Week 8: Viruses

Question 1

Did viruses exist before or after bacteria and archaea?

Answer 1

• Viruses existed before these entities

Question 2

What is one of the smallest viruses known?

Answer 2

• The parvovirus

- It has a genome of only 5,000bp that encodes 2 proteins

Question 3

When were viruses discovered?

Answer 3

• Viruses were discovered much later than bacteria as bacteria could be seen under light microscope
• In the 1870s Pasteur could not find a “germ” that could rabies and speculated about a pathogen too small to be observed by microscopy
• In the 1930s the influenza virus was discovered

Question 4

What are the defining characteristics of a virus?

Answer 4

• Infectious, intracellular obligate parasites
• Viruses are acellular
• The viral genome is made up of nucleic acid (RNA or DNA)
• The viral genome encodes the components needed for replication in the host cell
• Infectious progeny (virions) self-assemble
• Progeny virions transfer their genome to the next host cell to initiate the next infectious cycle

Question 5

What is the structure of a virus?

Answer 5

• Viruses consist of nucleic acid surrounded by a protective protein shell called a caspid
• The caspid proteins are very stable and protect the virus genome against many environmental stresses such as heat and pH
• In some cases the caspid will be surrounded by a membranous envelope (made up of lipid and membrane-associated proteins)
• The external surface of the virus (the caspid or the envelope with host glycoproteins) enables attachment to the host cells

Question 6

How are viruses classified by the Baltimore scheme?

Answer 6

• This scheme groups viruses into families depending on the type of nucleic acid in their genome
  e. g. DNA, dsRNA, -ssRNA, +ssRNA etc.
• The viruses much synthesise proteins so their genome must be converted into mRNA
• This can occur in a number of different ways depending on the type of nucleic acid in the viral genome:
  1. DNA viruses utilise the host cell DNA and RNA transcriptional machinery to make mRNA
  2. Orthomyxo viruses which have -RNA initially make copies of their -RNA using enzymes they carry with them to form +RNA, and mRNA is formed from the +RNA by host processes
  3. Retroviruses have +RNA but reverse transcriptase enzyme of the virus converts it into -DNA which integrates into the genome and will then undergo transcription into mRNA by the host cell machinery

Question 7

What is the basic process of viral replication inside a host cell?

Answer 7

1. Viral attachment
2. Release of viral genome into the cytoplasm
3. Host cell machinery are recruited to allow for the translation of viral proteins
4. The viral genome also replicates
5. The virions self-assemble
6. Release of the virions

Question 8

How do viruses attach to host cells?

Answer 8

• Viruses attach to host cells via different cell surface receptors
  e. g. Herpes interacts with herparan sulfate proteoglycan
  e. g. Influenza binds to sialic acids (very specifically)
  e. g. HIV interacts with 2 cell surface receptors on helper T cells, it interacts with CD4 to attach to the cells and then it binds to CCR5 (a chemokine receptor) to enter the cell
• People with mutations in CCR5 are resistant to HIV

Question 9

How do the viral receptors on HIV determine its species/tissues tropism?

Answer 9

• HIV only attaches to and infects activated/memory T cells (it only has receptors for CD4 and CCR5)
• HIV is usually sexually transmitted so it attaches to mucosal surfaces
• After this mucosal infection occurs activated T cells migrate to the site via the chemokine receptor CCR5
• By activating an immune response, the HIV virus is able to recruit activated CD4+ CCR5+ T cells which they are able to infect

Question 10

How do the viral receptors on Hepatitis B virus determine its species/tissues tropism?

Answer 10

• Hepatitis B virus has a receptor for NTCP
• NTCP is a bile transporter
• Heparin sulphate proteoglycans act as a co-receptor

Question 11

What are the different strategies of progeny virion release?

Answer 11

1. Lysis:
   - The host cell is lysed and the progeny are released
   - Used by poliovirus
2. Budding:
   - The virus buds off the host cell membrane, taking advantage of the cell’s exocytosis process
   - Used by many enveloped viruses such as measles
3. Exocytosis:
   - Some viruses are released from host cells via exocytosis
   - Herpes virus undergoes waves of transcription and it then self assembles and is released by exocytosis
4. Budding/cell-cell transfer:
   - Some viruses such as poxviradae (small pox) release factor that drive the proliferation of neighbouring cells, so when they either lyse or bud off their host cell there is an abundance of healthy host cells to infect

Question 12

What are the infection outcomes of animal viruses?

