Virology Flashcards
give 6 distinguishing features of viruses
• small size (20-2300 nm)
• obligate intracellular parasites: need a host cell for replication
• simple composition: simplest have only protein and nucleic acid
• unique mode of replication (not binary fission)
• great diversity: infect all cellular organisms, cause devastating plagues or asymptomatic
infections
• numerous: estimated 1031 virions in biosphere
how did we originally discover viruses were v small
Viruses were discovered as disease-causing agents that passed through filters that
retained all bacteria, and hence were very small.
Give the range of virus sizes, including examples
The smallest, such as foot and mouse disease
virus (FMDV), are only 20 nm in diameter, whereas others, such as poxviruses, are bigger (250
x 350 nm), and the largest, the mimiviruses, are up to ~700 (diameter) and ~2300 nm
(length).
True or false
Viruses are always smaller than bacteria
false
the largest, the mimiviruses, are up to ~700 (diameter) and ~2300 nm
(length). These are larger than the smallest bacteria (micrococci ~ 500 nm).
What is the simplest viral particle
What is it essentially
the virion
a nucleic acid (genome)
surrounded by a protein shell (capsid) that protects the genome from the environment and
delivers the virus genome from one susceptible cell to another.
What are capsids composed of
repeating protein subunits (capsomers) that are arranged in a
symmetrical array. Symmetry is, in nearly all cases, helical or icosahedral.
The capsid of plant some viruses is made of many repeated identical polypeptides. What does this mean for the viral genome
only one gene is needed to make the capsid as it is just lots of the same gene product bound together
How do animal virus capsids differ from plant virus capsid
animal viruses are often more complicated - each subunit may be composed of several polypeptides and there may be more than one type of subunit.
True or false
All viruses all contain protein and nucleic acid
Some viruses have only protein and nucleic acid, but others contain lipid and carbohydrate too.
How are viruses which contain lipid and carbohydrate different in structure to those that are only nucleic acid and protein
in virus with carbohyrate and lipid, the capsid is surrounded by a phospholipid membrane (envelope) that is acquired from the host cell
How is the envelope of some viruses often made
What is it embedded with and what can happen
often by budding of the nucleocapsid through
the plasma membrane.
The membrane is embedded with viral proteins which, like many membrane proteins, may be glycosylated.
Define the following:
virion
virus genome
capsid
Virus particle = virion
Viral nucleic acid = genome
Protein coat = capsid
what are the following
capsid protein
capsid+genome
viral membrane
Capsid proteins = those proteins found in the capsid
Capsid + genome = nucleocapsid
Viral membrane = envelope
What are the following
envelope proteins
structural proteins
non structural proteins
Envelope proteins = viral proteins embedded in envelope
Structural proteins = proteins found in the virion
Non-structural protein = virus protein expressed in the infected cell but absent from the virion
Describe the viral genome generally
Virus genomes are composed of DNA or RNA, which may be linear or circular, monopartite
or segmented, and double stranded (ds) or single stranded (ss)
What are the 2 classes of ssRNA genome
If the RNA is mRNA sense (i.e. can be
translated into protein) it is a positive-strand RNA genome. If the genome is complementary
to mRNA (i.e. the mRNA is obtained by transcribing the virus genome as template), it is a
negative-strand RNA genome
Is it more common for a viral genome to be segmented
no
Usually, the genome is a single nucleic acid molecule (monopartite), but a few viruses contain
several nucleic acid molecules (segmented); example, influenza virus and rotavirus.
what is the size of viral genome limited by?
the error prone nature of RNA polymerases.
If the genome is too big (> ~20 kb) replication creates too many mutations, which are lethal
What is the usual RNA genome size for a virus
> 15kb
What sizes are the largest RNA viral genomes
What does this size necessitate
slightly over 30kb
proof reading activity of the RNA pol
Which viruses have the largest genomes
dsDNA viruses (mimiviruses: up to 1500 kb).
In the viral genome, how much does 1kb code for
If virus genomes range from 3kb to 1500kb, how many proteins are coded for at each extreme
1 mid sized protein
n (333
aa = 35 kDa),
the smallest genomes code for just a few proteins and the largest ~1500
Most viruses have small genomes and so limited coding capacity. Therefore, coding potential is
used efficiently by… (4)
- Densely packed genes
- Small intergenic spaces with few non-coding spaces
- Overlapping reading frames, use of a same nucleic acid to code for > 1 protein
- RNA splicing
How are viruses classified
grouped into families (viridae), subfamilies (virinae), genera, species and strains.
How were viruses classified in the past
Why can this cause confusion
different parameters such as the type of disease
caused, mode of transmission, capsid structure, immunological relatedness, genome
sequence, protein structure and mode of replication.
German measles vs measles: Rubella virus (a togavirus, +ve ssRNA, German measles) and measles virus (a paramyxovirus, - ve ssRNA) are viruses causing similar type of illness, but are caused by quite different viruses.
patients with Chicken pox and small pox look similar therefore they are caused by similar viruses. True or false?
false
caused by either a poxvirus
(variola virus) or herpesvirus (varicella-zoster virus), respectively.
