read Virus_Tech page 1.
Many viruses carry RNA rather than DNA as their genetic material.
may be single or double-stranded.
Like DNA viruses, RNA viruses come in a wide variety of forms. The
model above is a togavirus (such as Semliki
Forest Virus (SFV) or Sindbis virus).The core of the virus is the
nucleocapsid - single-stranded RNA
packaged inside a protein capsid with icosahedral
symmetry (not an icosahedron, in this instance as there are
more than 20 triangular faces, but the symmetry is icosahedral).
packaged inside the togavirus capsid; note that
the capsid is fenestrated (it has 'windows').
nucleocapsid is partially covered by a coat of C
and enveloped by a phospholipid bilayer viral
the host cell's membrane
contains the viral protein spikes.
and Injection of DNA
protein spikes adhere to specific
on the target cell surface-membrane. The nucleocapsid,
with its C protein shell enters the host cytosol and the RNA is
released and escapes from the capsid.
replication of the RNA and the protein capsid and their packaging
are summarised in the diagram below.
The single-stranded RNA is a plus or positive-strand, meaning that it is of
the right sense to be immediately
[Some ssRNA viruses carry negative-strand
which must first be copied
into the complementary (+)-strand which is then translated.] The (+)-RNA contains
(AUG) codons and transcription from each of these results in the
synthesis of a different set of proteins.
In the early phase of infection,
translation proceeds from the first AUG codon, resulting in the
synthesis of a
long polyprotein (using the host's ribosomes) which is then
cleaved into separate early protein polypeptides
which fold into enzymes and proteins needed for RNA
replication, producing the complementary (-)-strand
RNA, using the original (+)-strand as a template.
Part of this (-)-strand is then copied to produce a short
(+)-strand mRNA which lacks the first START codon.
This is translated from the second START codon, producing a
different polyprotein which is cleaved to
produce the late
which form the virus particle, and include the C protein. In the
(-)-RNA is copied repeatedly to produce lots of (+)-strand RNA
genomes which are packaged into the
assembling virions. The nucleocapsid is assembled in the host
cytosol, where the C protein coat is added.
Spike proteins are manufactured by the rough endoplasmic reticulum
and Golgi apparatus of
before being added to the host cell-surface membrane, where they
form patches (excluding host proteins) to
which the assembled virions add and bud from the cell, acquiring
their envelope as they do so.
are plant pathogens that consist of circular ssRNA of about 300b
(220 to 380 bases, the smallest is
220b). E.g. potato spindle tuber viroid (PSTVd) which causes
infectious disease in potato plants. They code
for no proteins and have no protein capsid or protein-coat at all:
they are naked infectious RNA molecules
and thus one of the simplest parasites conceivable. Their
replication requires RNA polymerase II, provided
by the host cell and occurs by rolling
The RNA has a 2D/3D structure, with some
regions pairing by hydrogen-bonding between the bases to give
double-stranded regions, and the molecule
is rod-shaped. Some are ribozymes, meaning that they fold
to form structures with enzymatic activity, such
as catalysis of cutting the concatemers (produced by rolling
circle replication) into individual viroids.
D virus (HDV)
is the smallest known animal virus and has a
single-stranded RNA or (-)sscRNA of 1.7 kb, in which about 70% of
the nucleotides pair with other bases in
the molecule, forming a rod-like molecule. This virus is not able
to complete its life-cycle without a helper
in this case hepatitis B virus (HBV). HDV must coinfect the same
cell as HBV in order to complete its
development as it requires some of the HBV genes. A virus like HDV
is called a satellite virus (or subviral
satellite) and is thus parasitic on HBV. It is possible that HDV
evolved from a viroid or similar infectious RNA
(it is thought that undiscovered viroids may infect and cause
disease in animals).
Like a viroid, the HDV RNA has regions that can form catalytically
active ribozymes, which are required to cut
the concatemers produced during genome replication (by (+)RNA to
(-)RNA rolling-circle replication, which
first requires synthesis of the (+)RNA antigenome from the
original (-)RNA genome) into individual genomes.
This is the fastest known self-cleaving ribozyme in nature,
cutting the RNA in less than one second. Neither
encode their own RNA polymerase, required for RNA genome
replication, but use host RNA polymerase.
The HDV genome encodes only two proteins: the large and small
delta antigens (HDAg-S and HDAg-L) from
a single open reading frame (ORF). HDAg-S is produced early in
infection and is required for viral
replication. HDAg-L appears in the later stages and inhibits viral
replication and instead promotes viral
Baltimore scheme classifies viruses into the following groups,
based upon the nature of their genomic
material (different sources number the groups in different
with linear dsDNA: e.g. adenovirus (icosahedral symmetry), T4
symmetry) and poxviruses (complex structure), or with circular
dsDNA: e.g.hepatitis B virus.
