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