STRUCTURE OF

VIRUSES
Wallace Bulimo, PhD (Molecular
Virology)

Virus Structure

Size
17 nm 3000 nm diameter
Basic shape
Rod-like
Spherical

Protective Shell - Capsid

Made of many identical
protein subunits
Symmetrically organized
50% of weight
Enveloped or non-enveloped
Genomic material
DNA or RNA
Single- or double-stranded

Structure of a Virus
Questions Relating to Structure
Is it rigid?
How big is it?
Is it flexible

Structure Must Serve Virus

It should provide protection for genome
It should allow virus to move from one host to next
It should allow for attachment of virus on to new host

Structural Components
Viral Capsid
Virus capsid function in:
Packaging and protecting nucleic acid
Host cell recognition
Protein on coat or envelope feels or recognizes
host cell receptors
Genomic material delivery
Capsid means box
Capsid can be square, tetrahedron or icosahedron
Capsid is made up of protein
Capsid is the storage site for genome
Many capsids have a shell structure
Genome + Capsid = Nucleocapsid

Structural Components Cont..

Capsid is made up of polymeric proteins to
conserve genome
Ex. 5 Kb genome requires 30,000 a/a capsid,
which means 90 Kb genome just for
capsid!!
Solution: use multiple copies of same protein
Viral Envelope
It is the covering of the nucleocapsid
Made up of a phospholipid bilayer
It should allow for attachment of virus on to
new host

Tools for Studying Viral Structure

Electron Microscopy
Excellent tool with some limitations
High resolution
Image can be a distortion due to specimen
processing
X-ray Diffraction
Good for naked virions (no envelope)
Cryoelectron Microscopy
Flash frozen with liquid nitrogen

Structural Symmetries
Icosahedral Symmetry
20 triangular faces
It is a common capsid structure
Examples of viruses with icosahedral symmetry
Parvoviruses

These are simple viruses

5 Kb ssDNA genome
Capsid is formed with 60 copies of single protein
Protein is approximately 520 a/a
1/3 of genome is dedicated to capsid

Polio virus
Uses 180 copies of 3 subunit proteins
Much bigger virus

Icosahedral Symmetry
12 vertices
20 faces
(equilateral triangles)

5-3-2 symmetry axes

60 identical* subunits
in identical environments
can form icosahedral shell
* asymmetric

Caspar and Klugs Icosahedral

shell

But
Clear evolutionary pressure to make larger capsid
Using larger subunits helps very little
Using more subunits helps a lot

Not possible to form icosahedral shell (of identical units in identical

environments) with more than 60 subunits
Viruses with more than 60 subunits were observed
Question:
How can >60 subunits form an icosahedral shell?
Will any number of subunits work?
If so, how would they be organized?

Quasi-equivalence
In 1962, Caspar & Klug proposed the
theory of quasi-equivalence
Not all protein subunits are equivalent
Identical subunits in slightly different
environments

Only certain numbers of subunits will can be

packed into closed regular lattice.
Caspar & Klug, Cold Spring Harbor, 1962

Quasi-equivalence
Subunits are in minimally
different environments
Pentamers at vertices
Hexamers elsewhere

Predicts packing arrangements

of larger capsids
Shift from T1 to T4 packing
=> 8-fold increase in volume

Spherical viruses have icosahedral symmetry

Desmodium Yellow Mottle

Virus
X-Ray Crystallography
Icosahedral Symmetry

Other Structural Symmetries

Fig. 2.7 The helical nucleocapsid of tobacco mosaic virus.

Other Structural Proteins

Core Proteins
Can originate from host
Ex. Histones

Can also be virally coded

Their function is to condense viral genome
Scaffolding Proteins
Facilitate capsid formation
Facilitate docking of proteins
Facilitate stability of proteins during assembly
Not included inside virion

Viral Envelope

Lipid bilayer
Most originate from cellular host
Cholesterol and glycoproteins are present
In cases where budding occurs at the plasma
membrane (Ex. Influenza) envelope resembles
hosts plasma membrane i.e cholesterol and
phospholipids
In cases where budding occurs at the ER (Ex.
Flaviviruses) envelope has less cholesterol, similar
to ER

Viral Glycoproteins
Glycoproteins
Short cytoplasmic tail
Hydrophobic segment for anchoring (~20 amino acids)
Relatively large ectodomain (external domain)

