35. Virology Flashcards

Question

Describe the replication cycle for a virus (such as HIV).

Answer 1

1. Attachment to host cell 2. Binding to cell-surface receptors 3. Release of capsid into the cell 4. Uncoating of the capsid, releasing the genome 5. Replication of the viral genome 6. Transcription of genome 7. Translation of genome 8. Proteins and other components are assembled into a new virus particle 9. New virus is released from the host cell

Answer 2

No, they can also bind to carbohydrates, etc.

Answer 3

* Virus attachment proteins -\> GP120 * Cellular receptors -\> CD4 (and co-receptors CXCR4, CCR5)

Answer 4

Chemokine receptors CXCR4 and CCR5.

Answer 5

The cellular receptors on host cells determine which cells the virus can bind to using its attachment proteins.

Answer 6

Endocytosis, which is usually dependent on receptor binding.

Answer 7

* Acute -\> This is when you get ill for a short period, then you recovery from the virus * Persistent -\> This is when the virus is continually present in the body

Answer 8

Acute: * Must have at least some ability to avoid the innate and adaptive immune responses Persistent: * Must have immune evasion abilities, PLUS... * Ability to avoid apoptosis * Finding immune privileged sites * Latency by genome persistence

Answer 9

* In 1981, the inactivated antigen on hepatitis B cells was purified, allowing it to be used as a vacine * In 1986, recombinant technology allowed the same antigen to be produced in yeast, for use in a vaccine

Answer 10

* The HPV virus consists of a naked capsid * The vaccine is made by expressing just the capsid, without all of the virulent material inside, so that an immune response can be mounted without endangering the patient * This protects mucosa from the virus by covering them in IgG

Answer 11

Acyclovir: * Acyclovir has a similar structure to guanosine * The herpes virus' thymidine kinase enzyme adds a phosphate to the acyclovir * The host cell adds more phosphates to give the triphosphate version of the acyclovir * During DNA synthesis mediated by the infection, the acyclovir triphosphate is incorporated into the chain * This terminates synthesis because there is no 3' carbon on the acyclovir, so no more nucleotides can be added to the chain * This prevents the virus from completing the cycle This is selectively toxic to the virus because the human cell can differentiate between the guanosine and the acyclovir

Answer 12

They can be used as vectors in vaccines.

Answer 13

* Influenza viruses in humans cause influenza (the flu), an acute self-limiting febrile respiratory infection * This can involve mild to severe illness, and at times can lead to death

Answer 14

Orthomyxoviridae

Answer 15

* Influenza A viruses (humans, birds, pigs, horses, bats, etc.) * Influenza B virus (humans) * Influenza C virus (humans) * Influenza D virus (cattle, goats, pigs) A and B are responsible for most cases in humans.

Answer 16

* Epidemic = A disease that affects a large number of people within a community, population, or region. * Pandemic = An epidemic that's spread over multiple countries or continents.

Answer 17

Annual seasonal epidemics (caused by influenza A and B viruses): * Limited outbreaks every winter * Infection unpleasant but generally non-fatal * Up to ~ 1 billion infections, with up to 500,000 deaths Pandemics (caused by influenza A viruses): * Unpredictable outbreaks that spread rapidly and globally * Caused by novel influenza viruses emerging from the animal reservoir * Because of lack of pre-existing immunity in humans more infections and more deaths than usual * Typically more severe symptoms than in seasonal epidemics

Answer 18

* First infects the upper airway * Then spreads to the ciliated cells in the bronchus and bronchioli But it remains restricted to the lungs.

Answer 19

* Short incubation period * Fever appears around day 2 * High titres of the virus are seen then, meaning the individual is most infectious then * Innate immune responses typically supress the virus within a week * Adaptive immune response develops later, preventing subsequent infections

Answer 20

Severe complications include pneumonia. This can be primary viral pneumonia or secondary bacterial pneumonia.

Answer 21

* Group V * This means it has negative RNA, which can be transcribed directly into mRNA by RNA polymerase (which is then used to make the protein)

Answer 22

In culture: * Spherical virions * Around 120nm in diameter Clinical isolates: * Filamentous virions * Around 80nm wide, Over 250nm long

Answer 23

* Lipid bilayer derived from host cell, containing: * Haemagglutinin + Neuraminidase -\> 2 glycoproteins that are the main antigens * M2 ion channel (or BM2 protein in influenza B) * M1 matrix protein layer -\> Just below the lipid bilayer, Involved in structure of the virus * Non-structural proteins 1 + 2 (NS1 and NS2) * 8 viral ribonucleoprotein complexes -\> Contain the negative single-strand RNA of the virus

Answer 24

* Influenza A is responsible for pandemics, since it has many different subtypes of HA and NA. * Influenza B only has one type of HA and NA, plus there is an BM2 membrane channel protein instead of the M2 ion channel.