What are arboviruses
The arboviruses are a large group of viruses that are transmitted by biting insects (ARthropod
BOrne VIRUSES).
What is classification of viruses now based upon
How are families arranged? why is this useful?
genetic relatedness and structural characteristic
into larger groups based on type of nucleic acid genome
groups viruses with similar replication strategies
Give 5 ways to study viruses
EM PCR haemagluttination immunological evidence of infection plaque assay
How are infectious virus titres expresses
How high can a titre go
plaque forming units per mL
some are a high as 10e9 or 10e10
how is EM useful for virology
what is it useful for
how is it done
enabled virus particles to be seen and their
structure studied.
This was useful for diagnosis and quantification.
E.g. by mixing a virus
preparation with a suspension of small beads of known concentration and counting both
virions and beads under the e.m., the concentration of virions may be deduced.
what does an em of a virus preparation measure
total virus particles, not how many are infectious.
How is PCR useful in virology
What is a possible draw back
genome sequences of many viruses are
known, so specific primers can be used in PCR to identify and quantify virus genomes.
This is very sensitive and useful for diagnosis.
But, like e.m., this does not measure virus
infectivity
What is haemagluttination
Some viruses bind to red blood cells (rbc) and cause their
agglutination (clumping), haemagglutination. So a crude measure of virus concentration
can be made by mixing virus dilutions with a standard number of rbc and determining
the maximum dilution of virus that can agglutinate the rbc. Note, this is not measuring
virus infectivity
Is haemagluttination measuring infectivity
NO
How does immunological evidence of infection help the study of viruses
What is it useful for
Infection will be followed by an adaptive
immune response, i.e. the presence of (or an increase in) antibody or T cell responses to
virus antigens.
This is usually retrospective and so seldom provides rapid diagnosis.
Useful for epidemiological studies.
Which measurement of viruses measures infectivity
plaque assay
How does plaque assay work
A dilution series of virus is applied to lawns of
susceptible cells. Where a virus binds to and enters a cell, it replicates and releases new
virions. These infect and replicate in adjacent cells. Eventually, a visible area of cells is
destroyed by the virus. This is a plaque. Each plaque derives from one infectious virus
particle, so the titre of infectious virus particles can be calculated.
infectious virus titre given in pfu/ml
Can the total number of virus particles and the pfu/ml differ?
yes
This ratio is called the particle / pfu ratio. For some
enveloped RNA viruses, the particle / pfu ratio may be >100 or >1000 to one.
can all viruses be titrated by plaque assay
no: hepatitis B cannot
true or false
there
is a phase during virus replication when an infected cell contains no infectious virus particles
true
What are the 3 phases of the virus life cycle
- adsorption and penetration
- eclipse phase
- assembly and release
How are the 3 phases of the virus life cycle illustrated
infecting cells with virus and measuring the virus pfu at various times thereafter
(the cells in each sample are lysed artificially to release intracellular virus).
Shortly after infection the virus titre drops to close to zero and rises again at the end of the eclipse phase.
The final titre is much higher than the input titre because the virus has multiplied.
Are the general features of the virus growth curve common to all viruses?
yes
but the timescale and virus yield vary greatly.
What is the latent period of the virus life cycle
give examples to demonstrate the difference between viruses
The time taken to form new particles
it is about 20 mins when
bacteriophage T4 infects E. coli, whereas herpes simplex virus takes about 10 hrs inhuman epithelial cells.
what is the mean burst size
The average yield of virus particles / cell
reflects the specific
virus - host cell combination, and is
influenced by the cell metabolic activity
Describe the binding of HIV
The HIV envelope protein, gp120 (glycoprotein of 120,000 Mr) binds to CD4 and a chemokine
receptor (the co-receptor). CD4 is limited to T-lymphocytes and macrophage/dendritic cells.
The tropism of HIV is defined by this
describe the binding of influenza
The influenza virus envelope glycoprotein (haemagglutinin, HA) binds to sialic acid (the
terminal sugar on most glycoproteins). Since sialic acid is on almost all cell surfaces, influenza
binds to most cell types and receptor-binding does not define influenza virus tropism.
What does EBV bind to on host cells
Epstein-Barr virus (EBV) glycoprotein 340 (gp340) binding to the cell surface protein CD21
What are neutralising antibodies in relation to virology
Antibodies against receptor binding proteins usually inactivate the virus by blocking infection
What must the virus do after binding
How can this happen
penetrate into the cytoplasm.
Penetration may occur at the cell
surface, or the virus may be taken into vesicles by endocytosis or macropinocytosis and enter
the cytoplasm after disruption of the vesicle membrane
How does penetration occur with enveloped viruses
fusion of the virus envelope and a cell
membrane at either the cell surface (plasma
membrane, neutral pH) or after endocytosis
with the endosomal membrane (at low pH).
What does the process of membrane fusion require
how is this acheived
2 membranes to be drawn close together followed by membrane disruption
conformational change in the receptor binding protein
Describe the penetration of HIV after binding
binding of gp120 to CD4 results in a conformational change in the virus gp120/gp41
and the virus envelope fuses with the plasma membrane at the cell surface
What happens to influenza after binding to sialic acid
the virion is
endocytosed and the endosome is acidified. The reduction in pH causes a conformational
change in the HA drawing the viral envelope close to the vesicle membrane. A hydrophobic
fusion peptide in HA is inserted into the vesicle membrane thus promoting fusion.
