Genome Analysis of SARS-CoV-2 Isolate from Bangladesh

Microbiology Resource Announcements

This study reports the coding-complete genome sequence, with variant identifications and phylogenetic analysis, of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) P.1 variant (20J/501Y.V3), obtained from an oropharyngeal swab specimen from a female Bangladeshi patient diagnosed with coronavirus disease 2019 (COVID-19) with no travel history.

2020

Corona Virus Disease-2019 (COVID-19) warrants comprehensive investigations of publicly available Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2) genomes to gain new insight about their epidemiology, mutations and pathogenesis. Nearly 0.4 million mutations were identified so far in ∼60,000 SARS-CoV-2 genomic sequences. In this study, we compared 207 of SARS-CoV-2 genomes reported from different parts of Bangladesh and their comparison with 467 globally reported sequences to understand the origin of viruses, possible patterns of mutations, availability of unique mutations, and their apparent impact on pathogenicity of the virus in victims of Bangladeshi population. Phylogenetic analyses indicates that in Bangladesh, SARS-CoV-2 viruses might arrived through infected travelers from European countries, and the GR clade was found as predominant in this region. We found 2602 mutations including 1602 missense mutations, 612 synonymous mutations, 36 insertions and deletions with...

Microbiology Resource Announcements, 2020

We report the sequencing of three severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Bangladesh. We have identified a unique mutation (NSP2_V480I) in one of the sequenced genomes (isolate hCoV-19/Bangladesh/BCSIR-NILMRC-006/2020) compared to the sequences available in the Global Initiative on Sharing All Influenza Data (GISAID) database. The data from this analysis will contribute to advancing our understanding of the epidemiology of SARS-CoV-2 in Bangladesh as well as worldwide at the molecular level and will identify potential new targets for interventions.

Microbiology Resource Announcements, 2021

The coding-complete genome sequence of a coronavirus strain, SARS-CoV-2/human/BGD/G039392/2021, obtained from a symptomatic male patient with coronavirus disease 2019 (COVID-19) in Dhaka, Bangladesh, is reported. The strain G039392 is 99.9% identical to the UK variant B.1.1.7.

2020

The COVID19 pandemic caused by SARS-CoV-2 virus has severely affected most countries of the world including Bangladesh. We conducted comparative analysis of publicly available whole-genome sequences of 64 SARS-CoV-2 isolates in Bangladesh and 371 isolates from another 27 countries to predict possible transmission routes of COVID19 to Bangladesh and genomic variations among the viruses. Phylogenetic analysis indicated that the pathogen was imported in Bangladesh from multiple countries. The viruses found in the southern district of Chattogram were closely related to strains from Saudi Arabia whereas those in Dhaka were similar to that of United Kingdom and France. The 64 SARS-CoV-2 sequences from Bangladesh belonged to three clusters. Compared to the ancestral SARS-CoV-2 sequence reported from China, the isolates in Bangladesh had a total of 180 mutations in the coding region of the genome, and 110 of these were missense. Among these, 99 missense mutations (90%) were predicted to des...