Answer 25

* vRNP contains negative single-strand RNA * Each of the 8 vRNA segments contains one or two open reading frames * Each ORF is flanked by a non-coding region that is highly conserved * The two non-coding regions come together to make a loop of RNA -\> The RNA polymerase can interact with this region * The whole of the RNA molecule is bound to a long nucleoprotein molecule -\> The whole structure takes on a double-helix structure

Answer 26

It is a heterotrimer of: * Polymerase basic 1 * Polymerae basic 2 * Polymerase acidic

Answer 27

Based on their haemagglutinin and neuraminidase surface glycoproteins.

Answer 28

Influenza A: * There are 18 haemagglutinin (H1-H18) and 11 neuraminidase (N1-N11) subtypes recognised within the influenza type A viruses. Influenza B: * There are two **lineages**, the Victoria and Yamagata.

Answer 29

Yes, because there is a large degree on mutation over time, even within a subtype (such as the H3N2 subtype).

Answer 30

* Antigenic drift * Small changes in the antigenic structure due to random mutations within the antigen gene, caused for example by the error-prone RNA polymerase * Lead to epidemics (i.e. yearly seasonal outbreaks of the flu) * Antigenic shift * Large changes in the antigens due to obtaining a new gene for the antigens (haemagglutinin and neuraminidase) from e.g. swine flu * Lead to pandemics

Answer 31

Reassortment of a virus: * When two influenza viruses invade a cell at once, they each release their 8 vRNA segments into the cell * This means that there are theoretically 256 ways for the segements to be rearranged into new viruses * This is how RNA is transferred from one virus to the other, causing antigenic shift

Answer 32

It occurs by antigenic shift driven by reassortment of vRNA segments.

Answer 33

* H3N2 -\> Hong Kong flu * H1N1 -\> Swine flu

Answer 34

* Yes, certain avian influenza viruses, such as H5N1 can infect humans. * However, these tend to be sporadic outbreaks amongst bird-handlers and there is usually no transmission between humans. * But when there is transmission, it is very dangerous.

Answer 35

* H5N1 avian influenza causes severe multisystem disease in humans * This is suspected to be partly due to the virus causing excessive activation of the innate immune response * This leads to inflammation, which leads to problems such as acute respiratory distress syndrome

Answer 36

* Firstly, the virus infects a human, and although it is dangerous, it is not yet transmissible between humans * Therefore, it can either: * Adapt via mutation to become transmissible * Undergo reassortment (leading to antigenic shift) due to a simultaneous infection with a human virus * This can lead to a pandemic because there are new antigens that the human population has no immunity against Diagram is from: (Russell, 2005)

Answer 37

1. Entry into the cell -\> Virus binds to the cell surface proteins via viral attachment proteins, then enters by endocytosis 2. Entry of vRNPs into the nucleus 3. Transcription and replication of the viral genome 4. Export of the vRNPs from the nucleus 5. Assembly and budding of new virus at the host cell plasma membrane

Answer 38

* It is a negative single-strand RNA virus (Baltimore group 5) * However, it uses the cell nucleus for transcribing and replicating its RNA * This is unusual for an RNA virus, which usually have an entirely cytosolic life cycle

Answer 39

It has direct access to nuclear factors, such as splicing factors, for processing its mRNA.

Answer 40

* Virus attachment protein -\> Haemagglutinin (HA) * Host cell surface receptor -\> Sialic acid (on glycoproteins and glycolipids)

Answer 41

* Human influenza viruses prefer binding to sialic acid attached to galactose via a α-2,6 linkage, while avian influenza viruses prefer binding to sialic acid attached to galactose via a α-2,3 linkage. * The pig is a "mixing vessel" for both types of virus, since it can be infected by both types. * Some transmission to humans can also occur because we have sialic acid α-2,3 linkages in the lower respiratory tract.

Answer 42

* Avian -\> Lower respiratory tract -\> Because we have sialic acid α-2,3 linkages to galactose in the lower respiratory tract. * Human -\> Upper respiratory tract -\> Because we have sialic acid α-2,6 linkages to galactose in the upper respiratory tract. This partly explains why avian influenza viruses do not spread as easily between humans.