Why is hemagglutination not a problem for patients suffering from influenza
Influenza virus-induced ‘haemagglutinin’ is an ‘in vitro’ phenomenon that is useful for titrating influenza virus, but
has no in vivo significance.
What is the process of membrane penetration of non enveloped proteins
Binding of virus to receptor
• Conformational change of virus causing disruption of host membrane enabling
• Transfer of virus nucleic acid or entire capsid into cell
How does bacteriophage T4 penetrate the membrane
injects its DNA into E. coli by contraction of a syringe-like sheath
Why is it called the eclipse phase
What is happening
no infectious virus particles are present in the host cell.
The virus particle has been disassembled (‘uncoated’), the virus genome is being replicated and
virus proteins are being synthesised
What kind of control over virus protein synthesis is there
both temporal and quantitative
How is virus nucleic acid synthesis so regulated
Nucleic acid polymerases recognise specific sequence/structures (origins of replication).
Where do viral polymerases come from
Viruses must either provide their own
polymerases, or synthesise proteins that modify and exploit host polymerases.
What is the minimum requirement for a virus to code for
i) a virus-specific nucleic acid
polymerase (or evolve to utilise one from the host) and ii) for virus coat proteins.
What is a unifying theme for all virus despite their wide range of genome types and replication strategies
What does this mean
the need to translate their mRNAs on host cell ribosomes.
So if viruses are grouped according
to how they convert their genome into mRNA, viruses with common replicative strategies group
together.
Which viruses’ genomes cannot be translated and the host cell cannot transcribe them
How is this circumvented
negative strand ssRNA viruses (eg measles and rabies)
ds RNA viruses (rotavirus)
must use virus genomes must be transcribed into mRNAs by a RNA-dependent RNA polymerase encoded by the virus.
What does viral mRNA from negative sense ssRNA viruses act as
positive sense RNAs serve as mRNA and as a template from which more virus RNA (-ve sense) can be produced for packaging into new virions
True or false
purified virus RNA is NOT infectious
true
Where do most negative strand ssRNA viruses and dsRNA viruses replicate
Give an exception
Most of these viruses replicate in the cytoplasm, but influenza virus replicates in the nucleus.
Influenza is unusual in that it replicates in the nucleus. Why else is it unusual
it requires host DNA-dependent RNA polymerase II as well as the virus RNA polymerase to make virus mRNA
Name 6 positive strand ssRNNA viruses
poliovirus, foot and mouth disease virus, hepatitis A virus, rubella virus, yellow fever virus, chikungunya virus
What is the first step once a positive strand ssRNA virus enters the cell
genome is mRNA so can be directly translated
When the virus genome is mRNA the first step is translation. How does the virus replicate
The translated proteins include the RNA-dependent RNA polymerase that replicates the input virus genome via a complementary (-ve sense) RNA. This is then copied into more +ve RNA, which can be translated into more proteins or packaged into new virions
True or false
purified viral RNA is NEVER infectious
false
Purified viral RNA is infectious if injected into a susceptible cell.
What are retroviruses
+ve ssRNA viruses
but after entry the virus genome is
not translated.
retroviruses are not translated directly after entry into the cell. Why
Instead it is copied by reverse transcriptase (RNA dependent DNA polymerase) into a dsDNA intermediate that is integrated into the host genome (the provirus) .
Where is the reverse transcriptase found for retroviruses
within the virus particle
What is the strategy of the retrovirus after the action of the reverse transcriptase
The virus now has the strategy of a
DNA virus in that mRNA is transcribed by host DNA dependent RNA polymerase II
from the integrated provirus. The full length transcripts are either translated or packaged into new virus capsids within the cytoplasm. Some of the full length transcripts
need to be spliced to express some of the virus proteins.
Name 3 dsDNA viruses
adenoviruses, herpesviruses, papillomaviruses
Where do most DNA viruses replicate?
What does it use
what does this mean it will do as soon as it enters the cell
Most DNA viruses replicate in the
nucleus
use cellular machinery for the transcription,
transport and processing of
mRNA.
So after infection the virus
genome is transported into the
nucleus.
What does transcription of dsDNA virus genome use
Where is the mRNA translated
Where do the translated viral proteins go and what do they do here
DNA dependent RNA polymerase
II.
mRNAs are translated in the
cytoplasm
some of the proteins (DNA polymerase and capsid proteins) are transported back to the nucleus, where viral DNA is replicated and progeny genomes are package into new capsids.
Using your knowledge of dsDNA virus strategy and replication, tell me whether viral dsDNA is infection alone
it is infectious
the input virus particle has no nucleic acid polymerase. If virus DNA is purified and
injected into the nucleus, virus replication will occur. The viral DNA alone is infectious.
Why are poxviruses an odd type of dsDNA virus
replicate in the cytoplasm
Poxviruses also have dsDNA genomes but replicate in the cytoplasm. How is this possible?