Answer 12

• Infection outcome is a reflection of the damage caused by the infection process

1. Transformative outcomes:
   - Transformation of host cells from normal cells into tumour cells
   E.g. EBV causes Burkitt’s lymphome and HPV causes cervical cancer
2. Lytic infections:
   - The viral replication involves the death and lysis of the host cells
   - The process triggers inflammation
   E.g. Influenza, Rotavirus, Ebola
   - Common in acute infections
3. Persistant infections:
   - The virus is released from cells slowly and does not cause cell death
   - E.g. Measles, EBV- the virus can persist for 12 months
4. Latent infections:
   - The viral genome is integrated into the host cell genome but remains dormant
   - The infection will later emerge as a lytic infection
   E.g. HIV, HSV-1

Question 13

How are viruses classified in accordance to their disease outcome?

Answer 13

1. Respiratory viruses
   e. g. influenza, rhinovirus, adenovirus
2. Enteric viruses:
   - Rotavirus, norovirus
3. Arboviruses (arthorpod-borne viruses):
   - Dengue virus, Zika virus
4. Sexually transmitted viruses:
   - HIV, Herpes simplex and HPV
5. Hepatitis viruses:
   - Viruses that cause liver disease
   e. g. Hepatisis B

Question 14

What are the 4 Stages of Immune Defence against virus infection?

Answer 14

1. Physical barriers:
   e. g. mucous, skin, tears, stomach acids
2. Intrinsic:
   E.g. Interferons, autophagy, apoptosis, MicroRNAs, CRISPRs
3. innate:
   - NK cells, Complement system, APCs and neutrophils
4. Adaptive:
   - T cells and B cells

Question 15

How are intracellular pathogens detected in innate cells?

Answer 15

• Toll like receptor system
• TLRs are positioned on the cell surface membrane, inside the cytoplasm and on membranes of endosomes
  e. g. poliovirus is detected by TLRs on the outside of cells
• The TLR detection of viruses drives a signalling pathway driven by Nf-kB:
• Nf-kB is a proinflammatory transcription factors that drives the inflammatory response, it enters the nucleus of infected cells and drives the production of a set of cytokines called interferons
• Interferons interfere with viral replication

Question 16

What is the function of Type 1 interferons?

Answer 16

• Type I IFNs are produced by the infected cell and then they go out and signal (to other non-infected cells) via IFN receptors
• The signalling cascade from IFN binding to IFN receptors initiates an antiviral state in the cell by:

1. Inhibition of viral protein synthesis:
   - Activation of protein kinase R
   - PKR when activated bind to the viral genome and phosphorylates a protein translation initiation factor
   - This phosphorylation inhibits viral protein synthesis
   - This kills the cell, but prevents the transmission and limits the replication of the virus
2. Degradation of viral RNA:
   - Oligo A synthetase is first activated by detecting viral genomes
   - Oligo A synthetase activation causes the aggregation of Oligo A’s in the cell
   - Oligo A then binds to RNAase L, which causes the degradation of host and viral RNA
3. Inhibition of viral gene expression and virion assembly:
   - Mx GTPass cause the activation of oligomerisation
   - This process includes apoptosis which subsequently provides inhibition of viral gene expression and virion assembly

Question 17

How to Viruses combat the action of type I IFNs?

Answer 17

1. Influenza virus:
   - NS1 protein is encoded by the viral genome
   - NS1 inhibits the activity of PKR
2. Herpes virus:
   - Targets PKR
   - Targets RNAaseL
3. Pox virus:
   - Targets PKR
   - Targets the signalling of IFN
   - Targets oligo A synthetase

Question 18

How to antibodies neutralise pathogens such as viruses?

Answer 18

• Antibodies against a specific virus neutralise pathogens by binding to them and preventing the interaction between the virus and its host cell receptor which blocks attachment and prevents infection

Question 19

How does influenza avoid antibody binding?

Answer 19

• Influenza virus is a RNA virus that replicates via RNA polymerase so there is no proofreading ability which results in the introduction of mutations
• A small mutation in the gene that encodes for an attachment receptor will block the ability for an antibody against the virus to bind- as the antibody would have been specific to the original receptor
• The antibody binding sites of flu heamaglutanin accumulate mutations
• Therefore immunity to previous strains of influenza may not be effective

Question 20

How do CD8+ killer T cells target virally infected cells?

Answer 20

• CD8+ killer T cells can detect if a cell is infected with a virus as the viral proteins will be degraded and loaded onto MHC Class I
• The CD8+ T cells recognise that cells are infected and release granzymes and perforins which induce cell death in the infected cell

Question 21

How do viruses evade CD8+ Killer T cell Responses?