Answer 43

* There is gradual acidification of the endosome due to entry of H⁺ * Two things must now happen First, the viral envelope and endosome membrane must fuse: * Acidification causes major structural rearrangement of the haemagglutinin * This exposes the fusion peptide, a part of the haemagglutinin that enables fusion between the virus envelope and the endosomal membrane * This allows a pathway to be created, ready for the release of the vRNP complex Secondly, the vRNP complex must be released: * H⁺ions from the endosome enter the virion via the M2 ion channels (Note: Influenza B has an BM2 membrane channel protein instead) * This acidification of the virion leads to release of the vRNP complex from the virion

Answer 44

* The release of the vRNP complexes from the virion is caused by H⁺ entry into the virion via M2 ion channels. * This can be inhibited by M2 blockers, such as amantadine * However, these are rarely used clinically, since resistance to them has developed in most influenza viruses (Note: Influenza B has an BM2 protein instead)

Answer 45

It is either: * Replicated -\> This involves the production of an intermediate structure, known as the cRNP (complementary RNP), which then acts as a template to produce more vRNP molecules * Transcribed -\> To produce mRNA that can be translated to produce viral proteins

Answer 46

RNA-dependent RNA polymerase (a viral protein)

Answer 47

It has cap-snatching activity: * The enzyme can remove the first 10 to 20 residues of a host cell's RNA * It can then attach this cap to viral RNA to allow it to be translated

Answer 48

It has a high error rate because it lacks a proofreading mechanism -\> This contributes to antigenic drift in seasonal influenza viruses.

Answer 49

The structure has been determined by X-ray crystallography and cryo-EM. This has enabled targeting by various drugs.

Answer 50

* The mRNA is exported from the nucleus * In the cytoplasm, it is translated into proteins * Some of these (such as haemagglutinin and neuraminidase) are go to the plasma membrane * Some of these (such as the polymerase and nucleoprotein) return to the nucleus, where they are assembled into new vRNP complexes * These complexes are then also exported to the plasma membrane where they assemble * The virus is released from the cell by budding

Answer 51

It is dependent on neuraminidase, which cleaves sialic acid and therefore causes release of the virus.

Answer 52

Neuramidinidase inhibitors are used as antiviral drugs, since neuraminidase is required to cleave sialic acid, releasing new viruses. These are [IMPORTANT]: * zanamifir (Relenza) * oseltamivir (Tamiflu)

Answer 53

* zanamifir (Relenza) * oseltamivir (Tamiflu)

Answer 54

* The cells can recognise the virus and enter an anti-viral state, which stops or slows down viral replication. * RNA helicase RIG-I is a sensor for influenza virus RNA, and becomes activated upon binding to influenza virus RNA * This leads to the expression of interferons and antiviral cytokines * However, influenza has NS1 (non-stuctural protein 1), which antagonises the interferons: * By sequestering the viral RNA (hiding it) * By preventing RIG-I activation * By interfering with the polyadenylation machinery of the host cell, so that antiviral proteins cannot be produced

Answer 55

Non-structural protein 1 is a very potent inhibitor of immunity and allows influenza virus to efficiently escape the immune surveillance and to establish infection in the host.

Answer 56

* Inactivated influenza vaccine * Live attenuated influenza vaccine

Answer 57

* Virus grown in embryonated chicken eggs or cell culture * After this, it is chemically inactivated * The main antigen components of the vaccine are the haemagglutinin and neuraminidase * Thus, this induces mostly humoral immunity (anitbodies) * However, this means that it is strain-specific, since there is lots of variation in the antigens between strains * Regular update of vaccine composition is required

Answer 58

* Vaccine grown in embryonated chicken eggs * It is not killed, just attenuated, so it can infect the upper airway in a limited manner, but not cause disease or spread * It induces better immunity that the inactivated vaccine because it is live and can cause infection * Induces humoral and cellular immunity * Immunity induced is strain-specific, so it requires frequent updating

Answer 59

This is done by genetic reassortment: * A chicken embryo is co-infected by a virulent influenza virus that is predicted to be the major strain next winter and a non-virulent donor virus * Of the 256 possible resulting genotypes, ones are selected that have the genes that encode the virulent antigens, but the rest of the genes come from the donor virus * Selecting the right genotype can be difficult

Answer 60

* Vaccine development usually requires genetic reassortment, after which the right genotype must be selected so that there are the virulent antigens, but not the rest of the virulent genome * This genotype selection process is difficult, but it can be simplified by reverse genetics * This involves the cloning of individual RNA segments for just the virulent antigens and non-virulent other genes into plasmids * These can be inserted into the host cell, ensuring that the resulting vaccine has all the right proteins

Answer 61

WHO, around February of that year

Answer 62

There are efforts, which aim to target highly conserved regions, such as the stalk of the haemagglutinin or neuraminidase or ectoderm of the M2 ion channel.

Answer 63

Inflammation of the liver.