What does this mean for the infectivity of the purified viral DNA
encode enzymes required for transcription of the DNA genome (DNAdependent RNA polymerase, and capping and polyadenylating enzymes) and package these
within the virion. The virus DNA-dependent RNA polymerase is needed for transcription from
virus promoters, so purified viral DNA is not infectious.
In general which viral proteins are needed early and late
, virus enzymes for genome replication (such as polymerases), or
proteins that modify the host cell, are required early. In contrast, capsid proteins that are used
to build new virus particles are required late.
Name 2 types of virus that have very particular control over temporal protein expression
Both herpesviruses and poxviruses have several temporally distinct gene classes that are expressed in a regulated cascade, with expression of the next class of gene being dependent on proteins of the previous class. These have been referred to as immediate early, delayed early and late (herpesviruses) or early 1, early 2, intermediate and late (poxviruses).
How does the quantity of expressed protein differ for viruses
Early proteins have regulatory or enzymatic functions and so are needed in low amounts. Late
proteins are mostly constituents of new virus particles and so are needed in large amounts.
Why is eukaryotic mRNA monocistronic
How is this a problem for some viruses (use an example)
How is this overcome
unlike
prokaryotic ribosomes, do not re-initiate translation after a termination codon.
poliovirus must encode all virus proteins
Translate the mRNA into a single giant polypeptide (a 'polyprotein') that is post-translationally cleaved by proteases into several, smaller, mature polypeptides.
Which viruses use polyprotein processing to produce their capsid proteins from a polyprotein
are the proteases that perform this cleavage from the host or virus
retroviruses
virally encoded so are potential targets for chemotherapy
What is an alternative to a virus having a single mRNA encoding all the proteins?
eg
have a genome with several
different RNA segments, each encoding a different polypeptide (e.g., influenza).
How do retroviruses place the coding region for some proteins at the 5’end
How does HIV do this
How is HIV pol made
splicing
The HIV envelope
protein env is made this way and
then cleaved into gp120 and gp41.
Pol is made as a polyprotein by
ribosomal frameshifting.
What happens after the eclipse phase
which enzymes are always required here
new virus genomes and proteins assemble to form new virions.
“self-assembly” can occur, i.e. no catalytic process is involved.
what does the formation of the helical rod of tobacco mosaic virus involve during assembly
progressive addition of protein subunits around the nucleic acid
molecule
how is a complete nucleocapsid formed from an icosahedral
an icosahedral structure may form from protein subunits alone and the nucleic
acid is then inserted into these ‘empty’ capsids to form the complete nucleocapsid.
Why may a virus only become infectious during assembly
Sometimes production of infectious virions is associated with the cleavage of capsid proteins
into mature forms, a step that is necessary for the virion to become infectious, e.g. HIV.
How is the release of progeny most simply achieved
how can this be achieved
what must the virus be careful to do
cell lysis
Some bacteriophages encode a
protein that causes lysis of the bacterium.
This must only be expressed late during infection
how do many enveloped virus progeny leave the cell
‘bud’ out of the
plasma membrane over prolonged periods, acquiring their envelope in the process.
Is virus replication the only outcome of infection?
no
Some viruses can infect a cell and remain in a
quiescent state within the cell. This is called latent infection
What happens in a latently infected cell
contains
the viral genome but no virus multiplication occurs, yet the cell has the potential to produce
progeny virus - i.e., to switch from latency to the productive cycle.
Name 2 virus types that can become latent
retroviruses and herpesviruses
What happens after the retrovirus infects a cell broadly
When would it become latent
viral genome is converted to dsDNA by reverse transcriptase and then DNA integrates into a host chromosome to form the provirus
if the proviral DNA is not transcribed so no viral proteins are made
Why can it be hard for the body to eliminate all HIV infected cells
latent cells do not have any viral proteins so cannot be detected by the immune system
How can retroviruses be transferred vertically
if the virus integrates into germ cells
Give evidence that our evolution was driven by retroviruses and retrotransposons
The human genome is riddled with bits of retroviruses and retrotransposons that represent 8%
of our DNA.
In contrast, only 2% of our DNA codes for proteins
How do herpes viruses become latent in infected cells
they are dsDNA so must head straight to the nucleus to be transcribed.
but in some cell types there is no
transcription (or very limited transcription) of the viral genome. The viral DNA is quiescent -
does not integrate (with rare exception) but exists as an extrachromosomal
circular molecule called an episome)
What does the latent viral DNA in a cell infected with herpes exist as
as an extrachromosomal
circular molecule called an episome
How does a latent infection switch to a productive cycle
What is this called
might
occur when changes in the transcription factors in the cell allow recognition of viral promoters.
reactivation
give 2 examples of latent herpes infection
• herpes simplex virus (HSV-1) causes repeated cold sores
• varicella-zoster virus (VZV) primary infection causes chicken pox, reactivation
causes shingles
Virus infection of a cell is more than just replication followed by release. Give 8 ways in which the virus can modify an infected cell.
