Abstract

A new public health crisis has emerged with the appearance and global spread of the 2019 novel
coronavirus (2019-nCoV), now officially named severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2). The virus is believed to have originated in bats and was transmitted to humans
via an unidentified intermediate host in Wuhan, Hubei Province, China, in December 2019. As of
March 5, 2020, approximately 96,000 cases of coronavirus disease 2019 (COVID-19) and over
3,300 related deaths had been reported globally. COVID-19 is transmitted primarily through
inhalation of or contact with respiratory droplets from infected individuals. The incubation
period ranges from 2 to 14 days. Common clinical manifestations include fever, cough, sore
throat, shortness of breath, fatigue, and malaise. While the disease remains mild in the majority
of patients, elderly individuals and those with underlying comorbidities are at greater risk of
developing severe illness. Containing the spread of SARS-CoV-2 requires rigorous and timely
implementation of public health measures. However, such interventions are both logistically
challenging and time-consuming given the scale of the outbreak. Strategies such as follow-up
monitoring of confirmed cases via telephone on days 7 and 14, and the development of public
datasets by independent analytical groups, have proven useful in minimizing nosocomial
transmission and informing control efforts. Media sources, including newspapers and social
media, have also been instrumental in early outbreak reconstruction and case tracking. Travel
restrictions enacted by several countries may have contributed to slowing the global spread of the
virus. In response to the suspected zoonotic origin of SARS-CoV-2, temporary bans on wildlife
trade were implemented, underscoring the need for stronger, long-term policies to mitigate the
risk of future zoonotic spillovers. Currently, no licensed antiviral treatments or vaccines are
available for SARS-CoV, MERS-CoV, or SARS-CoV-2. Nevertheless, ongoing progress in
antiviral drug and vaccine development for other emerging infectious diseases holds promise for
rapid therapeutic innovation. Until effective countermeasures are developed, controlling the
pandemic will depend heavily on non-pharmaceutical interventions. Differential diagnosis of
COVID-19 should consider other viral respiratory infections such as respiratory syncytial virus,
rhinovirus, human metapneumovirus, and other coronaviruses, as well as atypical and bacterial
pneumonias, including those caused by Mycoplasma pneumonia and Chlamydia pneumonia.
Although viral RNA can be detected in blood and stool samples, respiratory specimens remain
the most reliable for laboratory confirmation of SARS-CoV-2 infection.

Nucleic Acid Amplification Tests (NAAT) for COVID-19 Virus

The gold standard method for confirming suspected cases of COVID-19 is the detection of
unique RNA sequences of the virus through reverse transcription polymerase chain reaction (RT-
PCR), along with nucleic acid sequencing if needed. The various viral genes identified so far
include N, E, S (N: nucleocapsid protein, E: envelope protein gene, S: spike protein gene), and
RdRP genes (RNA-dependent RNA polymerase gene). The virus has spread exponentially in
other countries, including South Korea, Italy, and Iran. Of those infected, 20% are in critical
condition, 25% have recovered, and 3,310 individuals (3,013 in China and 297 in other
countries) have died [2]. India, which had reported only 3 cases by March 2, 2020, has seen a
sudden increase in cases. By March 5, 2020, 29 cases were reported, mostly in Delhi, Jaipur, and
Agra, involving Italian tourists and their contacts. One case involved an Indian who traveled
back from Vienna and exposed a large number of schoolchildren at a birthday party in a city
hotel. Many contacts of these cases have been quarantined. These numbers are likely an
underestimate of the actual number of infected and deceased individuals due to limitations in
surveillance and testing. While SARS-CoV-2 originated from bats, the intermediary host has not
been conclusively identified. Another study conducted in South Korea on SARS-CoV-2 viral
load suggested that the viral kinetics of SARS-CoV-2 differ significantly from those of previous
CoV infections, including SARS-CoV [253]. SARS-CoV-2 transmission can occur early in the
viral infection phase; thus, diagnostic and isolation strategies for this virus require a different
approach compared to those used for SARS-CoV. Further studies are needed to establish any
correlation between SARS-CoV-2 viral load and cultivable virus. Recognizing patients with few
or no symptoms, who may have detectable viral RNA in the oropharynx for up to 5 days,
highlights the need for updated data on SARS-CoV-2 transmission dynamics and revised
screening protocols in clinical settings [82].

As of now, there have been 4,170,424 cases and 287,399 deaths worldwide. There is an urgent
need for a coordinated international effort to address unhealthy food practices in countries such
as China, encouraging vendors to adopt hygienic practices or close live-animal markets. It is also
essential to modify food policies at national and international levels to prevent further health
threats and economic consequences from emerging or reemerging pandemics due to close
animal-human interaction [2d5]. Although individuals of all ages and sexes are susceptible to
COVID-19, older individuals with underlying chronic conditions are at a higher risk of severe
infection [80]. Recent studies have also found that asymptomatic individuals can act as sources
of infection for susceptible individuals [81]. Both asymptomatic and symptomatic patients
secrete similar viral loads, indicating that the transmission capacity of asymptomatic or
minimally symptomatic patients is very high. Therefore, SARS-CoV-2 transmission can occur
early in the course of infection [82]. Atypical clinical manifestations have been reported in
COVID-19 patients, with fatigue being the only noticeable symptom. These patients may lack
respiratory signs such as fever, cough, and sputum production [83]. The SARS-CoV-2 strains
available in the National Center for Biotechnology Information and GISAID databases were
subjected to multiple-sequence alignment and phylogenetic analysis to study variations in the
viral genome [260]. All viral strains showed high homology, with a nucleotide similarity of
99.99% (99.91% to 100%) and an amino acid similarity of 99.99% (99.97% to 100%). Overall,
variation was low in the ORF regions, with 13 variation sites identified in regions such as la, lb,
S, 3a, M, 8, and N. Mutation rates of 30.53% (29/95) and 29.47% (28/95) were observed at
positions 28,144 (ORF8) and 8,782 (ORF1a), respectively. Due to these selective mutations,
some specific regions of SARS-CoV-2 should not be considered when designing primers and
probes. The SARS-CoV-2 reference sequence provides valuable insights into molecular biology,
pathobiology, and the development of diagnostic, prevention, and control strategies to combat
the virus [260].

SARS-CoV-2 nucleic acids can be detected in various samples, including bronchoalveolar

lavage fluid, sputum, nasal swabs, fiber bronchoscope brush biopsy specimens, pharyngeal
swabs, feces, blood, and urine, each with varying diagnostic sensitivity. At present, treatment for
sepsis and ARDS primarily involves antimicrobial therapy, source control, and supportive care.
Therapeutic plasma exchange may also be considered for managing severe conditions, and
further randomized trials are needed to assess its efficacy [311].

Potential Therapeutic Agents

Potent therapeutic agents to combat SARS-CoV-2 infection include virus-binding molecules,

molecules or inhibitors targeting specific enzymes involved in the virus’s replication and
transcription processes, helicase inhibitors, viral proteases and proteins, host cell protease
inhibitors, endocytosis inhibitors, short interfering RNA (siRNA), neutralizing antibodies,
monoclonal antibodies (MAbs) against the host receptor, MAbs interfering with the spike protein
receptor-binding domain (RBD), antiviral peptides targeting S2, and nanodrugs/medications [7,
166, 186]. The spike (S) protein serves as a critical target for developing CoV antivirals, such as
inhibitors of the S protein and its cleavage, neutralizing antibodies, RBD-ACE2 blockers,
siRNAs, fusion core blockers, and protease inhibitors [168]. These therapeutic approaches have
been studied in relation to viral load, which can help evaluate the progression of infection [291].
Additionally, sequencing and phylogenetic play a critical role in the accurate identification and
confirmation of the causative viral agent. They are also useful for establishing relationships with
previous isolates and sequences, and particularly during an epidemic, identifying nucleotide and
amino acid mutations and molecular divergence. The rapid development and implementation of
diagnostic tests for emerging novel diseases like COVID-19 face significant challenges due to
limited resources and logistical constraints associated with outbreaks [155]. SARS-CoV-2
infection can also be confirmed by isolation and culturing. Human airway epithelial cell cultures
have been found useful for isolating SARS-CoV-2 [3]. Efficient outbreak control depends on the
rapid diagnosis of the disease. In response to the COVID-19 outbreak, one-step quantitative real-
time reverse transcription-PCR assays have been developed to detect the ORF1b and N regions
of the SARS-CoV-2 genome [156]. This assay has been found effective for the rapid detection of
SARS-CoV-2. Nucleic acid-based assays offer high accuracy in diagnosing SARS-CoV-2.
Currently, no licensed antiviral drug is available for MERS- and SARS-CoV infections, and
clinical efforts remain focused on alleviating symptoms and providing supportive care [183-186].
Effective drugs for managing COVID-19 patients include remdesivir, lopinavir/ritonavir (alone
or combined with interferon beta), convalescent plasma, and monoclonal antibodies (MAbs).
However, the efficacy and safety of these treatments require further clinical trials [187, 281]. A
controlled trial of ritonavir-boosted lopinavir and interferon alpha 2b treatment was conducted on
hospitalized COVID-19 patients (ChiCTR2000029308) [188]. The use of hydroxychloroquine
and tocilizumab has also been proposed for their potential roles in modulating inflammatory
responses in the lungs and exerting antiviral effects. However, no definitive clinical trials have
been published [194, 196, 197, 261-272]. A recent clinical trial on adult patients with severe
COVID-19 revealed no benefit of lopinavir-ritonavir treatment over standard care [273].

Efforts to control SARS-CoV-2 infection use defined strategies similar to those against
MERS and SARS, while adapting to the spectrum of illnesses from the common cold to severe
and potentially fatal diseases such as SARS, MERS, and COVID-19. SARS-CoV-2 is one of the
seven members of the CoV family that infect humans [3] and belongs to the same lineage of
CoVs that cause SARS. However, this novel virus is genetically distinct. Until 2020, six CoVs
were known to infect humans, including HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-
HKU1, SARS-CoV, and MERS-CoV. While SARS-CoV and MERS-CoV caused outbreaks with
high mortality, the others were associated with mild upper respiratory tract illnesses [4]. The
emergence of new CoVs poses a significant threat to global public health. The current COVID-
19 outbreak is the third CoV outbreak in humans over the past two decades [5]. It is not
surprising that Fan et al. predicted potential SARS- or MERS-like CoV outbreaks in China
following pathogen transmission from bats [6]. COVID-19 emerged in China and rapidly spread
across the country and to other parts of the world. Given the severity of this outbreak and the
potential for global spread, the WHO declared it a public health emergency.

Reports of COVID-19 in companion and wild animals have steadily increased worldwide.
Further studies are needed to evaluate the potential role of animals (especially companion
animals) as efficient reservoir hosts that could alter the dynamics of human-to-human
transmission [330]. To date, two pet dogs (Hong Kong) and four pet cats (one each from
Belgium and Hong Kong, two from the United States) have tested positive for SARS-CoV-2
[335]. The World Organization for Animal Health (OIE) has confirmed COVID-19 diagnoses in
both dogs and cats due to human-to-animal transmission [331]. The genetic similarity observed
between SARS-CoV-2 from an infected pet owner and their dog further confirms human-to-
animal transmission [333]. Although asymptomatic, feline species should be considered a
potential route for animal-to-human transmission [326]. However, no evidence has been found to
suggest SARS-CoV-2 transmission from cats to humans. Based on current evidence, it is clear
that cats are susceptible to SARS-CoV-2 and can become infected from humans. However, no
evidence of cat-to-human transmission has been reported. SARS-CoV-2 uses ACE2 as its
receptor and human proteases to activate the virus's entry into host cells. Drugs that interfere with
this entry mechanism could be potential treatments for COVID-19. Umifenovir (Arbidol),
approved in Russia and China for treating influenza and other respiratory viral infections, targets
the interaction between the S protein and ACE2 and inhibits membrane fusion. In vitro studies
have shown that it has activity against SARS-CoV-2, and preliminary clinical data suggest it may
be more effective than lopinavir and ritonavir in treating COVID-19. However, other clinical
studies have shown that umifenovir might not accelerate SARS-CoV-2 clearance in patients with
mild to moderate COVID-19. Ongoing clinical trials are evaluating its efficacy in treating
COVID-19. Camostat mesylate, approved in Japan for treating pancreatitis and gastroesophageal
reflux disease (GERD), has been shown to prevent SARS-CoV entry by inhibiting TMPRSS2
activity and protecting mice from lethal SARS-CoV infection. Recent studies have shown that
camostat mesylate also blocks SARS-CoV-2 entry into human lung cells, making it a potential
antiviral drug against SARS-CoV-2, though sufficient clinical data to support its efficacy are still
lacking.

Limitations, including restricted access to medical care and social distancing measures, have
led to the closure of many cities, and individuals are being advised to work from home [232].
However, the current COVID-19 outbreak can be brought under control with the adoption of
strategic preventive and control measures, along with early isolation of subsequent cases. Reports
indicate that increased air traffic between China and African countries after the SARS outbreak
makes African countries vulnerable to the spread of novel coronaviruses [225]. Wuhan City was
completely shut down due to fears of the virus spread [233]. The immediate control of COVID-
19 outbreaks remains a major challenge, especially for developing countries with limited
resources for quarantine stations and screening infected individuals [234]. These countries should
prioritize preventive measures such as controlling entry from areas with active outbreaks and
isolating and quarantining infected or suspected individuals. Most Sub-Saharan African countries
have fragile health systems and are at a disadvantage due to the novel nature of this virus [36,
189]. Currently, the main treatments for severely affected SARS-CoV-2 patients include
mechanical ventilation, intensive care unit (ICU) admission, and supportive care. RNA synthesis
inhibitors (lamivudine and tenofovir), remdesivir, neuraminidase inhibitors, peptide-based
treatments (EKI), anti-inflammatory drugs, and traditional Chinese medicine (Lianhuaqingwen
and capsules) may help manage COVID-19, but further clinical trials are ongoing to assess their
safety and efficacy [7]. It may take months to a year to design, develop, and obtain regulatory
approval for effective drugs, therapeutics, and vaccines for COVID-19, followed by large-scale
production to meet global demand [9]. Ongoing efforts are also needed to identify and evaluate
drugs and immunotherapeutic regimens that have demonstrated efficacy against other viral
agents similar to SARS-CoV-2. Analysis of the initial cluster of infections suggests that the
infected individuals had a common exposure point, a seafood market in Wuhan, Hubei Province,
China (Fig. 6). This market is known for selling wild animals for human consumption [71]. The
Huainan South China Seafood Market also sells live animals, such as poultry, bats, snakes, and
marmots [72], which may have been the source of zoonotic (animal-to-human) transmission [71].
Although SARS-CoV-2 is believed to have originated from an animal host, human-to-human
transmission has been confirmed [6]. Further investigations are needed to rule out the possibility
of foodborne transmission, as it remains a latent concern [1]. Additionally, other potential
transmission routes, such as direct contact with contaminated hands or surfaces, need to be
further explored. Whether blood transfusion, organ transplantation, or perinatal transmission are
possible routes for SARS-CoV-2 transmission is still under investigation [276].

Conclusion

COVID-19 has spread at an alarming rate across the globe, challenging the world's economic,
medical, and public health infrastructures. The elderly and immunocompromised individuals are
particularly vulnerable to the virus's severe impacts. At present, no documented cure or vaccine
for the virus exists, although some treatment protocols have shown promise. As such, controlling
the virus primarily relies on the implementation of appropriate prevention strategies.
Furthermore, it is essential to develop systematic approaches to prevent future zoonotic
outbreaks. While clinical trials are ongoing, newly developed drugs cannot be widely marketed
due to the lack of end users and further regulatory approvals.

Vaccines

The spike (S) protein plays a crucial role in inducing protective immunity against SARS-CoV by
mediating T-cell responses and the production of neutralizing antibodies (168). Over the past few
decades, several attempts have been made to develop a vaccine targeting the S protein against
human coronaviruses (168, 169). However, these vaccines have had limited success, even against
closely related strains, primarily due to a lack of cross-protection. This limitation is mainly due
to the significant diversity among the various antigenic variants of the virus (104). The role of
other structural proteins, such as the spike (S), membrane (M), envelope (E), and nucleocapsid
(N) proteins, in inducing protective immunity has been evaluated by expressing them in a
recombinant parainfluenza virus type 3 (BHPIV3) vector. Notably, the results showed that the
expression of M, E, or other variants did not generate substantial cross-protection. Furthermore,
the receptor-binding region of the SARS-CoV S protein appears to be very similar to that of
SARS-CoV-2, suggesting that both viruses may utilize the same receptor for cell entry (17).

4.1 Virion Structure and Its Genome

Coronaviruses are structurally enveloped viruses belonging to the positive-strand RNA virus
category and have the largest known RNA genomes. These viruses typically exhibit spherical
shapes but can modify their morphology in response to environmental conditions, making them
pleomorphic. The viral envelope, which represents the outer membrane, typically contains
glycoprotein projections that cover the nucleocapsid, composed of a matrix protein and positive-
strand RNA. The RNA genome of coronaviruses is 5'-capped and 3'-polyadenylated, resembling
the structure of cellular mRNAs. The coronavirus structure includes several key proteins:
hemagglutinin esterase (HE) (present only in some beta-coronaviruses), spike (S), small
membrane (E), membrane (M), and nucleocapsid (N) proteins, as shown in Figure X. The
envelope containing glycoproteins is responsible for attaching to the host cell, with the primary
antigenic epitopes located in the spike protein. These viral proteins are involved in host cell entry
and immune response activation. Coronavirus infections in humans are commonly associated
with mild to severe respiratory diseases, including high fever, severe inflammation, cough, and
potential internal organ dysfunction that can lead to death (92). While most coronaviruses cause
mild respiratory symptoms like the common cold, this changed when SARS-CoV was identified,
leading to more severe forms of the disease in humans (22). Previous outbreaks of other
coronaviruses, such as SARS and MERS, have shown that COVID-19 is primarily transmitted
human-to-human via direct contact, droplets, and fomites (25). Recent studies have demonstrated
that SARS-CoV-2 can remain viable for hours in aerosols and up to days on surfaces, suggesting
that aerosol and fomite transmission play significant roles in its spread (257). The immune
response to coronavirus infection is crucial for controlling and eliminating the virus. However,
maladaptive immune responses can contribute to immunopathology, impairing pulmonary gas
exchange. Understanding the interaction between coronaviruses and the host's innate immune
system is essential for developing effective therapeutic strategies. Additionally, abnormal CT
scans have been used to diagnose COVID-19 in cases with negative molecular tests, and many of
these patients tested positive upon repeat molecular testing (22).

Differential Diagnosis [21]

The differential diagnosis for COVID-19 includes various types of respiratory viral infections,
such as influenza, parainfluenza, respiratory syncytial virus (RSV), adenovirus, human
metapneumovirus, and non-COVID-19 coronaviruses. Additionally, atypical organisms like
Mycoplasma and Chlamydia and bacterial infections must be considered. Clinically, it is not
possible to distinguish COVID-19 from these other infections through routine examination or
tests. Genetic studies have shown that the SARS-CoV-2 virus shares over 95% homology with
bat coronaviruses and approximately 70% similarity with SARS-CoV. Environmental samples
from the Huanan Seafood Market also tested positive for the virus, suggesting that the virus may
have originated there [7]. However, as the number of cases began to rise exponentially, some
individuals without direct exposure to the market indicated that human-to-human transmission
was occurring [8]. The first fatal case of COVID-19 was reported on January 11, 2020. The large
migration of Chinese people during the Chinese New Year fueled the epidemic, with cases
quickly spreading to other provinces in China and countries such as Thailand, Japan, and South
Korea. Transmission to healthcare workers who were caring for patients was first described on
January 20, 2020. By January 23, the 11 million residents of Wuhan were placed under
lockdown. Given the increasing global spread of the virus, it is important to emphasize proper
sanitation practices. Further research is needed to explore the potential for fecal-oral transmission
of SARS-CoV-2 and investigate the virus's persistence in various environmental conditions.
Understanding the correlation between fecal viral RNA concentrations and disease severity is
crucial, as well as studying gastrointestinal symptoms and the potential for detecting SARS-
CoV-2 RNA in feces during the incubation or convalescence phases of the disease [249-252].

For clinical diagnosis, lower respiratory tract sampling techniques, such as bronchoalveolar
lavage fluid aspirates, are considered more reliable than throat swabs, as they have a higher
positive rate for nucleic acid tests [148]. However, these techniques pose a risk to healthcare
workers due to close patient contact [152]. There have been reports of a patient with a high viral
load contaminating an entire endoscopy room by shedding the virus, which may remain viable
for extended periods [6.2].

Serological Testing

Serological surveys are considered one of the most effective tools in outbreak investigations,
providing valuable insights into the spread and dynamics of diseases. They enable a retrospective
assessment of the disease, such as estimating the attack rate and the extent of exposure in the
population. Recent literature suggests that paired serum samples can help clinicians diagnose
COVID-19, especially in cases where nucleic acid amplification tests (NAATs) yield false
negative results. In addition, both commercial and non-commercial serological tests are being
developed and considered to support clinicians in diagnosing COVID-19. These tests can provide
important information regarding past infections and the immune response to the virus. Several
studies have been published on COVID-19 that include serological data from clinical samples,
further highlighting the potential of serological testing in enhancing our understanding of the
disease.

Viral Sequencing

Viral sequencing serves multiple purposes beyond confirming the presence of the virus in
specimens. It is particularly valuable for monitoring viral genomic mutations, which can
significantly impact the effectiveness of medical countermeasures, including diagnostic tests.
Genomic sequencing allows for the detection of mutations that may alter the virus’s behavior or
resistance to treatments. Additionally, sequencing plays a crucial role in molecular epidemiology
studies, helping to track the spread and evolution of the virus. One notable application of viral
sequencing is in understanding the potential for intrauterine vertical transmission of COVID-19.
A study assessing this in nine infants born to infected mothers found that none of the infants
tested positive for the virus, and no evidence of vertical transmission was observed. This finding
aligns with previous research during the SARS and MERS epidemics, where no evidence of
intrauterine infection was found.
 The CDC has emphasized that infants born to mothers with confirmed COVID-19 are
considered persons under investigation (PUI). As a precaution, these infants should be
temporarily separated from their mothers and isolated to prevent potential transmission.

7.1 Breastfeeding and Infant Care

The available data to date is limited and cannot confirm whether COVID-19 can be transmitted
through breast milk. An assessment of breast milk samples from six patients showed negative
results for the presence of the virus. The CDC emphasizes that in cases of confirmed or
suspected COVID-19 infection, the decision to start or continue breastfeeding should be made by
the mother in collaboration with her family and healthcare providers. Mothers should take careful
precautions to prevent transmitting the virus to their infants through respiratory droplets during
breastfeeding. These precautions include wearing a face mask and practicing proper hand
hygiene.

Coronaviruses are enveloped, positive-sense RNA viruses ranging from 60 to 140 nm in

diameter, with spike-like projections on their surface that give them a crown-like appearance
under the electron microscope—hence the name "coronavirus" [3]. Four coronaviruses—HKU1,
NL63, 229E, and OC43—have been in circulation among humans and generally cause mild
respiratory illness.

In the past two decades, there have been two notable events where animal-origin
betacoronaviruses crossed over into humans, resulting in severe disease. The first such event
occurred in 2002–2003 with the SARS outbreak. Another significant event involved the
emergence of Swine Acute Diarrhea Syndrome Coronavirus (SADS-CoV), which was first
identified in suckling piglets suffering from severe enteritis. SADS-CoV belongs to the genus
Alphacoronavirus [10b]. The outbreak resulted in high mortality rates among piglets—24,693
deaths reported across four farms in China [134]. Genomic analysis showed that the virus
isolated from piglets was nearly identical to the horseshoe bat (Rhinolophus species) coronavirus
HKU2, with 95% genomic similarity, strongly suggesting a bat origin [106, 134, 135]. Notably,
the SADS-CoV outbreak began in Guangdong province, which is also near the origin of the
SARS pandemic [134]. Before this outbreak, pigs were not known to be infected with bat-origin
coronaviruses, indicating a cross-species transmission. This raises concerns about the potential
for further jumps, as pigs are known ―mixing vessels‖ for influenza A viruses due to their
susceptibility to both human and avian strains [136].

Similarly, pigs may serve as mixing vessels for coronaviruses as they are frequently in
contact with both humans and various wildlife species. Furthermore, pigs have been found
susceptible to human SARS-CoV and MERS-CoV infections, which increases the risk of new
zoonotic outbreaks [109, 137]. The most common symptoms of COVID-19 include fever, cough,
dyspnea (shortness of breath), expectoration, headache, and myalgia or fatigue.

Less common symptoms at the time of hospital admission include diarrhea, hemoptysis
(coughing up blood), and shortness of breath [14]. Recently, asymptomatic individuals have also
been suspected of transmitting the virus, complicating the understanding of transmission
dynamics [1]. Effective response strategies require in-depth understanding of the virus. As
SARS-CoV-2 is a novel pathogen, continued research is essential. Comparative genome analysis
between SARS-CoV-2 and closely related SARS/SARS-like CoVs revealed 27 amino acid
substitutions in the spike protein (which is 1,273 amino acids long). Of these, six substitutions
are located in the receptor-binding domain (RBD), and another six in the subdomain (SD) [16].
Phylogenetic analysis has shown that SARS-CoV-2 shares about 88% similarity with two bat-
derived SARS-like CoVs.
Individuals with underlying chronic medical conditions—such as lung disease, heart failure,
cancer, cerebrovascular disease, renal disease, diabetes, liver disease, immunocompromising
conditions, and pregnancy—are at higher risk for developing severe COVID-19 illness.
Management strategies include the implementation of infection prevention and control measures,
supportive care to manage complications, and, when necessary, advanced organ support.

Corticosteroids should generally be avoided unless specifically indicated, such as for

exacerbations of chronic obstructive pulmonary disease (COPD) or septic shock, as their use may
prolong viral replication, as observed in patients with MERS-CoV.

12 Early Supportive

Therapy and Monitoring

Management of patients with suspected or confirmed COVID-19 involves ensuring appropriate

infection control measures and providing supportive care. The WHO and CDC have published
clinical guidance for the management of COVID-19 [59]. Immediate therapy should include
supplemental oxygen for patients with severe acute respiratory infection (SARI), along with
respiratory support medications to prevent ventilator-associated lung injury, which can occur due
to human-machine coordination issues [122]. A clinical study involving four patients infected
with COVID-19 suggested that combination therapy using lopinavir/ritonavir, arbidol, and
Shufeng Jiedu capsules (a traditional Chinese medicine) was effective in managing COVID-19
pneumonia [193]. However, it is challenging to evaluate the therapeutic potential of a drug or
combination of drugs based on such a limited sample size. Before selecting the ideal therapeutic
agent for managing COVID-19, randomized controlled clinical trials with a larger study
population should be conducted.