Ectodomain
Extensively glycosylated preventing aggregation of virions
Glycosylation attracts water and reduces sticking (carried out in
ER)
Palmitoylation of cysteine residues is also extensive (carried out in
ER)

Most envelope proteins are type I

That means N-terminus facing out, C terminus near anchor domain
Some though are type II

Viral Budding
Several budding mechanims exist
Envelope proteins create 2-D pools excluding cellular
memberane proteins
Capsids can bind cytoplasmic tails of envelope
proteins
Binding of capsid proteins and envelope proteins is mediated
by matrix proteins in viruses with helical nucleocapsids (Ex.
influenza budding)

When budding takes place eventually, capsid wraps

itself around host plasma membrane

Influenza Viral Budding

Matrix protein (M) interacts with HA and NA

HA are glycoproteins on envelope
Interaction occurs at the level of their cytoplasmic tail
M protein also interacts with helical nucleocapsid proteins
RNP

Semliki Forrest Viral Budding

Direct interaction between icosahedral capsid and envelope

proteins
No Matrix protein involved
Interaction at the level of cytoplasmic tail of envelope protein

Replication
Learning Objectives:
Understand how the nature of a virus genome determines

its pattern of replication.

Describe a typical, generalized replication cycle of a

virus.
Compare the patterns of replication of each of the seven

major virus groups.

Classification of Viruses
The way in which viruses are classified has
altered as our perception of them has changed:

By disease: early civilizations

By morphology: 1930s-1950s
Functional classification

Investigation of Virus Replication

Bacteriophages have long been used by virologists
as models to understand the biology of viruses.
Two particularly significant experiments which
illustrate the fundamental nature of all viruses
were performed on bacteriophages:
Ellis and Delbruck in 1939
Hershey and Chase in 1952

Virus Replication
Following the development of plaque assays for animal
viruses in the 1950s, 'single burst' experiments have been
performed for eukaryote viruses.
The major difference between these viruses and
bacteriophages is the much longer time interval required
for replication, which is measured in terms of hours or
days rather than minutes.
This difference reflects the slower growth rate of
eukaryotic cells and the complexity of virus replication
in compartmentalized cells.

The Replication Cycle

The Replication Cycle

Virus replication can be divided into eight arbitrary
stages.
Regardless of their hosts, all viruses must undergo each
of these stages in some form to complete their
replication cycle.
Not all the steps described here are detectable as
distinct stages for all viruses.

1. Attachment
Virus attachment consists of specific binding of a virusattachment protein (or 'antireceptor') to a cellular
receptor molecule.
Target receptor molecules on cell surfaces may be
proteins (usually glycoproteins), or the carbohydrate
residues present on glycoproteins or glycolipids.
Some complex viruses (e.g. poxviruses, herpesviruses)
use more than one receptor and have alternative routes of
uptake into cells.

Virus Receptors
Virus receptors fall into many different
classes:
immunoglobulin-like superfamily molecules
membrane-associated receptors
transmembrane transporters and channels

Viruses have subverted molecules required

for normal cellular functions.

Virus Receptors

Many examples of virus receptors are now known.

Schematic representation of some virus receptors
- arrows indicate virus attachment site:

Plant Viruses
No plant virus is known to use a specific cellular
receptor of the type that animal and bacterial viruses use
for attachment.
Plant viruses rely on a breach of the integrity of a cell
wall to directly introduce a virus particle into a cell.
This is achieved either by the vector associated with
transmission of the virus or mechanical damage to cells.
After replication in an initial cell, the lack of receptors
poses special problems for plant viruses in recruiting
new cells to the infection.

Virus-Receptor Interactions
The major human rhinovirus (HRV) receptor molecule,
ICAM-1 (intercellular adhesion molecule 1), is an adhesion
molecule whose normal function is to bind cells to adjacent
substrates.
ICAM-1 is similar to an immunoglobulin molecule, with
constant (C) and variable (V) domains homologous to
those of antibodies and is a member of the immunoglobulin
superfamily of proteins.
The poliovirus receptor is also a member of this family,
with one variable and two constant domains.