• Subversion of cellular metabolism to make only viral macromolecules
• Stimulation of cell biochemistry to enhance yields of virus
• Expression of virus enzymes to enhance nucleoside triphosphate (NTP) pools and so
increase nucleic acid synthesis
• Cell membrane modifications
• Induction of morphological changes to the cell (cytopathic effect, cpe)
• Evasion of host sensing of infection - blocking activation of innate immunity
• Non-lytic infection – persistent or latent infection
• Cell transformation - cancer
Describe how poliovirus subverts cellular metabolism
Within 1 h of infection the infected cell stops making host proteins and only makes poliovirus proteins. The virus has turned the cell into a virus factory whose only purpose is poliovirus replication
How does poliovirus stop host ribosomes recognising host mRNA
viral protease cleaves 5’ cap binding complex so it can longer recognise 5’cap
How is poliovirus mRNA translated
host ribosome recognises viral IRES after 5’cap was cleaved
Name 3 ways the virus can shut off translation of host proteins
cleavage of 5’cap recognition complex
destruction of host DNA
destruction of host mRNA
How do poxviruses subvert cellular metabolism
encode enzymes that cleave off 5’-caps from virus and cellular
mRNAs. Virus mRNAs are much more abundant and so predominant. Therefore, the translated
proteins are viral
What is a benefit of the poxvirus method of subverting host cell metabolism
helps the virus switch from early to late virus gene
expression more rapidly because the early mRNAs are destroyed once their synthesis stops.
Why would a virus want to stimulate the cell cycle
DNA viruses require high levels of dNTPs, but in resting cells dNTP
pools are low. Non-replicating cells (i.e., most cells) are therefore poor hosts for DNA viruses
Having stimulated the cell, viral DNA
synthesis and capsid protein synthesis occur more efficiently.
How can a virus stimulate cell cycle
Some DNA viruses (papovaviruses, adenoviruses,
herpesviruses) synthesise factors that stimulate the cell into cycle (e.g simian virus 40 T
antigen) . These factors are made early in infection
Vaccinia virus expresses an epidermal growth factor that is secreted from the infected cell and stimulates neighbouring cells to divide, making them
ideal infection targets.
How do pox viruses stimulate cell cycle
Vaccinia virus expresses an epidermal growth factor that is secreted from the infected cell and stimulates neighbouring cells to divide, making them ideal infection targets.
Name a factor synthesised in a virally infected cell that stimulates cell cycle
simian virus 40 T antigen
Is stimulating cell cycle the only way to increase the virally infected cell’s pool of dNTPs
no
the virus to express its own enzymes
that produce dNTPs.
Why does poxvirus and herpes encode for thymidine kinase
Larger DNA viruses (poxviruses and herpesviruses) encode enzymes that produce dNTPs: for instance, thymidine kinase, thymidylate kinase and ribonucleotide reductase.
When might a poxvirus growth well in actively growing cells in culture but poorly in resting cells
How would they affect an animal
if they are lacking the genes for dNTP producing enzymes
cause no disease (are avirulent) in animals.
What are non essential genes in the viral genome
eg genes that code for dNTP producing enzymes
THIS DOES NOT MEAN THEY ARE NOT IMPORTANT IN VIVO - it just means they are unlike genes encoding capsid proteins or viral polymerases,
which are essential
Why do enveloped viruses modify the cell membrane
part of their replication cycle, because the plasma membrane
will become the virus envelope and must contain the proteins required for adsorption to and penetration of the next host cell.
What can the effect of viral modification of infected cell membrane be (2)
may be to change
the behaviour of a cell with respect to its neighbours,
make it a target for NK cell
recognition
How does measles affect the host membrane
s induces the infected cell to fuse with surrounding uninfected cells so spreading
virus to uninfected cells without exposure outside the cell (and a target for antibody)
What are cell-associated viruses
Name one
Viruses
that pass from cell to cell without an extracellular stage
Measles
What is cpe
cytopathic effect - when a virus-infected cell shows a strikingly different morphology to uninfected cells
What can cpe be caused by
e alterations to the cytoskeleton (actin and tubulin containing filaments), which are exploited by the virus to facilitate intracellular movement of virus particles.
Give 3 viruses that can be identified from the cpe they result in
Rabies virus: Negri bodies in Purkinje cells in cerebellum
• Human cytomegalovirus: nuclear inclusion bodies that resemble “owl eyes”
• Poxviruses: cytoplasmic, eosinophilic inclusion bodies
How do cells sense viral infection
what is the effect on the virus
Cells sense virus infection by detecting the presence of (PAMPs), such as virus nucleic acid, by pattern recognition receptors (PRRs).
leads to an innate immune response, which left unchecked are detrimental virus replication and spread
Give an example of how viruses mitigate the effect of the innate immune response
Large DNA viruses, such as herpesviruses and poxviruses, encode many proteins that block the innate immune response to infection
What are 3 rules to remember when considering if a viral infection is lytic or non lytic
The productive cycle of DNA viruses is lytic.
Non-enveloped RNA viruses are lytic.
Viruses that cause host shut-off are lytic.
Non-enveloped RNA viruses are lytic. What about enveloped RNA viruses?
some enveloped RNA viruses, including retroviruses, can multiply in cells without killing
them and so release virus particles over a long period of time.