Antiviral Drugs

Several commonly used antiviral drugs, such as oseltamivir (a neuraminidase inhibitor),

acyclovir, ganciclovir, and ribavirin, have no proven effect against COVID-19 and therefore are
not recommended [187]. Oseltamivir was used in some Chinese hospitals to treat suspected
COVID-19 cases, but it lacks proven efficacy against SARS-CoV-2 [7]. In vitro studies have
investigated the antiviral potential of FDA-approved drugs. One such approach involves the
peptide HR2, which can form a six-helix bundle with HR1, bringing viral and host membranes
into proximity and facilitating fusion. Sequence alignment studies between SARS-CoV and
SARS-CoV-2 revealed that the S2 subunit is highly conserved. The HR1 and HR2 domains
showed 92.6% and 100% sequence identity, respectively [210]. These findings underscore the
importance of HR1 and HR2 in viral entry, making the HR1 domain a target for fusion
inhibitors—an emerging therapeutic strategy in COVID-19 treatment. Beyond targeted antiviral
therapy, general supportive treatments also play a critical role in enhancing host immune
responses. Poor nutritional status is linked to weakened immunity, increasing susceptibility to
infection. Thus, nutritional assessment in COVID-19 patients is essential to understand the
relationship between diet and disease severity [205]. The Chinese government has encouraged
the public to resume consumption of animal meat, aiming to restore normalcy. However, this
raises concerns, as advisories have warned against contact with live or dead animals due to the
zoonotic origin of SARS-CoV-2. The possibility of viral mutation related to human-animal
interactions in markets remains a significant concern [284]. In January 2020, China imposed a
temporary ban on the sale of live or dead animals in wet markets. Despite this, many such
markets have since reopened without implementing proper food safety and sanitation measures
[286]. Wet markets are often unhygienic, with fresh blood contaminating surfaces and floors.
These conditions can facilitate the adaptation and mutation of pathogens, increasing the risk of
cross-species transmission.
To assess genetic variations of SARS-CoV-2, the 2019 Novel Coronavirus Resource at the China
National Center for Bioinformation analyzed 77,801 global SARS-CoV-2 genome sequences and
identified 15,018 mutations, including 14,524 single nucleotide polymorphisms (SNPs). Four
amino acid changes in the spike protein—V483A, L455I, F456V, and G476S—were found near
the receptor-binding domain (RBD), though their impact on host receptor binding remains
unclear. A notable mutation, D614G in the S1 subunit, has become dominant globally since
March 2020 and is a marker for the G clade. The G614 variant was associated with higher viral
loads, although no significant correlation with disease severity has been established. Pseudotyped
virus studies showed that the G614 variant produced higher infectious titers compared to the
D614 variant, suggesting increased infectivity [REF]. However, these in vitro results must be
validated through further studies using wild-type SARS-CoV-2 in animal and cellular models to
determine the true impact on transmissibility. Another significant mutation under study is a
single-nucleotide change linked to SARS-CoV-2 evolution, with antiviral therapies like
lopinavir-ritonavir previously used in SARS and MERS. A historical control study found that
SARS patients receiving lopinavir-ritonavir plus ribavirin had better outcomes than those treated
with ribavirin alone [15].

In a case series of 99 hospitalized COVID-19 patients in Wuhan, 76% received oxygen therapy,
13% non-invasive ventilation, 4% mechanical ventilation, 3% extracorporeal membrane
oxygenation (ECMO), 9% continuous renal replacement therapy (CRRT), 71% antibiotics, 15%
antifungals, 19% glucocorticoids, and 27% intravenous immunoglobulin therapy [15]. Antiviral
treatments—including oseltamivir, ganciclovir, and lopinavir-ritonavir—were administered to
75% of patients. The duration of non-invasive ventilation ranged from 4 to 22 days (median: 9
days).

Interestingly, cases reported outside Hubei Province and China overall were milder [6,17]. This
may be due to selection bias—where initial data from Wuhan primarily included severe cases—
or possible genetic predisposition, such as higher ACE2 receptor expression among Asians,
increasing vulnerability [11]. Children, including neonates and infants, generally experienced
milder illness than adults. In a study of 34 children hospitalized in Shenzhen between January 19
and February 7, there were 14 males and 20 females, with a median age of 8 years and 11
months. For 28 children, infection was linked to a family member. Elderly patients and those
with underlying conditions—especially hypertension and diabetes—were more likely to suffer
respiratory failure and poor outcomes. Early respiratory support improved prognosis and
facilitated recovery [18]. Acute Respiratory Distress Syndrome (ARDS) in COVID-19 results
from cytokine storms that trigger exaggerated immune responses and systemic immune
dysregulation, potentially leading to multi-organ failure [122]. In addition, the compensatory
proliferation of bile duct epithelial cells—due to liver involvement—may increase ACE2
expression in the liver, contributing to hepatic injury [123].

Corona Viruses in Animals and Zoonotic Lines — A Brief Viewpoint

Coronaviruses (CoVs) are known to cause diseases in various species of domestic and wild
animals, as well as in humans [23]. A wide range of animals have been found susceptible to CoV
infection, including horses, camels, cattle, swine, dogs, cats, rodents, birds, ferrets, minks, bats,
rabbits, snakes, and several other wildlife species [20, 30, 79]. Patients infected with COVID-19
are typically treated symptomatically, along with oxygen therapy. In cases where patients
deteriorate into respiratory failure and become unresponsive to oxygen therapy, mechanical
ventilation becomes necessary. COVID-19-induced septic shock can be managed with
appropriate hemodynamic support [299].

Currently, multiple classes of drugs are under evaluation for their potential therapeutic effects
against SARS-CoV-2. These agents can be broadly categorized into three main groups: Drugs
that inhibit viral entry into host cells, Drugs that inhibit viral replication and survival within the
host, and Drugs that modulate the host's immune response, particularly in severe cases [300]. A
hyperinflammatory response, commonly referred to as a cytokine storm, is frequently observed
in critically ill COVID-19 patients. These patients may benefit from timely administration of
anti-inflammatory treatments. Such therapies may include glucocorticoids, cytokine inhibitors,
JAK inhibitors, and chloroquine or hydroxychloroquine. However, these should only be
administered after a thorough assessment of the risk-to-benefit ratio in each individual patient
[301]. Currently, there are no conclusive studies specifically addressing the use of nonsteroidal
anti-inflammatory drugs (NSAIDs) in patients infected with COVID-19. Nevertheless, some
reasonable evidence suggests a potential link between NSAID use and COVID-19 outcomes,
which warrants further investigation.

5.2 Specimen Collection and Storage

Nasopharyngeal and oropharyngeal swabs should be collected using Dacron or polyester flocked
swabs. The samples must be transported to the laboratory at a temperature of 4°C. For optimal
viral detection, both swabs should be placed in the same tube to increase viral load. Depending
on the storage duration, samples should be stored at temperatures ranging between 4°C and –
70°C. Bronchoalveolar lavage fluid and nasopharyngeal aspirates should be collected in sterile
containers and transported under the same conditions (maintaining 4°C) to the laboratory.
Sputum samples, particularly those from the lower respiratory tract, must also be collected in
sterile containers and stored accordingly. Similarly, tissue samples obtained through biopsy or
autopsy should be placed in sterile containers with saline and stored at 4°C to –70°C in the
laboratory. Whole blood samples for antigen detection, especially during the first week of illness,
should be collected in appropriate collection tubes and stored between 4°C and –70°C. Urine
samples must also be collected using sterile containers and stored under the same conditions. It is
important to note that additional clinical trials in various phases are still ongoing to optimize
specimen handling and diagnostic procedures.

SARS-CoV-2 is known to elicit a strong immune response, which in severe cases may lead to
cytokine storm syndrome. Therefore, immunomodulatory agents that suppress excessive
inflammation may serve as potential adjunct therapies for COVID-19. Dexamethasone, a
corticosteroid widely used for its anti-inflammatory and immunosuppressive properties, has
demonstrated efficacy in COVID-19. Results from the RECOVERY trial revealed that
dexamethasone reduced mortality by approximately one-third in hospitalized patients who
required invasive mechanical ventilation, and by one-fifth in those receiving supplemental
oxygen. However, no benefit was observed in patients who did not require respiratory support.
Tocilizumab and sarilumab, monoclonal antibodies targeting the interleukin-6 (IL-6) receptor,
have shown promise in managing severe COVID-19 by mitigating the cytokine storm, as
observed in small uncontrolled clinical studies. Similarly, bevacizumab, an anti-vascular
endothelial growth factor (VEGF) agent, may reduce pulmonary edema in critically ill patients.
Eculizumab, a monoclonal antibody that inhibits the proinflammatory complement protein C5,
demonstrated a reduction in inflammatory markers, including C-reactive protein (CRP), in
preliminary observations. This suggests potential utility in treating severe forms of COVID-19.
Although these therapeutic approaches have demonstrated in vitro and in vivo antiviral activity
against coronaviruses, most lack comprehensive support from large-scale, randomized clinical
trials. Therefore, their clinical applicability remains limited until further validated. Additionally,
the interaction between SARS-CoV-2 and ACE2 receptors contributes to pneumonia through
dysregulation of the renin-angiotensin system (RAS). The resulting pulmonary inflammation
may be alleviated with ACE inhibitors or angiotensin II type 1 receptor (AT1R) blockers [207].

Multiple studies have also explored small-molecule inhibitors as potential treatments. Screening
of FDA-approved compounds identified several agents—chlorpromazine, chloroquine,
loperamide, and lopinavir—which inhibited MERS-CoV replication. These compounds also
showed activity against SARS-CoV and other human coronaviruses [208].

Finally, therapies utilizing monoclonal antibodies or compounds that neutralize cytokines and
their receptors hold promise in controlling the host inflammatory response. Drugs targeting the
respiratory tract specifically may offer additional benefits by limiting localized viral activity and
associated inflammation.

Prevention [21, 30]

As there are currently no approved treatments for COVID-19, prevention remains the most
critical strategy in controlling the spread of the virus. Several characteristics of SARS-CoV-2
pose challenges to effective prevention. These include: Nonspecific symptoms that resemble
other common illnesses, Infectivity during the incubation period, even before the onset of
symptoms, Transmission from asymptomatic individuals, A relatively long incubation period,
Viral tropism for mucosal surfaces such as the conjunctiva, Prolonged duration of illness, and
Continued viral transmission even after apparent clinical recovery.

To minimize transmission, home isolation is recommended for confirmed or suspected cases

with mild illness. The home environment should be well-ventilated and exposed to sunlight, as
UV light can help inactivate the virus. Infected individuals should wear a simple surgical mask
and consistently practice respiratory hygiene, including covering the mouth and nose while
coughing or sneezing.

For breastfeeding mothers infected with COVID-19, the following precautions are advised to
prevent transmission to the infant: Wear a facemask during feeding, Practice proper hand
hygiene before touching the baby or any feeding equipment, Ensure that breast pumps are
thoroughly cleaned after each use, If possible, a healthy caregiver should feed the expressed
breast milk to the infant. These measures help reduce the risk of viral transmission while
supporting the benefits of breastfeeding.

7.2 Children and Elderly Population

According to available reports, children account for approximately 1–5% of confirmed COVID-
19 cases. This age group does not appear to be at higher risk of severe illness compared to adults.
Furthermore, there is no significant difference in the clinical symptoms of COVID-19 between
children and adults. However, children diagnosed with COVID-19 typically experience milder
symptoms and have a low mortality rate [48, 49]. In contrast, the elderly population, particularly
those aged 65 years and above, is at a higher risk of developing severe disease. In the United
States, an estimated 31–59% of individuals aged 65–84 years with confirmed COVID-19
required hospitalization. Additionally, 11–31% needed intensive care, and 4–11% succumbed to
the illness [50].

A confirmed case is defined as a suspected case with a positive molecular test. Clinical
presentation can vary, and some cases may be asymptomatic or afebrile, making clinical
diagnosis challenging in areas with ongoing transmission or exposure history. Specific diagnosis
relies on molecular testing (RT-PCR) performed on respiratory samples such as: Throat swabs
Nasopharyngeal swabs Sputum Endotracheal aspirates Bronchoalveolar lavage (BAL) In some
cases, the virus can also be detected in stool samples or blood in severe disease. It is important to
note that multiplex PCR panels currently available do not include SARS-CoV-2, and commercial
tests are still limited in availability. In India, samples from suspected cases must be sent to
designated reference laboratories or the National Institute of Virology in Pune for confirmation.
In severe cases, SARS-CoV-2 induces an inflammatory cascade marked by the release of
proinflammatory cytokines, particularly IL-1 and IL-33. This suggests that anti-inflammatory
cytokines targeting the IL-1 family could be beneficial [92]. Additionally, research indicates that
actin proteins in host cells are involved in viral entry and pathogenesis. Drugs that modulate actin
activity—such as ibuprofen—may have potential as adjunctive therapies [174].

Elevated levels of angiotensin II have been observed in COVID-19 patients, correlating with
viral load and lung injury. This provides a rationale for using angiotensin receptor blockers
(ARBs) as a possible therapeutic strategy [121].

German scientist Rolf Hilgenfeld has been actively engaged in developing antiviral agents
targeting coronaviruses since the first SARS outbreak [19]. For example, the S2 subunit of the
SARS-CoV-2 spike protein plays a vital role in membrane fusion and viral entry, making it a
target of therapeutic interest. Genomic analysis shows that the receptor-binding domain (RBD)
of the S protein in coronaviruses isolated from pangolins is nearly identical (differing by one
amino acid) to that of SARS-CoV-2. This suggests a likely recombination event between
pangolin-CoV-like and bat-CoV-RaTG13-like viruses. Increasing human–wildlife interactions,
especially under the pressure of climate change, elevate the risk of zoonotic spillovers [142]. To
prevent future outbreaks: High-risk pathogens in wildlife should be systematically identified,
Serological surveillance should be carried out among people living near wildlife habitats,
Biosecurity protocols in the wildlife trade must be strengthened [1, 12, 146].

Serological studies in populations near bat caves in rural China have confirmed prior exposure to
SARS-related coronaviruses, highlighting ongoing spillover risks [147].

Recent computational (in silico) studies identified promising antiviral compounds, including: 4-
(cyclopent-1-en-3-ylamino)-5-(4-iodophenyl)hydrazinyl-1,2,4-triazole-3-thiol 4-(cyclopent-1-en-
3-ylamino)-5-[2-(4-chlorophenyl)hydrazinyl]-1,2,4-triazole-3-thiol

These compounds were docked into the active site of MERS-CoV helicase nsp13, showing high
binding affinity [21]. Although encouraging, these findings require further preclinical and
clinical testing to evaluate their therapeutic potential in the context of COVID-19.

Passive Immunization, Antibody Therapy, and Monoclonal Antibodies (MAbs)

Monoclonal antibodies (MAbs) have demonstrated potential utility in the prevention and
treatment of COVID-19, particularly among individuals exposed to the virus. Patients who
recovered from SARS infections were found to develop robust neutralizing antibody responses
against the virus [164]. Similarly, several MAbs targeting the S protein of MERS-CoV,
specifically those recognizing six epitope groups involved in receptor binding, membrane fusion,
and sialic acid-binding domains, have shown efficacy in blocking viral entry [198, 199]. Passive
immunization with both weakly and strongly neutralizing antibodies provided significant
protection in murine models against lethal MERS-CoV infection.

Further research has explored the use of fully human antibodies, such as human single-chain
variable fragments (HuscFvs) and humanized nanobodies (single-domain antibodies: sdAbs,
VH/VHH), which can act as "transbodies." These antibodies are capable of penetrating virus-
infected cells and interfering with the biological functions of viral proteins during replication.
Such an approach has shown promise in the context of other viral infections, including influenza,
hepatitis C, Ebola, and dengue virus [206]. Developing similar intracellularly active antibodies
targeting essential viral components of coronaviruses—such as papain-like protease (PLpro),
cysteine-like protease (3CLpro), and other non-structural proteins (nsps)—may present a
promising strategy for both prophylaxis and therapy in COVID-19.
In one clinical case series, the administration of convalescent plasma to five critically ill COVID-
19 patients with severe pneumonia yielded encouraging outcomes. The transfused plasma,
collected from individuals who had recovered from COVID-19, contained SARS-CoV-2-specific
ELISA antibody titers exceeding 1:1,000 and neutralizing antibody titers greater than 1:40. These
findings suggest that convalescent plasma therapy may aid recovery in severely ill patients and
augment the host’s humoral immune response.

Neutralizing antibodies targeting the receptor-binding domain (RBD) of the SARS-CoV-2 spike
protein are particularly crucial. Their ability to cross-neutralize other coronaviruses depends
significantly on the similarity between RBD sequences. For instance, SARS-CoV RBD-specific
MAbs could neutralize the bat-SL-CoV strain WIV1 (with only eight amino acid differences
from SARS-CoV), but not the strain SHC014 (which has 24 amino acid differences) [200]. Thus,
evaluating and identifying RBD-specific MAbs based on comparative sequence analysis between
SARS-CoV and SARS-CoV-2 is a vital step toward developing broadly neutralizing antibodies
against emerging CoVs.

In the United States, the biotechnology company Regeneron has actively pursued the
development of potent and specific MAbs for combating COVID-19. A combination therapy
consisting of MAbs and the antiviral agent remdesivir has been proposed as a promising
therapeutic approach [201]. Additionally, the SARS-CoV-specific human monoclonal antibody
CR3022 was found to bind the SARS-CoV-2 RBD, suggesting its potential therapeutic value
[140]. However, some early studies lacked control groups, and clinical trials of antivirals such as
favilavir often involved small sample sizes, highlighting the need for large-scale randomized
controlled trials to ascertain efficacy conclusively.

Moreover, the antiretroviral drugs lopinavir and ritonavir have exhibited in vitro inhibitory
activity against both SARS-CoV and MERS-CoV [141, 142]. Though their clinical utility for
COVID-19 remains under investigation, these findings provide a rationale for further evaluation
in controlled studies.

Zoonotic Potential of Animal Coronaviruses

Coronaviruses are widely distributed among various animal species and possess significant
zoonotic potential. Bovine coronaviruses (BoCoVs), for instance, infect multiple domestic and
wild ruminants and are responsible for a range of diseases in cattle, including neonatal calf
diarrhea, winter dysentery (bloody diarrhea), and bovine respiratory disease complex (shipping
fever) [126]. Notably, BoCoV-like viruses have also been detected in humans, suggesting a
possible zoonotic transmission [127].

In felines, two major coronaviruses have been identified: feline enteric coronavirus (FECV) and
feline infectious peritonitis virus (FIPV). These viruses affect the gastrointestinal system,
abdominal cavity, respiratory tract, and even the central nervous system [128]. Similarly, canine
coronaviruses belong to different genera. Canine enteric coronavirus (CECoV), classified under
Alphacoronavirus, targets the gastrointestinal system, whereas canine respiratory coronavirus
(CRCoV), under Betacoronavirus, affects the respiratory tract [129, 130].

Among avian species, the infectious bronchitis virus (IBV), a Gammacoronavirus, causes
significant morbidity and economic losses in poultry due to its effects on the respiratory, urinary,
and reproductive systems [131, 132]. Additionally, various laboratory animals harbor their own
species-specific coronaviruses. For example, mouse hepatitis virus, rat sialodacryoadenitis virus,
as well as guinea pig and rabbit coronaviruses, have been associated with enteritis, hepatitis, and
respiratory illnesses in their respective hosts [10, 133].
These observations underscore the importance of surveillance and control of animal
coronaviruses, not only for veterinary health but also for anticipating and mitigating potential
spillover events into the human population.

Swine acute diarrhea syndrome coronavirus (SADS-CoV), along with SARS-CoV and MERS-
CoV, represents a group of coronaviruses with significant zoonotic and pathogenic potential
[117].

SARS-CoV-2, the causative agent of COVID-19, primarily targets the lung parenchyma, leading
to severe interstitial inflammation. Radiological examination using computed tomography (CT)
often reveals ground-glass opacities in the lungs. These lesions initially appear in a single lobe
but typically progress to involve multiple lobes as the disease advances [118]. Histopathological
analysis of lung biopsy samples from COVID-19 patients has revealed features consistent with
acute respiratory distress syndrome (ARDS), including diffuse alveolar damage, cellular
fibromyxoid exudates, hyaline membrane formation, and desquamation of pneumocytes [119].

Lymphocytopenia is commonly observed in patients infected with SARS-CoV-2 and may occur
with or without leukocyte abnormalities. The severity of lymphocytopenia has been found to
correlate positively with disease prognosis, thus serving as a potential indicator of disease
progression [118].

Pregnant women are considered at higher risk for COVID-19 infection, with potential adverse
fetal outcomes such as intrauterine growth restriction, spontaneous abortion, preterm delivery,
and perinatal death. However, the risk of intrauterine vertical transmission of coronaviruses is
considered low and was not observed during the outbreaks of SARS or MERS [120].

Countries with fragile healthcare infrastructures are particularly vulnerable during pandemics.
The effective management of COVID-19 poses significant challenges in low-income countries
due to limited healthcare resources and inadequate response capacity [65]. Containing imported
cases remains a crucial strategy to prevent community transmission in previously unaffected
regions. The estimated probability of sustained human-to-human transmission from an imported
case is 0.41; however, this can be reduced to 0.012 by minimizing the interval between symptom
onset and hospitalization—an outcome achievable only through robust disease surveillance
systems [235].

Silent transmission by asymptomatic or presymptomatic individuals has played a key role in the
global spread of COVID-19. Despite the travel ban implemented in Wuhan [89], individuals who
left the city before the lockdown may have contributed to seeding outbreaks in other regions
[236]. In the context of globalization, novel infectious diseases such as COVID-19 cannot be
easily contained within national borders. This underscores the necessity for strong international
collaboration in disease monitoring and response efforts.

During previous pandemics, such as influenza, public health guidelines permitted patients to
return to work or school once afebrile for 24 hours or by the seventh day of illness, without the
requirement for negative molecular test results. At the community level, public health measures
should include avoiding crowded areas, postponing non-essential travel to affected locations, and
encouraging cough etiquette (e.g., coughing into a sleeve or tissue) and frequent hand hygiene
every 15–20 minutes. Individuals displaying respiratory symptoms should wear surgical masks to
reduce transmission.

While the World Health Organization (WHO) does not currently recommend the use of masks by
healthy individuals in public settings due to insufficient evidence of their effectiveness in
preventing respiratory viral infections, authorities in China have mandated public mask usage,
particularly in crowded environments and during large-scale gatherings, such as in entertainment
parks.

China declared a public health emergency on 31 January 2020, and the World Health
Organization officially declared COVID-19 a pandemic on 11 March 2020. Currently, no
approved vaccines or specific antiviral drugs exist for the treatment of human coronavirus
infections [7–9]. Thus, the global response has largely focused on prevention and containment
through non-pharmaceutical interventions and public health strategies.

In domestic animals, infections with coronaviruses (CoVs) are associated with a broad spectrum
of pathological conditions. Aside from infectious bronchitis virus, canine respiratory CoV, and
mouse hepatitis virus, CoVs are predominantly linked to gastrointestinal diseases [10]. The
emergence of novel CoVs may be facilitated by the simultaneous maintenance of multiple CoVs
in their natural hosts, increasing the likelihood of genetic recombination [10]. High genetic
diversity and the ability to infect multiple host species result from the high mutation rates in
CoVs, attributed to the low fidelity of RNA-dependent RNA polymerase and a high frequency of
homologous RNA recombination [10, 11].

Identifying the origin of SARS-CoV-2 and understanding its evolutionary pathway are critical
for effective disease surveillance [12]. However, a major limitation of the currently available
diagnostic kits is that they only detect active infections, restricting their usefulness to the early
stages of the disease. To overcome this limitation, several laboratories worldwide are developing
antibody-based diagnostic tests for SARS-CoV-2 [157].

Chest computed tomography (CT) is considered an ideal diagnostic tool for identifying viral
pneumonia, demonstrating far greater sensitivity than standard X-ray imaging. CT findings in
patients infected with COVID-19 commonly include patchy infiltrates that progress to ground-
glass opacities [158]. Early signs of COVID-19 pneumonia may not be apparent in chest X-rays;
in such cases, CT imaging is recommended due to its high specificity for COVID-19 pneumonia
[118]. Patients with COVID-19 typically exhibit these ground-glass opacities on chest CT
images [154]. Elevated plasma levels of angiotensin II have also been observed in COVID-19
patients. These levels correlate linearly with viral load and lung injury, indicating angiotensin II's
potential as a diagnostic biomarker [121]. Notably, CT imaging abnormalities indicative of
COVID-19 pneumonia have been detected even in asymptomatic individuals.

Several therapeutic and preventive strategies—including vaccines, immunotherapeutics, and

antiviral drugs—have been explored in response to previous coronavirus outbreaks, such as
SARS-CoV and MERS-CoV [8, 104, 164–167]. These approaches have been evaluated for their
potency, efficacy, and safety, and continue to guide ongoing research aimed at developing
effective treatments for COVID-19 [7, 9, 19, 21, 36].

The primary reason for the lack of approved commercial vaccines or therapeutics for SARS-CoV
and MERS-CoV is the limited attention they received from the biomedical and pharmaceutical
industries. These viruses did not cause the same level of global disruption and panic as SARS-
CoV-2. Furthermore, during such outbreaks, the demand for vaccines and therapeutics tends to
be short-lived, lasting only until the outbreak is contained. The relatively low global infection
rates of SARS-CoV and MERS-CoV failed to attract sufficient interest from drug and vaccine
manufacturers. Consequently, by the time effective treatments were developed, the outbreaks
were already under control through public health interventions.

Coronaviruses are a diverse group of viruses that infect a wide range of animals and can cause
respiratory illnesses in humans, ranging from mild to severe. In 2002 and 2012, two highly
pathogenic zoonotic coronaviruses—SARS-CoV and MERS-CoV—emerged and caused fatal
respiratory diseases in humans, highlighting the growing public health threat posed by emerging
coronaviruses in the 21st century.

In late 2019, a novel coronavirus known as SARS-CoV-2 emerged in Wuhan, China, leading to
an outbreak of atypical viral pneumonia. Due to its high transmissibility, this disease—named
coronavirus disease 2019 (COVID-19)—spread rapidly worldwide. It has far exceeded SARS
and MERS in both the number of cases and geographic spread. The ongoing COVID-19
pandemic poses an unprecedented global public health challenge.

This review summarizes the current understanding of the nature of SARS-CoV-2 and COVID-
19. Based on recent studies, it comprehensively covers the virus’s basic biology, including
genetic features, potential zoonotic origins, and receptor-binding mechanisms. Additionally, the
review discusses the clinical and epidemiological characteristics of the disease, diagnostic
approaches, and available countermeasures.

Emergence and Spread

In late December 2019, several health facilities in Wuhan, Hubei Province, China, reported
clusters of patients suffering from pneumonia of unknown origin[^6]. Similar to patients infected
with SARS and MERS, these individuals exhibited symptoms typical of viral pneumonia, such as
fever and cough. The envelope (E) protein plays an important role in the virulence of
coronaviruses. The absence of this protein is associated with altered pathogenicity, which is
believed to result from changes in viral morphology and tissue tropism[^54]. Structurally, the E
protein comprises three domains: a short hydrophilic amino-terminal domain, a large
hydrophobic transmembrane domain, and an efficient C-terminal domain[^51]. The E protein of
SARS-CoV-2 shares a similar amino acid composition with its counterparts in other
coronaviruses, with no significant substitutions detected[^16].

N Protein

The nucleocapsid (N) protein of coronaviruses serves multiple functions. It assists in the
formation of complexes with the viral genome, facilitates interaction with the membrane (M)
protein during virion assembly, and enhances the efficiency of viral transcription[^55,^56]. The
N protein consists of three highly conserved and distinct domains: the N-terminal domain (NTD),
the RNA-binding domain or linker region (LKR), and the C-terminal domain (CTD)[^57].

The NTD is believed to bind to the 3′ end of the viral genome, likely via electrostatic
interactions, and is highly variable in both sequence and length[^58]. The LKR, which is rich in
serine and arginine residues (also referred to as the SR domain), plays a critical role in RNA
binding and is capable of direct interaction with RNA in vitro[^59]. This domain is also involved
in cell signaling[^60,^61] and modulates the host’s antiviral response by antagonizing interferon
activity.

Practice Points from an Indian Perspective

At the time of writing this article, the risk of coronavirus transmission in India remains extremely
low. However, this may change in the coming weeks. Therefore, the following measures are
recommended:

 Healthcare providers should obtain a thorough travel history from all patients presenting with
respiratory symptoms, including any international travel within the past two weeks, and
inquire about contact with individuals who have recently traveled abroad and are showing
symptoms of illness.
 Triage systems should be implemented in outpatient departments to identify patients with
respiratory illness. Such patients should be provided with a basic surgical mask upon entry.
Healthcare workers examining them should also wear surgical masks.
 Clinicians must stay informed about the latest global and local developments regarding the
spread of COVID-19 and adapt clinical practices accordingly.
 Non-essential international travel should be avoided at this time to minimize the risk of viral
spread.
 The general public should refrain from circulating myths and misinformation about COVID-
19. Instead, they should help reduce panic and anxiety by sharing accurate, verified
information.