Answer 21

1. Interfering with MHC Class I presentation:
   - Some viruses e.g. herpes viruses and pox viruses (mainly DNA viruses) have envolved a mechanism so that killer T cells do not recognise them too early
   - They do this by encoding proteins which target different elements of the host cell processing and presenting pathway such as the the processing and presentation pathway by blocking the processing of viral proteins, the transport and loading onto MHC Class I and the secretion of loaded MHC Class I to the surface
2. Mutation of CD8+ Killer T cell Targets:
   - RNA viruses and HIV
   - predominantly mutate CD8+ T cell targets via mutation
   - By mutating the peptides that are derived from them so T cell recognition is abolished or peptide binding to the MHC is abolished

Question 22

What are viromes?

Answer 22

• Viromes are the part of our metagenome that comes from viral DNA
• It is estimated that each human may be infected by 4-5 viruses at once
• This enables a somewhat symbiotic relationship between viruses and hosts (the hightened inflammation protects the host from more virulent infections)
• The enhanced inflammation may also be associated with the development of autoimmune disease

Question 23

What is small pox?

Answer 23

• Smallpox is an infectious disease characterised by the development of pustules on the skin surface filled with replicating virus
• It is caused by the poxviridae virus which is a large DNA virus
• These pox viruses are largely invariant as they have a slow mutation rate

Question 24

What has the history of smallpox care been?

Answer 24

• It was recognised early that if you survived smallpox you would not succumb to a secondary epidemic
• Variolation (giving a small dose of smallpox sourced from scabs blown into someones respiratory tract) was developed by the Chinese and introduced into a standard of care in 1775 in England but had a slight risk of death
• Jenner recognised that milkmaids that contracted cowpox were protected from smallpox
• Jenner used the cowpox virus to innoculate a child that became protected against small pox
• This principle was used by Pasteur to develop the fowl cholera vaccine
• Smallpox has been eradicated from the world via vaccination

Question 25

What is the longevity of B cell and T cell immunity to smallpox?

Answer 25

B cell Immunity:

• Decreases over time
• Requires revacination every 5-10 years
• However antibody immunity is maintained through life and only 1 vaccination is needed to maintain high levels of neutralising antibody

T Cell Immunity:

• Long lived but with a half life of 10-15 years
• There is some decrease in the number of T cells over time

Question 26

What is Picornaviridae?

Answer 26

• Also called polio virus
• Is a very small simple virus with no envelope
• Replicates in host cells via lysis
• Enteric virus that are transmitted via the oral-fecal route
• Polio epidemics are a consequence of better sanitation as improved sanitation means there is less endemic exposure and thus less immunity (e.g. maternal Abs transferred to babies) to the virus in the population
• Less protections against the virus leads to a greater risk of developing neurological symptoms and poliomyelitis

Question 27

What is poliomyelitis?

Answer 27

• The infectious disease caused by the polio virus
• Damaged motor neuronal cells
• This leads to muscle wasting and paralysis (when it occurred in diaphragm muscles people had to use iron lung machines)
• Drop foot/withered leg syndrome is another symptom

Question 28

What are the two vaccines developed against polio?

Answer 28

1. IPV Salk Vaccine:
   - Used inactivated poliovirus that was fixed with formaldehyde
   - This was administered as an injection
   - This resulted in the significant reduction of cases but then a plateu occurred
2. OPV Sabin Vaccine:
   - Used live attenuated poliovirus (cultured in monkeys) of 3 subtypes
   - The type 3 virus differs from the wildtype virus by only 10 mutations
   - The attenuated virus is given orally
   - More effective that the IPV but in rare cases type 3 virus given could revert back to the wildtype and cause polio
   - In Australia only the IPV is given

Question 29

What is Flavivaradae?

Answer 29

• Also called Yellow Fever virus
• Transmitted via mosquito vectors (an arbovirus)
• Causes yellow fever:
• Acute symptoms: 3-4 days of fever
• 15-20% of cases develop vomiting, epigastric pain, jaundice, renal failure
• There is a 20-50% mortality rate upon renal failure
• In rare cases encephalitis can occur

Question 30

What is the yellow fever vaccine?

Answer 30

• Live attenuated vaccine (has 20 AA differences to the WT)
• Been used for over 65 years
• Protection is achieved in >98% of recipients
• The vaccine has been used as a vaccine vector for novel antigens from other flaviviruses, malaria and cancer

Question 31

Why is the yellow fever vaccine so good?