Virus-Receptor Interactions
In human rhinoviruses (HRVs), there is a deep cleft known
as the 'canyon' in the surface of each face of the icosahedral
capsid, formed by the flanking monomers, VP1, VP2, and
VP3.
The interaction between ICAM-1 and the virus particle
occurs in this canyon.
Unlike other areas of the virus surface, the amino acid
residues forming the internal surfaces of the canyon are
relatively invariant.
These regions are protected from antigenic pressure because
the antibody molecules are too large to fit into the cleft .

Poliovirus Receptor Binding

Influenza Virus
Receptor Binding
The influenza haemagglutinin protein is one of two types
of glycoprotein spike on the surface of influenza virus
particles, the other type being the neuraminidase protein.
Each haemagglutinin spike is composed of a trimer of
three molecules, while the neuraminidase spike consists
of a tetramer.
The haemagglutinin spikes are responsible for binding
the influenza virus receptor, which is sialic acid (N-acetyl
neuraminic acid).
As a result, there is little cell-type specificity imposed by
this receptor interaction and therefore influenza viruses
bind to a wide variety of different cell types.

Influenza Virus
Receptor Binding

Neuraminidase
Attachment to cellular receptors is usually reversible.
Neuraminidase is an esterase which cleaves sialic acid from
sugar side-chains.
Because the receptor molecule is so widely distributed, the
virus tends to bind inappropriately to a variety of cells and
cell debris.
Elution from the cell surface after receptor binding has
occurred often leads to changes in the virus (e.g. loss or
structural alteration of virus-attachment protein) which
decrease or eliminate the possibility of attachment to other
cells.

Cell Tropism
The expression of receptors on the surface of cells
largely determines the tropism of a virus, i.e. the type of
host cell in which it is able to replicate.
This initial stage of replication has a major influence on
virus pathogenesis and in determining the course of a
virus infection.

Multiple Receptors (1)

In some cases, interactions with more than one protein are
required for virus entry - neither protein alone is a functional
receptor.
Adenovirus receptor-binding is a two stage process
involving an initial interaction of the virion fibre protein
with a range of cellular receptors, including MHC class I
molecule and the coxsackievirus-adenovirus receptor (CAR).
Another virion protein, the penton base, then binds to the
integrin family of cell surface heterodimers allowing
internalization of the particle via receptor-mediated
endocytosis.
Most cells express primary receptors for the adenovirus fibre
coat protein; however, the internalization step is more
selective.

Multiple Receptors (2)

The primary receptor for HIV is the T cell antigen, CD4.
Transfection of human cells which do not express CD4 with
recombinant CD4-expression constructs makes them permissive for
HIV infection.
Transfection of rodent cells with human CD4 does not permit
productive HIV infection.
If HIV DNA is added to rodent cells by transfection, virus is produced
- no intracellular block to infection.
These are a. Several members of a family of proteins known as chemokine receptors play a role in the entry of HIV into cells, and their
distribution may be the primary control for the tropism of HIV for
different cell types (lymphocytes, macrophages, etc).

2. Penetration
Penetration of the target cell normally occurs a very short
time after attachment of the virus to its receptor in the cell
membrane.
Unlike attachment, cell penetration is generally an
energy-dependent process, i.e. the cell must be
metabolically active for this to occur.
Three main mechanisms are involved.

3. Translocation
1) Translocation of the entire virus
particle across the cytoplasmic
membrane of the cell.
This process is relatively rare
among viruses and is poorly
understood.
It is mediated by proteins in the
virus capsid and specific
membrane receptors.

3a. Endocytosis
2) Endocytosis of the virus into
intracellular vacuoles is probably
the most common mechanism.
Does not require any specific
virus proteins (other than those
utilized for receptor binding) but
relies on the formation and
internalization of coated pits at
the cell membrane.
Receptor-mediated endocytosis is
an efficient process for taking up
and concentrating extracellular
macromolecules.

3b. Fusion
3) Fusion of the virus envelope
with the cell membrane, either
directly at the cell surface or in
a cytoplasmic vesicle.
Fusion requires the presence of
a fusion protein in the virus
envelope which promotes
joining of the cell and virus
membranes, resulting in the
nucleocapsid being deposited
directly in the cytoplasm.
There are two types of virusdriven membrane fusion: pHdependent and pHindependent.