What does it mean to say a virus transforms a cell
the
cell now exhibits uncontrolled growth, fails to respond to the presence of neighbouring cells
(contact inhibition), and has many of the properties associated with malignant cells in vivo
What amount of human cancers are caused by viruses
20%
How do certain DNA viruses transform the cell
stimulate cell metabolism to create a suitable environment for virus
replication. This stimulation (by an ‘early’ virus protein) is normally followed by virus DNA
synthesis, virus capsid protein synthesis, the appearance of new particles and cell death
Give an example of a DNA virus transforming a cell
What can go wrong
papilloma viruses, which induce cell proliferation (resulting in a wart)
before synthesis of new virus takes place.
However, occasionally the virus replication cycle fails
(i.e. DNA synthesis and capsid protein synthesis do not occur) but ‘stimulation’ continues and
the cell continues to divide.
In the case of certain human papilloma viruses (HPVs) (notably HPV strains 16 and 18) cervical carcinoma may result.
How can retroviruses induce transformation
capture of oncogenes
integration to dysregulate cell division
How does retrovirus capture of oncogenes occur
Retroviruses can occasionally acquire a host cell gene during replication. If the cellular gene
plays an important role in the control of cell growth, then the resultant virus will ‘transform’
cells because the gene will be expressed at abnormally high levels, and lacks normal regulation,
when the virus infects a cell.
What is Rous sarcoma virus
an acute transforming retrovirus
it is an avian retrovirus that acquired src gene leading to src RTK being overexpressed
Why are acute transforming viruses usually replicative defective
What do they now require
Usually the acquisition of host gene is accompanied by loss of virus sequences.
co-infection by a helper virus to replicate
What makes Rous sarcoma virus replication defective
lacks the envelope
gene (env) and cannot replicate unless a helper virus provides this
How can a retrovirus lead to cancer other than acquisition of an oncogene
random integration may disrupt a tumour suppressor gene or activate/overexpress an oncogene
this is rare
how commonly do retroviruses, other than acute transforming viruses, lead to transformation
very rarely
True or false
transformation occurs frequently in most viral infections
false
cell transformation by viruses is a rare event because it requires an abortive infection
(DNA viruses) or the activation of a key host gene (retroviruses)
more likely to occur when the virus persists in an individual for a long time
Name 5 virus types that are associated with neoplasia
some herpesviruses (EBV & HHV-8),
papillomaviruses (HPV 16 and HPV 18),
retroviruses (HTLV-1),
hepadnaviruses (HBV)
flavivirus (HCV
What must a virus do to survive a multicellular host
gain entry to the host, replicate despite the host defences, and be released in a manner enabling transmission to new hosts.
What are ‘portals’ in virology
Viruses generally enter and leave a host by a specific route (portals of entry and exit) and
these are closely linked to transmission between hosts
Do viruses have to enter and leave through the same tissue
All superficial (local) infections must use the same entry and exit tissue
Some systemic infections also use the same entry and exit routes.
What are the physical barriers that a virus must evade to gain entry (5)
the skin,
the cilia that beat on our mucosal surfaces to sweep foreign particles such as viruses and bacteria out of the respiratory system,
the mucous secretions that bathe these surfaces,
the proteases of the stomach and intestine
the low pH of the
stomach.
How do viruses overcome the physical barriers to their entry
eg?
they are specially adapted
viruses that enter via
the alimentary canal, such as poliovirus, must be highly resistant to the acid pH of the
stomach and the proteases that are present here and within the intestine. If other viruses that
do not usually enter via this route are ingested they would be destroyed quickly.
How are viral infections sensed by the innate immune system
nucleic acids that may either be in an unusual place (DNA in the
cytoplasm) or have an unusual structure (RNA with a 5’ triphosphate) and these are sensed as
foreign by PRRs.
Once viral nucleic acids are detected by PRRs, what happens
activate signalling cascades that
culminate in activation of transcription factors, eg NF-κB or IRFs.
Once activated, these transcription factors translocate into the nucleus where they promote
transcription of a wide range of genes that activate innate immunity. These include:
interferons, chemokines (that recruit leukocytes to the site of infection) and cytokines that
promote the inflammatory response (such as IL-1β and TNF).
What are interferons in relation to viruses
secreted glycoproteins that bind to specific receptors on cells to induce
activation of an anti-viral state. Subsequently, if a virus enters an IFN-treated cell it will be
unable to replicate
Give 2 ways to illustrate that IFNs are v important anti-virus chemicals
the much greater sensitivity to virus infection in the absence of IFNs or their receptors,
• the fact that very many viruses, probably all mammalian viruses, have at least one way of
avoiding or disabling IFNs, or the functions of IFN-induced proteins
How can a virus be detected once it has infected a cell, if not by a PRR
TLRs on the endosomes that contain the virus
Give the cascade following detection of a virus by a PRR
PRR activates IRF3 and NF-κB, which activate IFN beta transcription
IFNβ is secreted from the cell where it binds to the type I IFN-R on adjacent cells.
activates JAK-STAT pathway, activating ISGF-3
ISGF-3 binds to ISRE and ISGs are activated, rendering the cell resistant to viral infection
What are the following
a) ISGF-3
b) ISRE
c) ISG
a) a transcription factor complex interferon stimulated gene factor 3 (activated by JAK-STAT pathway)
b) interferon stimulated response element, which ISGF-3 binds to
c) interferon stimulated genes, whose protein product leads to priming of the cell to be resistant to viral infection
give 3 examples of ISGs
protein kinase R (PKR),
2’-5’ oligoadenylate synthetase (OAS)
the Mx protein.