Conclusions

The emergence of SARS-CoV-2 has posed significant challenges to the healthcare, economic,
and public health infrastructure of China and, to a lesser extent, neighboring countries. Its
eventual impact on India remains to be seen. Nonetheless, future outbreaks of zoonotic viruses
are likely to persist. Therefore, in addition to current efforts to control this outbreak, proactive
strategies must be developed.

For instance, the inclusion of negative fecal viral nucleic acid test results as an additional
discharge criterion in laboratory-confirmed COVID-19 cases has been proposed[^326]. Although
the virus is genetically distinct, the pattern of emergence and transmission largely mirrors
previous encounters with other pathogenic coronaviruses. The key difference lies in its genetic
makeup and the timing of its emergence.

Mutations in the receptor-binding domain (RBD) of coronaviruses have enhanced their capacity
to infect new hosts, expanding their range globally[^85]. This represents a substantial threat to
both human and animal health. Advanced phylogeographic analysis using Bayesian methods
suggests that SARS-CoV-2 most likely originated from a SARS-like coronavirus circulating in
the Rhinolophus bat family[^86].

Further phylogenetic analysis of 10 whole-genome sequences of SARS-CoV-2 revealed

similarities to two bat-origin coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, both
reported in China in 2018[^17]. It has been confirmed that SARS-CoV-2 utilizes ACE2 as its
entry receptor and exhibits an RBD structure closely resembling that of SARS-CoV.

To mitigate severe illness and reduce exposure risks during outbreaks, the implementation of
robust surveillance and control measures remains essential[^53]. Research collaborations
between the human and veterinary health sectors are also necessary to identify animal reservoirs,
evaluate transmission risks, and formulate effective responses to emerging zoonotic diseases.

9. Vaccines

The novel coronavirus outbreak in Wuhan, China—now officially termed COVID-19—has

rapidly spread worldwide and poses a serious global health threat. Due to its pandemic nature,
various institutions, including the National Institutes of Health (NIH) and several pharmaceutical
companies, are actively involved in the development of vaccines against COVID-19. Xu
Nanping, China's Vice-Minister of Science and Technology, announced that the first vaccine
candidate was expected to be ready for clinical trials in China by the end of April 2020[^54]. As
of now, there is no approved vaccine or specific treatment available for COVID-19 infections.
Vaccine development efforts are being supported by the Biomedical Advanced Research and
Development Authority (BARDA), which is part of the Office of the Assistant Secretary for
Preparedness and Response (ASPR). For instance, Sanofi is utilizing its egg-free recombinant
DNA technology to produce a precise genetic match to viral proteins involved in COVID-
19[^55]. Protecting the mental health of medical workers involved in pandemic response is also
of paramount importance. The stress placed on healthcare professionals can impair their
attention, decision-making abilities, and overall performance. Thus, timely interventions to
safeguard their psychological well-being are crucial for an effective outbreak response[^229].

Since live mammals sold in wet markets are suspected to act as intermediate hosts for SARS-
CoV-2, there is an urgent need to strengthen regulatory mechanisms governing the wildlife
trade[^13]. The number of confirmed COVID-19 cases continues to rise, while the recovery rate
remains comparatively low, complicating disease control efforts. The Chinese government has
undertaken various emergency measures to contain the outbreak, including the rapid construction
of hospitals dedicated to treating COVID-19 patients[^230]. Effective control of SARS-CoV-2
transmission requires aggressive public health interventions such as intensive contact tracing,
mandatory quarantine for suspected cases, and isolation of confirmed patients. The combined
implementation of such preventive and control strategies is essential to reduce the basic
reproduction number (R₀) and limit further spread of the virus[^228]. COVID-19 should be
managed with infection control protocols similar to those used for Category A biological agents
(e.g., cholera, plague). Patients should be placed in individual rooms or cohorted. While negative
pressure rooms are not mandatory, all surfaces, rooms, and equipment must be regularly
disinfected—preferably using sodium hypochlorite. Healthcare workers should be equipped with
properly fitted N95 respirators, protective gowns, gloves, and goggles. Airborne precautions
should be implemented during aerosol-generating procedures, such as intubation, suctioning, and
tracheostomy. All contacts, including healthcare providers, must be actively monitored for the
development of COVID-19 symptoms. Patients may be discharged from isolation once they have
been afebrile for at least three consecutive days and have tested negative for SARS-CoV-2 on
two successive molecular tests taken at least 24 hours apart. This differs from discharge
protocols for pandemic influenza, where viral shedding patterns vary.

Animal Models and Cell Cultures

To evaluate the efficacy of vaccines and therapeutics against coronaviruses—including

SARS-CoV, MERS-CoV, and the emerging SARS-CoV-2—appropriate animal models that
accurately replicate human disease are essential[^211,^212]. Various animal models have been
tested for their suitability in studying SARS and MERS infections, including mice, guinea pigs,
golden Syrian hamsters, ferrets, rabbits, and non-human primates such as rhesus macaques,
marmosets, and cats[^185,^213–^218]. One major obstacle in developing effective animal
models has been the virus's specificity to human angiotensin-converting enzyme 2 (hACE2), the
receptor utilized by SARS-CoV. To overcome this barrier, transgenic mouse models have been
created by introducing the hACE2 gene into the mouse genome, thereby allowing SARS-CoV
infection and replication[^219]. Similarly, MERS-CoV has shown limited replication in the
respiratory tracts of mice, hamsters, and ferrets, which has posed challenges in model
development. This issue has been addressed by genetically engineering mouse models that
express human dipeptidyl peptidase 4 (hDPP4), the MERS-CoV receptor. These include hDPP4-
transduced mice and transgenic mice expressing human DPP4, which are now being used for
evaluating novel drugs and vaccine candidates against MERS-CoV[^220,^245,^246].

Small animal models such as mice and hamsters are particularly valuable due to their genetic
modifiability and cost-effectiveness. Modifications such as human receptor expression enhance
their utility in mimicking human infections and disease progression. In relation to SARS-CoV-2,
viral loads in infected individuals were measured using N gene-specific quantitative RT-PCR.
Throat swab and sputum samples indicated that viral loads peaked approximately 5 to 6 days
after symptom onset, with concentrations ranging from 10⁴ to 10⁷ copies/mL during this
period[^151]. Additional studies have shown that viral loads are typically higher in nasal swabs
compared to throat swabs in symptomatic COVID-19 patients[^82].

Although early assumptions linked high viral load to severe outcomes, some case reports have
documented asymptomatic individuals carrying high viral titers[^247]. In one study involving 17
symptomatic patients, higher viral loads were observed soon after symptom onset, particularly in
nasal swabs. The viral shedding pattern of SARS-CoV-2 resembled that of influenza more than
that of SARS-CoV, indicating a different transmission dynamic. Interestingly, viral loads in
asymptomatic individuals were comparable to those in symptomatic patients, highlighting the
significant risk of transmission from individuals showing few or no clinical signs[^82].

6.1 Laboratory Testing for Coronavirus Disease 2019 (COVID-19) in Suspected

Human Cases

The assessment of patients suspected to have COVID-19 should be based on a combination of

clinical symptoms and epidemiological risk factors. Screening protocols must be adapted to the
local context to ensure relevance and efficacy[^31]. A cornerstone of outbreak control is the
prompt collection and testing of clinical specimens from suspected individuals. The
recommended diagnostic method is nucleic acid amplification testing (NAAT), particularly
reverse transcription polymerase chain reaction (RT-PCR), which detects SARS-CoV-2 RNA in
respiratory tract samples. If local diagnostic capacity is lacking, specimens should be shipped to
WHO-designated reference laboratories[^32].

In addition to testing for SARS-CoV-2, it is advisable to screen for other common respiratory
pathogens—such as influenza viruses, parainfluenza virus, adenovirus, respiratory syncytial
virus, and rhinovirus—according to local laboratory protocols. This differential diagnosis helps
rule out other causes of respiratory illness that may present similarly. A case is confirmed when
SARS-CoV-2 nucleic acid is detected in respiratory tract aspirates, saliva, or blood samples
using RT-PCR or when sequencing confirms the presence of SARS-CoV-2 genetic
material[^80]. A patient is considered cured once they are afebrile for at least three consecutive
days and yield two consecutive negative RT-PCR results from oral swabs collected at 24-hour
intervals[^153].

Recent studies have also demonstrated the reliability of self-collected saliva as a non-invasive
sample for diagnosis, offering a practical alternative in certain settings[^152]. However, it is
important to note that some COVID-19 patients may initially test negative by RT-PCR despite
showing positive chest CT findings. This underscores the importance of repeated RT-PCR
testing and CT imaging to minimize false-negative results and improve diagnostic
accuracy[^154]. Despite being the gold standard, RT-PCR has limitations, such as the inability to
assess disease severity or progression. In this context, droplet digital PCR (ddPCR) may be used
for more precise quantification of viral load, especially from lower respiratory tract samples.

Lastly, phylogenetic analyses—such as SplitsTree based on the spike (S) protein—have helped
clarify the classification of SARS-CoV-2 within the Sarbecovirus subgenus. SARS-CoV-2
sequences cluster closely with bat SARS-like CoVs and SARS-CoV, reaffirming its zoonotic
origin. Subgenera like Merbecovirus and Embecovirus form distinct clusters representing MERS-
CoV and other human and animal CoVs, respectively, while Nobecovirus and Hibecovirus
appear more distantly related but still share a common bat origin.
Current Worldwide Scenario of SARS-CoV-2

The novel coronavirus, SARS-CoV-2, belongs to the Sarbecovirus subgenus of the

Orthocoronavirinae subfamily. It is genetically distinct from other known human coronaviruses,
although it uses the angiotensin-converting enzyme 2 (ACE2) receptor to enter human cells—
similar to SARS-CoV[^17,^87,^254,^255]. Early in the outbreak, several countries issued travel
advisories for individuals planning to visit China[^88,^89]. Initially, the human-to-human
transmission efficiency of SARS-CoV-2 was thought to be lower than that of SARS-CoV and
MERS-CoV, based on the relatively lower infection rates among healthcare workers compared to
past outbreaks of these fatal coronaviruses[^2]. However, superspreading events—which played
a central role in the transmission of both SARS and MERS—are also suspected in the case of
COVID-19[^90,^91]. In fact, nearly half of MERS-CoV cases in Saudi Arabia were attributed to
secondary transmission from both symptomatic and asymptomatic individuals[^92]. Although
the full extent of superspreading in COVID-19 is still under investigation, it remains a likely
contributor to the virus's rapid global spread. Similar to SARS and MERS, SARS-CoV-2
primarily infects the lower respiratory tract, but often presents with milder symptoms[^27]. The
estimated basic reproduction number (R₀) for COVID-19 ranges from 2.8 to 3.3 based on real-
time case data, and from 3.2 to 3.9 based on predictive modeling[^84]. These figures indicate a
high potential for sustained transmission in human populations.

Importantly, virological, radiological, and pathological studies conducted in monkeys have

shown that re-exposure to the virus does not lead to reinfection. Monkeys that had recovered
from initial SARS-CoV-2 infection remained protected upon rechallenge, similar to non-
rechallenged controls. These results suggest that primary infection may confer protective
immunity, providing important insight into disease prognosis and supporting efforts toward
vaccine development[^274].

Prevention, Control, and Management

In contrast to its response during the 2002 SARS outbreak, China demonstrated notable political
transparency in addressing the COVID-19 pandemic. The country promptly reported the
outbreak, rapidly sequenced the virus at multiple levels, and shared genomic data globally within
days of identifying SARS-CoV-2[^225]. This action marked a significant advancement in global
health security and international collaboration. Despite the enforcement of a complete lockdown
in Wuhan, the massive internal migration that occurred during the Lunar New Year contributed
to the rapid spread of the virus to neighboring provinces and other countries. As a result, large-
scale screening programs became essential in early identification and containment of the virus.
SARS-CoV-2 is primarily transmitted through respiratory droplets produced when an infected
person coughs, sneezes, or speaks. These droplets can settle on surfaces and remain viable for
days under favorable environmental conditions. However, they are effectively inactivated within
minutes by common disinfectants such as sodium hypochlorite and hydrogen peroxide[^13].
Infection can occur either through direct inhalation of these droplets or by contact with
contaminated surfaces followed by touching the eyes, nose, or mouth.

Evidence also suggests the presence of the virus in stool, raising concerns about aerosolized
fecal-oral transmission and possible contamination of water supplies[^6]. However, current
studies indicate that transplacental transmission from infected pregnant women to the fetus has
not been documented, although postnatal transmission to neonates has been observed[^14]. The
incubation period for COVID-19 ranges from 2 to 14 days, with a median of 5 days.
Understanding this timeline is crucial for effective quarantine and monitoring measures.

From a molecular perspective, the SARS-CoV-2 genome encodes several open reading frames
(ORFs), including ORF1a/b, which occupies most of the 5′ end of the genome. Translation of
this region produces two polyproteins (pp1a and pp1ab) via a -1 ribosomal frameshift between
ORF1a and ORF1b[^31,^32]. These polyproteins are cleaved into nonstructural proteins (nsps)
by viral proteases such as main protease (Mpro), chymotrypsin-like protease (3CLpro), and
papain-like proteases (PLPs)[^42].

One distinguishing feature of SARS-CoV-2 compared to other coronaviruses is the presence of a

novel short putative protein within ORF3b, and a secreted protein encoded by ORF8, which
contains an alpha-helix and six-stranded beta-sheet[^31]. Additionally, coronaviruses, including
SARS-CoV-2, encode four major structural proteins: Spike (S) – facilitates viral entry by binding
to host receptors, Membrane (M) – shapes the viral envelope, Envelope (E) – involved in viral
assembly and release, Nucleocapsid (N) – binds the viral RNA genome and is critical for
replication and packaging.

These molecular insights are essential for understanding the virus’s pathogenicity and for guiding
the development of targeted therapeutics and vaccines.

S Glycoprotein

The spike (S) glycoprotein of coronaviruses is a large, multifunctional class I transmembrane

protein that plays a critical role in viral entry into host cells. This protein facilitates attachment to
the host cell receptor and subsequent fusion of the viral and host membranes, making it a key
target for vaccine and antiviral development.

Based on molecular characterization, SARS-CoV-2 is classified as a novel Betacoronavirus

within the subgenus Sarbecovirus[^3]. Although it shares its genus with other zoonotic
coronaviruses such as SARS-CoV and MERS-CoV, SARS-CoV-2 is genetically distinct. For
instance, the conserved open reading frame 1a/b (ORF1a/b) shares less than 90% sequence
identity with other betacoronaviruses[^3]. SARS-CoV-2 has an overall nucleotide identity of
approximately 80% with the original SARS-CoV, and a similar degree of identity with bat-
derived SARS-related coronaviruses ZC45 and ZXC21[^2,^31,^36]. Furthermore, an 82%
sequence identity was found between SARS-CoV-2 and human SARS-CoV strains Tor2 and
BJO1 (2003)[^31]. In contrast, the sequence identity between MERS-CoV and SARS-CoV-2 is
much lower, at only 51.8%[^37]. Phylogenetic analysis of structural genes reveals that SARS-
CoV-2 is most closely related to bat SARS-related coronaviruses, suggesting that bats are likely
the natural reservoir for this virus[^31]. This is consistent with the origins of both SARS-CoV
and MERS-CoV, which also trace back to bats, with civets and camels acting as intermediate
amplifier hosts, respectively[^38,^39]. While the exact cross-species transmission route of
SARS-CoV-2 remains unclear, current evidence suggests the involvement of one or more
intermediate hosts. Understanding the zoonotic spillover mechanisms remains a key priority in
pandemic prevention. Until clinically approved vaccines became widely available, personal
preventive behaviors—such as mask-wearing, social distancing, and hand hygiene—combined
with public health strategies like active testing, contact tracing, and limitations on social
gatherings, remained the most effective methods to curb viral transmission. Despite the surge in
research publications, our understanding of SARS-CoV-2 remains limited, and many aspects—
including its pathogenesis, host-virus interactions, and evolutionary trajectory—are yet to be
fully elucidated.

Several vaccine candidates targeting the S glycoprotein have shown promising results in early
trials: A recombinant adenovirus vector vaccine developed by the University of Oxford induced
neutralizing antibodies in 100% of 1,077 participants following a second dose during a
randomized, controlled phase I/II trial. The vaccine was also reported to have an acceptable
safety profile[^63]. The mRNA-1273 vaccine, co-developed by Moderna and the U.S. National
Institute of Allergy and Infectious Diseases (NIAID), encodes a stabilized prefusion form of the
SARS-CoV-2 S protein. It elicited robust dose-dependent neutralizing antibody responses, as
demonstrated in a phase I trial, with significantly boosted responses after the second dose[^64].
In China, a whole-virus inactivated vaccine underwent a successful phase I/II clinical trial with
320 participants. It demonstrated a low rate of adverse reactions and effectively induced
neutralizing antibodies, supporting its advancement to phase III trials for evaluating protective
efficacy in larger populations[^65].

These vaccine strategies, centered around the S glycoprotein, underscore its central role in both
viral infectivity and immune targeting, making it a crucial component of ongoing efforts to
control and eventually eliminate SARS-CoV-2.

Future Perspectives

COVID-19 represents the third major outbreak of a highly pathogenic human coronavirus
following SARS-CoV and MERS-CoV. While its case fatality rate is lower, the unprecedented
transmissibility of SARS-CoV-2 has rendered it the most significant global health crisis of the
21st century. The virus has sustained transmission for over half a year since its emergence, and
continues to spread globally—often driven by asymptomatic or mildly symptomatic individuals.
Radiological findings play a critical role in COVID-19 management. Lung abnormalities
typically begin as focal, unilateral ground-glass opacities and can progress to diffuse bilateral
patterns, often evolving into or coexisting with lung consolidations within 1 to 3 weeks after
symptom onset[^159]. In this context, radiologists are essential not only in the early detection of
pulmonary involvement but also in evaluating disease severity, identifying progression to acute
respiratory distress syndrome (ARDS), and detecting secondary bacterial infections[^160].

Although chest CT has been recognized as a valuable tool in diagnosing COVID-19 pneumonia,
its extensive use for routine screening—especially in asymptomatic or low-risk individuals—
raises concerns regarding the risk-benefit ratio. Overuse may lead to unnecessary radiation
exposure and increased risk of cross-infection in healthcare settings. Thus, CT imaging should be
used judiciously, particularly in high-risk populations or when clinical indications strongly
warrant it[^292]. In parallel, significant strides have been made in the development of novel
diagnostic technologies. One promising advancement is reverse transcription loop-mediated
isothermal amplification (RT-LAMP) assays, such as iLACO, which enable rapid, sensitive, and
colorimetric detection of SARS-CoV-2[^345,^347,^350–^352]. These methods offer practical
alternatives to traditional PCR-based tests, particularly in resource-limited settings. On the
therapeutic front, several agents have shown in vitro antiviral activity against SARS-CoV-2.
However, many of these candidates lack validation through randomized animal or human clinical
trials, limiting their clinical utility at this stage of the pandemic[^7,^9,^19–^21]. Robust clinical
evaluation is critical to translate these findings into safe and effective treatments.

This comprehensive review has discussed the key molecular, clinical, diagnostic, and
epidemiological features of SARS-CoV-2 and COVID-19. It has also compared SARS-CoV-2
with its predecessors—SARS-CoV and MERS-CoV—and outlined the veterinary and zoonotic
perspectives. Understanding the One Health implications of this and other emerging
coronaviruses is vital for the development of integrated management strategies that include
human, animal, and environmental health components.

As research continues, emphasis must be placed on: Unraveling the molecular mechanisms of
viral infection and immune evasion, Clarifying the animal origin and interspecies transmission
pathways, Refining diagnostic tools for early and accurate detection, Developing broadly
protective vaccines and evidence-based therapeutics, and Establishing sustainable global
surveillance and response systems. Only through such multidisciplinary and collaborative efforts
can we hope to effectively mitigate the impact of this pandemic and better prepare for future
zoonotic outbreaks.

The Virus (SARS-CoV-2)

Coronaviruses (CoVs) are positive-sense, single-stranded RNA viruses with a broad natural host
range and the ability to affect multiple organ systems[^23,^24]. They are known to cause a
spectrum of clinical illnesses in humans, ranging from mild upper respiratory infections (e.g., the
common cold) to severe respiratory syndromes such as SARS and MERS[^17,^279]. The most
recent member of this group, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2),
has caused widespread devastation, originating in China and evolving into a global pandemic,
with profound public health, social, and economic impacts[^10,^11]. Epidemiology and
Transmission SARS-CoV-2 can infect individuals of all age groups and is primarily transmitted
via respiratory droplets expelled during coughing, sneezing, or speaking by symptomatic
individuals. Importantly, transmission can also occur from asymptomatic individuals and during
the presymptomatic phase of infection[^9]. Studies show higher viral loads in nasal swabs
compared to throat swabs, with no significant difference in viral burden between symptomatic
and asymptomatic individuals[^12]. Infected individuals may remain contagious throughout their
symptomatic period and even after clinical recovery. Notably, superspreading events have played
a critical role in viral dissemination. One such case involved a UK national who, after attending a
conference in Singapore, infected 11 others during a stay in the French Alps before returning to
the UK[^6]. Infected droplets can travel 1–2 meters and contaminate surfaces, facilitating fomite-
based transmission. Pregnancy and Neonatal Concerns
The impact of SARS-CoV-2 infection during pregnancy has drawn significant attention. While
vertical (in utero) transmission remains controversial, some studies from China have documented
elevated levels of IgM, IgG, and inflammatory cytokines in neonates born to COVID-19-positive
mothers, despite negative RT-PCR results for viral RNA in these infants[^283]. There is also
evidence linking SARS-CoV-2 to preterm delivery and its complications[^240–^243]. Clinical
Features and Disease Severity Indicators
COVID-19 is frequently associated with viral pneumonia, which may progress to acute
respiratory distress syndrome (ARDS). Several blood biochemical markers are correlated with
disease severity, including reduced levels of albumin and lymphocytes, and elevated levels of
neutrophils, lactate dehydrogenase (LDH), C-reactive protein (CRP), aspartate aminotransferase
(AST), alanine aminotransferase (ALT), bilirubin, and particularly D-dimer[^121,^244].
Immunology and Vaccine Targets
Evidence suggests that antibodies targeting SARS-CoV-2 structural proteins, especially the spike
(S) and nucleocapsid (N) proteins, are promising candidates for vaccine
development[^170,^294]. Subunit vaccines under development in Asia specifically target the S,
E, M, and N proteins of SARS-CoV-2[^295]. Within the S protein, the C-terminal domain of the
S1 subunit is considered an immunodominant region, as demonstrated in porcine
deltacoronavirus, and is likely a crucial epitope for SARS-CoV-2 vaccine design as well[^171].
Efforts are ongoing to map the immunodominant epitopes within SARS-CoV-2 for the
development of more effective vaccines. Studies exploring T-cell epitope conservation across
SARS-CoV and MERS-CoV have raised the possibility of designing a universal vaccine
targeting shared regions among pathogenic coronaviruses[^172]. Given the close genetic
similarity between SARS-CoV-2 and SARS-CoV (over 80% nucleotide identity), cross-reactive
vaccine strategies are under investigation[^173,^174]. Zoonotic and Cross-Species Transmission.

Coronaviruses are known for their zoonotic potential, with bats considered a major natural
reservoir. For example, MERS-CoV can be shed by infected animals—including milk, urine,
feces, and nasal secretions—and has been detected in raw animal organs, raising public health
concerns[^108]. In a susceptibility study, llamas and pigs were also found to be potential
intermediate hosts for MERS-CoV, suggesting broader interspecies transmission routes[^109].
Following the 2003 SARS outbreak, SARS-CoV-like viruses were isolated from Himalayan
palm civets and raccoon dogs in live-animal markets in Guangdong, China. These animal-
derived isolates retained a 29-nucleotide sequence absent in most human SARS-CoV isolates,
implying host-specific adaptation and potential spillover[^78]. Coronaviruses have also been
found circulating in Chinese horseshoe bats (Rhinolophus sinicus), with evidence of host-
pathogen coevolution and genetic recombination[^78]. These observations underscore the urgent
need to monitor animal reservoirs, understand interspecies transmission, and strengthen One
Health approaches to prevent future zoonotic pandemics.

13. Convalescent Plasma Therapy

Convalescent plasma therapy (CPT) has emerged as a promising supportive treatment for
critically ill COVID-19 patients. According to Guo Yanhong, a senior official from China’s
National Health Commission (NHC), this method involves transfusing plasma collected from
individuals who have recovered from SARS-CoV-2 infection into patients with severe disease.
The rationale lies in the presence of neutralizing antibodies in the donor’s plasma, which may
help to reduce viral load and enhance clinical recovery. The first convalescent plasma donations
in Wuhan were collected from recovered patients on February 1 and 9, 2020, and subsequently
administered to critically ill patients in Jiangxia District. Notably, one such patient recovered and
was discharged from the hospital by mid-February, as reported by Chinese science authorities.
Plasma donation is considered safe for donors, with only plasma being extracted; the red blood
cells, white blood cells, and platelets are reinfused into the donor’s body. Typically, 200–300 mL
of plasma is collected, and donors generally regenerate this volume within one to two weeks
post-donation. Donors must meet strict eligibility criteria, including confirmed recovery and
discharge from the hospital.

Genomic analysis using MegAlign software revealed that SARS-CoV-2 isolates share 99.4%–
100% nucleotide identity among themselves. Comparatively, the highest sequence similarity with
other known coronaviruses was observed with bat-SL-CoV, with a nucleotide identity ranging
from 88.12% to 89.65%. In contrast, the similarity with previously reported SARS-CoV isolates
ranged between 70.6% to 74.9%. Similarity to other betacoronavirus subgenera (Hibecovirus,
Nobecovirus, Merbecovirus, and Embecovirus) ranged between 45.0% and 55.4%. These data
suggest that SARS-CoV-2 likely originated from bat coronaviruses, specifically those within the
subgenus Sarbecovirus, although further complete genomic studies are needed to confirm these
evolutionary relationships.

In the absence of virus-specific antivirals, various repurposed drugs have been investigated for
potential use against COVID-19. Drugs such as lopinavir/ritonavir and interferon-β1b, originally
developed for HIV and hepatitis, have demonstrated in vitro activity against MERS-CoV. In vivo
experiments in marmosets showed protective effects, and these agents were used in the
MIRACLE trial for MERS treatment.

In the context of SARS and COVID-19, lopinavir/ritonavir combined with ribavirin

demonstrated some clinical benefit; however, evidence from randomized trials in COVID-19 has
been inconclusive. Supportive care—including oxygen therapy, fluid resuscitation, and broad-
spectrum antibiotics for secondary infections—remains the cornerstone of treatment for
hospitalized patients[^192]. Some studies have explored the use of hydroxychloroquine and
azithromycin; however, results have been inconsistent. Several patients experienced QT interval
prolongation, and in some cases, therapy had to be discontinued[^307]. Therefore, further well-
controlled randomized clinical trials are required. Ivermectin, an FDA-approved antiparasitic
agent, has been shown to inhibit SARS-CoV-2 replication in vitro, with a ~5,000-fold reduction
in viral RNA after 48 hours in cell cultures[^308]. However, the cytotoxicity and high
concentrations required for effective viral inhibition limit its clinical applicability. Formulation
adjustments and pharmacokinetic modifications are under exploration, though therapeutic plasma
levels in humans are unlikely to match those effective in vitro. Chloroquine and
hydroxychloroquine initially showed promise in reducing fever and viral load, but subsequent
clinical evidence failed to confirm their efficacy across broader populations. Tocilizumab, an IL-
6 receptor antagonist, has been employed in selected cases to control the cytokine release
syndrome associated with severe COVID-19. Although based on theoretical immunopathology
and preliminary data, its role remains adjunctive and investigational[^66].