Answer 64

* Non-specific symptoms at first * Generally feel off color * Nausea and vomiting * Hepatomegaly * Jaundice * Pale stool/dark urine

Answer 65

After a short period of lag: * First, there is an increase in alanine aminotransferase (ALT) -\> Derived from hepatocytes and therefore a marker of hepatocyte injury. * Then there is an increase in bilirubin and alkaline phosphatase (biliary) * In severe disease, there may also be decreased synthetic activity of the liver (e.g. albumin synthesis)

Answer 66

* Virus itself may be relatively non-cytopathic (i.e. it does not directly cause cell death) * Most changes are due to host respones: * Includes lymphocytes, polymorphs and macrophages * Cell-mediated immune response -\> Cytotoxic T-cells kill cells and there is release of mediators like IFNγ, TNFα that are important in inflammation * There is killing of bystander cells in addition to the infected cells * The damage is relatively non-specific and common to various viruses

Answer 67

Cell-mediated immunity -\> This is leads to bystander cell death and therefore damage to the liver, as well as inflammation.

Answer 68

Cytotoxic T-cells

Answer 69

Therefore, it is important to note that hepatitis is not only caused by hepatitis viruses.

Answer 70

HAV, HBV, HCV, HDV, etc. These correspond to hepatitis A, hepatitis B, etc.

Answer 71

* Hepatitis B (HBV) * Hepatitis C (HCV)

Answer 72

* Transmission -\> Feco-oral route * Virus type -\> Picornavirus * Symptoms -\> Mild and transient * Diagnosis -\> Detecting Hepatitis A IgM * Vaccine -\> Effective vaccine

Answer 73

Quite distinct genetically and have different routes of transmission, but share “hepatotropism” (i.e. they all go to the liver)

Answer 74

* Hepatitis is acute if it resolves within six months, and chronic if it lasts longer than six months. * Acute hepatitis can resolve on its own, progress to chronic hepatitis, or (rarely) result in acute liver failure.

Answer 75

Chronic hepatitis tends to be characterised by an imbalance between the pro-inflammatory drive (e.g. caused by alcohol) and natural tolerance mechanisms. i.e. Increased inflammation + Reduced tolerance = Sustained inflammation

Answer 76

* Acute -\> Hepatitis A, B, C and E mostly, plus some other types like Yellow Fever * Chronic -\> Hepatitic B and C mostly

Answer 77

Group VII: * Have (partly) double-stranded DNA * Use RNA polymerase to produce mRNA. When this mRNA enters cells, reverse transcriptase is used to produce double-stranded DNA. This is then transcribed into mRNA.

Answer 78

* Hepatitis B enters the host cell via endocytosis and uncoats, releasing its genetic material (in the form of rcDNA - relaxed circular DNA) * cccDNA (covalently closed circular DNA) is formed in the nucleus from the rcDNA -\> This is a source of new virions * This can remain in the nucleus for a long time, so it makes it hard to get rid of the virus * The cccDNA is trancribed, producing mRNA that can be translated to give viral proteins * It also produces RNA that can be combined with the viral proteins to produce RNA-containing virions * This RNA is then converted into DNA by reverse transcriptase, finishing the production of the new virion

Answer 79

Reverse transcriptase is required to convert RNA into DNA in newly-synthesised virions, meaning that RT inhibitors can be used as antiviral drugs.

Answer 80

2-6 months

Answer 81

Blood, semen, or other body fluids -\> Sex, sharing needles, or mother to baby at birth. (Mostly via blood for HCV)

Answer 82

* Resolution (95% of cases) * Chronic carriage (5% of cases)

Answer 83

Immunoglobulins are produced after the incubation period: * First IgM increases, but then the levels fall * Then IgG increases and remains high Some HBV DNA may remain in the liver at very low levels.

Answer 84

This occurs when the body does not produce a sufficient immune response against the virus, so it remains in the body chronically.

Answer 85

All carriers have HBs antigens , but there are: * High level carriers -\> Have no antibodies against HBe, so they are HBe positive * Low level carriers -\> Have antibodies against HBe, so they are HBe negative The high level carriers are at high risk of progression and cancer, due to continued T cell recruitment, as well as transmission.

Answer 86

Intravenous immunoglobulins (passive immunisation)

Answer 87

* Most cases are asymptomatic and are not treated * Severe cases may progress to cirrhosis and liver cancer * It is the pre-cirrhosis and pre-cancer cases that are treated using interferon-alpha or lamivudine, tenofovir, entecavir and other reverse transcriptase antagonists

Answer 88

* Hepatocellular carcinoma (this is a type of liver cancer) * It occurs in severe cases of chronic hepatitis infection

Answer 89

* The core elements that make up the virus itself are on the left * The rest of the genome is non-structural proteins that are involved in replication of the virus

Answer 90

HCV has a higher diversity, which is because it has been within the human population for a longer time.