What do PKR and OAS require for activation
What do they do
what are the consequences (2)
dsRNA
(produced during infection by both DNA and RNA viruses)
inhibit protein synthesis (host and viral)
no virus
replication, and cell death.
Give 4 ways viruses can interfere with the interferon
Do any viruses exploit ALL of the these strategies
• stopping activation of the PRR-induced signalling cascades, so IFNβ is not produced
• releasing soluble proteins to bind IFNs and stop IFNs binding to the IFN-Rs on cells
• inhibiting the JAK-STAT signalling cascade to block induction of ISGs
• targetting the ISG proteins directly to block their action (e.g. 2’5’-oligo adenylate
synthetase, and protein kinase R)
yes poxviruses
Programmed cell death of a virally infected cell can be an effective way to limit spread of infection. How do viruses block apoptosis?
by blocking the action of
caspases (needed for induction of apoptosis), or targetting Bcl-2 family pro-apoptotic
proteins, which function at the mitochondrion to induce apoptosis.
What are chemokines
small chemo-attractant cytokines that recruit leukocytes to the site of infection. The recruited leukocytes then produce more IFNs or cytokines to activate T cells and
macrophages to fight the infection
why are inflammatory cytokines important during the response to viral infection
they drive the development of cellular immunity, such as CD8+ cytotoxic T lymphocytes
(CTL) that recognise and remove virus-infected cells. CTL are particularly important for
recovery from systemic virus infections.
How do herpesvirus and poxviruses block cytokine and chemokine action
secrete proteins from the cell that bind these molecules
outside the cell and stop them reaching their natural receptors
How does EBV block cytokine response
Epstein-Barr virus, expresses a viral cytokine (vIL-10)
that drives the immune system towards a Th2, rather than Th1 response.
How do NK cells kill virally infected cells
an antigen-independent manner.
NK cells kill virally infected cells in an antigen independent manner. what does this mean?
Normally cells express class I MHC molecules and the presence of class I MHC instructs the NK
cell not to lyse the cell. However, if class I MHC molecules are low or missing, as can happen
during virus infection, the NK cell is activated and kills the cell. Thus the cell may be destroyed
before virus replication is complete.
How is the killing of virally infected cells by NK cells different from CD8+ CTLs?
different activating stimuli:
For CD8+ CTL, the target cell is identified by the presence of specific virus peptides associated with class I MHC molecules on the cell surface, and this is antigen-dependent.
• In contrast, NK cells recognise the absence of class I MHC - may be antigen independent
NK cells are important early after infection before an antigen-specific CD8+ T-cell response
develops.
True or false:
NK cells can also develop pathogen-specific memory
true
What is the role of antibodies in a viral infection
how do they do this
Abs help prevent infection or diminish spread by free virions after an infection has
been established
bind to and neutralise virus particles, either alone or in combination with
complement.
What is mucosal IgA important for
preventing infection by viruses that enter by the
respiratory system
True or false
Abs are vital for removal of virally infected cells
false
more important in preventing infection or spread by free virions
What is the role of cytotoxic T cells in viral infections
CTL are unable to combat free virus particles, but are efficient at recognising and
destroying virus-infected cells
What kind of viruses are CTLs important in combating
viruses that remain largely cell associated (e.g. HCMV and measles virus) and for those that cause systemic infections.
Name a virus that is well adapted to block the CTL response
How
herpesviruses
have many strategies to block the presentation of peptides on class I MHC molecules
Herpesviruses have many strategies to block the presentation of peptides on class I MHC molecules. Give 4 examples
• Block generation of peptides by the proteasome
• Block transport of peptides into endoplasmic reticulum (HSV and adenovirus)
• Destroy class I MHC molecules by inducing their transport back into the cytosol for
proteolytic degradation (HCMV)
• Retain class I MHC molecules intracellularly and so preventing their transport to the cell
surface (adenovirus, VZV and HCMV)
Give 3 ways for viruses to escape adaptive immunity
• Latency. Hide from the immune system.
• Express Fc receptors on cells and virions. The Fc region of antibodies that are bound to
virus antigens on cells or virions is then not available to bind host Fc receptors.
• Antigenic variation: influenza, HIV and hepatitis C virus.
What are the 4 outcomes after a cell is infected by a virus
latency
cell death
persistent infection
cell transformation
Which cell types can poliovirus destroy?
What must you remember about this?
motor anterior horn cells in the CNS
leads to paralysis
it is unusual for poliovirus to escape the gut and enter the CNS This has no benefit for the virus, for the route of exit to find new hosts is via the gut.
What affects the outcome of a viral infection
virus dose, the route of infection, and the age, sex and physiological state of the host.
How does viral dose affect outcome
Low doses are less likely to establish productive infection and cause disease.
High doses, on the other hand, may overwhelm the local innate response and cause disease.