15. HOME CARE

Home management may be appropriate for patients with mild COVID-19 infection who can be
adequately isolated in an outpatient setting. The primary goals of care are to prevent transmission
to others and to monitor for clinical deterioration, which may necessitate hospitalization. Interim
recommendations on home care management for COVID-19 patients are available from relevant
health authorities.

The pathogenesis of SARS-CoV-2 infection in humans ranges from mild symptoms to severe
respiratory failure. Upon binding to epithelial cells in the respiratory tract, SARS-CoV-2 begins
replicating and spreads down the airways, eventually infecting alveolar epithelial cells in the
lungs. Rapid viral replication may trigger a strong immune response. A cytokine storm can lead
to acute respiratory distress syndrome (ARDS) and respiratory failure, which are the primary
causes of death in patients with COVID-19. Older adults (over 60 years) and individuals with
serious pre-existing conditions are at a higher risk of developing ARDS and fatal outcomes.
Multi-organ failure has also been observed in some cases.

Histopathological findings in COVID-19 patients primarily involve the lungs. Histological

analysis has revealed bilateral diffuse alveolar damage, hyaline membrane formation,
pneumocyte desquamation, and fibrin deposition in the lungs of severely affected patients. In
some cases, exudative inflammation was also present. Immunohistochemistry studies detected
SARS-CoV-2 antigens in the upper airway, bronchiolar epithelium, submucosal gland
epithelium, type I and II pneumocytes, alveolar macrophages, and hyaline membranes.

Animal models used to study SARS-CoV-2 pathogenesis include non-human primates (rhesus
macaques, cynomolgus monkeys, marmosets, and African green monkeys), wild-type and
transgenic mice expressing human ACE2, ferrets, and golden hamsters. These models,
particularly rhesus macaques, exhibit clinical features similar to those observed in human
COVID-19 cases, including viral shedding, replication, and immune responses.

Initially, the epicenter of the SARS-CoV-2 outbreak was China, with 84,458 laboratory-
confirmed cases and 4,644 deaths reported by 13 May 2020. By that time, confirmed cases had
been reported in over 210 countries. COVID-19 had spread to all continents except Antarctica.
Italy initially became the focus due to high case numbers, with 221,216 cases and 30,911 deaths,
but the United States later reported the highest numbers globally, with 1,322,054 cases and
79,634 deaths. The United Kingdom subsequently surpassed Italy in both case count and
mortality. The Johns Hopkins University web platform has provided daily updates on the global
epidemiology of the pandemic. In vitro studies evaluating the antiviral potential of FDA-
approved drugs—including ribavirin, penciclovir, nitazoxanide, nafamostat, and chloroquine—
compared to broad-spectrum antivirals such as remdesivir and favipiravir, found that remdesivir
and chloroquine were most effective in vitro. Ribavirin, penciclovir, and favipiravir required
higher concentrations to achieve efficacy and may not be viable in vivo options. Since remdesivir
and chloroquine are already approved for human use, they are being explored for COVID-19
treatment.
Several therapeutic agents—such as lopinavir/ritonavir, chloroquine, and hydroxychloroquine—
have been considered for clinical use. Molecular docking studies targeting the RNA-dependent
RNA polymerase (RdRp) of SARS-CoV-2 showed that ribavirin, remdesivir, galidesivir,
tenofovir, and sofosbuvir bind tightly to the enzyme, indicating potential antiviral
[Link] the first 27 hospitalized cases, most were epidemiologically linked to the
Huanan Seafood Wholesale Market in Wuhan, which sold seafood and live animals, including
poultry and wildlife. A retrospective study suggested that the earliest known case dates back to 8
December 2019. On 31 December, the Wuhan Municipal Health Commission reported a
pneumonia outbreak of unknown cause and informed the World Health Organization
(WHO).Through metagenomic RNA sequencing and virus isolation from bronchoalveolar lavage
fluid, Chinese scientists identified a novel betacoronavirus as the causative agent. The
identification was publicly announced on 9 January 2020. The first genome sequence of the virus
was published on 10 January, with additional sequences released via the GISAID database by 12
January. Later, more cases were identified without any link to the market, suggesting human-to-
human transmission. Familial clusters and nosocomial infections were also reported. The
outbreak coincided with the Lunar New Year, during which travel likely accelerated the spread
across China and beyond.

Multiple COVID-19 vaccine candidates are in preclinical and clinical development. These
include live attenuated and inactivated virus vaccines, adenovirus vector vaccines, lipid
nanoparticle (LNP)-encapsulated mRNA vaccines, DNA plasmid vaccines, and subunit protein
vaccines using S protein, S-trimer, or Ii-Key peptide antigens. Although vaccine development
typically takes around ten years, accelerated processes—like those used during the Ebola
outbreak—have shortened this to around five years. For COVID-19, rapid development has been
enabled by advances in computational biology, gene synthesis, protein engineering, and
manufacturing technologies. A pan-coronavirus vaccine producing cross-reactive antibodies is
considered a critical long-term goal.

N Protein

The nucleocapsid (N) protein of coronaviruses is multifunctional. Among its various roles, it
forms a complex with the viral genome, facilitates interaction with the membrane (M) protein
during virion assembly, and enhances viral transcription efficiency (55, 56). It comprises three
highly conserved and distinct domains: the N-terminal domain (NTD), a central RNA-binding
linker region (LKR), and the C-terminal domain (CTD) (57).

The NTD binds to the 3′ end of the viral genome, likely through electrostatic interactions, and
shows substantial variability in both length and sequence among coronaviruses (58). The linker
region (LKR), which is rich in serine and arginine residues, is also referred to as the SR
(serine/arginine) domain (59). This domain can directly interact with RNA in vitro and is also
involved in cellular signaling pathways (60, 61).

Moreover, the N protein modulates the host antiviral response by acting as an antagonist of
interferon (IFN) signaling and RNA interference mechanisms (62). Compared to the N protein of
SARS-CoV, that of SARS-CoV-2 contains five amino acid substitutions: two in the intrinsically
disordered region (IDR; at positions 25 and 26), and one each in the NTD (position 103), LKR
(position 217), and CTD (position 334) (16).

Non-Structural and Accessory Proteins

Preventing zoonotic spillover from mammalian species is essential to avoid future outbreaks of
coronaviruses (1).
 Personal protective equipment (PPE), such as face masks, plays a critical role in preventing
the spread of respiratory infections like COVID-19. Masks not only protect individuals from
infectious aerosols but also reduce transmission from infected individuals to others, particularly
in public transportation settings (313). Another key preventive measure is maintaining hand
hygiene. However, its effectiveness against respiratory viruses like SARS-CoV-2 largely
depends on the size of the droplets. Hand hygiene is most effective if transmission occurs via
large droplets (314). Therefore, overemphasizing hand hygiene as a primary preventive measure
may create a false sense of security and inadvertently contribute to the spread of COVID-19.
Although airborne transmission of SARS-CoV-2 has not been definitively confirmed, droplet and
fomite transmission remains a major concern, especially in situations involving close and
unprotected contact. Hand hygiene remains an important, though not sole, preventive strategy.

The spike (S) protein of SARS-CoV-2 differs from that of SARS-CoV in five key amino acid
residues that are critical for binding to the ACE2 receptor: Y455L, L486F, N493Q, D494S, and
T501N (FIG. 5b, c). These mutations enhance the binding affinity of SARS-CoV-2 to the human
ACE2 (hACE2) receptor by stabilizing two virus-binding hotspots on the receptor surface (REF
50). A unique four-residue motif (G-V-E-G; positions 482–485) in the receptor-binding motif
(RBM) of SARS-CoV-2 forms a more compact hACE2-binding ridge, facilitating stronger
interactions with the N-terminal helix of hACE2.

As with other coronaviruses, the S protein of SARS-CoV-2 must be cleaved by host proteases for
activation and cellular entry via the endocytic pathway. Host proteases involved include
TMPRSS2, cathepsin L, and furin. Single-cell RNA sequencing has revealed co-expression of
TMPRSS2 and ACE2 in nasal epithelial cells, lungs, and bronchial branches, supporting the
observed tissue tropism of SARS-CoV-2 (REFs 56, 57). Pseudovirus entry assays show that
TMPRSS2 and cathepsin L act synergistically with furin to facilitate viral entry (55). Cryo-
electron microscopy analysis has demonstrated that the receptor-binding domain (RBD) of the
SARS-CoV-2 S protein primarily adopts a "lying-down" conformation, in contrast to the
"standing-up" and "lying-down" states seen in SARS-CoV. While the "lying-down" state may
limit receptor binding, it may aid immune evasion (55).

Laboratory and Clinical Features

Initial laboratory findings in COVID-19 cases are often nonspecific. White blood cell counts may
be normal or low, and lymphopenia (lymphocyte count <1,000/µL) is commonly associated with
severe cases. Platelet counts are typically normal or mildly reduced. Inflammatory markers such
as CRP and ESR are usually elevated, whereas procalcitonin levels remain normal—elevated
levels may suggest bacterial co-infection. Other laboratory abnormalities in severe disease
include elevated ALT/AST, prolonged prothrombin time, increased creatinine, D-dimer, CPK,
and LDH levels.

Radiographic findings on chest X-ray (CXR) often reveal bilateral infiltrates but may appear
normal early in the disease course. CT imaging is more sensitive and specific, commonly
showing ground-glass opacities and subsegmental consolidation.

Therapeutic Approaches

Neutralizing antibodies targeting the receptor-binding interface (RBI) of the S protein have
shown therapeutic potential in COVID-19. These antibodies may be used alone or in
combination with other effective neutralizing agents (202). SARS-CoV-specific antibodies such
as m396 and CR3014 do not bind SARS-CoV-2 S protein, underscoring the need for structural
similarity in RBDs for cross-reactivity.
Broad-spectrum antiviral agents are under investigation. Remdesivir has shown promise due to
its wide antiviral activity and is being evaluated for efficacy in human COVID-19 cases.
Chloroquine, an antimalarial drug, inhibits virus-cell fusion by increasing endosomal pH and
disrupts virus-receptor interaction by affecting ACE2 glycosylation (196). A multicenter clinical
trial in China reported that chloroquine phosphate is both effective and safe in treating SARS-
CoV-2-associated pneumonia (197). Hydroxychloroquine, often combined with azithromycin,
demonstrated viral load reduction in early studies, although these trials involved small sample
sizes and require further validation (271).

Passive immunotherapy using convalescent plasma or immune serum—such as that from MERS-
immune camels—has shown protective effects in animal models and is being explored for
treating critically ill COVID-19 patients (204, 205).

Epidemiology and Preparedness

Epidemiological modeling estimated a doubling time of 1.8 days during the early phase of the
outbreak [10]. On February 12, 2020, China revised its case definition to include clinically
diagnosed cases without positive molecular tests, leading to a single-day increase of 15,000 new
cases [6]. As of March 5, 2020, over 96,000 cases had been reported worldwide, including
80,000 in China, across 87 countries and one international cruise ship (Diamond Princess) [2].
While new cases declined in China, they surged in other countries like South Korea, Italy, and
Iran.

Approximately 20% of infected individuals develop critical illness. Asymptomatic and atypical
cases—presenting with nonspecific symptoms like fatigue without respiratory symptoms—
complicate diagnosis and containment efforts. Clinicians must maintain a high index of suspicion
to avoid missed diagnoses.

Future Directions

The current SARS-CoV-2 outbreak was, in many ways, anticipated. Although containment is
expected, the key concern remains: how prepared are we for the next coronavirus pandemic?
Most bat coronaviruses remain uncharacterized. Proactive screening, isolation, and genetic
characterization of coronaviruses in wildlife, especially bats in China, should be prioritized. Both
in vitro and in vivo studies, using relevant animal models, are crucial for preparedness and future
outbreak mitigation.

Keywords: 2019-nCOV, SARS-C0V-2,

COVID-19, Pneumonia, Review

Introduction

The 2019 novel coronavirus (2019-nCoV), now officially named severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2), originated in Wuhan City, Hubei Province, China, and
has since spread rapidly across the globe [1]. As of March 5, 2020, approximately 96,000 cases
of coronavirus disease 2019 (COVID-19) and over 3,300 deaths had been reported worldwide
[2]. At that time, India had confirmed 29 cases. Fortunately, children appeared to be infrequently
affected, with no reported fatalities. However, the future trajectory of this viral outbreak remains
uncertain. This article provides a concise overview of the virological features of SARS-CoV-2,
focusing particularly on its key antigenic epitopes, especially those targeted by neutralizing
antibodies. Among the structural proteins, the spike (S) protein plays a pivotal role in viral entry.
This protein undergoes conformational changes to facilitate the fusion of the viral envelope with
the host cell membrane [19, 20]. Recent studies on SARS-CoV have demonstrated that the
angiotensin-converting enzyme 2 (ACE2), a membrane-bound exopeptidase, serves as the
functional receptor for SARS-CoV-2, enabling the virus to enter human cells [21].

Figure 1.

The coronavirus S (spike) protein is a large, multifunctional class I viral transmembrane protein,
ranging in size from approximately 1,160 amino acids (as in infectious bronchitis virus in
poultry) to 1,400 amino acids (in feline coronavirus, FCoV) [43]. It assembles into a trimer on
the surface of the virion, giving the virus its characteristic crown-like ("corona") appearance.

Functionally, the S protein is essential for viral entry into host cells, as it interacts with various
cellular receptors [44]. It also plays a critical role in determining host range and tissue tropism
[45]. Importantly, the S protein is a major immunodominant antigen capable of eliciting strong
host immune responses.

Structurally, the S protein's ectodomain is divided into two subunits: S1 and S2. The S1 subunit
is responsible for receptor binding, while S2 mediates membrane fusion. Within S1, two
subdomains—the N-terminal domain (NTD) and the C-terminal domain (CTD)—function as
receptor-binding domains (RBDs), with the CTD containing the receptor-binding motif (RBM)
[45].
In the trimeric spike configuration, the S1 subunits are located on top of the S2 subunits.

Animal Model Observations:

In ACE2-transgenic mice infected with SARS-CoV-2, typical interstitial pneumonia developed,
and viral antigens were predominantly detected in bronchial epithelial cells, macrophages, and
alveolar epithelial cells. Some mice succumbed to the infection [70,71]. A mouse-adapted strain
carrying the N501Y mutation in the RBD of the S protein also caused interstitial pneumonia in
both young and aged wild-type mice.

Golden hamsters exhibited classical respiratory symptoms post-infection, while cats and ferrets
supported viral replication mainly in the upper respiratory tract without showing severe illness
[43,78]. Notably, SARS-CoV-2 transmission through direct contact and aerosols was observed in
ferrets and hamsters, making them valuable models for studying transmission dynamics [77–79].

These animal models provide critical insights into SARS-CoV-2 pathogenesis and are essential
tools for evaluating the efficacy of antiviral drugs and vaccines.

Clinical and Epidemiological Features

SARS-CoV-2 infection can affect individuals across all age groups, though the median age of
infection is around 50 years. Clinical outcomes, however, vary significantly with age. In general,
older males (>60 years) with pre-existing comorbidities are more likely to develop severe
respiratory illness requiring hospitalization. Regarding the origin of SARS-CoV-2, sequence
comparisons have shown that pangolin coronaviruses from Guangxi province are less similar to
SARS-CoV-2 than those from Guangdong, sharing only ~85.5% genome identity [39]. Despite
having receptor-binding domains (RBDs) that resemble those of SARS-CoV-2 [40], the
pangolins infected during illegal smuggling events exhibited clinical illness and histopathological
changes, such as interstitial pneumonia and inflammation in multiple organs. This suggests that
pangolins may not be the natural reservoirs of the virus, unlike bats, which typically remain
asymptomatic carriers. Instead, pangolins might have acquired the virus after spillover from a
natural host, likely during illegal wildlife trade. This parallels previous coronavirus outbreaks,
where intermediate hosts played a pivotal role—for example, palm civets in SARS-CoV and
dromedary camels in MERS-CoV. In those cases, viruses found in the intermediate hosts were
nearly genetically identical to those infecting humans (>99% sequence identity).

Although the pangolin coronavirus RBDs are nearly identical to SARS-CoV-2’s, their overall
genome identity remains below 92%, making it unlikely that pangolins were the intermediate
host responsible for SARS-CoV-2's emergence [REF 42]. Current evidence does not support a
direct role of pangolins in initiating the outbreak. Genomic analyses have also identified a single
nucleotide polymorphism at position 28,144, resulting in a Serine-to-Lysine substitution at
position 84 of the ORF8 protein. Variants carrying this mutation belong to a specific subclade,
referred to as ―clade S‖ [33, 34]. However, available genomic data remain insufficient to
definitively reconstruct the early global transmission history of SARS-CoV-2. Factors such as
travel patterns, founder effects, and public health interventions have also significantly influenced
the spread of specific viral lineages, often independently of biological differences between
variants.

Animal Host and Spillover

Bats are recognized as natural reservoirs for many alphacoronaviruses and betacoronaviruses.
The closest known relative to SARS-CoV-2 is a bat coronavirus named RaTG13, which was
detected in Rhinolophus affinis bats from Yunnan Province, China. The full-length genome of
RaTG13 shares 96.2% sequence identity with SARS-CoV-2, including more than 90% identity
across all open reading frames (ORFs), even in highly variable regions such as the spike (S) gene
and ORF8 [REF 11].

Phylogenetic analyses consistently show that SARS-CoV-2 clusters closely with RaTG13,
strongly supporting the hypothesis that bats, particularly Rhinolophus species, serve as the
primary reservoir for the virus [35]. More recently, another related coronavirus was detected in a
Rhinolophus malayanus bat, further reinforcing the role of bats in the evolutionary origin of
SARS-CoV-2. Despite their genetic closeness, SARS-CoV-2 is still distinct from SARS-CoV
and MERS-CoV, sharing approximately 79% and 50% genomic similarity with them,
respectively [17]. Clinically, SARS-CoV-2 infection is universally associated with pulmonary
involvement, presenting with characteristic chest CT findings, including multiple ground-glass
opacities, often located in multiple lung lobes. These lesions may coexist with consolidation
shadows, providing radiographic clues that support the diagnosis of COVID-19 [18].

Diagnosis of SARS-CoV-2 (COVID-19)

The diagnosis of SARS-CoV-2 (COVID-19) primarily relies on the detection of viral RNA,
using real-time reverse transcription polymerase chain reaction (RT-PCR) or next-generation
sequencing (NGS) methods [148, 149, 245, 246]. Currently, RT-PCR is the gold standard for
confirming COVID-19 infection in clinical settings [148]. In response to the global demand,
multiple companies and laboratories worldwide have developed and marketed SARS-CoV-2-
specific nucleic acid detection kits. For instance, Shuoshi Biotechnology has developed a double
fluorescence PCR kit for SARS-CoV-2 detection [150]. As of March 30, 2020, the U.S. Food
and Drug Administration (FDA) had issued 22 Emergency Use Authorizations (EUAs) for in
vitro diagnostic tests, including the CDC-developed RT-PCR diagnostic panel, which enables
both universal detection of SARS-like betacoronaviruses and specific detection of SARS-CoV-2
[258, 259]. Serological testing complements molecular diagnostics, particularly for retrospective
assessments or late-stage infections. These tests detect antibodies against nucleocapsid (N) or
spike (S) proteins, but vary in sensitivity and specificity. Their interpretation must consider the
timing of infection and variability in immune response, which remains not fully understood.
Future approaches may also explore T-cell response assays.

Typical symptoms of COVID-19 include fever, fatigue, and dry cough. Less frequent symptoms
are sputum production, headache, hemoptysis, diarrhea, anorexia, sore throat, chest pain, chills,
nausea, and vomiting. In some countries like Italy, patients frequently reported loss of smell
(anosmia) and taste (ageusia) [85]. The incubation period ranges from 1 to 14 days, with a
median of around 5 days. In many cases, dyspnea and pneumonia develop within a median of 8
days from symptom onset. According to a report on 72,314 COVID-19 cases in China,

 81% were mild

 14% were severe (requiring hospitalization)
 5% were critical, involving respiratory failure, septic shock, or multi-organ dysfunction [86].

On imaging, chest CT scans frequently reveal bilateral, multilobar ground-glass opacities,

predominantly in peripheral or posterior lung regions [118, 119]. These findings are especially
helpful when RT-PCR results are negative but clinical suspicion remains high. In such cases, CT
imaging combined with repeated swabs is suggested. Laboratory findings often show marked
lymphopenia, especially in non-survivors, mirroring observations in SARS and MERS patients.

Introduction

Over the past two decades, coronaviruses (CoVs) have been responsible for significant disease
outbreaks, particularly in East Asia and the Middle East. The severe acute respiratory syndrome
(SARS) emerged in 2002, followed by the Middle East respiratory syndrome (MERS) in 2012.
Most recently, a novel coronavirus—severe acute respiratory syndrome coronavirus 2 (SARS-
CoV-2)—was identified in late 2019, causing coronavirus disease 2019 (COVID-19). This virus
has led to a global pandemic, affecting nearly every country and territory worldwide [1]. The
novel coronavirus, initially named 2019-nCoV, was first reported in Wuhan City, Hubei
Province, China, on 12 December 2019. On 11 February 2020, the World Health Organization
(WHO) officially named the disease COVID-19, and its causative agent SARS-CoV-2. The
earliest identified cluster of cases was linked to the Huanan South China Seafood Market in
Wuhan [2].

Coronaviruses belong to the family Coronaviridae, subfamily Coronavirinae, and infect a broad
range of hosts. Although SARS-CoV-2 shares high genome sequence similarity with SARS-like
CoVs, comparative analyses have revealed unique features. Notably, a furin-like cleavage site in
the spike (S) protein of SARS-CoV-2, which is absent in other SARS-like CoVs, is hypothesized
to enhance viral entry and pathogenicity, and may serve as a potential therapeutic target for furin
inhibitors [99].

Additionally, a stabilizing mutation in the endosome-associated protein-like domain of

nonstructural protein 2 (nsp2) may contribute to the higher transmissibility of SARS-CoV-2
compared to earlier coronaviruses. Conversely, a destabilizing mutation near the phosphatase
domain of nsp3 might reflect a functional divergence from related CoVs [100]. Despite the case
fatality rate (CFR) for COVID-19 being lower than those for SARS and MERS, the sheer scale
of transmission has resulted in more deaths than SARS and MERS combined [101]. Further
insights into viral attenuation have been gained from the discovery of an 832-nucleotide deletion
in ORF8, which appears to reduce viral replication and results in a less virulent phenotype [256].

Coronaviruses are a prime example of emerging zoonotic pathogens with pandemic potential. As
Fan et al. [6] previously predicted, another outbreak was likely—and the emergence of SARS-
CoV-2 affirms this warning. While the current pandemic may eventually be contained, the more
critical question is how prepared we are to face future zoonotic CoV epidemics, which could
arise within the next 5 to 10 years—or even sooner (Fig. 7).

14. Antiviral Therapy

COVID-19 is an infectious disease caused by the novel coronavirus SARS-CoV-2, which is

closely related to the virus responsible for SARS. In an effort to identify effective treatments, the
Ministry of Science and Technology of the People's Republic of China initially proposed three
potential antiviral drugs: Favilavir, chloroquine phosphate, and remdesivir. Clinical trials
indicated that Favilavir demonstrated efficacy in treating patients with COVID-19, while the
other two drugs were primarily effective against malaria, and showed limited benefit against
COVID-19 [62].

In the United States, the National Institutes of Health (NIH) found that remdesivir was effective
in treating Middle East respiratory syndrome coronavirus (MERS-CoV), another zoonotic
coronavirus. Based on these findings, remdesivir was later repurposed for use in patients with
COVID-19. Additionally, the combination of lopinavir and ritonavir, both protease inhibitors
used in HIV therapy, was proposed as a potential treatment option for COVID-19, though with
limited conclusive evidence [62].

Understanding the inflammatory response in the lungs associated with SARS-CoV-2 is crucial in
evaluating the effectiveness of antiviral therapies [24].
SARS, caused by a previously unidentified animal coronavirus, emerged from wet markets in
southern China in 2002, adapting to human hosts and enabling human-to-human transmission
[90]. The SARS outbreak (2002–2003) resulted in 8,098 confirmed cases and 774 deaths, with a
case fatality rate (CFR) of 9.6% [93]. Although the CFR of SARS-CoV-2 is lower, its rapid and
widespread transmission, akin to that of influenza viruses, poses serious challenges to public
health systems and has triggered a global pandemic [95, 96].

MERS, first reported in Saudi Arabia in 2012, had a much higher CFR of approximately 35%
[97]. Despite differences in severity, the incubation period for SARS-CoV-2 is similar to that of
SARS-CoV and MERS-CoV, with the longest reported duration being 14 days. Consequently,
individuals suspected of infection are typically isolated for 14 days to limit further transmission
[98].

Studies on SARS-CoV-2 viral load have revealed active replication in the upper respiratory tract,
and importantly, prolonged viral shedding even after clinical symptoms resolve. Viral RNA has
also been detected in stool samples, raising concerns about fecal–oral transmission and
necessitating updates to biosafety protocols and case definitions [248]. In a study of 17 patients,
53% had detectable viral RNA in stool samples collected between days 0 and 11 after symptom
onset. Although these viral loads were lower than those found in respiratory samples, the
findings have biosafety implications, particularly during sample handling [151].

A separate study of 18 patients in Singapore, all of whom had traveled from Wuhan, detected
viral RNA in stool and whole blood, but not in urine, further supporting the need for multi-
specimen testing [288]. Additionally, SARS-CoV-2 has been identified in various clinical
samples, including bronchoalveolar lavage fluid. In pediatric case series, all infected children
recovered with basic treatment and did not require intensive care [17].

There is anecdotal experience with the use of remdesivir, originally developed to treat Ebola
virus, as a broad-spectrum antiviral agent in COVID-19 patients [27]. However, more rigorous
clinical data are needed before firm treatment recommendations can be made. Other proposed
therapies include:

 Arbidol, an antiviral agent available in Russia and China

 Intravenous immunoglobulin (IVIG)
 Interferons
 Chloroquine and hydroxychloroquine
 Convalescent plasma from recovered COVID-19 patients [21, 28, 29]

In addition, the use of traditional Chinese medicine has been incorporated into the national
COVID-19 treatment guidelines in China [21].

Prevention [21, 30]

One notable molecular feature of SARS-CoV-2 is the presence of a polybasic cleavage site
(RRAR) at the S1–S2 junction of the spike (S) protein, which allows for efficient cleavage by
host proteases such as furin [2]. This site is not found in all related viruses of the Sarbecovirus
subgenus, with the exception of RmYN02, a bat-derived coronavirus isolated from Rhinolophus
malayanus in China. RmYN02 contains a three–amino acid insertion (PAA) at a similar location
[28], which, although not a functional polybasic cleavage site, supports the hypothesis that such
insertions can occur naturally in related viruses.

Structural analyses suggest that the furin cleavage site may reduce the stability of the spike
protein, facilitating the conformational changes necessary for binding of the receptor-binding
domain (RBD) to the ACE2 receptor [29]. While this feature has been proposed as a contributor
to the higher transmissibility of SARS-CoV-2 compared to SARS-CoV, a definitive gain-of-
function role for the cleavage site has yet to be experimentally confirmed [26].

Another distinguishing factor of SARS-CoV-2 is the presence of a novel accessory gene, ORF8,
which encodes a protein that shares only 40% amino acid identity with the ORF8 protein of
SARS-CoV. Unlike SARS-CoV, the SARS-CoV-2 ORF8 does not contain a motif that activates
intracellular stress pathways [23]. Interestingly, a 382-nucleotide deletion encompassing the
entire ORF8 gene has been identified in several SARS-CoV-2 cases in Singapore, mirroring
similar deletions (29- and 415-nucleotide) observed in late-phase human SARS-CoV variants
during the 2002–2003 outbreak [30]. These deletions may signal a process of viral adaptation to
human hosts following cross-species transmission.