Answer 91

* Resolution (20% of cases) * Persistence (80% of cases) In both cases, anti-HCV antibodies develop, but in resolution, there is no chronic viremia, while in persistence there is.

Answer 92

* It is highly dependent on host responses and viral escape from them. * Resolution is increased in those with: * Better CD4+ T cell responses * Better CD8+ T cell responses * Better innate responses (IL28B)

Answer 93

(Ge, 2009) showed that the IL28B locus polymorphism has a huge impact on spontaneous control of HCV. Thus this demonstrates the importance of the innate immune response in outcomes of HCV infection.

Answer 94

* In patients who present with acute HCV infection, the virus will evolve under selection pressure from the immune response. * The likelihood of clearance of the virus, and therefore resolution of the infection, is partly dependent on how much the virus evolves during the infection. * During infection, there are periods of time where different antibodies are produced against the different emerging strains, and later there might be more broad cross-reactive antibodies.

Answer 95

* Immunogenetics studies (Class I and II) * Depletion studies in chimps * Human correlative studies * Protection studies in chimps (vaccine)

Answer 96

* Viral Escape -\> Changes to the structure of the virus through selection pressures, so that it can no longer be recognised * Exhaustion -\> Over-exposure to high levels of antigen leading to T cell dysfunction

Answer 97

* A vaccine would attempt to increase the number of resolutions of infection instead of them developing into persistent chronic infections * Resolution is highly depedent on T-cells * Therefore, a vaccine would need to drive T-cell action

Answer 98

* Hepatitis B has a vaccine * Hepatitis C does not currently have a vaccine

Answer 99

* Most cases are asymptomatic and are not treated * Severe cases may progress to cirrhosis and liver cancer * It is the pre-cirrhosis and pre-cancer cases that are treated using interferon-alpha in combination with ribavirin (an antiviral drug) and protease inhibitors * Recently, inhibitors of the non-structural proteins in the virus have been used (including NS5B, NS5A, NS3/4A inhibitors) (Therefore, both hep B and C are treated using interferon-alpha, which is a cytokine involved in the innate immune response)

Answer 100

* 1st Wave = Protease inhibitors (-previrs) -\> Act on NS3 * 2nd Wave = Polymerase inhibitors (-buvirs) -\> Act on NS5B * 3rd Wave = NS5A inhibitors (-asvirs) All three must be used together, or there is a high risk of viral escape.

Answer 101

EBV (Epstein-Barr virus) is on the left hand side of the spec, but chickenpox, shingles, oral & genital herpes and cytomegalovirus are all on the right hand side.

Answer 102

Baltimore group 1 -\> Linear double-stranded DNA genome

Answer 103

* 170 kb linear double-stranded DNA genome (Baltimore group 1) * Contained within an icosahedral protein capsid * Capsid coated in viral tegument proteins and a lipid bilayer envelope

Answer 104

They can produce lytic, acute infection, which may progress to be latent infections.

Answer 105

Note: Only HHV-4 (EBV) is on the right of the spec. HHV 1,2,3 and 5 are right-hand side content.

Answer 106

* HHV-1 and HHV-2 are very common and tend to be what we think of when herpes is mentioned. * HHV-1 infects primarily the lip area, establishing latency in the trigeminal ganglion. It has a 60% prevalence in the US. * HHV-2 (genita herpes) infects primarily the ano-genital region through sexual transmission, establishing latency in the sacral ganglion. It has a 20% prevalence in the US. How it establishes latency: * There is lytic replication in the epithelial cells * The virus then enters neuronal terminals * The viruses are transported along the axons * Latency is established in the nucleus of the neuron * A reactivation stimulus may cause replication and anterograde transport

Answer 107

* It is called the Varicella Zoster Virus * It causes chickenpox (varicella) and shingles (zoster)

Answer 108

It can be spontaneous or triggered by immunosuppression (e.g. during surgery).

Answer 109

EBV (Esptein-Barr virus)

Answer 110

* Infection is usually asymptomatic * Late primary infection can lead to infectious mononucleosis (glandular fever) [IMPORTANT] * Most of the population are chronic carriers, but the virus may re-emerge if immune surveillance is lacking (e.g. in HIV and AIDS)

Answer 111

Via saliva (thus glandular fever is also known as the 'kissing disease')

Answer 112

* EBV is spread by saliva * Infects the epithelial cells of the pharynx and also B cells * It causes cell lysis in the epithelial cells and plasma cells (derived from the B cells) * Latent infection of B cells is enabled by circularisation of the virus' genome and decreased viral gene expression, which confers resistance to host adaptive immunity

Answer 113

CD8+ responses

Answer 114

* Beta-1 integrin (on epithelial cells) * CD21, a complement receptor (on B cells) * MHC II is a co-receptor