How does route of entry affect the outcome of a viral infection
eg?
The same dose of virus given by different routes can give different
outcomes.
eg the use of variola virus (the poxvirus that causes smallpox) to prevent severe disease if given by dermal infection (variolation), rather than by inhaling the virus naturally (respiratory infection).
Give 3 examples of viruses which have different outcomes depending on the age or sex of the host
varicella zoster virus
hepatitis B
EBV
How is varicella zoster virus affected by age
causes chickenpox after the primary
infection. Infection with VZV in early childhood is generally a mild infection, but it is much more serious as an adult
How does EBV infection differ with age
Usually EBV
infection in childhood is asymptomatic, but if infection is acquired as a young adult the
outcome may be glandular fever (infectious mononucleosis).
How does age and sex affect the outcome from a Hep B infected patient
HBV infection of a
neonate, from an HBV-infected
mother, gives a much greater chance of establishing a chronic infection
than if the infection is acquired later in
life, when the outcome is more likely to be an acute infection
for males it is worse than females. So if a male is born to an HBV-infected mother, becomes infected and no action is taken, he has a 90% chance of developing chronic HBV infection, and a 50% chance of dying from liver cancer due to this chronic HBV infection.
What can a chronic HBV infection lead to
strong chance of developing into liver
cancer (hepatocellular carcinoma,
HCC)
What is the difference in HBV outcome between the sexes
if a male is born to an HBV-infected mother, becomes infected and no action is taken, he has a 90% chance of developing chronic HBV infection, and a 50% chance of dying from liver cancer due to this chronic HBV infection
How does the physiological state of the host affect the outcome of a viral infection
Stress and immunological deficiency are both factors that increase
the likelihood of severe infection.
Both these conditions contribute to the frequency of
reactivation of herpesvirus infections, for instance.
How do we know varicella zoster virus is more potent in stressed hosts
From NASA: there is an increase in varicella zoster virus in the saliva of astronauts during space travel.
Why can FMDV, VZV, measles and rubella not be classified by their target organ
all acquired by the respiratory route, but they would not be described as ‘respiratory infections’.
What happens in superficial infections
Virus replication occurs in the epithelium at the initial infection site (portal of entry) but does not spread to other tissues
they are acute with a short incubation period and short duration period
Give 5 features of a superficial virus infection
remain at portal of entry
acute
short incubation period
short duration
independent of specific immune responses
Give 3 examples of superficial infections
common cold, influenza, gastroenteritis (rotavirus).
How does a viral systemic infection differ from a superficial one
The virus replicates at the portal of entry but then spreads by various routes (lymphatics,
bloodstream, nerves) to other sites where further replication occurs. These infections have a longer incubation period, are more severe, and the outcome is very dependent on specific immune responses (especially CTL).
name 4 viral systemic infections
smallpox, measles, chickenpox, foot and mouth disease
Which virus have we used to define the characteristics of systemic infection
ectromelia virus (the cause of mousepox)
this still remains the paradigm
Describe the route of systemic mousepox infection (6)
enters and replicates in epithelium
- ->draining lymph node
- -> blood stream
- -> amplification in internal organs eg spleen, liver and vascular endothelium
- -> released in higher titres into blood stream
- -> replicates in lungs and skin of hot for transmission to new hosts (portal of exit)
What is primary and secondary viraemia
primary: first time systemic viral infection enters blood stream after infecting the portal of entry and then passing to the draining lymph node
secondary: when the virus is released into the blood in much greater titres after replicating in the liver etc
What are the most common routes of spread for systemic viral infections?
What else can be used>
blood and lymph
viruses like rabies can use nerve tracts
Why is the common cold only ever superficial
rhinoviruses (common cold) grow well at 32 ºC but not at 37 ºC and so replicate
well only in upper respiratory tract epithelium.
Why does budding affect whether a viral infection is superficial or systemic
influenza buds from apical surface of respiratory epithelial cells and so virions are released into the airways (local). This is determined by trafficking of the virus glycoproteins to that cell surface.
In contrast, a virus that budded from a basal layer (into
tissue) might have greater chance of establishing a systemic infection.
Which factors influence whether a viral infection is superficial or systemic (3 examples)
eg temperature it grows best at
location of budding
interaction with phagocytes
How do interactions with phagocytes affect whether a viral infection is superficial or systemic?
several viruses that cause systemic infection (yellow fever virus and ectromelia virus) can grow in macrophages.
what are the 3 categories for viruses based off their ability to persist in the host
acute
persistent/ chronic
persistent/ latent
What happens usually in acute viral infections
What happens if this does not happen? Use an example to illustrate
In these infections the virus is cleared
after an acute infection. This is the
normal outcome in the normal host
Measles virus mutants can persist in the CNS and cause a chronic demyelinating disease (SSPE) with a frequency of about one per million infection
How long can a chronic viral infection last
Name 2 viruses which almost always establish persistence
for years or even life long
HIV and hep c
Is hep B chronic or acute
cleared after the acute phase in about 90% of normal adults, the
remaining 10% become persistently infected.
In contrast, 90% of infected male neonates become infected chronically.
which herpes viruses establish latency and are not cleared
all