Besides the important structural proteins, the SARS-CoV-2 genome contains 15 nsps, nspl to
nsp10 and nsp12 to nsp16, and 8 accessory proteins (3a, 3b, p6, 7a, 7b, 8b, 9b, and ORF14) (16).
All these proteins play a specific role in viral replication (27). Unlike the accessory proteins of
SARS-CoV, SARS-CoV-2 does not contain 8a protein and has a longer 8b and shorter 3b
protein (16). The nsp7, nsp13, envelope, matrix, and p6 and 8b accessory proteins have not been
detected with any amino acid substitutions compared to the sequences of other coronaviruses
(16).The virus structure of SARS-CoV-2 is depicted in Fig. 2

Spike glycoprotein (S) (required for the

entry ofthe infectious virion particle)
Membrane protein (M)
(most abundant viral protein)Major
structural proteins

Envelope glycoprotein (E) (smallest among the

major structural proteins)
Nucleocapsid protein (N) + single-stranded positive sense RNA genome
Lipid bilayer

out on the isolated virus confirmed th there is a potential risk for the reemergence of SARS-
CoV infection from the viruses that are currently circulating in the bat population (105).

Clinical Pathology of SARS-CoV-2 (COVID-19)

The disease caused by SARS-CoV-2 is also referred to by several names, including severe
specific contagious pneumonia (SSCP), Wuhan pneumonia, and, more recently, COVID-19
[110]. Compared to SARS-CoV, SARS-CoV-2 is associated with less severe clinical outcomes
but exhibits greater transmissibility, as evidenced by the rapid global spread of COVID-19 cases
[111].

The incubation period of SARS-CoV-2 in familial clusters ranges from 3 to 6 days, with a mean
incubation period of approximately 6.4 days (range: 2.1–11.1 days) [112, 113]. In a cohort of the
first 425 confirmed cases, the median age was 59 years, with a higher incidence in males [114].
As with SARS and MERS, the severity of COVID-19 tends to be higher among individuals over
50 years of age [2, 115].

Common symptoms include fever, cough, myalgia, and fatigue, while headache, hemoptysis, and
diarrhea are less frequently reported [116, 282]. Early in the outbreak, travel history was a useful
diagnostic clue, but as community transmission became widespread, its relevance diminished.

Treatment [21, 23]

Management of COVID-19 is primarily supportive and symptomatic. The initial step is to ensure
adequate isolation to prevent virus transmission to contacts, other patients, and healthcare
workers. Mild cases can be managed at home, with counseling on warning signs that warrant
medical attention.

Key treatment principles include:

 Maintaining hydration and nutritional support

 Controlling fever and cough
 Avoiding unnecessary use of antibiotics and antivirals such as oseltamivir in confirmed
COVID-19 cases

For patients with hypoxia, oxygen therapy may be administered using nasal prongs, a face mask,
or high-flow nasal cannula, depending on severity.

8. Prevention

The World Health Organization (WHO) and agencies such as the Centers for Disease Control
and Prevention (CDC) have issued several protective guidelines to reduce the transmission of
COVID-19. These include: Frequent hand washing using soap and water or alcohol-based hand
sanitizers (at least 60% alcohol) for a minimum of 20 seconds. Avoiding close contact with
individuals exhibiting symptoms of illness, especially those coughing or sneezing. Maintaining a
minimum distance of 1 meter from others in public settings. Avoiding touching the face,
particularly the eyes, nose, and mouth, to reduce the risk of virus entry. Covering the mouth and
nose with a tissue, cloth, or the elbow crease when coughing or sneezing. Wearing face masks in
public settings, particularly where social distancing is difficult. Staying home if sick and limiting
outings, especially for individuals at higher risk for severe illness (e.g., elderly or
immunocompromised). Daily disinfection of frequently touched surfaces such as phones,
doorknobs, and light switches [51, 52].

Additional public health strategies are essential given the zoonotic origins of SARS-CoV-2. The
One Health approach, which integrates human, animal, and environmental health, is crucial for
coordinated pandemic prevention and control efforts [317–319]. The presymptomatic spread of
COVID-19 from Wuhan led to independent, self-sustaining outbreaks across multiple global
cities. Localized outbreaks have been observed in many parts of China, reinforcing the urgent
need for timely public health interventions to slow or stop transmission [231]. The spread of
COVID-19 on cruise ships has offered insight into transmission dynamics. These ships create
closed environments that are highly conducive to respiratory outbreaks. With passengers from
various countries onboard, they also facilitate cross-border pathogen spread [320]. Notable cruise
ships associated with COVID-19 outbreaks include: Diamond Princess, Grand Princess,
Celebrity Apex, Ruby Princess These incidents highlight the importance of infection control in
confined environments and during international travel.
Origin and Spread of COVID-19

In December 2019, an outbreak of COVID-19 emerged in Wuhan, the capital city of Hubei
Province in China. This new virus, later identified as SARS-CoV-2, has caused a global
pandemic. Early research indicated that BCG (Bacillus Calmette-Guérin) vaccination, originally
derived from a live attenuated strain of Mycobacterium bovis, might offer some protective
benefit against SARS-CoV-2. To explore this potential, three clinical trials have been initiated to
assess the role of BCG vaccination in preventing COVID-19 infection.

A cohort study was recently conducted to evaluate whether childhood BCG vaccination
influenced COVID-19 PCR positivity rates. However, the results of this study indicated no
significant difference in the rate of COVID-19-positive test results between those who had
received the BCG vaccine in childhood and those who had not. This finding suggests that BCG
vaccination may not provide protective effects against SARS-CoV-2 infection, and further
studies are needed to determine if any long-term benefits exist from childhood vaccination. On
the genetic front, population genetic studies on 103 SARS-CoV-2 genomes have identified two
major viral types: L-type and S-type. The L-type is expected to be the most prevalent, making up
approximately 70% of cases, while the S-type accounts for around 30%. This discovery has
important implications for vaccine development, as an effective vaccine must be capable of
targeting both viral strains. Currently, the genetic differences between the L and S types are
minimal and are unlikely to affect immune responses. However, ongoing genetic evolution of the
virus could lead to the emergence of new variants in the future, which may necessitate the
development of updated vaccines to account for these potential changes.

Concluding Remarks

Several years after the global SARS epidemic, the ongoing SARS-CoV-2/COVID-19 pandemic
underscores how rapidly novel pathogens can emerge and spread through human populations,
leading to significant public health crises. This pandemic has provided valuable insights into the
dynamics of zoonotic transmission and the evolving nature of coronaviruses.

Future research must focus on developing and evaluating animal models for SARS-CoV-2 to
better understand viral replication, transmission dynamics, and pathogenesis. These models will
be essential for the development of therapeutic strategies to combat zoonotic coronavirus
outbreaks in the future. Given the climate change and ecological shifts occurring globally, the
likelihood of new coronavirus outbreaks remains high, often exacerbated by increasing human-
animal interactions, particularly in environments like live animal markets. The Huanan South
China Seafood Market, for example, may have been a key site for cross-species transmission of
the virus, further highlighting the risk of genetic recombination in coronaviruses and the potential
for new, more dangerous strains to emerge [323–325].

The clinical presentation of COVID-19 is marked by a range of symptoms, including fever,

cough, headache, myalgia, and fatigue. The disease also manifests with asymptomatic cases and
atypical presentations. As we continue to learn more about SARS-CoV-2, particularly through in
vitro and in vivo research, our understanding of its effects on the respiratory system and other
organs, including the intestinal lymphocytes, renal cells, and T lymphocytes, will expand. In
particular, the virus has been shown to induce T-cell apoptosis, which may lead to immune
system dysregulation and an increased susceptibility to secondary infections.

Regarding therapeutic interventions, several antiviral agents are currently under investigation.
Remdesivir (GS-5734) has shown promise in vitro and in clinical settings, demonstrating
potential to shorten recovery times for hospitalized patients with COVID-19. This medication
has been granted emergency use authorization by the FDA and is one of the first approved
options for the treatment of severe COVID-19 cases requiring supplemental oxygen. Ongoing
clinical trials continue to assess its efficacy and safety.

Another antiviral agent, Favilavir (T-705), has shown efficacy in reducing disease progression
and shortening the time to viral clearance in patients with mild to moderate COVID-19. Its use
has been approved in China, Russia, and India, and results from clinical trials indicate promising
rates of clinical improvement, particularly for those with less severe forms of the disease.
However, the complexity of COVID-19 pathophysiology, combined with variations in patient
responses, highlights the need for further research into replication inhibitors, immune
modulators, and targeted therapies. As our understanding of SARS-CoV-2 evolves, it will be
essential to develop comprehensive, adaptable treatment protocols to address the wide-ranging
impacts of the virus on different populations.

Interestingly, disease in patients outside Hubei province has been observed through both in vivo
and in vitro experiments. There is an enhanced nasal secretion observed along with local oedema
because of the damage of the host cell, which further stimulates the synthesis of inflammatory
mediators. In addition, these reactions can induce sneezing, difficulty breathing by causing
airway inhibition and elevate mucosal temperature. These viruses, when released, chiefly affect
the lower respiratory tract, with the signs and symptoms existing clinically. Also, the virus
further affects the intestinal lymphocytes, renal cells, liver cells and T- lymphocytes.
Furthermore, the virus induces T-cell apoptosis, causing the reaction of the T- cell to be erratic,
resulting in the immune system's complete collapse.24, 25

5.1 Mode of Transmission

The initial outbreak of COVID-19 was linked to a seafood market in Wuhan, China, known for
selling live animals. Most of the early cases were individuals who had either worked at or visited
this market, leading to the assumption that the virus was transmitted from animals to humans at
this location. However, the exact origin and mode of initial transmission remain unclear, and
subsequent cases were reported in individuals who had no direct exposure to the market. This
indicates that human-to-human transmission became the primary mode of spread shortly after the
virus emerged. Despite ongoing research, our understanding of the full transmission dynamics of
SARS-CoV-2 remains incomplete.

COVID-19 is primarily spread through respiratory droplets produced when an infected person
coughs, sneezes, or talks. Transmission may also occur via contact with contaminated surfaces,
followed by touching the nose, mouth, or eyes. Airborne transmission in enclosed or poorly
ventilated settings, and fecal-oral transmission in certain scenarios, have also been considered but
are less clearly defined. The basic reproduction number (R₀) for COVID-19 was initially
estimated to range between 1.4 and 2.5. More recent data suggest an R₀ between 2.24 and 3.58,
indicating a higher potential for spread than MERS-CoV (R₀ < 1) but somewhat lower than
SARS-CoV (R₀: 2–5). These figures highlight the virus's significant transmission potential and
the need for robust public health interventions.

To mitigate spread, governments must rely not solely on lockdowns, but also on alternative
strategies, including: Large-scale testing, Contact tracing, Targeted quarantine of suspected
cases, Timely isolation of confirmed cases. Lockdowns should primarily serve to slow disease
progression, preventing healthcare systems from being overwhelmed and allowing time to scale
up medical infrastructure.

10. Recombinant Subunit Vaccine

Clover Biopharmaceuticals is developing a recombinant subunit vaccine targeting the trimeric
spike (S) protein of SARS-CoV-2, which plays a crucial role in viral entry into host cells. This
vaccine aims to stimulate a protective immune response by presenting a highly immunogenic
part of the virus without the use of live components, thus enhancing safety.

In parallel, Vaxart is advancing the development of an oral recombinant vaccine using its
proprietary tablet-based vaccine platform. This oral formulation offers the potential for improved
ease of distribution and administration, particularly in large-scale immunization campaigns, by
eliminating the need for injections and cold-chain logistics.

11. Clinical Management and Treatment

In severe COVID-19 cases, treatment should be provided to support vital organ functions. People
who think they may have been exposed to COVID-19 should contact their healthcare provider
immediately. Healthcare personnel should care for patients in an Airborne Infection Isolation
Room (AIIR). Precautions must be taken by healthcare professionals, such as contact precautions
and airborne precautions with eye protection.⁵⁶

Individuals with a mild clinical presentation may not require primary hospitalization. Close
monitoring is needed for persons infected with COVID-19. Elderly patients and those with pre-
existing chronic medical conditions, such as cardiovascular disease, diabetes, or respiratory
illness, are at higher risk of developing complications.

Angiotensin-converting enzyme 2 (ACE2) has been identified as the receptor through which the
virus enters the respiratory mucosa.¹¹ The basic case reproduction rate (BCR) is estimated to
range from 2 to 6.47 in various modelling studies.¹¹ In comparison, the BCR of SARS was 2 and
1.3 for the pandemic flu H1N1 in 2009.²

Clinical Features [8, 15–18]

The clinical features of COVID-19 are varied, ranging from an asymptomatic state to acute
respiratory distress syndrome (ARDS) and multi-organ dysfunction. The common clinical
features include fever (though not always present), cough, sore throat, headache, fatigue,
myalgia, and breathlessness. Conjunctivitis has also been reported. Thus, these symptoms are
indistinguishable from those caused by other viral respiratory infections.

Cases of COVID-19 in countries outside China were reported in individuals with no history of
travel to China, suggesting that local human-to-human transmission was occurring in these
countries.⁹ Airports in different countries, including India, implemented screening mechanisms
to detect symptomatic travelers returning from China, isolating them and testing them for
COVID-19.

It soon became evident that the infection could also be transmitted by asymptomatic individuals
and even before the onset of symptoms. Therefore, countries including India, which evacuated
their citizens from Wuhan through special flights or received travelers returning from China,
placed all individuals—symptomatic or not—in isolation for 14 days and tested them for the
virus.

Cases continued to increase exponentially, and modelling studies provided projections for
the ongoing spread.

Pieces of evidence are available that link NSAID use with the occurrence of respiratory and
cardiovascular adverse effects. Hence, as a cautionary approach, it is advisable not to recommend
NSAIDs as the first-line option for managing COVID-19 symptoms (302). The use of
corticosteroids in COVID-19 patients remains controversial and requires further systematic
clinical studies. The guidelines proposed for managing critically ill adults suggest the use of
systemic corticosteroids in mechanically ventilated adults with ARDS (303). However,
generalized use of corticosteroids is not indicated in COVID-19, as there are concerns regarding
their effects in cases of viral pneumonia. Stem cell therapy using mesenchymal stem cells
(MSCs) is another promising strategy that can be applied in clinical cases of COVID-19 due to
its potential immunomodulatory properties. MSCs may help attenuate the cytokine storm
observed in severe SARS-CoV-2 infections, thereby reducing mortality. Among the various
types of MSCs, expanded umbilical cord MSCs have shown promise as a therapeutic agent,
though further validation is required to confirm their efficacy in managing critically ill COVID-
19 patients (304). Repurposed broad-spectrum antiviral drugs and the administration of
recombinant adenovirus-based vaccines have shown encouraging results. In BALB/c mice, these
vaccines were found to induce long-lasting neutralizing immunity against MERS spike
pseudotyped viruses, characterized by the induction of systemic IgG, secretory IgA, and lung-
resident memory T-cell responses (177). Immunoinformatics methods have been used for
genome-wide screening of potential vaccine targets among the various immunogens of MERS-
CoV (178). The N protein and potential B-cell epitopes of the MERS-CoV E protein have been
suggested as immunoprotective targets capable of inducing both T-cell and neutralizing antibody
responses (178, 179).

A collaborative effort by researchers from Rocky Mountain Laboratories and Oxford University
is focused on developing a chimpanzee adenovirus-vectored vaccine to combat COVID-19 (180).
The Coalition for Epidemic Preparedness Innovations (CEPI) has launched three programs aimed
at designing vaccines for SARS-CoV-2 (181). CEPI is collaborating with Inovio to develop a
MERS-CoV DNA vaccine that may provide effective immunity. Additionally, CEPI and the
University of Queensland are working on a molecular clamp vaccine platform for MERS-CoV
and other pathogens, which could facilitate more efficient antigen recognition by the immune
system.

4. VIROLOGY

Coronaviruses, a family of viruses within the Nidovirales superfamily, are further classified into
four genera: alpha-, beta-, gamma-, and deltacoronaviruses (α-, β-, γ-, and δ-coronaviruses).
Among these, alpha- and beta-coronaviruses are capable of infecting only mammals, whereas
gamma- and delta-coronaviruses primarily infect birds but can also infect mammals.¹³˒¹⁴

Two of these genera include human coronaviruses (HCoVs): alpha-coronaviruses, which

comprise human coronavirus 229E (HCoV-229E) and human coronavirus NL63 (HCoV-NL63),
and beta-coronaviruses, which include human coronavirus HKU1 (HCoV-HKU1), human
coronavirus OC43 (HCoV-OC43), Middle East respiratory syndrome coronavirus (MERS-CoV),
and severe acute respiratory syndrome coronavirus (SARS-CoV).¹⁵

The severe acute respiratory syndrome coronavirus 2

(SARS-CoV-2) is now referred to as the novel coronavirus disease 2019 (COVID-19). Genome
sequencing and phylogenetic research revealed that the virus responsible for COVID-19 is a
beta-coronavirus that belongs to the same subgroup as the SARS virus, but exists as a distinct
variant. When patients present with severe symptoms, interventions such as the use of prongs,
face masks, high-flow nasal cannula (HFNC), or non-invasive ventilation are indicated. In more
critical cases, mechanical ventilation and even extracorporeal membrane oxygenation (ECMO)
may be required. Some patients may also need renal replacement therapy. Antibiotics and
antifungals are necessary if co-infections are suspected or confirmed. The role of corticosteroids
remains uncertain. While the current international consensus and WHO advise against their
routine use, Chinese guidelines recommend short-term therapy with low-to-moderate doses of
corticosteroids for patients with COVID-19-induced ARDS. Detailed critical care management
guidelines have been issued by the WHO. As of now, there is no approved treatment for COVID-
19. However, antiviral drugs such as ribavirin and lopinavir-ritonavir have been administered
based on previous experiences with SARS and MERS. Historically, it is only a matter of time
before another zoonotic coronavirus crosses the species barrier and causes an epidemic.

The host spectrum of coronaviruses broadened when a novel strain, SW1, was identified in the
liver tissue of a captive beluga whale (Delphinapterus leucas). In recent decades, various novel
coronaviruses have been identified across different animal species. Bats, in particular, can harbor
these viruses asymptomatically and are chronically infected. As the only mammals capable of
sustained flight, bats can migrate long distances and are globally distributed, comprising
approximately one-fifth of all mammalian species. This makes them an ideal reservoir host for
numerous viral agents, including several coronaviruses not yet identified. Given the repeated
emergence of bat-origin coronaviruses, it is imperative to conduct comprehensive molecular
surveillance to study Betacoronaviruses in animal populations, particularly in the Rhinolophus
bat family. Chinese bats, in particular, are commercially significant, as they are used in
traditional medicine and the wildlife trade.

Initially, the epicenter of the SARS-CoV-2 pandemic was China, reporting 84,458 laboratory-
confirmed cases and 4,644 deaths as of 13 May 2020. By the same date, SARS-CoV-2 cases had
been confirmed in more than 210 countries outside of China. COVID-19 had been reported on
every continent except Antarctica. For several weeks, Italy garnered attention due to its large
number of cases—221,216 confirmed and 30,911 deaths. However, the United States soon
surpassed all countries, reporting 1,322,054 confirmed cases and 79,634 deaths. The United
Kingdom also exceeded Italy, with 226,467 confirmed cases and 32,692 deaths. Johns Hopkins
University has developed a web-based platform providing daily epidemiological updates on the
COVID-19 outbreak.

Coronavirus infections are linked to a wide range of clinical manifestations, including enteritis in
cows and pigs, upper respiratory disease in chickens, and fatal respiratory infections in humans.
Among coronavirus genera, Alphacoronavirus and Betacoronavirus infect mammals, while
Gammacoronavirus and Deltacoronavirus primarily infect birds and fish, and occasionally
mammals. Several novel Deltacoronaviruses have been discovered in birds, including Wigeon
coronavirus HKU20, Bulbul coronavirus HKU11, Munia coronavirus HKU13, White-eye
coronavirus HKU16, Night-heron coronavirus HKU19, and Common moorhen coronavirus
HKU21, as well as in pigs, such as Porcine coronavirus HKU15. Other porcine coronaviruses
include transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), and
porcine hemagglutinating encephalomyelitis virus (PHEV). Among them, TGEV and PEDV are
responsible for severe gastroenteritis in piglets, with high morbidity and mortality. PHEV can
also cause enteric infections but is capable of inducing encephalitis due to its neurotropic nature.

Molecular diagnostic assays offer high accuracy for detecting SARS-CoV-2. However, their
utility is limited by the global shortage of test kits, contributing to ongoing transmission, as only
a fraction of suspected cases are confirmed. In such contexts, conventional serological assays—
such as enzyme-linked immunosorbent assay (ELISA)—which detect IgM and IgG antibodies
specific to COVID-19, serve as high-throughput alternatives. Currently, no widely available
diagnostic kit exists for detecting SARS-CoV-2 antibodies. Antibody profiling has shown that
IgM persists for over one month, indicating prolonged viral replication, while IgG levels rise
during the later stages of infection. These findings show that the antibody profiles of SARS-
CoV-2 and SARS-CoV are similar and can be leveraged to develop specific serological tests for
rapid diagnosis. Though diagnostic kits that detect viral RNA sequences already exist, their
availability is limited due to the surging number of COVID-19 cases. One major issue is viral
shedding; the virus may remain viable for at least three days, posing a significant risk to
uninfected individuals and healthcare workers. Notably, anal swabs have yielded more positive
results than oral swabs in the later stages of infection. Thus, clinicians should exercise caution
when discharging patients based solely on negative oral swab results, given the possibility of
fecal-oral transmission.

Although the viral loads in stool samples were found to be lower than those in respiratory
samples, strict precautionary measures must be followed when handling stool samples from
suspected or confirmed COVID-19 patients (151). Children infected with SARS-CoV-2 typically
experience only mild illness and recover quickly after treatment. However, it was recently found
that stool samples from SARS-CoV-2-infected children who had negative throat swab results
remained positive for up to ten days after those negative results. This indicates the possibility of
fecal-oral transmission of SARS-CoV-2, particularly in children (290). Therefore, to prevent
fecal-oral transmission of SARS-CoV-2, infected patients should only be considered negative
once they test negative for SARS-CoV-2 in their stool samples. SARS-CoV-2, the virus
responsible for COVID-19, is classified as a group 2B coronavirus and is closely related to the
viruses that caused MERS-CoV and SARS-CoV (3). Genome sequences obtained from SARS-
CoV-2-infected patients show a 79.5% sequence similarity with that of SARS-CoV (63).

As of 13 May 2020, confirmed COVID-19 cases have been reported in more than 210 countries,
with 287,399 deaths recorded (WHO Situation Report 114). Transmission can also occur directly
from the reservoir host to humans without receptor-binding domain (RBD) adaptations. The
currently circulating bat coronavirus possesses "poised" spike proteins that can infect humans
without requiring further mutations or adaptations (105). Overall, various bat species around the
world carry a vast number of coronaviruses (106).

The high plasticity in receptor usage, coupled with the potential for adaptive mutation and
recombination, may result in frequent interspecies transmission of coronaviruses from bats to
animals and humans (106). The pathogenesis of most bat coronaviruses remains unknown, as
many of these viruses have not yet been isolated or studied (4). Hedgehog coronavirus I-HKU31,
a Betacoronavirus, has been identified in Amur hedgehogs in China. Studies suggest that
hedgehogs serve as reservoirs for Betacoronaviruses, and evidence of recombination has also
been found (107). Current scientific evidence on MERS infection suggests that dromedary
camels are the major reservoir and primary animal source of MERS infection in humans (97).
Infected camels may not show visible signs of illness, making detection and control difficult.
Given the potential for adaptive evolution, close monitoring of viral mutations that occur during
human-to-human transmission is essential.

M Protein

The M protein is the most abundant viral protein present in the virion particle and gives the viral
envelope its defined shape (48). It binds to the nucleocapsid and acts as a central organizer in
coronavirus assembly (49). Although coronavirus M proteins exhibit high diversity in their
amino acid sequences, they maintain overall structural similarity across different genera (50).
The M protein contains three transmembrane domains, flanked by a short amino terminus on the
exterior of the virion and a long carboxy terminus inside the virion (50). Overall, the viral
scaffold is maintained by M-M interactions. Notably, the M protein of SARS-CoV-2 does not
exhibit any amino acid substitutions compared to that of SARS-CoV (16).
E Protein

The coronavirus E protein is the smallest and most enigmatic of the major structural proteins
(51). It plays a multifunctional role in the pathogenesis, assembly, and release of the virus (52).
The E protein is a small integral membrane polypeptide that functions as a viroporin (ion
channel) (53). The inactivation or inhibition of this protein can significantly impact viral
replication and pathogenesis. Furthermore, diagnostic methods, such as RT-LAMP, have been
developed for the rapid and colorimetric detection of this virus (354). RT-LAMP serves as a
simple, rapid, and sensitive diagnostic method that does not require sophisticated equipment or
highly skilled personnel (349).

An interactive web-based dashboard for tracking

SARS-CoV-2 in real time has been designed (238). A smartphone-integrated, home-based point-
of-care testing (POCT) tool, combined with a paper-based POCT and LAMP (loop-mediated
isothermal amplification), is a useful diagnostic method at the point of care (353). The Abbott ID
Now COVID-19 molecular POCT-based test, which uses isothermal nucleic acid amplification
technology, has been designed as a point-of-care test for very rapid detection of SARS-CoV-2 in
just 5 minutes (344). A CRISPR-based SHERLOCK (specific high-sensitivity enzymatic reporter
unlocking) diagnostic tool for rapid detection of SARS-CoV-2, without the requirement of
specialized instrumentation, has been reported as highly useful in clinical diagnosis of COVID-
19 (360). Additionally, a CRISPR-Cas12-based lateral flow assay has been developed for the
rapid detection of SARS-CoV-2 (346). Artificial intelligence, using a three-dimensional deep
learning model, has been developed for the sensitive and specific diagnosis of COVID-19 via CT
images (332).

Tracking and mapping the rising incidence rates, disease outbreaks, community spread,
therapeutics, and drug regimens to counter emerging viruses are critical (161—163, 280). Several
attempts are being made to design and develop vaccines for COVID-19 infection, primarily by
targeting the spike glycoprotein. However, due to the extensive diversity in antigenic variants,
the cross-protection provided by vaccines is significantly limited, even within strains of the same
phylogenetic subcluster (104). In the current scenario, due to the lack of effective antiviral
therapy and vaccines, we must rely solely on implementing effective infection control measures
to reduce the risk of possible nosocomial transmission (68). Recently, the receptor for SARS-
CoV-2 was identified as the human angiotensin-converting enzyme 2 (hACE2), and the virus
was found to enter host cells primarily through endocytosis. Major components involved in viral
entry include PIKfyve, TPC2, and cathepsin L. These findings are crucial because these
components may serve as candidates for vaccines or therapeutic drugs against SARS-CoV-2
(293).