2. ssDNA, e.g. parvoviruses
(icosahedral) such as adenoassociated virus.
3. dsRNA, e.g. reovirus
4. (+)ssRNA, e.g. togaviruses
5. (-)ssRNA, e.g. rhabdoviruses
6. RNA, with a DNA step in replication, e.g. retroviruses (e.g.
virus is a (-)ssRNA virus whose genome is divided into 8 separate chromosomes (unusual for a
virus!). Influenza B, which infects humans, has a genome size of
14.648 kb and forms particles which are
spherical to filamentous). These 8 RNA segments are packaged into
8 helical ribonucleoprotein particles
(RNPs) enclosed in a protein capsid (made of the matrix or M1 protein) surrounded by a
bilayer envelope (with the M protein
lining the inside of the envelope). Embedded in the envelope are
types of glycoprotein spike: haemagluttinin
(HA or H) so-called
because it will cause red blood cells to stick
together, and neuraminidase
(NA or N).
The virus is 80-120 nm in diameter and up to 2000 nm long
third type of projection, the short proteins (unshaded rods) that
are not labelled in this
diagram, and which project from between the M1 protein (unshaded
circles) capsid, are M2 ions
channels. Two RNPs are visible in the above section. The detailed
structure of an RNP is shown
of the HA spikes
haemagluttinin is involved in cell binding and each strain of
influenza has one of 16
subtypes of H (designated H1 to H16). Human influenza is
characterised by possessing H1, H2
or H3. Three identical copies of the haemagluttinin polypeptide
form a single haemagluttinin
spike (it is trimeric, specifically a homotrimer).
HA binds sialic acid-containing receptors on the target cell
surface membrane. This is referred to
as docking, binding or adsorption. Sialic acid is a component of
carbohydrate chains borne on
the cell surface (the glycocalyx) and also of mucus
The virus then tricks the target cell to take it up (by activating
the receptor upon binding to it)
and it is taken-up by (coated-pit) endocytosis into a vesicle
called a coated vesicle. Acidic
endosomes fuse with this vesicle, as the cell attempts to digest
the virus. HA then facilitates the
fusion of the viral and endosome vesicle membranes. This happens
when endosomes fuse with
the coated-vesicle, acidifying it. When the pH drops below 6, the
HA changes shape, partially
unfolding, which exposes a hydrophobic region (hydrophobic
literally means 'water-fearing' and
refers to substances that prefer to dissolve in lipids, rather
than water) which attaches to the
endosome membrane, like a grappling hook, then the HA stabilises
and refolds, retracting as it
does so and bringing the viral membrane so close to the endosomal
membrane that the two
of the N spikes
neuraminidase is a sialidase, an enzyme which cuts sialic acid
residues from the ends of
carbohydrate chains. This breaks-up the long carbohydrate chains
that form the slimey lining of
respiratory airways and makes the mucus of the respiratory tract
more watery, which helps the
virus move easily to its target cells (one of the functions of
mucus is to entangle foreign
particles, such as viruses, and the N spikes counter this by
cutting the entangling threads). The
N spikes help new virus progeny spread from cell to cell. The N
spikes will also cleave sialic acid
residues to which HA binds, if the target is inappropriate (such
as a mucoprotein in the mucus
layer rather than the cell receptor).
There are also several types of N and the H and N types carried by
a particular strain
charcterise the virus. For example, avian flu is H5N1 (avian
influenza has one of H1 to H16 and
one of N1 to N9).
of the M2 ion channels
are activated by the low pH when the endosome fuses with the
the virus. They import protons and are involved in triggering
uncoating - the disassembly of the
protein capsid which allows the RNPs to enter the host cytosol.
of the three polymerase peptides
in the cytosol the nucleoprotein which packages the RNA of each
RNP, allows movement
of the RNPs into the host cell nucleus. Once inside the nucleus,
the three polymerase units (PA,
PB1 and PB2) initiate transcription of the viral RNA. PB2 attaches
to the cap present at the head
end (5') of host mRNA, PB1 then cleaves this cap which attaches to
PB2 - the virus steals the 5'-
cap off host RNA to make itself look like mRNA! PB1 also adds the
usual 3' tail to the end of the
viral RNA, so now it resembles host mRNA ready to be transcribed!
PB1 and PA then synthesise
more viral RNA, both mRNA ((+)ssRNA) which is translated by host
ribosomes in the cytoplasm
to make viral proteins, and new copies of the viral genome, which
remain in the nucleus.
synthesis results in a high concentration of NP protein in the
cytoplasm, viral mRNA
synthesis stops but synthesis of genomic RNA continues - this
occurs in the late
infection and switches the virus from protein synthesis
mode, into assembly mode, in which the
synthesised components are assembled into new virus particles.