Answer 115

* EBV infects the pharyngeal epithelial cells, which undergo lysis * The EBV then infects naive and memory B cells * EVC mimicks the signals that trigger the activation and proliferation of naive and memory B cells * This proliferation is balanced by the T-cell immune response that kills cells since they present viral peptides on the surface * The circular genome of the virus means that there is a latent infection of memory B cells

Answer 116

* EBV can emerge from latency due to presence of the antigen that the B cell is specific to, but the virus itself can drive the process too * Either way, the host B cell differentiates to become a plasma cell, while also regenerating the memory B cell population * Differentiation to become a plasma cell triggers the virus to return to its lytic form, so it replicates and the viruses are released * The viruses infect epithelial cells and new B cells, but the CD8+ cells are primed this time and are likely to stop the spread easily

Answer 117

EBV expresses very few genes during latency (this limits the adaptive immune response).

Answer 118

* Latency 0 -\> When the virus is in the memory B cell reservoir * Latency 1/2 -\> When the virus is in the germinal centre (sites within secondary lymphoid organs where mature B cells proliferate, differentiate, and mutate their antibody genes) * Latency 3 -\> When the virus is naive B cells and memory B cells (not in the memory cell reservoir)

Answer 119

Cytomegalovirus

Answer 120

* Primary infection (via body fluids) usually asymptomatic or mild, with the potential of a life-long immune response * Recurrence associated with immunodeficiency (e.g. in AIDS) * Most common congenital viral infection (around 1% of births): * About 10% of these symptomatic * Petechiae (red spots), jaundice, microcephaly, hearing loss, and intellectual disability * 20% mortality

Answer 121

The viral proteins and microRNA inhibit: * MHC I pathway * Block MHC I expression and promote MHC I degradation * Inhibit the immunoproteasome that normally generates peptides for presentation * Block TAP transporter that normally pumps the peptides into the ER for loading onto the MHC * NK cell activation * Block expression of activatory NK ligands * Virally-encoded inhibitory ‘decoy’ NK ligands

Answer 122

(Barton, 2007): * Mice were infected with herpes and then later infected with Listeria * If the Listeria infection came several weeks later, then the herpes group performed better in terms of survival than the control group * This suggested that the herpes could be a symbiont that improves survival (Roberts, 2010): * Elderly patients with anti-CMV (anti-herpes) antibodies were shown to have worse survival during the following years than the group without the antibodies * This suggested that herpes was not a symbiont and it instead reduces survival

Answer 123

* Aciclovir [IMPORTANT] and ganciclovir [EXTRA] * Herpes viruses have thymidine kinase (TK) genes * These convert the aciclovir and ganciclovir into triphosphates that act as chain terminators in DNA replication * They can be used against HHV-1, HHV-3 and HHV-5, but they are not effective in latency because TK is not expressed

Answer 124

* Used to treat herpes infections (HHV-1, 3 and 5) * Acts by being converted into a triphosphate that acts as a chain terminator in DNA replication

Answer 125

* Cellular latency -\> Persistence of viral genomes in cells without overt expression of new viruses. * Clinical latency -\> Temporary absence of symptoms in spite of infection. This may be the result of cellular latency, active immunity, etc.

Answer 126

* Herpes * HIV

Answer 127

* Normally causes only infectious mononucleosis (glandular fever) * Predisposes to Burkitt’s lymphoma (BL) and nasopharyngeal carcinoma (NPC) -\> Other cofactors are required for this.

Answer 128

* Glandular fever * It is caused by EBV (human herpes virus 4), which is spread by saliva * It causes: * Extreme tiredness * Swollen glands in your neck * High temperature

Answer 129

* A cancer of the lymphatic system, particularly B lymphocytes found in the germinal center. * EBV (human herpes virus 4) predisposes to Burkitt's lymphoma

Answer 130

* The most common cancer originating in the nasopharynx * EBV (human herpes virus 4) predisposes to this

Answer 131

* Some benign tumours are induced as part of the normal cycle of infection * Malignant tumours are rare, ‘accidental’ consequences of viral infection Immunodeficiency increases the incidence of tumours.