Answer 31

1. The vaccine induces a very robust immune response:
   - Gene arrays show that after the vaccine is administered all the genes involved in the immune response to a virus were activated
   - All of the genes activated in response to the vaccination were co-regulated by one or two transcription factors (IRF7 or IRF9)
   - IRF7/9 are activated when there is ligation of TLRs
   - Therefore the yellow fever vaccine is able to engage the innate immune system in a robust manner: both in terms of a type 1 antiviral response and the maturation of the adaptive immune response

Question 32

What strategies are being considered to develop a vaccine for HIV?

Answer 32

• Currently there is no vaccine against HIV
• Current development include:

1. MERK/NIH STEP trial:
   - Ues recombinantly expressed HIV proteins: gag, pol and nef in adenovirus serotype 5
   - Adenovirus induces a robust immune response in humans so it was thought that expressing the HIV targets in the adenovirus would cause the development of immunity against them also
   - The adenovirus HIV vaccine was administered to 3000 high risk participants in a stage III clinical trial
   - It was shown that there was no difference in HIV infection rte for those who did not respond to the vaccine or vector
   - For those that did respond, there were more infected individuals in those who did receive the vaccine
   - Therefore the vaccination resulted in increased incidence of HIV infection
   - It is thought that this occurred because the vaccine was given as an injection and leads to an immune response that involves the activation of T cells
   - Activated vaccine specific T cells will express CD4 and CCR5 and if HIV infection occurs they will migrate to the infection site and act as a reservoir of cells for infection

Question 33

Describe the Ebola outbreak of 2014-2016:

Answer 33

• Ebola is caused by a type of filoviridae virus
• The virus infects endothelial cells and causes a haemorrhagic fever
• It is spread through direct contact
• The latest outbreak lasted an unusually long time due to a delay in control measures and cultural practices
• 1/3 of people infected in this outbreak died
• Given the high mortality rate- it is difficult for Ebola to be transmitted outside of the area where it is prevalent

Question 34

What is SARS?

Answer 34

• Severe acute respiratory syndrome
• Due to corona virus
• Epidemic occurred in 2003
• First presented in China
• Was predominantly limited to SE Asia but did spread to North America
• Bats were the reservoir for the virus and palm civets were the intermediate carrier
• SARS was limited because the infection had limited human-human transmission and was mainly occurring in a hospital setting

Question 35

What is MERS?

Answer 35

• Middle East respiratory syndrome
• Due to Corona virus
• High fatality rate (26%)
• Bats were the reservoir and camels were the intermediate carriers

Question 36

What is the Zika Virus outbreak?

Answer 36

• Due to a flaviridae virus (similar to yellow fever)
• Not a lethal infection but can leads to birth defects such as microencephaly and Guillen-barre syndrome (neurological disease)
• The Zika virus can be transmitted across the placental barrier and it attacks neuronal cells in the foetus
• Bats are the reservoir for the virus and mosquitos were the intermediate vectors

Question 37

What is the origin of human viruses?

Answer 37

• All human viruses have emerged from another host (started out as a zoonotic infection)
• 70% of current viruses of concern are vector-borne or zoonotic
  E.g.1 Measles is part of the morbillivirus family that came from cattle
  E.g.2. HIV1 M came from a similar virus SIV which was found in chimpanzees- transmission of this virus to humans came through the harvesting of bush meat

Question 38

What factors are promoting the emergence of vector-borne and zoonotic infections?

Answer 38

1. Dominance of human:
   - There is a disruption to the ecosystem
   - There is an increased density of people closer to the animal reservoirs which increases the likelihood of transmission
2. Climate change:
   - Pathogens can adapt to climate change
   E.g. Ross river virus has spread from tropic North Queensland to the East coast of Australia

Question 39

What type of host-virus interactions are there?

Answer 39

1. Resistant:
   - Certain hosts may be resistant to certain viruses
   - Vaccinations aim to increase the number of resistant hosts
2. Evolving:
   - The virus or host may evolve e.g. a virus may become immune to an antibody
3. Stable:
   - The virus is maintained and the host does not die
4. Dead-end:
   - The virus causes catastrophic effects in the host

Question 40

What type of virus-host interactions result in emerging infections?

Answer 40

• Emerging infections are predominantly occurring from stable viruses evolving or becoming dead-end viruses

Question 41

How do the various outcomes of Influenza A virus model the different virus-host interactions?