RNPs are assembled in the
host cell nucleus and are then exported to the cytoplasm.
M protein, HA and N accumulate together in the host cell-surface
membrane (after being
processed and delivered there by the rough endoplasmic reticulum
and Golgi apparatus of the
host cell). The RNPs assemble here and then the virus buds from
the host cell surface,
becoming enclosed in the phospholipd envelope containing the viral
fever (38-39 C)
weakness, fatigue, aches and pains in joints and especially
in the back and legs,
headache, eye irritation and reddening, reddening of the
face and nose.
pain in children.
that may occur include pneumonia, bronchitis, sinus and ear
chemotherapeutic agents have been developed to combat influenza.
inhibitors, block the M2 proton channels with the aim of
preventing the viral RNA
entering the cell
cytosol, e.g. amantadine (1-aminoadamantane).
inhibitors, e.g. Tamiflu (Oseltamivir) and relenza
sialic acid for the enzyme, slowing-down the action of the
A vaccine is available, consisting of inactive materials from
three different virus strains, which
stimulates the body to produce natural antibodies to influenza.
Influenza replication cycle
The replication or life cycle of influenza is illustrated below.
This illustrates many of the features
of a 'typical' animal cell virus, such as:
(attachment) of the virus particle (virion) to specific
on the target cell
adhesion triggers uptake
(endocytosis) of the virion by the target cell.
and release of the genetic material into the host cell
nucleus in this case. This genetic material commandeers the
the host cell to
make more proteins and replicate the viral genome.
of new virions on the host cell membrane and their
host cell, taking
host cell phospholipid, modified with virus proteins, with
them as the viral
retrovirus of the lentivirus type, e.g. human
immunodeficiency virus (HIV).
two (+)ssRNA molecules in its genome, represented above as the
spirals (red) in the centre of
the elongated inner core (yellow) which are both identical copies
of the genome wound with
packaging proteins to form ribonucleoprotein. The elongated conical core shell (the shape
of which is characteristic of the lentivirus variety of
retrovirus, the core being icosahedral in
some retroviruses). HIV is enveloped, that is it is enclosed in a
phospholipid bilayer membrane
(cyan) derived from the host cell-surface membrane. This envelope
spikes. Just beneath the envelope is a protein shell 9inner shell
or matrix) which stabilises the
structure of the envelope.
HIV is well-known as the causative agent of AIDs
(Acquired-immunodeficiency syndrome or
acquired immune-deficiency syndrome) in which destruction of key
components of the body's
immune system leaves it very susceptible to many other infections.
This occurs because HIV
targets certain immune cells, especially T-helper cells (cells
that act as alarms and 'officers' for
the immune system - activating and directing other immune cells).
HIV will target these cells,
enter them and turn them into virus factories!
Cycle - example HIV
1. Adsorption/adhesion and entry
usual, the virus must bind to specific receptors on its target
cell. These receptors are more-
or-less specific, since viruses infect only one or a few cell
types. In the case of HIV, the gp120
spikes bind to CD4 receptors on T-cells (HIV can also infect a few
other cell types, such as
macrophages). This is the initial adhesion, which is transient and
unstable. This is followed by a
secondary and more stable adhesion between the vrius and a second
receptor on the cell
surface (CCR5 or CXCR4). Once stably bound or adsorbed, the lipid
envelope of the virus
fuses with the host cell membrane (this fusion is triggered by
gp41). The inner core is then
released into the cell.
Replication of viral genome
replicate their RNA via a DNA intermediate. They use their RNA as
a template to
synthesise first a complementary ssDNA molecule (creating an
RNA/DNA hybrid molecule with
the RNA then be degraded leaving ssDNA) and then the ssDNA is used
as a template to
generate a dsDNA intermediate. To complete this unusual task, of
synthesising dsDNA from a
ssRNA template, HIV carries the viral enzyme reverse
- blue spheres
inside inner core in the diagram above. This enzyme is responsible
i) Synthesising the ssDNA complementary strand by using the RNA as
a template, that is
working as an RNA-dependent DNA polymerase, resulting in the
formation of an RNA/DNA
ii) Digesting away the RNA strand of the RNA/DNA hybrid duplex (RNAse
activity, present as a
separate enzyme or bound to RT and called RNase H) producing
iii) Synthesising the second DNA strand, using the ssDNA as a
template, that is working as a
DNA-dependent DNA polymerase, producing dsDNA.