Answer 132

* Some viruses rely on the host cell for replication, so it is advantageous to speed up the cell cycle * Some viruses cause chronic infection, inflammation and repair that lead to cancers * Some viruses suppress apoptosis and/or other aspects of host immune responses, leading to cancers

Answer 133

* EBV stimulates proliferation and inhibits apoptosis of host cells * If co-factors are present, it may proceed to tumours: * Malaria is a co-factor that leads to Burkitt lymphoma (cancer of the B cells) * Environmental co-factors lead to nasopharyngeal carcinoma

Answer 134

* A reciprocal translocation between chromosomes 8 and 14 is characteristic of Burkitt lymphomas * This translocation is common in this particular lymphoma because the virus opens up the region on chromosome 8 for transcription * The translocation brings the myc gene (responsible for stimulating cell proliferation) next to an IgH gene for an immunoglobulin heavy chain * Now the myc gene is under the control of the IgH enhancer and is therefore over-expressed, leading to rapid cell proliferation * This leads to tumours

Answer 135

* Common warts (benign tumours) * 6 strains predispose to uterine cervix cancers

Answer 136

* In basal cells of the skin, the 'early' promoter (P97) is active -\> This leads to transcription of the E1-E7 (e for early) proteins, some of which are involved in driving the cell cycle * In epithelial cells, the 'late' promoter (P670) is active -\> This leads to transcription of the L1-L2 (l for late) structural proteins

Answer 137

As the host cell passes through different levels of differentiation, the virus expresses different genes.

Answer 138

When a mitogenic signal is received, two pathways are triggered: * CDK inhibits the RB1 that inhibits the cell cycle -\> Thus, proliferation is stimulated * p53 stimulates apoptosis and inhibits the CDK pathway via p21 When there is survival signalling, the p53 pathway is downregulated, so apoptosis does not occur and instead proliferation happens.

Answer 139

The HPV proteins interact with the cell cycle control proteins, causing proliferation to be favoured over apoptosis.

Answer 140

If the viral DNA gets integrated with the host genome by non-homologous end-joining, and the E5, E6 and E7 proteins (that are responsible for driving the cell-cycle) are conserved, then a malignant tumour may form. This is not advantageous for the virus.

Answer 141

* The major HPV capsid protein, L1, is produced by gene cloning and expression in yeast or insect cells * L1 assembles spontaneously into virus-like structures, which are highly immunogenic, but non-infectious This is a subunit vaccine.

Answer 142

Retrovirus of the lentivirus family

Answer 143

The 2008 Nobel prize was won for elucidating that HIV was a retrovirus: * Found that the ctopathic effect of the infection was the fusion of lymphocytes with each other into giant cells * Used electron microscopy to isolate the virus particles and found that they contained the distinctive core of retro- and especially lentiviruses * They were then able to demonstrate the action of the reverse transcriptase enzyme during HIV infection, which indicates a retrovirus

Answer 144

The infection itself is not usually life-threatening itself, but: * Opportunistic infections from normally harmless bacteria can occur * Disease from chronic viral infection and other infections can be exacerbated * Tumours can be exacerbated and become life-threatening

Answer 145

Majority of infected people in sub-Saharan Africa. West Africa and Asia also badly affected.

Answer 146

Baltimore group 6 -\> Enveloped, positive single-stranded RNA with reverse transcriptase

Answer 147

It is a single-stranded RNA with 3 reading frames that contain 3 main open reading frames (gag, pol and env), as shown in the diagram. It encodes 16 proteins.

Answer 148

* Outer lipid envelope with glycoproteins (gp120 and gp41) * Matrix just within this, made of repeating units of P17 (encoded by the gag ORF) * Two identical strands of positive single-strand RNA within a capsid (made of repeating P24 units)

Answer 149

1. The virus attaches to: * CD4 and CCR5 on T cells and macrophages * CD4 and CXCR4 on naive T cells 2. Viral core enters the cell via fusion of the viral and plasma membranes. 3. Viral RNA is reverse transcribed to give DNA 4. The viral core arrives at the nuclear pore and the genome enters the nucleus 5. The proviral DNA is integrated into the host DNA 6. In activated cells, the DNA is transcribed to give spliced and unspliced mRNA 7. Viral proteins and genome are assembled 8. New viruses bud out of the cell and are released

Answer 150

* HIV-1 has glycoproteins in the envelope that enable binding and entry: gp120 and gp41 * gp120 binds to CD4 on T cells and macrophages * This triggers a conformational change in gp120 that enables it to bind to CCR5 (on T cells and macrophages) or CXCR4 (on naive T cells) * This in turn leads to even more conformational changes that allow the gp41 to extend out in an alpha helical arrangement -\> They 'harpoons' the plasma membrane, causing pore formation * The capsid can enter the cell due to membrane fusion

Answer 151

No, it is dependent on binding of receptors on the virus to host cell receptors.