The majority of treatment options and strategies currently being evaluated for SARS-CoV-2
(COVID-19) are based on our previous experiences in treating SARS-CoV, MERS-CoV, and
other emerging viral diseases. Several therapeutic approaches have been proposed, particularly
regarding the spike (S) protein, which locates itself on top of the trimeric S2 stalk (45). Recently,
structural analyses of the S proteins of COVID-19 revealed 27 amino acid substitutions within a
1,273-amino-acid stretch (16). Six substitutions are located in the receptor-binding domain
(RBD) (amino acids 357 to 528), while four substitutions are in the receptor-binding motif
(RBM) at the C-terminal domain (CTD) of the S1 domain (16). Notably, no amino acid change
has been found in the RBM, which binds directly to the angiotensin-converting enzyme-2
(ACE2) receptor in SARS-CoV (16, 46). The main emphasis is currently on understanding how
many differences are required to alter host tropism. Sequence comparisons revealed 17
nonsynonymous changes between the early sequence of SARS-CoV-2 and the later isolates of
SARS-CoV.
These changes were scattered across the virus genome, with nine substitutions in ORF1ab, ORF8
(four substitutions), the spike gene (three substitutions), and ORF7a (one substitution) (4).
Notably, the same nonsynonymous changes were observed in a familial cluster, suggesting that
viral evolution occurred during person-to-person transmission (4, 47). Such adaptive evolution
events are frequent and constitute an ongoing process as the virus spreads among new hosts (47).
While no functional changes are associated with this adaptive evolution, close monitoring of the
viral mutations is necessary.

The SARS-CoV-2 virus was initially detected in environmental samples from the Huanan
Seafood Market, suggesting that the virus may have originated from there [7]. The number of
cases began to increase exponentially, with some cases not linked to the market, indicating that
human-to-human transmission was occurring [8]. The first fatality from the virus was reported on
January 11, 2020. The mass migration of people during the Chinese New Year helped fuel the
epidemic. Cases in other provinces of China, as well as in Thailand, Japan, and South Korea,
were quickly reported in individuals who had recently returned from Wuhan. Transmission to
healthcare workers caring for patients was reported on January 20, 2020. On January 23, the
entire 11 million population of Wuhan was placed under lockdown with strict entry and exit
restrictions. The genome of SARS-CoV-2 shares over 90% amino acid identity with SARS-CoV,
particularly in its structural genes, except for the spike (S) gene, which shows a divergence. The
replicase gene accounts for two-thirds of the 5’ genome and encodes a large polyprotein (pp1ab)
that is cleaved into 16 non-structural proteins involved in virus replication and transcription.
Most of these non-structural proteins in SARS-CoV-2 exhibit more than 85% amino acid
sequence identity with SARS-CoV [25].

Phylogenetic analysis of the whole genome shows that SARS-CoV-2 clusters with SARS-CoV
and SARS-related coronaviruses (SARSr-CoVs) found in bats, placing it within the subgenus
Sarbecovirus of the genus Betacoronavirus. Within this clade, SARS-CoV-2 is grouped in a
distinct lineage with four horseshoe bat coronavirus isolates (RaTG13, RmYN02, ZC45, and
ZXC21), as well as recently identified novel coronaviruses in pangolins, which are
phylogenetically parallel to SARS-CoV. The virus spread exponentially to other countries,
including South Korea, Italy, and Iran. Among the infected, 20% have become critically ill, 25%
have recovered, and 3,310 individuals (3,013 in China and 297 in other countries) have died [2].
India, which reported only three cases as of March 2, 2020, saw a sudden rise in cases by March
5, 2020, with 29 reported cases, mostly among Italian tourists and their contacts in Delhi, Jaipur,
and Agra. One case involved an Indian national who had returned from Vienna and exposed a
large group of schoolchildren at a birthday party at a city hotel. Many of the contacts have been
quarantined.

These numbers likely underestimate the actual number of infections and deaths due to limitations
in surveillance and testing. Although SARS-CoV-2 originated from bats, the intermediary host
remains unclear.

The interferon response is a key innate immunity defense against viral infections. Interferons
induce the expression of a wide range of interferon-stimulated genes that can interfere with viral
replication at various stages. Previous studies have identified type I interferons as a promising
therapeutic candidate for SARS [149]. In vitro data suggests that SARS-CoV-2 is more sensitive
to type I interferons than SARS-CoV, indicating the potential effectiveness of interferons in the
early treatment of COVID-19 [150]. In China, vapor inhalation of interferon-α is included in
COVID-19 treatment guidelines [151], and clinical trials are ongoing globally to evaluate the
efficacy of different interferon therapies, either alone or in combination with other treatments
[152].
Immunoglobulin Therapy. Convalescent plasma treatment is another potential adjunctive therapy
for COVID-19. Preliminary findings have suggested an improvement in clinical status following
this treatment. The U.S. Food and Drug Administration (FDA) has provided guidance for the use
of COVID-19 convalescent plasma under an emergency investigational new drug application.
However, this treatment may lead to adverse effects such as antibody-dependent enhancement of
infection, transfusion-associated acute lung injury, and allergic transfusion reactions.

Monoclonal antibody therapy is an effective immunotherapy for treating certain viral infections
in selected patients. Recent studies have reported specific monoclonal antibodies capable of
neutralizing SARS-CoV-2 infection. Caregivers should wear surgical masks when in the same
room as the patient and practice proper cough hygiene. In addition, hand hygiene should be
performed every 15–20 minutes.

The greatest risk associated with COVID-19 is transmission to healthcare workers. During the
2002 SARS outbreak, 21% of those infected were healthcare workers. To date, nearly 1,500
healthcare workers in China have been infected, with six reported deaths. The physician who first
raised the alarm about the virus has also passed away. Protecting healthcare workers is crucial to
maintaining continuity of care and preventing further transmission to other patients. Although
COVID-19 is transmitted via respiratory droplets and is classified as a Category B infectious
agent—similar to highly pathogenic H5N1 and SARS—by the China National Health
Commission, the recommended infection control measures are those used for SARS-related
coronaviruses (SARSr-CoVs) (see FIG. 2). Using sequences from five conserved replicative
domains in pp1ab—3C-like protease (3CLpro), nidovirus RNA-dependent RNA polymerase
(RdRp)-associated nucleotidyltransferase (NiRAN), RdRp, zinc-binding domain (ZBD), and
helicase (HELD)—the Coronaviridae Study Group of the International Committee on Taxonomy
of Viruses estimated the pairwise patristic distances between SARS-CoV-2 and other known
coronaviruses. Based on this analysis, SARS-CoV-2 has been assigned to the existing species
SARSr-CoV. Although phylogenetically related, SARS-CoV-2 is distinct from all other
coronaviruses identified in bats and pangolins within this species.

The SARS-CoV-2 spike (S) protein consists of 1,273 amino acids, which is longer than that of
SARS-CoV (1,255 amino acids) and known bat SARS-related coronaviruses (SARSr-CoVs),
which range from 1,245 to 1,269 amino acids. It is distinct from the S proteins of most members
of the Sarbecovirus subgenus, sharing only 76.7–77.0% amino acid sequence similarity with
SARS-CoVs isolated from civets and humans. In a pediatric cohort, one case was linked to
exposure through a family member, and 26 children had a history of travel to or residence in
Hubei Province, China. All patients were either asymptomatic (9%) or presented with mild
disease; no severe or critical cases were observed. The most common symptoms were fever
(50%) and cough (38%). All patients recovered with symptomatic therapy, and no deaths were
reported. However, one case of severe pneumonia with multiorgan dysfunction in a child has
been documented [19]. Similarly, reported neonatal cases have been mild [20].

Diagnosis [21]

A suspected case is defined as an individual with fever, sore throat, and cough who has a history
of travel to China or other areas with ongoing local transmission, or who has had contact with
patients with similar travel histories or with confirmed infection.

The development of a vaccine that can produce cross-reactive antibodies is essential. However,
the success of such a vaccine greatly depends on its ability to provide protection not only against
current strains of the virus but also against future variants that may emerge. This can be achieved
by identifying antibodies that are capable of recognizing relatively conserved epitopes—regions
of the virus that remain unchanged despite significant mutations (362). Although multiple
vaccine clinical trials are currently underway around the world, pregnant women have been
entirely excluded from these studies. Pregnant women are highly vulnerable to emerging
infectious diseases such as COVID-19 due to changes in the immune and other physiological
systems associated with pregnancy. Consequently, if a vaccine is successfully developed,
pregnant women would be unable to access it (361). Therefore, it is recommended that pregnant
women be included in ongoing vaccine trials, as successful vaccination during pregnancy would
protect not only the mother but also the fetus and newborn.

The heterologous immune effects induced by the Bacillus Calmette–Guérin (BCG) vaccine
represent a promising strategy for controlling the COVID-19 pandemic, although further
investigation is required. BCG is widely used as a vaccine against tuberculosis, particularly in
countries with a high burden of the disease. Experimental animal models, such as high-mice and
hDPP4-transgenic (hDPP4-Tg) mice—which express the human DPP4 receptor—have been used
to study MERS-CoV infection (221). The CRISPR-Cas9 gene-editing tool has also been
employed to introduce genomic alterations in mice, making them susceptible to MERS-CoV
infection (222). Efforts are ongoing to identify suitable animal models for SARS-CoV-
2/COVID-19, determine the receptor affinity of the virus, investigate disease pathology in
experimental animals, and explore virus-specific immune responses and protection mechanisms.
These endeavors aim to accelerate the development of effective vaccines and therapeutic drugs to
combat this emerging virus. Various cell lines, such as monkey epithelial cell lines (LLC-MK2
and Vero-B4), goat lung cells, alpaca kidney cells, dromedary umbilical cord cells, and advanced
ex vivo three-dimensional tracheobronchial tissue models, have been used in studies of human
coronaviruses, including MERS-CoV (223, 224). Vero cells and Huh-7 cells (a human liver
cancer cell line) have also been employed to isolate SARS-CoV-2 (194).

Recently, an experimental study involving rhesus monkeys revealed no detectable viral loads in
nasopharyngeal and anal swabs, and no evidence of viral replication in primary tissues five days
after reinfection. These findings were supported by subsequent virological, radiological, and
pathological assessments. The COVID-19 outbreak has also had profound global economic
consequences, primarily due to the sudden disruption of international trade and supply chains.
These disruptions forced multinational companies to make critical decisions that resulted in
substantial financial losses (66). The recent surge in the number of critically ill COVID-19
patients has exceeded the capacity of intensive care resources, limiting access to intensive care
services to only a small fraction of patients in need (67). This shortage may have contributed to
the increased case fatality rate observed during the pandemic.

Viewpoint on SARS-CoV-2 Transmission, Spread, and Emergence

The novel coronavirus (SARS-CoV-2) was identified within one month (28 days) of the initial
outbreak—an impressively rapid timeline compared to the 125 days it took to identify SARS-
CoV, which was first reported in Foshan, Guangdong Province, China (68). Immediately
following confirmation of the viral etiology, Chinese virologists promptly released the genomic
sequence of SARS-CoV-2. This swift action played a critical role in controlling the spread of the
newly emerged novel coronavirus to other parts of the world (69).

The possible origin of SARS-CoV-2 and the initial mode of transmission remain subjects of
investigation.

Origin and Spread of COVID-19

In December 2019, adults in Wuhan—the capital city of Hubei Province and a major
transportation hub in China—began presenting to local hospitals with severe pneumonia of
unknown origin. Many of the initial cases had a common exposure to the Huanan Wholesale
Seafood Market, which also sold live animals. The surveillance system, established following the
SARS outbreak, was promptly activated, and respiratory samples from patients were sent to
reference laboratories for etiological investigation.

On December 31, 2019, China officially notified the World Health Organization (WHO) about
the outbreak, and on January 1, the Huanan Seafood Market was closed. By January 7, the
causative virus was identified as a novel coronavirus, showing over 95% genetic homology with
coronaviruses found in bats. Given the high transmission rates, frequent disease outbreaks,
community spread, clustered transmission events, hot spots, and superspreader potential of
SARS-CoV-2/COVID-19, there is a strong need to fully utilize real-time disease mapping. This
can be achieved through the use of geographical information systems (GIS), such as the Kosmo
3.1 GIS software, as well as web-based real-time tools and dashboards, mobile applications, and
other advances in information technology (356–359).

Researchers have also developed several prediction tools and models, including the Prediction
model Risk Of Bias Assessment Tool (PROBAST) and the Critical Appraisal and Data
Extraction for Systematic Reviews of Prediction Modeling Studies (CHARMS). These tools can
assist in estimating the risk of infection and in predicting clinical outcomes. However, many of
these models may be subject to bias and therefore cannot yet be considered fully reliable,
highlighting the need for the development of new, robust predictive tools (360).

Vaccines, Therapeutics, and Drugs

The recent emergence of viruses such as Zika, Ebola, and Nipah, along with the serious threats
they pose to human health, has initiated a global race to design and develop advanced vaccines,
prophylactics, therapeutics, and drug regimens to counter emerging viruses. In the case of SARS-
CoV-2, viral RNA has been detected in nasal washes, saliva, urine, and feces for up to eight days
after infection. Moreover, a few naïve ferrets that had only indirect contact tested positive for
viral RNA, suggesting the potential for airborne transmission. Additionally, transmission through
the ocular surface and the prolonged presence of SARS-CoV-2 viral RNA in fecal samples have
been documented [101,102]. Coronaviruses are known to persist on inanimate surfaces for
several days, and this may also be true for SARS-CoV-2, which could contribute to an extended
risk of infection [103]. These findings help explain the rapid global spread of COVID-19. Public
health interventions aimed at reducing transmission—such as widespread testing, contact tracing,
quarantine, and social distancing—have proven beneficial in mitigating the epidemic, as
demonstrated by the success seen in China and several other countries, including South Korea.

Diagnosis

Early diagnosis is crucial for controlling the spread of COVID-19. Molecular detection of SARS-
CoV-2 nucleic acid remains the gold standard. Numerous commercial detection kits are
available, targeting genes such as ORF1b (including RdRp), N, E, or S [11,106–109]. The time
required for detection varies from several minutes to hours depending on the technology used.

However, molecular detection can be influenced by several factors. Although SARS-CoV-2 has
been identified in various respiratory samples—including throat swabs, posterior oropharyngeal
saliva, nasopharyngeal swabs, sputum, and bronchial fluid—the viral load tends to be higher in
samples from the lower respiratory tract. Additionally, viral nucleic acid has been found in
intestinal and blood samples even when respiratory samples tested negative [116].
Moreover, the viral load often begins to decline from its peak around the onset of symptoms [96,
109]. As a result, false negatives are common when only oral swabs are used. Therefore, multiple
detection methods should be employed to confirm a COVID-19 diagnosis [117,118].

To address limitations in molecular testing, other diagnostic methods have been utilized. In
Wuhan, when molecular testing capacity was overwhelmed, chest CT scans were used to rapidly
identify patients. CT imaging often reveals lung consolidation and abnormalities—even in
asymptomatic patients or those without clinical signs of lower respiratory tract involvement. In
fact, abnormal chest CT findings have aided in diagnosing COVID-19 in suspected cases with
initially negative molecular test results, many of whom tested positive upon repeat testing [22].

Differential Diagnosis [21]

The differential diagnosis of COVID-19 includes a broad range of respiratory viral infections
such as influenza, parainfluenza, respiratory syncytial virus (RSV), adenovirus, human
metapneumovirus, and other non-COVID-19 coronaviruses. It also includes atypical pathogens
like Mycoplasma pneumoniae and Chlamydia pneumoniae, as well as typical bacterial infections.

It is not possible to distinguish COVID-19 from these infections based solely on clinical
presentation or routine laboratory tests. Therefore, epidemiological factors—particularly recent
travel history—are important for diagnosis. However, as the epidemic progresses, reliance on
travel history becomes less useful due to widespread community transmission.

Additionally, for certain diagnostic tests, urine samples must be collected using sterile containers
and stored at controlled temperatures ranging from 4°C to –70°C to ensure sample integrity [32].

7. Pregnancy

Currently, there is a lack of knowledge and data regarding the consequences of COVID-19
during pregnancy [40–42]. However, pregnant women seem to be at higher risk of developing
severe infections and complications during the 2019-nCoV outbreak [41–43]. This speculation is
based on previous scientific reports on coronaviruses during pregnancy (SARS-CoV and MERS-
CoV) as well as the limited number of COVID-19 cases involving pregnant women [41–43]. An
analysis of the clinical features and outcomes of 10 newborns (including two sets of twins) in
China, whose mothers were confirmed COVID-19 cases, revealed that perinatal infection with
2019-nCoV may lead to adverse outcomes for neonates, such as premature labor, respiratory
distress, thrombocytopenia with abnormal liver function, and even death. It is still unclear
whether COVID-19 can be transmitted to the fetus during pregnancy through the transplacental
route [42]. A recent case series, which assessed intrauterine vertical transmission of COVID-19,
concluded that the possibility of such transmission is still not definitively confirmed. Therefore,
precautionary measures should be taken by healthcare providers when examining such patients,
with regular hand hygiene practices.

 Suspected cases should be referred to government-designated centers for isolation and testing
(in Mumbai, this is currently Kasturba Hospital). Commercial kits for testing are not yet
available in India.
 Patients admitted with severe pneumonia and acute respiratory distress syndrome (ARDS)
should be evaluated for travel history and placed under contact and droplet isolation.
Surfaces should be regularly disinfected. They should be tested for etiology using multiplex
PCR panels if logistics permit. If no pathogen is identified, samples should be referred for
SARS-CoV-2 testing.
Our knowledge of the animal origin of SARS-CoV-2 remains incomplete. The natural reservoirs
of the virus have not been conclusively identified. It is still unknown whether SARS-CoV-2 was
transmitted to humans through an intermediate host and which animals might serve as this host.
Detection of RaTG13, RmYN02, and pangolin coronaviruses suggests that various coronaviruses
similar to SARS-CoV-2 are circulating in wildlife. Additionally, as previous studies have shown
that RNA recombination might be the origin of some sarbecoviruses, such as SARS-CoV, it
cannot be excluded that viral RNA recombination between different related coronaviruses
contributed to the evolution of SARS-CoV-2. Therefore, extensive surveillance of SARS-CoV-2-
related viruses in China, Southeast Asia, and other regions—particularly in bats, wild and farmed
pangolins, and other wildlife species—will help better understand the zoonotic origins of SARS-
CoV-2.

In addition to wildlife, researchers have investigated the susceptibility of domesticated and

laboratory animals to SARS-CoV-2 infection. Experimental studies showed that SARS-CoV-2
replicates efficiently in cats and in the upper respiratory tract of ferrets, while dogs, pigs,
chickens, and ducks were not susceptible to the virus [43]. The susceptibility of mink was
documented in a report from the Netherlands about an outbreak of SARS-CoV-2 infection in
farmed mink. While most infected mink had mild symptoms, some developed severe respiratory
distress and died from interstitial pneumonia [44]. Both virological and serological testing found
evidence of natural SARS-CoV-2 infection in two dogs from households with human COVID-19
cases in Hong Kong, although the dogs were asymptomatic [45]. Another serological study
detected SARS-CoV-2 neutralizing antibodies in cat serum samples collected in Wuhan after the
COVID-19 outbreak, providing evidence of SARS-CoV-2 infection in cat populations in Wuhan.
However, the potential for SARS-CoV-2 transmission from cats to humans is still uncertain [46].

Receptor Use and Pathogenesis

SARS-CoV-2 uses the same receptor as SARS-CoV, angiotensin-converting enzyme 2 (ACE2)

[11,47]. Besides human ACE2 (hACE2), SARS-CoV-2 also recognizes ACE2 from pigs, ferrets,
rhesus monkeys, civets, cats, pangolins, rabbits, and dogs [11,43,48,49]. The broad receptor
usage of SARS-CoV-2 suggests that it may have a wide host range, and the varied efficiency of
ACE2 usage in different mammals may indicate their differing susceptibilities to SARS-CoV-2
infection. The spike (S) protein of a coronavirus is further divided into two functional domains:
an N-terminal domain and a C-terminal domain. Structural and biochemical analyses have
identified a 211 amino acid region (amino acids 319–529) at the S protein's C-terminal domain of
SARS-CoV-2 as the receptor-binding domain (RBD), which plays a key role in virus entry and is
the target of neutralizing antibodies (FIG. 5a). The receptor-binding motif (RBM) mediates
contact with the ACE2 receptor (amino acids 437–507 of SARS-CoV-2’s S protein), and this
region in SARS-CoV-2 differs from that in SARS-CoV by five critical residues. The cytokine
profile of SARS-CoV-2 infection is characterized by a significant elevation of plasma cytokines,
suggesting an immunopathological process caused by a cytokine storm in this cohort of patients.
Around 2.3% of individuals died within a median time of 16 days from disease onset [86]. Men
older than 68 years had a higher risk of respiratory failure, acute cardiac injury, and heart failure,
which led to death, regardless of a history of cardiovascular disease [86] (FIG. 4). Most patients
recovered sufficiently to be discharged from the hospital within 2 weeks [80] (FIG. 4).

Early Transmission and Spread The initial transmission of SARS-CoV-2 in Wuhan in December
2019 was linked to the Huanan Seafood Wholesale Market, which was suggested as the source of
the outbreak [92, 93]. However, community transmission might have occurred before this [88].
Later, ongoing human-to-human transmission propagated the outbreak. It is generally accepted
that SARS-CoV-2 is more transmissible than SARS-CoV and MERS-CoV. However,
determining an accurate reproduction number (R₀) for COVID-19 is not yet possible, as many
asymptomatic infections cannot be fully accounted for at this stage. An estimated R₀ of 2.5
(ranging from 1.8 to 3.6) has been proposed for SARS-CoV-2, compared with 2.0–3.0 for SARS-
CoV [90]. Notably, early human-to-human transmission of SARS-CoV-2 in China occurred
primarily within family clusters, and large outbreaks were also observed in other settings, such as
migrant worker communities, slaughterhouses, and meat-packing plants, highlighting the
importance of isolating infected individuals [91-93]. Nosocomial transmission was not a
significant source of transmission in China due to the implementation of infection control
measures in healthcare settings. By contrast, a higher risk of nosocomial transmission was
reported in other countries [93]. Environmental Contamination and Wastewater,
Increasing reports of SARS-CoV-2 presence in sewage and wastewater warrant further
investigation, as this suggests a potential for fecal-oral transmission. SARS-CoV-2 present in
environmental compartments like soil and water will eventually enter wastewater and sewage
sludge in treatment plants [328]. As a result, we must reassess current wastewater and sewage
sludge treatment procedures and introduce advanced techniques that are specific and effective
against SARS-CoV-2. Since SARS-CoV-2 is actively shed in stool, the prevalence of infections
in large populations can be studied using wastewater-based epidemiology. Recently, reverse
transcription quantitative PCR (RT-qPCR) was used to quantify the copies of SARS-CoV-2
RNA collected from wastewater treatment plants [327]. The calculated viral RNA copy numbers
can help estimate the number of infected individuals. Monoclonal Antibodies Compared with
convalescent plasma, which has limited availability and cannot be amplified, monoclonal
antibodies can be developed in larger quantities to meet clinical requirements. These antibodies
provide the possibility for the treatment and prevention of COVID-19. The neutralizing epitopes
of monoclonal antibodies also offer valuable information for vaccine design. However, the high
cost and limited manufacturing capacity, along with issues related to bioavailability, may restrict
the widespread use of monoclonal antibody therapy.

Vaccines

Vaccination is the most effective long-term strategy for the prevention and control of COVID-19.
Several vaccine platforms targeting SARS-CoV-2 are currently in development, including
recombinant vectors, DNA, mRNA in lipid nanoparticles, inactivated viruses, live attenuated
viruses, and protein subunits [159-161]. As of October 2, 2020, there were 51 vaccine candidates
in human clinical trials (COVID-19 vaccine and therapeutics tracker). Many of these candidates
were in Phase II testing, and some had already advanced to Phase III trials. One such vaccine,
developed by CanSino Biologicals and the Academy of Military Medical Sciences of China, is
an adenovirus-vectored vaccine expressing the SARS-CoV-2 spike (S) protein. A randomized
double-blind Phase II trial involving 603 adult volunteers in Wuhan demonstrated that the
vaccine was safe and induced significant humoral and cellular immune responses after a single
dose [62]. Another vectored vaccine, ChAdOx1, is also undergoing trials. In addition, the
development of multiepitope subunit vaccines, which are based on advanced immunoinformatics
tools, holds promise as an effective preventive strategy against COVID-19. These vaccines can
be designed using in silico methods, evaluated using docking studies, and further tested in animal
models [365].

Clinical Diagnosis

The symptoms of COVID-19 are similar to those of past respiratory epidemics, such as SARS
and MERS. These symptoms can range from mild rhinitis to severe conditions such as septic
shock. Intestinal disturbances, though observed in previous epidemics, are generally absent in
COVID-19. Clinical examination typically reveals unilateral or bilateral pneumonia, with
multiple lobular and sub-segmental consolidations observed in patients in intensive care units.
Patients with comorbidities tend to have a more severe course of disease than expected based on
previous epidemics. To diagnose COVID-19, a complete travel history and contact information
should be gathered, along with laboratory testing. Serological screening is especially useful as it
can help identify asymptomatic infections. Several serological tests for SARS-CoV-2 are in
development [14, 30]. Further genetic analysis of SARS-CoV-2 and its related strains, such as
SARS-CoV, will help in evaluating the potential for repurposed vaccines. This approach will be
valuable in case of future outbreaks, as preliminary evaluations, including in vitro studies, would
already be completed for these vaccine candidates.

The COVID-19 outbreak in China escalated rapidly, with the number of confirmed cases rising
sharply in January 2020. The World Health Organization (WHO) declared a public health
emergency of international concern on January 30, 2020, and the outbreak was officially labeled
as a pandemic on March 11, 2020. By that time, China had implemented strict public health
measures, including the lockdown of Wuhan on January 23, 2020, which effectively reduced the
number of new cases. However, despite the declining number of cases in China, the virus spread
rapidly to other regions, accelerated by international travel. By March, the case numbers in
Europe and the United States surged.

As of August 2020, over 20 million COVID-19 cases had been reported globally, with more than
733,000 deaths. High mortality was particularly evident in regions where healthcare resources
were overwhelmed. The United States had the highest number of cases and deaths at that time.
While some antiviral drugs, such as lopinavir and ritonavir, showed limited benefits in the
treatment of COVID-19, they appeared more effective when combined with other treatments,
like ribavirin and interferon beta-1b [143, 144]. The RECOVERY trial, a large clinical study
conducted in the UK, stopped treatment with lopinavir and ritonavir after finding no significant
benefits in a randomized trial with 1,596 patients. Despite these setbacks, researchers continue to
explore other potential therapeutics. Genetic evidence suggests that SARS-CoV-2 is a naturally
occurring virus, likely originating in animals. However, the exact time and location of its initial
transmission to humans remain uncertain. Although some of the first reported cases in Wuhan
had no direct link to the seafood market, it has been suggested that the market may not have been
the original source of the human infection.

A study from France detected SARS-CoV-2 through PCR in a stored sample from a patient who
had pneumonia at the end of 2019, suggesting that the virus may have spread in France earlier
than the officially recognized start of the outbreak. However, this early case does not provide
definitive evidence regarding the origin of SARS-CoV-2 or potential contamination, and a false-
positive result cannot be ruled out. To resolve this highly controversial issue, further
retrospective studies involving a larger number of stored samples from patients, animals, and
environmental sources are necessary. These studies should utilize well-validated assays to
provide more clarity.

Genomics, Phylogeny, and Taxonomy

As a novel beta coronavirus, SARS-CoV-2 shares 79% genome sequence identity with SARS-
CoV and 50% with MERS-CoV. Its genome organization is similar to that of other beta
coronaviruses. The six functional open reading frames (ORFs) are arranged in the following
order from 5' to 3': replicase (ORF1a/ORF1b), spike (S), envelope (E), membrane (M), and
nucleocapsid (N). Additionally, seven putative ORFs encoding accessory proteins are
interspersed between the structural genes. Many of the proteins encoded by SARS-CoV-2 have
similarities to those of SARS-CoV and MERS-CoV, which aids in understanding its
pathogenesis. These proteins also serve as targets for vaccine development and immune response
evaluation. For example, recombinant vaccines using rabies virus (RV) as a viral vector have
shown promise in eliciting immune responses. The RV vector can be engineered to express the
MERS-CoV spike protein, thereby inducing immunity against MERS-CoV. This method has
been found to elicit faster antibody responses and stronger cellular immunity compared to other
vector-based vaccines, such as the Gram-positive enhancer matrix (GEM) particle vaccine.
However, the GEM vaccine can induce high antibody responses at lower doses.