This dsDNA can then be integrated into the host chromosome - it
inserts into the DNA of the
host-cell, with the help of the viral enzyme integrase. In this integrated
dsDNA state the virus is
called a provirus. Note that as this step
proceeds efficient gene expression, the virus must
carry integrase, RNase and reverse transcriptase with it. All
these enzymes are represented by
the blue spheres inside the viral core.
HIV is unusual in that it can insert its provirus and replicate
inside non-dividing cells. To do this
it has to gain access to the nucleus by passing the nuclear pore complex (NPC). It does this
with the help of at least two viral proteins: MA, which apparently
acts as a key granting access
past the NPC and Vpr. replication of the viral RNA takes about 6
hours after cell-infection.
Transcription and expression of viral genes
synthesis of virus proteins only begins efficiently once the
provirus is integrated into the
host DNA. The primary transcript (the RNA initially produced by
transcription by RNA
polymerase) covers all nine or so genes of the HIV genome and is
spliced (cut-up by enzymes)
into more than 30 separate mRNA - 9 genes produce more than 9
proteins, many of which have
multiple functions - a way of minimising on the amount of DNA that
must be packaged and
carried by the virion.
following structural proteins are produced:
associates with the host cell-surface membrane and recruits
two copies of
the viral RNA
genome and other structural proteins for virion assembly and
the host. It is
then cleaved, after the virus has budded and while it is
maturing, into the
(matrix or p17) which forms the inner protein shell beneath
which stabilises the virion structure and is also involved
in transport of the
viral RNA to the
(capsid or p24) which forms the conical core or capsid,
which coats the genomic RNA during packaging into the virion
required for the incorporation of the viral protein Vpr into
the virion and
of budding virus.
- a protein produced from mRNA that encodes
and adjacent pol
Some 95% of the time, Gap is produced, but 5% of the time,
frame (due to a signal carried on the Gag mRNA and so misses
STOP codon and
continues onto pol which is encoded on the same mRNA,
Gag-Pol. A viral
protease (Pro) then cleaves the Gag from the Pol and cuts up
polypeptide into RT
(reverse transcriptase, p50), In
(integrase, p31), Pro
(p15, 50% of which remains linked to RT). Pro cleaves Gag
About 20 Gag are
produced to every Gag-Pol.
- Env -
envelope glycoprotein -Env is sent to the host cell's Golgi
are added to it (glycosylation) to convert it into a
A host cell
protease then cleaves Env into gp41 and gp120. These form
spikes of HIV: gp41
spans the envelope membrane and the gp120 ligand binds to
(by a non-covalent
following regulatory proteins are produced:
(transcriptional transactivator) which binds HIV genomic RNA
and increases the
efficiency of its
- Rev -
switches from early to late gene expression.
following accessory proteins are produced
(negative factor) which is produced early and downregulates
the CD4 receptor from
the infected cell
(preventing superinfection?). It is also packaged into
virions and cleaved
by viral protease
during virion maturation and greatly increases virion
- Vpr -
incorporated/pacakged into virions; helps the viral DNA gain
access to the cell
nucleus (binds the
DNA to the NPC?).
- Vpu -
essential for release of budding virus from the host cell
surface; prevents CD$
inside the cell
from binding to Env and blocking its incorporation into
by causing the cell
to degrade any CD4 bound to Env.
- Vif -
essential for replication; incorporated into the virion;
possibly counters a host cell antivirus mechanism.
from the cell
gp41 and gp120 gather in patches in the host cell membrane and
recruit viral RNA and
other components of the virion. The virus then buds from the host
cell, acquiring the lipid
envelope and then completes its maturation.
the host's immune system
has several tricks for evading the defences of its host.
Antibodies produced by the host
can, for example, bind to gp120 and prevent new viruses from
infecting cells. To combat this,
HIV uses antigenic
In particular, gp120 contains five hypervariable regions, that is
regions whose amino acid sequence and structure differ greatly
between one HIV strain and
another. [Recall that proteins and polypeptides are
polymers of amino acids]. The HIV
polymerase (RT + RNase H) also lacks a proof-reading function - it
does not check for errors
and so it makes mistakes fairly frequently, causing HIV to mutate
extremely rapidly, again
increasing variation. Antigens, e.g. gp120, are exposed regions of
foreign proteins and other
large molecules, which the immune system can target and develop
antibodies against. By
rapidly varying its antigens, HIV can stay one step ahead of the
immune system, changing to a
new form once antibodies are developed, making those antibodies
redundant. This helps to
explain why antibodies indicate HIV infection and the possibility
of developing full-blown AIDS -
the function of the antibodies is impaired!
14/2/2018 - proofreading and correcting of errata in text