4. Uncoating
Uncoating is a general term for the events which occur after
penetration.
Uncoating is one of the stages of virus replication that has
been least studied and is relatively poorly understood.
The product of uncoating depends on the structure of the virus
nucleocapsid.
The structure and chemistry of the nucleocapsid determines
the subsequent steps in replication.

5. Genome Replication
and Gene Expression

All viruses can be divided into seven groups - a scheme

was first proposed by David Baltimore in 1971.
Originally, this classification included only six groups,
but it has since been extended to include the
hepadnaviruses and caulimoviruses.
For viruses with RNA genomes in particular, genome
replication and the expression of genetic information
are inextricably linked, so both are taken into account.

Class I: Double-stranded DNA

This class can be subdivided into two further groups:
A)Replication is exclusively nuclear. The replication of
these viruses is relatively dependent on cellular factors.
B)Replication occurs in cytoplasm (Poxviridae). These
viruses have evolved (or acquired) all the necessary
factors for transcription and replication of their genomes
and are therefore largely independent of the cellular
machinery.

Class I: Double-stranded DNA

Class II: Single-stranded

DNA
Replication
occurs in the
nucleus,
involving the
formation of a
double-stranded
intermediate
which serves as a
template for the
synthesis of
single-stranded
progeny DNA.

Class III: Double-stranded RNA

These viruses
have segmented
genomes.
Each segment is
transcribed
separately to
produce
individual
monocistronic
mRNAs.

Class IV: Single-stranded

(+)sense RNA
These can be subdivided into two groups:
Viruses with polycistronic mRNA. As with all the
viruses in this class, the genome RNA forms the mRNA.
This is translated to form a polyprotein product, which
is subsequently cleaved to form the mature proteins.
Viruses with complex transcription. Two rounds of
translation (e.g. Togavirus) or subgenomic RNAs (e.g.
Tobamovirus) are necessary to produce the genomic
RNA.

Class IV: Single-stranded

(+)sense RNA

Class V: Single-stranded (sense

RNA
The genomes of these viruses can be divided into two
types:
Non-segmented genomes
(order Mononegvirales)
Segmented genomes

Class V: Single-stranded
()sense RNA

 Retrovirus
genomes are
(+)sense RNA
but unique in
that they are
diploid, and do
not serve directly
as mRNA, but as
a template for
reverse
transcription into
DNA.

Class VI: Single-stranded (+)sense RNA

with a DNA Intermediate

Class VII: Double-stranded DNA

with
RNA
This group
of viruses
also Intermediate
relies on reverse transcription.
Unlike the retroviruses (class VI), this occurs inside the
virus particle during maturation.
On infection of a new cell, the first event to occur is repair
of the gapped genome, followed by transcription.

Class VII: Double-stranded DNA

with RNA Intermediate

6. Assembly
Assembly involves the collection of all the components
necessary for the formation of the mature virion at a particular
site in the cell.
During assembly, the basic structure of the virus particle is
formed.
The site of assembly depends on the site of replication within
the cell and on the mechanism by which the virus is eventually
released.
in picornaviruses, poxviruses and reoviruses assembly
occurs in the cytoplasm
in adenoviruses, polyomaviruses and parvoviruses it occurs
in the nucleus

7. Maturation

Maturation is the stage of the replication-cycle at which the

virus becomes infectious.
Maturation usually involves structural changes in the virus
particle which may result from specific cleavages of capsid
proteins conformational changes in proteins.
Virus proteases are frequently involved in maturation,
although cellular enzymes or a mixture of virus and cellular
enzymes are used in some cases.

8. Release
Apart from plant viruses which have evolved particular
strategies to overcome the structure of plant cell walls, all
other viruses escape the cell by one of two mechanisms:
For lytic viruses (most non-enveloped viruses), release is a
simple process - the infected cell breaks open and releases
the virus.
Enveloped viruses acquire their lipid membrane as the virus
buds out of the cell through the cell membrane or into an
intracellular vesicle prior to subsequent release. Virion
envelope proteins are picked up during this process as the
virus particle is extruded - this process is known as budding.

Budding

Summary
Virus replication involves three broad stages which are carried
out by all types of virus:
Initiation of infection
Replication and expression of the genome
Release of mature virions from the infected cell
At a detailed level, there are many differences between the
replication processes of different viruses.
Nevertheless, it is possible to derive an overview of virus
replication with common stages which are followed by all viruses.

 Thank you