Recently, dual vaccines have gained popularity. One example is a vaccine developed using
inactivated rabies virus particles expressing the MERS-CoV spike protein. This dual vaccine
induced immune responses against both MERS-CoV and rabies virus. Mice vaccinated with this
approach were fully protected against MERS-CoV challenges. Infection Control for Healthcare
Workers. Healthcare workers are at high risk of contracting COVID-19 due to direct exposure to
infected patients. Therefore, proper training and strict preventive measures are essential for
protecting both healthcare staff and patients. This includes the use of appropriate personal
protective equipment (PPE), such as N95 or FFP3 masks, eye protection (goggles), gowns, and
gloves. These measures help reduce the risk of infection from both droplet and airborne
transmission, which are the primary modes of human-to-human transmission for SARS-CoV-2.
Mental health support for healthcare workers is also crucial, as the ongoing pandemic has placed
significant emotional and psychological strain on them. It's important to ensure their well-being
so they can continue to care for patients effectively.

4.2 Viral Replication

Coronavirus replication typically occurs within the cytoplasm and is closely associated with the
endoplasmic reticulum and other cellular membrane organelles. Human coronaviruses are
believed to enter cells primarily through different receptors. For example, 229E utilizes
aminopeptidase-N (AP-N), while OC43 uses a sialic acid-containing receptor to facilitate entry.
Once the virus enters the host cell and the uncoating process occurs, the viral genome is
transcribed and translated. A characteristic feature of coronavirus replication is that all mRNAs
share a typical 3' end structure, with only specific regions of the 5' ends being translated. In total,
approximately seven mRNAs are produced. The shortest mRNA encodes structural proteins,
while others may contribute to the synthesis of additional genome segments, including the
nucleoprotein. At the cell membrane, these proteins are assembled, and genomic RNA is
packaged to form mature viral particles, which then bud from internal cell membranes.

5. Pathogenesis

Coronaviruses exhibit high specificity, with most infections occurring in the airway epithelial
cells, as observed in both in vivo and in vitro studies. Traditional Chinese medicine (TCM) has
also been explored for its potential role in managing these infections. The handling of bats,
especially for trade purposes, poses a significant risk of zoonotic coronavirus (CoV)
transmission, potentially leading to epidemics (139).

Given the potential role of both farm and wild animals in SARS-CoV-2 infection, the World
Health Organization (WHO) recommended avoiding unprotected contact with these animals (25).
Live animal markets, such as the one in Guangdong, China, provide an environment where
animal coronaviruses can amplify and be transmitted to new hosts, including humans (78). These
markets are considered critical points for the origin of zoonotic diseases, with enormous public
health implications in the event of an outbreak. Bats, known reservoirs of various viruses, are
likely involved in the current outbreak, although their exact role in SARS-CoV-2 transmission
remains unclear (140). A qualitative study evaluating zoonotic risk factors in rural communities
of southern China identified frequent human-animal interactions and low levels of environmental
biosecurity as significant contributors to the emergence of zoonotic diseases (141, 142).

A comprehensive sequence analysis of bat coronaviruses revealed that RmYN02, a novel bat
virus discovered in Yunnan, is 93.3% identical to SARS-CoV-2 across the genome, with an even
higher similarity (97.2%) in the long lab gene. This is more than the similarity to RaTG13 (REF).
Phylogenetic analysis also places bat coronaviruses ZC45 and ZXC21, detected in Rhinolophus
pusillus bats from eastern China, within the SARS-CoV-2 lineage of the subgenus Sarbecovirus
(FIG. 2). These findings suggest that bats are likely reservoirs for SARS-CoV-2 (REF).
However, the divergence between SARS-CoV-2 and these related bat coronaviruses indicates
that they are likely evolutionary precursors but not direct progenitors of SARS-CoV-2 (REF).

In addition to bats, pangolins are another wildlife host potentially linked to SARS-CoV-2.
Several SARS-CoV-2-related viruses have been identified in Malayan pangolins smuggled from
Southeast Asia to southern China between 2017 and 2019. The viruses from these pangolins,
which were seized by provincial customs in Guangxi and Guangdong, fall into two distinct
sublineages (39-41). The Guangdong strains, isolated and sequenced by different research
groups, show 99.8% sequence identity with one another, exhibiting a 92.4% similarity to SARS-
CoV-2. Notably, the receptor-binding domain (RBD) of the Guangdong pangolin coronaviruses
is highly similar to that of SARS-CoV-2, with only one amino acid difference in the receptor-
binding motif (RBM), and it is identical to SARS-CoV-2 in five critical areas. This similarity
further supports the potential role of pangolins in SARS-CoV-2 transmission.

SARS-CoV-2's high transmissibility may be attributed to its unique virological characteristics.

While SARS-CoV transmission primarily occurred after illness onset and peaked with disease
severity, SARS-CoV-2 shows a high viral load in the upper respiratory tract during the first week
of symptoms. Consequently, the risk of viral shedding is particularly high early in the infection,
even in mild or asymptomatic cases (96, 97). It has been estimated that undocumented infections
may account for up to 79% of documented cases, as the virus is transmissible during the
asymptomatic period. SARS-CoV-2-infected individuals can shed the virus in respiratory
droplets when speaking, but aerosolized particles, which are much smaller and more numerous,
can also linger in the air for extended periods and penetrate deep into the lungs when inhaled by
others. Airborne transmission was observed in ferret experiments, highlighting the need for
enhanced precautions to prevent spread (REF).

In response to the spread of SARS-CoV-2, international measures initially included widespread

travel restrictions to China, with individuals returning from or evacuated from China being
isolated and tested for COVID-19 for 14 days, even if asymptomatic. With the virus's rapid
global spread, these travel restrictions were extended to other countries. However, the
effectiveness of these measures in slowing the viral spread remains uncertain.

A Candidate Vaccine is Under Development

Several vaccine candidates for COVID-19 are currently under development, utilizing diverse
platforms, such as mRNA, viral vectors, and inactivated viruses. These candidates are focused on
stimulating immune responses that target the spike protein of the SARS-CoV-2 virus, which
facilitates viral entry into human cells. The spike protein undergoes structural rearrangements
during viral entry, enhancing the fusion between the viral membrane and the host cell membrane.
Understanding the critical epitopes recognized by neutralizing antibodies has been pivotal in
guiding vaccine development. A key focus has also been on the role of the angiotensin-
converting enzyme 2 (ACE2) receptor, which has been identified as a major entry point for the
virus into human cells. ACE2 is present on the surface of various human cells, particularly in the
respiratory tract, and serves as the primary receptor for SARS-CoV-2. Targeting this receptor, in
addition to the spike protein, could offer a multi-pronged approach to preventing viral infection.

Practice Points from an Indian Perspective

COVID-19 presents differently across various populations, with individuals experiencing mild,
moderate, or severe symptoms. The disease may progress to pneumonia, acute respiratory
distress syndrome (ARDS), and multi-organ dysfunction, particularly in patients with underlying
comorbidities such as diabetes, hypertension, or cardiovascular diseases. However, many
infected individuals remain asymptomatic, making the disease particularly challenging to control.
The case fatality rate (CFR) for COVID-19 is estimated to range from 2% to 3%, though this rate
can vary depending on various factors, including the healthcare infrastructure and the patient's
comorbidities. Diagnosis is primarily through molecular tests, such as RT-PCR, which detect the
virus in respiratory secretions. Common laboratory findings include normal or low white blood
cell counts, alongside elevated C-reactive protein (CRP), indicating inflammation. A chest
computed tomography (CT) scan may reveal abnormalities even in individuals who show no
symptoms or have only mild disease, which is a significant feature of COVID-19.

Treatment remains largely supportive, with no established role for antiviral agents as of now.
Most patients with mild disease can recover through home isolation and supportive care.
Prevention includes strict infection control measures, such as contact and droplet precautions in
healthcare settings, as well as home isolation for suspected cases or individuals with mild
symptoms to reduce transmission. As the virus spreads primarily through respiratory droplets,
including during speech and breathing, it poses a significant risk in crowded settings. The role of
masks, hand hygiene, and other infection control measures remains essential in controlling the
spread of the disease, particularly in areas with high transmission rates.
FIGURE 1

The spike (S) protein of coronaviruses is a large, multifunctional class I viral transmembrane
protein. The size of this abundant S protein ranges from 1,160 amino acids (for Infectious
Bronchitis Virus, IBV, in poultry) to 1,400 amino acids (for Feline Coronavirus, FCoV) (43). It
exists as a trimer on the viral surface, giving the virion a corona or crown-like appearance.
Functionally, the S protein is required for the entry of infectious virion particles into host cells
through interaction with various host cellular receptors (44).

Additionally, the S protein is a critical factor for tissue tropism and the determination of the host
range (45). Notably, the S protein is one of the key immunodominant proteins of coronaviruses
(CoVs) capable of inducing host immune responses (45). The ectodomains of all CoV S proteins
share similar domain organizations, which are divided into two subunits, S1 and S2 (43). The S1
subunit helps with host receptor binding, while the S2 subunit is responsible for fusion. The S1
subunit is further divided into two subdomains: the N-terminal domain (NTD) and the C-terminal
domain (CTD). Both of these subdomains function as receptor-binding domains, interacting
efficiently with various host receptors (45). The CTD of S1 contains the receptor-binding motif
(RBM). In each coronavirus spike protein, the trimeric S1 subunit is positioned on top of the
trimeric S2 subunit (Table 2) (80, 245, 246).

The viral loads of SARS-CoV-2 were measured using N-gene-specific quantitative RT-PCR in
throat swab and sputum samples collected from COVID-19-infected individuals. The results
indicated that the viral load peaked around 5 to 6 days following the onset of symptoms, ranging
from 10^4 to 10^7 copies/mL during this period (151). In another study, the viral load was found
to be higher in nasal swabs compared to throat swabs from symptomatic COVID-19 patients
(82). Although it was initially thought that a higher viral load would correlate with worse
outcomes, some case reports have shown asymptomatic individuals with high viral loads (247).
Recently, the viral load in nasal and throat swabs of 17 symptomatic patients was determined,
with higher viral loads recorded shortly after symptom onset, particularly in the nasal swabs
compared to throat swabs. The viral nucleic acid shedding pattern in SARS-CoV-2-infected
patients was similar to that observed in influenza patients but differed from the pattern seen in
SARS-CoV patients. The viral load detected in asymptomatic patients was found to be similar to
that of symptomatic patients, as seen in a study conducted in China. This finding highlights the
transmission potential of both asymptomatic and mildly symptomatic patients (82).

6.1 Laboratory Testing for Coronavirus Disease 2019 (COVID-19) in Suspected Human
Cases

The assessment of patients with COVID-19 should be based on clinical features as well as
epidemiological factors. Screening protocols must be developed and implemented according to
the local context. The collection and testing of specimen samples from suspected individuals are
considered key principles in controlling and managing the outbreak within a country. Suspected
cases must undergo thorough screening to detect the virus, primarily using nucleic acid
amplification tests such as reverse transcription polymerase chain reaction (RT-PCR). If a
country or region lacks the necessary facilities for testing, specimens from suspected individuals
should be sent to the nearest reference laboratories as listed by the WHO.

It is also recommended that suspected patients be tested for other respiratory pathogens by
performing routine laboratory investigations based on local guidelines, mainly to differentiate
COVID-19 from other viruses such as influenza virus, parainfluenza virus, adenovirus,
respiratory syncytial virus, rhinovirus, and human metapneumovirus. In another study, the
average reproductive number (R₀) of COVID-19 was found to be 3.28, which is significantly
higher than the initial WHO estimate of 1.4 to 2.5. However, it is still too early to determine the
exact R₀ value, as there may be bias due to insufficient data. A higher R₀ indicates a greater
potential for SARS-CoV-2 transmission in a susceptible population. This is not the first time that
Chinese culinary practices have been blamed for the origin of a novel coronavirus infection in
humans. Previously, animals sold in live-animal markets were identified as intermediate hosts
during the SARS outbreak in China. Several wildlife species have been found to harbor
potentially evolving coronavirus strains capable of crossing species barriers. One of the core
principles of traditional Chinese food culture is the belief that animals freshly slaughtered are
more nutritious.

After four months of efforts, from December 2019 to March 2020, the COVID-19 situation in
China appeared to be under control. However, wet markets have since reopened, and people have
resumed buying bats, dogs, cats, birds, scorpions, badgers, rabbits, pangolins (scaly anteaters),
minks, palm civet soup, ostriches, hamsters, snapping turtles, ducks, fish, Siamese crocodiles,
and other animals. A suspected case of COVID-19 is confirmed if respiratory tract aspirates or
blood samples test positive for SARS-CoV-2 nucleic acid using RT-PCR, or if the genetic
sequence of SARS-CoV-2 is identified in these samples. A patient is considered cured when two
consecutive oral swab results are negative. Recently, live virus has been detected in the self-
collected saliva of COVID-19 patients, supporting the use of saliva as a noninvasive specimen
for diagnosing infection in suspected cases.

It has also been observed that initial RT-PCR tests may yield negative results despite suggestive
chest CT findings. Therefore, accurate diagnosis requires a combination of repeated RT-PCR
testing and CT scanning to minimize the risk of false negatives. RT-PCR remains the most
widely used diagnostic test for COVID-19; however, it has limitations from a clinical standpoint,
as it provides no information on disease progression. Droplet digital PCR (ddPCR) may be used
to quantify viral load in samples taken from the lower respiratory tract. Evidence of human
infection from animals exists, but cat-to-human transmission remains unconfirmed and requires
further study. Rather than waiting for definitive proof of animal-to-human transmission,
preventive measures should be adopted, including social distancing practices for companion
animals from different households. One leading veterinary diagnostics company, IDEXX,
conducted large-scale COVID-19 testing on samples from dogs and cats, with all results
returning negative.

A study investigating the potential of various animal species to act as intermediate hosts for
SARS-CoV-2 found that both ferrets and cats can be infected via experimental inoculation.
Moreover, infected cats were able to efficiently transmit the virus to uninfected cats. In ferrets,
SARS-CoV-2 infection and subsequent transmission closely resembled the clinical features of
COVID-19 in humans. Infected ferrets shed the virus through multiple routes—saliva, nasal
discharge, feces, and urine—making them a valuable animal model for studying transmission.
Experimental inoculation in other animals revealed that dogs have low susceptibility, while
chickens are largely unaffected.

SplitsTree Phylogeny Analysis

In an unrooted phylogenetic tree of various betacoronaviruses based on the spike (S) protein,
virus sequences from different subgenera formed distinct clusters. SARS-CoV-2 sequences from
Wuhan and other countries showed close relationships and appeared in a single cluster.
Coronaviruses from the Sarbecovirus subgenus grouped into three subclusters: SARS-CoV-2, bat
SARS-like CoV (bat-SL-CoV), and SARS-CoV.

In other subgenera, such as Merbecovirus, all sequences formed a single cluster. In Embecovirus,
species including camel respiratory CoVs, bovine CoVs, equine CoVs, and the human OC43
strain clustered together. Isolates from the Nobecovirus and Hibecovirus subgenera were found
to be phylogenetically separate from other reported SARS-CoVs but shared a bat origin.
Current Worldwide Scenario of SARS-CoV-2

The novel virus SARS-CoV-2 belongs to the subgenus Sarbecovirus of the Orthocoronavirinae
subfamily and is genetically distinct from previously known coronaviruses. It utilizes the same
cellular entry receptor as SARS-CoV, namely ACE2, although differences in binding affinity and
host interactions have been observed. Several countries have issued travel advisories for
individuals traveling to China. Compared to previous coronavirus outbreaks caused by SARS-
CoV and MERS-CoV, the human-to-human transmission efficiency of SARS-CoV-2 was
initially thought to be lower. This assumption was based on early reports indicating that
healthcare workers were less frequently affected than in prior outbreaks of deadly coronaviruses.

Superspreading events were significant contributors to the widespread transmission seen in

SARS and MERS outbreaks. For instance, nearly half of the MERS-CoV cases reported in Saudi
Arabia were of secondary origin, resulting from direct contact with infected individuals—either
symptomatic or asymptomatic. The possibility of superspreading events during the COVID-19
outbreak cannot be ruled out and requires careful evaluation. Similar to SARS and MERS,
COVID-19 primarily infects the lower respiratory tract, though it often presents with milder
symptoms. The basic reproduction number (R₀) of COVID-19 has been estimated to range from
2.8 to 3.3 based on real-time data and from 3.2 to 3.9 based on predictive modeling of case
numbers. Virological, radiological, and pathological studies have shown that monkeys with prior
exposure to SARS-CoV-2 did not experience reinfection upon rechallenge. These findings
suggest that primary infection with SARS-CoV-2 may confer protective immunity against
subsequent exposures. This has important implications for understanding disease prognosis and
for guiding the development of effective vaccines against COVID-19.

Prevention, Control, and Management

In contrast to their response during the 2002 SARS outbreak, China demonstrated significant
political transparency in reporting the COVID-19 outbreak promptly. The country also conducted
rapid sequencing of the virus at multiple levels and shared the genomic data globally within days
of identifying the novel coronavirus. This action marked a new chapter in global health security
and diplomacy. Despite the complete lockdown implemented following the outbreak in Wuhan,
large-scale human movement led to the rapid spread of infections to nearby provinces and other
countries. Mass screening programs were initiated to curb the transmission. The virus is known
to persist on surfaces for several days under favorable atmospheric conditions, but it can be
inactivated within a minute by common disinfectants such as sodium hypochlorite and hydrogen
peroxide. Transmission occurs primarily through inhalation of respiratory droplets or by touching
contaminated surfaces and subsequently touching the nose, mouth, or eyes. The virus has also
been detected in stool samples, raising the possibility of contamination of water supplies and
transmission via aerosolization or fecal–oral routes. According to current evidence, there is no
confirmed transplacental transmission of SARS-CoV-2 from pregnant women to fetuses.
However, cases of neonatal infection due to postnatal transmission have been reported.

The incubation period for COVID-19 ranges from 2 to 14 days, with a median of approximately
5 days. Studies have also indicated that animals such as cats and camels may act as amplifier
hosts in coronavirus transmission cycles. Coronavirus genomes and their subgenomes encode six
open reading frames (ORFs). The majority of the 5′ end is occupied by ORF1a/b, which
translates into 16 non-structural proteins (nsps). Two polyproteins, pp1a and pp1ab, are initially
synthesized from ORF1a/b via a −1 ribosomal frameshift. These polyproteins are then cleaved
into individual nsps by virus-encoded proteases, including the main protease (Mpro),
chymotrypsin-like protease (3CLpro), and papain-like proteases (PLPs). SARS-CoV-2 encodes
the same nsps, and their functions have been recently elucidated. A notable difference between
SARS-CoV-2 and other coronaviruses is the discovery of a novel, short putative protein encoded
within the ORF3 region, as well as a secreted protein with both alpha-helix and six-stranded
beta-sheet structures encoded by ORF8.

Coronaviruses also encode four major structural proteins that are essential for viral assembly and
infectivity: spike (S), membrane (M), envelope (E), and nucleocapsid (N) proteins. These
structural components are discussed in further detail in subsequent sections.

S Glycoprotein

The coronavirus spike (S) glycoprotein is a large, multifunctional, class I transmembrane protein
crucial for viral entry into host cells. Based on molecular characterization, SARS-CoV-2 is
classified as a novel betacoronavirus belonging to the subgenus Sarbecovirus. Other notable
zoonotic viruses, including MERS-CoV and SARS-CoV, also fall under the same genus.
However, SARS-CoV-2 has been identified as a distinct virus due to significant genetic
differences. Specifically, the conserved open reading frame 1a/b (ORF1a/b) of SARS-CoV-2
shares less than 90% sequence identity with other betacoronaviruses. An overall nucleotide
identity of approximately 80% has been observed between SARS-CoV-2 and the original SARS-
CoV, including similarities to bat SARS-related coronaviruses ZC45 and ZXC21. Additionally,
there is around 82% identity between SARS-CoV-2 and two human SARS-CoV strains: Tor2
and BJ01 (2003). In contrast, the sequence identity between MERS-CoV and SARS-CoV-2 is
much lower, at only 51.8%. Phylogenetic analysis of structural genes has also revealed that
SARS-CoV-2 is more closely related to bat SARS-related coronaviruses, suggesting that bats are
the most likely original host, with potential intermediate amplifier hosts facilitating transmission
to humans.

It is worth noting that the two other zoonotic coronaviruses—MERS-CoV and SARS-CoV—also
originated in bats, with civet cats and camels identified as intermediate hosts, respectively. Given
the evolutionary patterns, it is plausible that SARS-CoV-2 may establish a long-term niche in the
human population. Until clinically approved vaccines become widely available, the most
effective means of protection remain individual preventive behaviors, such as mask-wearing and
social distancing, along with public health strategies including active testing, contact tracing, and
limiting mass gatherings. Despite the rapid and substantial volume of SARS-CoV-2 research
being published weekly, much remains unknown. The precise animal origin and the mechanism
of cross-species transmission have not yet been definitively identified. Similarly, many
molecular mechanisms underlying SARS-CoV-2 infection, pathogenesis, and virus-host
interactions remain under investigation.

Several vaccine candidates have shown promising results. A viral vector vaccine developed by
the University of Oxford demonstrated the induction of neutralizing antibodies in all 1,077
participants after a second dose in a randomized, controlled phase I/II clinical trial, with an
acceptable safety profile. Another candidate, mRNA-1273—co-developed by NIAID and
Moderna—is a lipid nanoparticle-formulated mRNA vaccine encoding a stabilized prefusion
form of the SARS-CoV-2 S protein. Phase I trials confirmed its immunogenicity, showing strong
neutralizing antibody responses in a dose-dependent manner, which increased after the second
dose. In addition, an inactivated whole-virus COVID-19 vaccine underwent a successful phase
I/II clinical trial in China, involving 320 participants. It demonstrated a low incidence of adverse
effects and effectively induced neutralizing antibodies. The demonstrated safety and
immunogenicity of these vaccine candidates support their progression into phase III trials, which
are critical to assess their efficacy in protecting healthy populations from SARS-CoV-2 infection.
Future Perspectives

COVID-19 represents the third highly pathogenic coronavirus disease affecting humans,
following SARS and MERS. Although its case fatality rate is lower than that of SARS or MERS,
the rapid and extensive global transmission of SARS-CoV-2 has made it the most severe public
health crisis of the 21st century. The pandemic has persisted for over half a year, with ongoing
transmission likely to involve asymptomatic carriers who contribute silently to the spread of the
virus. Radiological findings play a critical role in the diagnosis and management of COVID-19.
Chest CT imaging reveals a progression from focal, unilateral ground-glass opacities to diffuse,
bilateral abnormalities, often accompanied by lung consolidation within 1 to 3 weeks of
symptom onset. Radiologists are therefore essential in early detection of COVID-19-associated
pneumonia, assessment of disease severity, identification of complications such as acute
respiratory distress syndrome (ARDS), and detection of secondary bacterial infections. However,
widespread use of CT imaging as a screening tool—especially in asymptomatic individuals—
may carry an unfavorable risk-benefit ratio due to radiation exposure and the potential for
nosocomial transmission. Consequently, CT imaging should be reserved for high-risk cases and
used judiciously.

To address the limitations of RT-PCR and imaging in rapid screening, several novel diagnostic
tools have been developed. One example is the reverse transcription loop-mediated isothermal
amplification (RT-LAMP) assay, such as iLACO, which allows for rapid, colorimetric detection
of SARS-CoV-2 and offers potential for decentralized testing. While multiple therapeutic agents
have demonstrated antiviral activity against SARS-CoV-2 in vitro, few have progressed to
randomized clinical trials in humans or animal models. This lack of clinical validation restricts
their current application in routine patient care and underscores the urgent need for rigorous
evaluation of candidate therapeutics.

This comprehensive review has outlined the key characteristics of SARS-CoV-2, including its
pathogenesis, diagnostic strategies, vaccine development efforts, and therapeutic potentials. It
has also provided a comparative analysis with previous outbreaks of SARS and MERS, discussed
the veterinary and zoonotic perspectives of coronaviruses, and emphasized the importance of
One Health approaches in managing emerging zoonotic threats. Moving forward,
interdisciplinary collaborations and sustained global health efforts will be essential in mitigating
the impact of COVID-19 and preventing future pandemics.

The Virus (SARS-CoV-2)

Coronaviruses are positive-sense single-stranded RNA viruses with a broad and promiscuous
host range in nature, capable of infecting multiple species and organ systems (23, 24). In
humans, coronaviruses are known to cause a spectrum of clinical illnesses, ranging from the
common cold to more severe respiratory diseases such as Severe Acute Respiratory Syndrome
(SARS) and Middle East Respiratory Syndrome (MERS) (17, 279). The newly emergent SARS-
CoV-2 has caused widespread disruption, beginning with an outbreak in China and rapidly
escalating into a global pandemic. This novel virus has led to unprecedented public health,
social, and economic challenges worldwide, affecting millions of individuals and straining
healthcare systems across nations.

Epidemiology and Pathogenesis [10, 11]

SARS-CoV-2 affects individuals of all age groups. Transmission occurs primarily via large
respiratory droplets produced by coughing and sneezing from symptomatic individuals; however,
asymptomatic and presymptomatic individuals can also transmit the virus [9]. Studies have
demonstrated higher viral loads in the nasal cavity compared to the throat, with no significant
difference in viral load between symptomatic and asymptomatic individuals [12]. Patients may
remain infectious throughout the duration of symptoms and, in some cases, even after clinical
recovery. Certain individuals, known as "superspreaders," can infect a disproportionately large
number of secondary cases. For instance, a UK citizen who attended a conference in Singapore
was linked to the infection of 11 others while staying at a ski resort in the French Alps and after
returning to the UK [6]. Respiratory droplets can travel 1–2 meters and deposit on surfaces,
contributing to fomite transmission. Although parallels are drawn from SARS and MERS
outbreaks, particular attention is being given to the potential impact of SARS-CoV-2 on
pregnancy. A few reports from China suggest the possibility of in utero transmission, based on
elevated levels of IgM, IgG, and cytokines in neonates born to infected mothers. However, RT-
PCR testing has not confirmed the presence of viral RNA in these neonates [283]. Some studies
have also linked preterm delivery and its complications with maternal SARS-CoV-2 infection.
Despite this, evidence of vertical transmission remains inconclusive [240–243].

Clinically, COVID-19 is frequently associated with pneumonia and, in severe cases, progression
to acute respiratory distress syndrome (ARDS). Laboratory markers such as hypoalbuminemia,
lymphopenia, elevated lactate dehydrogenase (LDH), C-reactive protein (CRP), and D-dimer
levels are indicative of disease severity [121, 244]. Altered levels of liver enzymes (AST, ALT),
bilirubin, and leukocyte counts are also common.

The viral spike (S) and nucleocapsid (N) proteins contain antigenic epitopes that make them
attractive vaccine targets [294]. In particular, subunit vaccines targeting the S, E, M, and N
proteins are under development, especially in the Asian population [295]. Identifying
immunodominant regions within the S protein—especially within the C-terminal domain of the
S1 subunit—is essential for developing effective vaccines, as demonstrated in porcine delta
coronavirus studies [171].

Efforts to develop a universal coronavirus vaccine based on T-cell epitope similarities between
SARS-CoV and MERS-CoV suggest the possibility of cross-reactivity [172]. This raises the
potential for shared vaccine targets among related coronaviruses. Given the genetic similarity
between SARS-CoV-2 and SARS-CoV [173, 174], such strategies may be feasible. Zoonotic
transmission remains a central concern in coronavirus epidemiology. In MERS-CoV, animals
such as dromedary camels have been shown to shed the virus via milk, urine, feces, and
respiratory secretions [108]. Other species, such as llamas and pigs, have also demonstrated
susceptibility, suggesting that MERS-CoV could circulate in a broader range of animal hosts
[109].