Answer 41

• Influenza A are orthomyxoviridae viruses
• They have genomes consisting of (-) sense RNA
• It is a respiratory infection as it infects epithelial cells in the airways
• Attaches to host cell sialic acid via hemagglutinin- then replicates and buds to exist the host cells
• It is a model for stable and dead-end outcomes:
  1. Stable: wild aquatic bird reservoir
  2. Evolving: 2009 pandemic in humans
  3. Dead-end: Bird flu

Question 42

How does Influenza A attach to host cells?

Answer 42

• Influenza A strains are characterised by the surface glycoproteins they express:
• Hemagglutinin (H) and neuraminidase (N)
• Different HN types segregate into different hosts
  e. g. Influenza viruses that infect humand are H3N2 and H1N1
• The hemagglutinin (HA) molecule on the surface of the Influenza A virus is a trimer that recognises sialic acids
• The type of HA recognises how sialic acid is linked to the end of the galactose chains
  e. g. Human influenza recognises sialic acid using an a2,6-SLN linkage
• The specificity of the receptor dictates the viruses ability to bind to host cells and infect

Question 43

What is antigenic drift?

Answer 43

• Antigenic drift is the small mutations that occur in attachment receptors (such as HA in influenza A)
• This alters the ability for antibodies to detect the virus, so the initial immunity developed is no longer protective
• This is the mechanism by which seasonal influenza persists

Question 44

What is antigenic shift? When did it occur in Influenza?

Answer 44

• A human virus (H3N2) and a bird virus (H5N1) can both infect pigs (an intermediate host)
• This is because pigs have sialic linkages that enable the attachment of both these HA’s (a2,6-SLN and a2,3-SLN)
• When the viruses infect the intermediate host cells there can be mixed/chimeric viruses produced
• These chimeric viruses contain human genes for replication and transmission, but have altered receptors (different HA and N) so that pre-existing immunity is ineffective)
• The H5N2 chimeric virus produced in pigs spread to humans and was highly virulent causing the swine flu pandemic

Question 45

What factors favour an Influenza A pandemic?

Answer 45

• No pre-existing immunity to an influenz A pandemic strain
• The ability for the virus to spread from human to human (not a dead end virus-host interaction)
• The pre-cursors are endemic in animal reservoirs so there must be the chance for the virus to re-assort with human viruses

Question 46

What are the characteristics of an influenza pandemic?

Answer 46

• Associated with the introduction of a new-subtype into circulation (so there is no existing immunity in population)
• Occurs rapidly with no warning
• There is rapid global spread
• There are waves of infection, with increasing virulence
• Most pandemics originate from Asia

Question 47

Describe the Influenza Pandemic in 1918: Spanish Flu

Answer 47

Influenza A pandemic

• The Spanish flu
• Occurred in 1918-1919
• This strain of flu (H1N1) was highly virulent and affected young, healthy adults due to over-activity of the immune system in the lungs due to the upregulation of inflammatory genes
• There was a second wave of infection that was more virulent as it was adapted to human hosts as it had an increased capacity to bind a2,6-SLN (the first wave could bind a2,3, SLN linkages as well because the virus likely originated from pigs)

Question 48

Describe the 2009 Swine Flu Pandemic:

Answer 48

• It was a swine origin influenza A virus (H1N1) that was antigenically distinct to current H1N1 viruses
• In early April it emerged in Mexico and California
• By Early May it had spread to 30 countries
• The source of the virus was 3 different strains of swine flu (triple assortment) that could bind α2,3 and α2,6 SLCs
• This pandemic flu has now become the stable, seasonal flu

Question 49

What may the likely source of the next influenza pandemic?

Answer 49

• H5N1/H7N9 bird flu
• This bird flu affects domestic poultry and can exist as low pathogenic or highly pathogenic forms
• The infection comes from wild birds
• There is concern that highly pathogenic H5N1 bird flu may be tranmitted to humans
• Highly pathogenic H7N5 bird flu has now emerged that transmits directly from birds into humans
• Currently H5N1 bird flu infects humans but does not transmit from human-human
• This is because the upper aiways have a low of a2,6, so when viruses that bind a2,6 replicate they can be spread easily through sneezing
• Lower airways express higher levels of a2,3 which H5N1 can bind to, so humans are infected with H5N1 if it can get low enough into the respiratory tract but it is difficult to transmit because it is restricted to the lower respiratory tract
• If the H5N1 virus mutates so it can bind a2,6 it could be spread from humans to humans