Microbiology resource announcements, 2021

Mutations, deletions, and the emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may pose a serious health threat. Here, we report the genome sequences of SARS-CoV-2 viruses that were collected from SARS-CoV-2-infected patients during the end phase of the first wave of the COVID-19 pandemic in Dhaka, Bangladesh. S evere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (family Coronaviridae, genus Betacoronavirus) is the causative agent of coronavirus disease 2019 (COVID-19). New variants of SARS-CoV-2 were detected as part of the second wave of the COVID-19 pandemic starting in March 2021 (https://www.worldometers.info/coronavirus/country/bangladesh/). Between November 2020 and February 2021, the rate of COVID-19 cases started to decrease and remained relatively low in Bangladesh. To analyze the types of SARS-CoV-2 variants which were circulating during the end phase of the first wave, nasopharyngeal swabs from SARS-CoV-2-infected patients were collected from the Department of Virology, Bangabandhu Sheikh Mujib Medical University (BSMMU), during November and December 2020. (International, national, and/or institutional guidelines were followed according to the Institutional Review Board [IRB] of BSMMU; the ethical approval number is BSMMU/2020/ 6320.) Nasopharyngeal swabs were tested for SARS-CoV-2 RNA via real-time reverse transcription-PCR (RT-PCR), and 23 RT-PCR-positive samples (cycle threshold [Ct], #25) were selected for the study. Viral RNA was extracted from the nasopharyngeal samples using the QIAamp viral minikit (Qiagen; catalog number 52904). cDNA synthesis and library preparation were performed using the Illumina RNA prep kit with enrichment (catalog number 20040537) and IDT for Illumina DNA/RNA UD indexes (catalog number 20027213), followed by enrichment with the Respiratory Virus Oligos Panel v2 (Illumina; catalog number 20044311). All procedures were conducted according to the Illumina RNA prep with enrichment (L) tagmentation reference guide (1000000124435 v03). Sequencing was performed on the Illumina MiniSeq system. The genomes were then processed using the DRAGEN RNA pathogen detection app. The low-quality raw reads were trimmed using Trimmomatic v0.36, and the de novo genome assembly was performed using SPAdes v03. These steps were executed using default parameters (1, 2). In total, 23 contigs were obtained and compared with the SARS-CoV-2 isolate Wuhan-Hu-1 (GenBank accession number NC_045512.2); the genome coverage was 99.86% to 99.93%. A phylogenetic tree was constructed as previously described (3) (Fig. 1). In short, the FASTA files of the assembled genome sequences were aligned using MAFFT (keeping the parameters unchanged), and the tree was created using FastTree v2.1.10 (4, 5)

2021

We announce the complete genome sequences of 12 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sublineage B.1.617.2 strains (Delta variant) obtained from nasopharyngeal and oropharyngeal swab samples from 12 pediatric patients in Chittagong, Bangladesh, displaying COVID-19 symptoms. Oxford Nanopore MinION sequencing technology was used to generate the genomic sequences. ABSTRACT We announce the complete genome sequences of 12 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sublineage B.1.617.2 strains (Delta variant) obtained from nasopharyngeal and oropharyngeal swab samples from 12 pediatric patients in Chittagong, Bangladesh, displaying COVID-19 symptoms. Oxford Nanopore MinION sequencing technology was used to generate the genomic sequences.

Microbiology Resource Announcements

The complete genome sequence of a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) isolate obtained from a nasopharyngeal swab from a patient with COVID-19 in Bangladesh is reported.

bioRxiv, 2020

Genomic mutation of the virus may impact the viral adaptation to the local environment, their transmission, disease manifestation, and the effectiveness of existing treatment and vaccination. The objectives of this study were to characterize genomic variations, non-synonymous amino acid substitutions, especially in target proteins, mutation events per samples, mutation rate, and overall scenario of coronaviruses across the country. To investigate the genetic diversity, a total of 184 genomes of virus strains sampled from different divisions of Bangladesh with sampling dates between the 10th of May 2020 and the 27th of June 2020 were analyzed. To date, a total of 634 mutations located along the entire genome resulting in non-synonymous 274 amino acid substitutions in 22 different proteins were detected with nucleotide mutation rate estimated to be 23.715 substitutions per year. The highest non-synonymous amino acid substitutions were observed at 48 different positions of the papain-l...

bioRxiv, 2021

Rationale The global public health is in serious crisis due to emergence of SARS-CoV-2 virus. Studies are ongoing to reveal the genomic variants of the virus circulating in various parts of the world. However, data generated from low- and middle-income countries are scarce due to resource limitation. This study was focused to perform whole genome sequencing of 151 SARS-CoV-2 isolates from COVID-19 positive Bangladeshi patients. The goal of this study was to identify the genomic variants among the SARS-CoV-2 virus isolates in Bangladesh, to determine the molecular epidemiology and to develop a relationship between host clinical trait with the virus genomic variants. Method Suspected patients were tested for COVID-19 using one step commercial qPCR kit for SARS-CoV-2 Virus. Viral RNA was extracted from positive patients, converted to cDNA which was amplified using Ion AmpliSeq™ SARS-CoV-2 Research Panel. Massive parallel sequencing was carried out using Ion AmpliSeq™ Library Kit Plus. ...