Following the SARS outbreak in China, SARS-CoV-like viruses were isolated from Himalayan
palm civets (Paguma larvata) and raccoon dogs (Nyctereutes procyonoides) in live animal
markets in Guangdong. These animal strains retained a 29-nucleotide sequence absent in most
human isolates, suggesting interspecies transmission [78]. Subsequent surveillance identified
SARS-like coronaviruses circulating in Chinese horseshoe bats (Rhinolophus sinicus), further
supporting the theory of bat-origin zoonotic spillover. The high genetic diversity of bat
coronaviruses in this region suggests a long history of host-pathogen coevolution.

13. Convalescent Plasma Therapy

Convalescent plasma therapy has emerged as a promising treatment for patients with severe
COVID-19. Guo Yanhong, an official from the National Health Commission (NHC) of China,
emphasized its significance in managing critical cases. In Wuhan, one of the earliest epicenters
of the outbreak, convalescent plasma therapy was administered to several severely ill patients,
with at least one patient discharged following treatment, according to Chinese scientific
authorities (17 February 2020, Beijing). The first doses of convalescent plasma were collected
from recovered COVID-19 patients on 1st and 9th February 2020 at a hospital in Jiangxia
District, Wuhan. The therapeutic effect is primarily attributed to the presence of neutralizing
antibodies in the plasma, which help reduce the viral load in recipients. According to Dr.
Guiqiang Wang, the donation process poses minimal risk to donors. Only plasma is extracted
during the process, while red blood cells (RBCs), white blood cells (WBCs), and platelets are
returned to the donor's bloodstream. Donors typically recover their plasma volume within one to
two weeks after donating 200–300 mL.

Animal studies have demonstrated that antibodies from convalescent plasma can confer
significant protection—such as in mice challenged with lethal doses of MERS-CoV. These
findings suggest that antibodies targeting the spike (S) protein, particularly its receptor-binding
domain (RBD), may enhance protective humoral responses against emerging coronaviruses. The
effectiveness of cross-neutralizing monoclonal antibodies (MAbs) depends on the similarity of
RBDs among different coronaviruses. For instance, SARS-CoV RBD-specific MAbs were able
to neutralize bat-SL-CoV strain WIV1 (which shares eight amino acid differences with SARS-
CoV) but not strain SHC014 (which has 24 differences) [200]. Therefore, identifying MAbs with
cross-neutralizing capabilities requires careful comparative analysis of the RBD of SARS-CoV-2
with related coronaviruses. Regeneron, a U.S.-based biotechnology company, has been actively
working to identify potent and specific MAbs for COVID-19 therapy. One promising candidate
is the human MAb CR3022, which binds to the SARS-CoV-2 RBD, suggesting potential for
therapeutic application.

Combination therapies, such as MAbs paired with antiviral agents like remdesivir, have been
proposed as an ideal approach for combating SARS-CoV-2 [201]. However, more robust clinical
data are required to confirm their efficacy. For example, early studies on favipiravir suggested
potential benefits, but these lacked control arms and were limited by small sample sizes. Larger
randomized controlled trials are essential for conclusive evidence.

Pathogenesis, Transmission, and Global Response

Swine acute diarrhea syndrome coronavirus (SADS-CoV), like SARS-CoV and MERS-CoV,
belongs to the Coronaviridae family and is a reminder of the zoonotic and pandemic potential of
emerging coronaviruses [117]. SARS-CoV-2 primarily invades the lung parenchyma, leading to
severe interstitial inflammation. Computed tomography (CT) scans of affected individuals
commonly reveal ground-glass opacities, initially localized to a single lobe and later progressing
to multiple lobes [118]. Histological analyses of lung tissue from COVID-19 patients have
shown diffuse alveolar damage, fibromyxoid exudates, hyaline membrane formation, and
desquamation of pneumocytes—all consistent with acute respiratory distress syndrome (ARDS)
[119]. Hematological findings often include lymphocytopenia, which may be accompanied by
other leukocyte abnormalities. The degree of lymphocytopenia is positively correlated with
disease severity, making it a valuable prognostic marker [118]. Pregnant women are considered
at higher risk of severe illness, and coronavirus infections in pregnancy have been associated
with adverse fetal outcomes, including intrauterine growth restriction, spontaneous abortion,
preterm delivery, and perinatal death. Nevertheless, the risk of vertical transmission appears low
and was not documented in prior SARS and MERS outbreaks [120].

Effective management of COVID-19 is particularly challenging in low-income countries with

fragile healthcare infrastructures. Delays in diagnosis and response can hinder containment and
contribute to wider transmission [65]. Modeling studies estimate that the probability of an
imported COVID-19 case leading to sustained local transmission is approximately 0.41;
however, this can be reduced to 0.012 if the time from symptom onset to hospitalization is
minimized, which requires robust surveillance systems [235]. Silent importation of infected
individuals—especially asymptomatic carriers—contributed significantly to the global spread of
the virus. Despite the travel ban in Wuhan, individuals who traveled before its implementation
likely triggered outbreaks in other regions [236]. In our globalized world, emerging infectious
diseases like COVID-19 can rarely be contained within national borders. International
collaboration is critical for early detection, information sharing, and implementation of
containment measures. Public health recommendations at the community level include avoiding
crowded places, delaying non-essential travel to high-transmission areas, practicing cough
etiquette (e.g., coughing into the elbow or a tissue), and frequent hand hygiene every 15–20
minutes.

Symptomatic individuals should wear surgical masks to prevent spread. However, routine mask
use by healthy individuals in public has not been definitively proven to prevent respiratory viral
infections and was not initially recommended by the World Health Organization (WHO). In
contrast, countries like China mandated mask use in public, particularly in crowded areas, and
prohibited large gatherings in spaces such as amusement parks.

On 31 January 2020, the WHO declared the outbreak a Public Health Emergency of International
Concern (PHEIC), and by 11 March 2020, it was classified as a pandemic. As of now, no
specific antiviral treatments or approved vaccines for SARS-CoV-2 exist, although global efforts
continue to focus on developing preventive and therapeutic strategies [7–9].

Coronaviruses in domestic animals are associated with a wide range of diseases. In addition to
respiratory pathogens like infectious bronchitis virus, canine respiratory coronavirus, and mouse
hepatitis virus, most animal CoVs are implicated in gastrointestinal disorders [10]. The
emergence of novel CoVs is likely driven by the maintenance of multiple coronaviruses in
natural reservoirs, promoting opportunities for recombination events. The high genetic diversity
of coronaviruses is attributed to the inherent error-prone nature of RNA-dependent RNA
polymerases and frequent homologous recombination [10, 11]. This genomic flexibility allows
cross-species transmission and adaptation. Understanding the origin and evolutionary dynamics
of SARS-CoV-2 is essential for disease surveillance, preparedness, and the development of
future diagnostics and vaccines [12]. One limitation of current nucleic acid-based diagnostics is
that they only detect active infection, reducing their utility in the later or post-infectious stages.
To address this, several research laboratories worldwide are developing antibody-based
diagnostic assays that can detect past exposure to SARS-CoV-2, enabling broader
epidemiological tracking [157].

Chest CT is an ideal diagnostic tool for detecting viral pneumonia, with superior sensitivity
compared to X-ray screening. The chest CT findings in COVID-19 patients often include
characteristic patchy infiltrates that progress to ground-glass opacities, which are highly
indicative of the disease [158]. Early manifestations of COVID-19 pneumonia may not be
apparent on chest X-ray, making CT imaging a more reliable diagnostic option. It is considered
highly specific for diagnosing COVID-19 pneumonia, with ground-glass opacities being a
hallmark feature on chest CT scans [154]. In addition to radiological findings, COVID-19
patients exhibit elevated plasma levels of angiotensin II, which have been found to correlate
linearly with viral load and lung injury, suggesting its potential as a diagnostic biomarker for the
disease [121]. Interestingly, CT imaging abnormalities associated with COVID-19 pneumonia
have also been observed in asymptomatic patients, underlining the diagnostic value of chest CT
in various stages of infection. The therapeutic landscape for coronaviruses has evolved over the
years, with several strategies, including vaccines, immune therapies, and antiviral drugs, being
evaluated for previous outbreaks like SARS-CoV and MERS-CoV [8, 104, 164–167]. However,
the primary obstacle to the development and availability of effective vaccines and therapeutics
for SARS-CoV and MERS-CoV was the relatively limited global impact of these viruses
compared to the SARS-CoV-2 pandemic. The lesser global threat posed by these earlier
outbreaks did not generate sufficient demand for mass vaccine or drug production, leading to
limited attention from the biomedicine and pharmaceutical industries [19]. Furthermore, the
short-lived nature of such outbreaks often meant that the need for vaccines and drugs existed
only during the peak of the outbreak, further hindering investment in long-term solutions.

Coronaviruses are a diverse group of viruses that infect a wide range of animals and can cause
diseases ranging from mild respiratory infections to severe pneumonia in humans. Two highly
pathogenic zoonotic coronaviruses, SARS-CoV (2002) and MERS-CoV (2012), emerged in
humans and caused fatal respiratory illnesses, highlighting the potential public health risks posed
by novel coronaviruses. At the end of 2019, a new coronavirus, SARS-CoV-2, emerged in
Wuhan, China, triggering a global pandemic of coronavirus disease 2019 (COVID-19). COVID-
19 has rapidly surpassed both SARS and MERS in terms of the number of infections and the
global spread of the disease. The ongoing outbreak has posed an extraordinary threat to global
public health. This review summarizes the current understanding of SARS-CoV-2, covering its
genetic characteristics, potential zoonotic origin, receptor binding, as well as the clinical,
epidemiological, and diagnostic features of COVID-19. The review also discusses the
countermeasures being developed to combat the ongoing pandemic.

Emergence and Spread of COVID-19

In late December 2019, several health facilities in Wuhan, Hubei province, China, reported
clusters of patients presenting with pneumonia of unknown etiology [6]. Similar to patients
infected with SARS-CoV and MERS-CoV, these individuals exhibited symptoms of viral
pneumonia, including fever and cough. This new disease, later identified as COVID-19, rapidly
spread within China and to other countries, prompting global concern. The SARS-CoV-2 virus
shares several structural and molecular features with its predecessors, SARS-CoV and MERS-
CoV. One such feature is the presence of the E protein, which plays a critical role in the viral life
cycle. The E protein consists of three distinct domains: a short hydrophilic amino terminal, a
large hydrophobic transmembrane domain, and a functional C-terminal domain [51]. In SARS-
CoV-2, the E protein reveals a similar amino acid structure to that of other coronaviruses, with
no significant substitutions in its sequence [16]. The presence and functionality of this protein are
linked to the virus’s ability to infect host cells, with its absence contributing to altered virulence
and changes in the virus’s morphology and tropism [54].

N Protein

The nucleocapsid (N) protein of coronaviruses is multifunctional, serving several critical roles in
the virus lifecycle. It is involved in complex formation with the viral genome, facilitates
interaction with the membrane (M) protein during virion assembly, and enhances the
transcription efficiency of the virus [55, 56]. The N protein consists of three highly conserved
domains: the N-terminal domain (NTD), the RNA-binding domain (RBD) or linker region
(LKR), and the C-terminal domain (CTD) [57]. The NTD binds to the 3' end of the viral genome,
potentially through electrostatic interactions, and exhibits significant variation in length and
sequence [58]. The LKR, rich in serine and arginine, is also referred to as the SR (serine-
arginine) domain [59]. This region can directly interact with RNA in vitro and plays an essential
role in cell signaling [60, 61]. Additionally, the LKR modulates the host's antiviral response by
acting as an antagonist to interferon signaling, thereby influencing the host's immune response.

Practice Points from an Indian Perspective

At the time of writing this article, the risk of coronavirus in India remains extremely low, but the
situation may change rapidly in the coming weeks. Therefore, the following measures are
recommended:
 Healthcare Providers: Healthcare providers should take a comprehensive travel history from
all patients presenting with respiratory symptoms, including recent international travel within
the past two weeks or any contact with individuals who have traveled internationally.
 Triage System: A triage system should be set up for patients with respiratory illness in the
outpatient department, and these patients should be given simple surgical masks to wear.
Healthcare providers should also use surgical masks while examining these patients to reduce
the risk of transmission.

Virology of SARS-CoV-2 The virus responsible for COVID-19 has been designated SARS-
CoV-2 by the International Committee on Taxonomy of Viruses (ICTV). SARS-CoV-2 is part of
the Severe Acute Respiratory Syndrome-related Coronavirus category, closely related to SARS-
CoV [26]. This virus belongs to the order Nidovirales, the family Coronaviridae, and the
subfamily Orthocoronavirinae, which is divided into four genera: Alphacoronavirus,
Betacoronavirus, Gammacoronavirus, and Deltacoronavirus [3, 27]. Alphacoronaviruses and
Betacoronaviruses primarily originate from bats, whereas Gammacoronaviruses and
Deltacoronaviruses are typically found in birds and swine [24, 28, 29, 275].

SARS-CoV-2 shares a common origin with other zoonotic coronaviruses, which explains its
ability to spill over from animal hosts to humans, creating potential for widespread outbreaks.

Coronaviruses possess an unsegmented, single-stranded, positive-sense RNA genome,

approximately 30,000 bases in length, enclosed by a 5' cap and a 3' poly(A) tail [30]. The
genome of SARS-CoV-2 is 29,891 base pairs long, with a G+C content of 38% [31]. These
viruses are surrounded by an envelope, but certain species, such as ducks and pigs, are not
susceptible to SARS-CoV-2 infection [329].

Interestingly, the National Veterinary Services Laboratories of the USDA have reported cases of
COVID-19 in tigers and lions that exhibited respiratory symptoms like dry cough and wheezing.
These zoo animals are believed to have been infected by an asymptomatic zookeeper [335]. With
the growing number of COVID-19 cases in humans, the risk of viral spillover to other species,
such as pigs, increases. Evidence from the SARS-CoV outbreak suggests that pigs can become
infected with SARS-CoV-2 [336]. However, experimental inoculation with SARS-CoV-2 has
failed to infect pigs in laboratory settings [329].

Further research is required to identify potential animal reservoirs of SARS-CoV-2 and assess
the seasonal variation in the circulation of these viruses within animal populations. There is a
growing need for collaborative research between human and animal health sectors to evaluate
and understand the risk factors for transmission between animals and humans. This collaboration
will be vital in devising effective strategies for managing emerging zoonotic diseases.

Recommendations for Clinicians and Public Health Measures

 Clinicians should stay updated on the latest developments, including the global spread of the
disease, and adjust their practices accordingly.
 Non-essential international travel should be avoided at this time to limit the spread of the
virus across borders.
 The public should stop spreading myths and false information about the disease to prevent
panic and anxiety. Efforts should focus on calming the population and promoting accurate
information about the ongoing situation.
Conclusions

The outbreak of this novel virus has posed significant challenges to the economic, medical, and
public health infrastructure of China, as well as to some extent, neighboring countries. The long-
term impact of this virus on India is still uncertain. However, it is clear that future outbreaks of
viruses and zoonotic pathogens are likely to continue. Therefore, alongside efforts to control the
current outbreak, there is a need to strengthen preparedness for future events, including the
introduction of additional diagnostic criteria, such as negative fecal viral nucleic acid test results,
as part of the discharge protocols for laboratory-confirmed COVID-19 cases [326].

The COVID-19 pandemic does not introduce fundamentally new challenges beyond those posed
by previous zoonotic viruses. What sets SARS-CoV-2 apart is its genetically distinct nature and
its origin from a novel pathogen. The likely cause and outcomes are familiar, as they echo earlier
encounters with deadly coronaviruses. The main difference lies in the timing of the outbreak and
the genetic characteristics of the virus involved. Mutations in the Receptor Binding Domain
(RBD) of coronaviruses have enhanced their ability to infect new hosts, allowing these viruses to
expand their reach worldwide [85]. This phenomenon poses a continuing threat to both animal
and human health.

Advanced studies, including Bayesian phylogeographic reconstruction, have identified the most
likely origin of SARS-CoV-2 as a bat SARS-like coronavirus circulating within the Rhinolophus
bat family [86]. Phylogenetic analysis of whole-genome sequences of SARS-CoV-2 confirmed
its relationship with two bat-origin coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21,
which were reported in 2018 in China [17]. It has also been confirmed that SARS-CoV-2 uses
ACE2 as an entry receptor, with its RBD resembling that of earlier SARS-related viruses,
highlighting the shared pathophysiology of these infections.

9. VACCINES

The COVID-19 outbreak, which originated in Wuhan, China, has rapidly spread across the
globe, posing a significant threat to public health. Due to its pandemic nature, efforts to develop
a vaccine for COVID-19 have become a global priority. The National Institutes of Health (NIH),
alongside pharmaceutical companies, are actively involved in vaccine development. In late April
2020, Xu Nanping, China's Vice Minister of Science and Technology, announced that the first
vaccine candidate was expected to enter clinical trials in China.

As of now, there is no approved vaccine or treatment for COVID-19 infections. Vaccine

development is being sponsored and supported by the Biomedical Advanced Research and
Development Authority (BARDA), a division of the Office of the Assistant Secretary for
Preparedness and Response (ASPR). Sanofi is one of the companies leading the charge, utilizing
its egg-free, recombinant DNA technology to produce a vaccine that mimics the genetic structure
of the virus proteins. This approach aims to develop a highly specific and effective vaccine. The
pandemic's impact extends beyond physical health, affecting the mental wellbeing of individuals,
especially healthcare workers on the frontlines. The mental strain experienced by these workers
can diminish attention, concentration, and decision-making abilities, potentially compromising
efforts to control the virus. As such, protecting the mental health of medical personnel should be
prioritized alongside physical health measures to ensure an effective response to the outbreak
[229].

The emergence of SARS-CoV-2, suspected to have originated from mammals sold in wet
markets, highlights the importance of strengthening regulatory frameworks for the wild animal
trade [13]. The rising number of confirmed COVID-19 cases and the relatively low cure rate
complicate the control of the disease. In response, the Chinese government has enacted several
emergency control measures, including the construction of dedicated hospitals for COVID-19
patients. Additional facilities are being built to accommodate the growing number of cases [230].
To effectively control the spread of SARS-CoV-2/COVID-19, comprehensive interventions are
necessary. These include intensive contact tracing, quarantine measures for suspected cases, and
isolation protocols for confirmed cases. Rigorous control and preventive measures will help
reduce the transmission rate and control the basic reproduction number (R₀) of the virus [228].

Animal Models and Cell Cultures

Evaluating the potential of vaccines and therapeutics against coronaviruses (CoVs), including
SARS-CoV, MERS-CoV, and the emerging SARS-CoV-2, requires suitable animal models that
can replicate the clinical disease. Various animal models have been assessed for SARS-CoV and
MERS-CoV, including mice, guinea pigs, golden Syrian hamsters, ferrets, rabbits, nonhuman
primates like rhesus macaques and marmosets, and cats [185, 211-218].

One significant challenge in developing animal models is the specificity of the virus to the
human ACE2 (hACE2) receptor, which SARS-CoV uses for entry into cells. This specificity has
hindered the development of suitable animal models. However, a transgenic mouse model for
SARS-CoV has been developed by inserting the hACE2 gene into the mouse genome, enabling
these mice to mimic human infection [219]. Similarly, MERS-CoV's inability to replicate
effectively in the respiratory tracts of animals such as mice, hamsters, and ferrets has also been a
barrier. To overcome this, a genetically modified MERS-CoV mouse model has been created,
which is now widely used for testing novel drugs and vaccines [220]. Small animals like mice
and hamsters have been particularly useful due to their humanized structures. For example, mice
have been genetically altered to express human DPP4 (hDPP4), the receptor for MERS-CoV,
making them valuable models for studying MERS-CoV infection.

These animal models have been crucial for evaluating the effectiveness of various therapeutic
approaches. In vitro studies have shown promising results for several therapeutics, but their
efficacy needs to be confirmed through randomized animal or human trials. Many potential
treatments, although showing promise in vitro, may have limited applicability until proven in
more comprehensive trials. The interaction of SARS-CoV-2 with the ACE2 receptor exacerbates
pneumonia, potentially disrupting the renin-angiotensin system (RAS). Studies suggest that ACE
inhibitors and angiotensin type-I receptor (AT1R) blockers may reduce viral-induced pulmonary
inflammation, highlighting their potential as therapeutic options [207].

Additionally, several small-molecule inhibitors have been identified for their potential to control
CoV infections. Drugs from the FDA-approved compound library, including chlorpromazine,
chloroquine, loperamide, and lopinavir, have shown efficacy in inhibiting MERS-CoV
replication. These compounds have also demonstrated activity against SARS-CoV and human
CoVs [208]. Further research into therapies that target specific antibodies or compounds to
neutralize cytokines and their receptors could help mitigate excessive host inflammatory
responses. Drugs that act specifically within the respiratory tract may be particularly beneficial
for managing viral infections in the lungs.

Prevention [21, 30]

Given that no approved treatments are currently available for COVID-19, prevention remains the
most effective strategy. Several characteristics of the virus make prevention challenging. These
include the nonspecific nature of the disease, the ability of the virus to spread even before
symptoms appear during the incubation period, and transmission from asymptomatic individuals.
Other complicating factors are the long incubation period, the virus's affinity for mucosal
surfaces like the conjunctiva, and prolonged illness duration, which can lead to continued
transmission even after clinical recovery. For individuals with mild illness, isolation at home is
recommended. The home should be well-ventilated, with exposure to sunlight, as this can help
reduce viral load. Patients should wear a simple surgical mask and practice proper cough hygiene
to minimize the risk of transmission.

For breastfeeding mothers, it is crucial to follow additional hygiene measures. The mother should
wear a face mask and practice hand hygiene before feeding the baby. Breast pumps should be
thoroughly cleaned after each use. If possible, it is recommended that a healthy individual feed
the expressed breast milk to the infant to minimize direct contact with the mother, further
reducing the risk of transmission [42].

7.2 Children and Elderly Population

Based on available reports, COVID-19 among children accounts for 1-5% of confirmed cases.
Children do not appear to be at higher risk for contracting the virus compared to adults. In fact,
symptoms in children seem to be milder, and the mortality rate is low [48, 49]. However, the
elderly population, especially those aged 65 years and older, are at significantly higher risk of
developing severe disease. In the United States, approximately 31-59% of individuals between
the ages of 65 and 84 with confirmed COVID-19 required hospitalization. Of those, 11-31%
required intensive care unit (ICU) admission, and 4-11% died [50]. In general, children with
COVID-19 have a milder disease course compared to adults, with a lower incidence of severe
outcomes. On the other hand, older adults face higher risks, including severe illness,
hospitalization, and death. It is also important to note that cases may be asymptomatic or show
mild symptoms, such as fever, especially in individuals who may have had persistent local
transmission or contact with patients who have similar travel histories or confirmed COVID-19
infections. A confirmed case is a suspect case with a positive molecular test.

For specific diagnosis, molecular tests on respiratory samples (such as throat swabs,
nasopharyngeal swabs, sputum, endotracheal aspirates, and bronchoalveolar lavage) are
recommended. The virus may also be detected in stool and, in severe cases, blood. Currently,
multiplex PCR panels do not include COVID-19, and commercial tests are not yet available. In
India, suspect cases must have their samples sent to designated reference labs or the National
Institute of Virology in Pune for testing. As the epidemic progresses, commercial tests for the
respiratory tract will help in reducing virus-triggered immune pathologies associated with
COVID-19 [209].

The later stages of the inflammatory response in COVID-19 are characterized by the release of
proinflammatory interleukin-1 (IL-1) family members, such as IL-1 and IL-33. Anti-
inflammatory cytokines from the IL-1 family may be potential treatments for mitigating
inflammation. Additionally, actin protein, a host factor involved in viral entry and pathogenesis
of SARS-CoV-2, could be a target for therapeutic intervention. Drugs like ibuprofen, which
modulate the biological activity of actin, may have potential applications in managing COVID-
19 [174]. Further research has shown that plasma angiotensin 2 levels are markedly elevated in
COVID-19 infections and are correlated with viral load and lung injury. Therefore, angiotensin
receptor blockers might hold potential for treating COVID-19 infection [121]. German scientist
Rolf Hilgenfeld has been studying drugs to treat coronaviral infections since the first SARS
outbreak [19].

Moreover, the SARS-CoV-2 spike (S) protein plays a significant role in virus fusion and entry
into host cells. The binding region (RBD) of the S protein from pangolin-derived CoVs was
nearly identical to that of SARS-CoV-2, with only one amino acid difference. This suggests that
pangolins could act as an intermediate host for SARS-CoV-2 [145].
Human-wildlife interactions are on the rise, particularly in the context of climate change [142].
These interactions are considered high-risk factors for the emergence of zoonotic diseases,
including SARS-CoV. COVID-19 is suspected to have a similar mode of origin, making it
crucial to prevent future zoonotic spillovers. To mitigate these risks, coordinated efforts are
needed to identify high-risk pathogens harbored by wild animal populations. Surveillance should
be conducted in communities that are at high risk of zoonotic spillover, particularly those in
proximity to wildlife habitats. Additionally, strengthening biosecurity measures related to the
wildlife trade is essential [146]. Previous serological surveillance studies in individuals living
near bat caves have confirmed the presence of SARS-related coronaviruses in humans. People
living at the wildlife-human interface, particularly in rural areas of China, are frequently exposed
to these viruses [147]. These findings underscore the importance of continued surveillance in
high-risk populations, but their significance remains limited without further studies on the viral
activity and potential for spillover.

Among the compounds evaluated for their potential therapeutic effects, two compounds—4-
(cyclopent-1-en-3-ylamino)-5-[2-(4-iodophenyl)hydrazinyl]-4H-1,2,4-triazole-3-thiol and 4-
(cyclopent-1-en-3-ylamino)-5-[2-(4-chlorophenyl)hydrazinyl]-4H-1,2,4-triazole-3-thiol—have
shown promise. These compounds were evaluated through in silico studies and molecular
docking into the active binding site of the MERS-CoV helicase (nsp13). While these compounds
have shown potential in preliminary studies, further research is necessary to evaluate their
therapeutic efficacy in managing COVID-19 infection.

Passive Immunization/Antibody Therapy/Monoclonal Antibodies (MAb)

Monoclonal antibodies (MAbs) have shown potential in the treatment of diseases caused by
coronaviruses (CoVs). For instance, patients who recovered from SARS demonstrated robust
neutralizing antibodies against the virus [164]. A series of MAbs targeting specific domains of
the MERS-CoV spike (S) protein, including those that interact with receptor-binding, membrane
fusion, and sialic acid-binding sites, are critical for viral entry [198, 199]. Passive immunization
with both weakly and strongly neutralizing antibodies has been shown to offer significant
protection in mice against MERS-CoV infection.

The development of fully human antibodies, such as human single-chain antibodies (HuscFvs) or
humanized nanobodies (single-domain antibodies; sdAb, VH/VHH), could also prove beneficial
in blocking viral replication. These agents are capable of crossing cell membranes (known as
transbodies), allowing them to interfere with the biological functions of replicating virus
proteins. Similar transbody-based therapies have been used for other viruses, including influenza,
hepatitis C, Ebola, and dengue [206]. By producing transbodies that target key intracellular
proteins of coronaviruses—such as papain-like proteases (PLpro), cysteine-like protease
(3CLpro), or other non-structural proteins (nsps) essential for viral replication and
transcription—this approach could provide a promising and safer passive immunization strategy
for individuals exposed to the virus and could offer effective treatment for infected patients.

In a case study involving five critically ill patients with severe pneumonia due to COVID-19,
administration of convalescent plasma was found to be beneficial. The plasma, which contained a
high titer of SARS-CoV-2-specific antibodies (ELISA titer greater than 1:1,000) and neutralizing
antibodies (titer greater than 40), was collected from recovered patients and transfused into the
critically ill individuals, contributing to their successful recovery.