Virus morphology
Macromolecular aggregates Different shapes and size that are family specific Size range 18 nm- 300 nm Enveloped, non-enveloped, helical and complex type of structure classes
The basic assembly
The subunits: structural proteins The capsomeres: structural proteins coming together to form a subunit The capsid: Outer shell The envelope: Viral or/and host membranes on the outside The core: Contains the viral genome DNA/RNA
Tools for studying virus structure
Electron microscopy X ray diffraction techniques NMR and other spectroscopy tools Cryo-EM
Icosahedral shells
20 sided solid with five fold axis of symmetry: Most of the non-enveloped viruses have this symmetry
Quasiequivalent structures
Not exact icosahedrons but similar
More complex icosahedral shells
Pentameric assembly units (papovaviruses) Trimeric assembly units (adenoviruses) Multishelled architecture (ds RNA viruses) The icosahedral surface may undergo rerrangements (ds DNA phages)
Helical symmetry
T4 phage, TMV, M13
Capsomeres organize around a central axis to form a helix Pitch and central canal Genome resides in central canal
Packing of the genome Positive stranded RNA viruses
RNA packaging signal that is recognized by structural proteins Tandem RNA hairpins and coat protein dimer interactions Specific packaging signals like Psi in retroviruses (Zinc knuckle modules) packs RNA only Polyamines
dsDNA genome
T4 phage, animal viruses
The DNA genome has a scaffold protein that drives the structural proteins to form the iscosahedral head Herpesviruses have similar mechanism Adenoviruses have AT rich sequence in left hand of genome that drives structural protein (protein VII) assembly In phage PRD1 a protein called IVa2 is an ATPase that drives energy dependent packaging
Negative strand RNA genomes
Influenza has the N protein that tightly condenses the RNA cores and packaging occurs through a sequential mechansim Measles show similar sequential packaging events
dsRNA genome
Segmented viruses (rota, reo pahse psi6) A 12 protein complex forms with ATP, structural proteins and RNA genome Energy driven process, RNA inserts into a simultaneously assembling shell
Why is studying structure so important?
Understand receptor binding (host & virus) Mechanisms of morphogenesis Host factors in assembly Crucial final events in virus formation Develop antiviral compounds
Structural similarities among viruses
Very distant viruses at genome level can show identical morphologic relationship (picornaviruses and plant viruses) The fibre structure of adeno and reo viruses Suggests evolutionary lineages
Jellyroll beta barrel and HK97 folds
A stretch of protein sequence where alpha helical stretches fold into compact domains (Picorna, adeno, reo) A steep fold seen in the capsid of phage HK97 that provides a deep groove on the surface. Also conserved in higher animal viruses
> 30.000 virus isolates
3 orders 63 genetically and morphology-defined families
31 vertebrate specific virus families
23 human specific virus families
ICTV 2005
MORPHOLOGICAL VIRAL DIAGNOSTICS
A Rhabdovirus !
Chandipura virus
Lancet 2004;364:869
Chikungunya virus, AP 2006 isolate from CSF
Negative stain, unfixed sample Infected vero TCF 5th day pi
A glimpse of a few interesting diagnostic situations
Lab confirmation of Influenza A
Lab confirmation of wild type polio
Throat swab, respiratory illness, Murshidabad 2004
Fecal specimen, polio case, Mumbai 2006
Severe GI illness, family
SARS corona virus Frankfurt Vero cells
Gelderblom H, Basu A, et al. EID 2004
Suspected Avian Influenza, 2006, India
ORTHMYXOVIRUS
Clarified and fixed fecal sp from dead bird prepared under containment lab, no further I.d ?
Poxviruses
Lesion from farmers hand direct TEM imaging of vesicular fluid
UAc
AMdate
PTA
Parapoxirus
Some human hepatitis viruses
Definitely a Public Health problem, specially A & E
HAV Outbreaks, epidemics 20-30 nm particles Picornavirus
HEV Outbreaks 20 nm Calici-like
HBV Blood borne 40 nm particles
Negative stained images in TEM
HIV: ultrathin section TEM of mature particles
Cryo EM
Reality of structures in zero artifact ?
Fast freezing in liquid ethane Native hydrated structures in amorphous ice Low dose TEM imaging Computer aided image reconstructions Electron tomography
Low dose cryo-TEM imaging of plunge-frozen cytomegalovirus capsids
An example of particle reconstruction
The nano-rover images of the virus surface
The tegument