Answer 152

* CCR5 (R5) viruses are the transmitted type of HIV-1 * They can enter activated/memory CD4+ T cells and also macrophages/dendritic cells since they present CD4 and CCR5 * However, CXCR4 (X4) viruses evolve in ~50% of infected people, where they gain the ability to enter naive CD4+ T cells also, since they present CD4 and CXCR4 * This typically happens in individuals who progress to AIDS

Answer 153

* SERINC5 inhibits entry into cells, but it is inhibited by Nef * APOBEC3G inhibits reverse transcription, but it is inhibited by Vif * Tetherin inhibits release of new viruses, but it is inhibited by Vpu

Answer 154

It can go by two methods: * Cell-free spread -\> Where new viruses are released and diffuse randomly new new host cells * Cell to cell spread across a virological synapse -\> This involves a transient adhesive junctions between cells that enable direct viral spread between them

Answer 155

1. Acute/Primary infection 2. Chonic infection 3. AIDS

Answer 156

* Viral load -\> Measured using the concentration of RNA in the blood * CD4+ T-cell concentraion

Answer 157

8-10 years

Answer 158

The viral load (the larger, the sooner AIDS develops)

Answer 159

When the CD4+ T cell numbers are \<200/µL blood.

Answer 160

The SIV infection in macaque monkeys has a very similar immuno-pathogenesis to HIV, except that AIDS is reached usually within 2 years, as opposed to 10. This makes it a good model for study.

Answer 161

* In some cases, in spite of viral load remaining high, there is no progression to AIDS and the CD4+ T-cell population recovers * This suggests that viral load does not correlate with progression to AIDS, but instead tbe primary correlate is non-specific systemic lymphocyte activation and cell death * A related correlate is protection of the gut epithelial barrier from long-term damage

Answer 162

* Normally, the gut has commensal flora in the lumen, surrounded by an intact epithelial layer that has GALT (Gut-associated lymphoid tissue) * In HIV infection, the inflammation can breakdown the epithelial layer (physical barrier) and also causes helper T-cell death (immune barrier) * Therefore, local immune homeostasis is not maintained, since bacteria can cross the barriers more easily

Answer 163

Note: The main driving force for T-cell death in HIV infection is activation-induced lymphocyte death, which occurs when bacterial products translocate across the gut epithelium and activate immune cells in a non-specific way. The lymphocytes are programmed to apoptose after this.

Answer 164

1. Direct HIV-1 killing of infected CD4+ T cells 2. Indirect killing of T cells by non-specific activation-induced cell death 3. Killing of HIV-1-infected CD4+ T cells by cytotoxic T cells and NK cells These all lead to lost T-cell helper function, and therefore compromised co-ordination of the immune response.

Answer 165

* HIV-1 can infect macrophages and T-cells (which can become memory T cells) * When these cells are in long-term reservoirs, they are not active and therefore there is no transcription of the viral genome -\> Thus, there is no immune response against the viral proteins and the virus is latent * These viruses in these cells are resistant to drugs and the immune system

Answer 166

The problem with HIV is that a latent infection is very difficult to treat. The approaches include: * 'Berlin' and 'London' patients, who received bone marrow transplants from individuals with no CCR5 receptors on their cells -\> This resulted in there being no detectable virus for many years, making these patients essentially cured. However, this is not widely viable for every HIV patient. * 'Kick and kill' approach, where latency is reversed by activating transcription in infected memory T-cells (so that they can be killed by cytotoxic T-cells) and then re-infection of new cells is prevented using strong anti-retroviral drugs

Answer 167

* Genito-urinary * Blood

Answer 168

* The virus crosses the genital or rectal epithelium through gaps in the epithelium or via dendritic cells * Infected dendritic cells and T-helper cells take the virus to lymph nodes * These lymph nodes distribute infected cells to all parts of the body

Answer 169

* T-helper cells and plasma dendritic cells are recruited to the site of infection at the genital/rectal epithelium * These can be infected but they also release chemokines and cytokines, which lead to recruitment of more cells * Myeloid dendritic cells take up viral antigens arnd present them to helper T cells * If the dendritic cell is infected, the antigens are also presented to cytotoxic T cells * This leads to activation and clonal proliferation of helper and cytotoxic T cells * Helper T cells help cytotoxic cell and B cell activity

Answer 170

Note: CTL stands for cytotoxic T cells.

Answer 171

* Cytotoxic T cells specific to HIV increase throughout infection, then plateau * HIV-specific T cells increase slightly and then fall to nothing -\> This is because

Answer 172

Non-neutralising antibodies form first: * IgM rises at first, but it quickyl replaced by IgG that has higher affinity * This is also followed by IgA (also at mucosa) * They bind internal viral proteins, and are therefore not very effective, but are useful for HIV diagnosis Neutralising antibodies: * It can take many months for neutralising antibodies to form and they are generally specific only to the virus present at the time * They are more effective at stopping spread, since they bind envelope proteins * In about 20% of individuals, broadly-neutralising antibodies appear after years, and can neutralise a wider range of HIV strains

Answer 173

There is a large degree of antigenic variation due to: * Low fidelity of reverse transcriptase [IMPORTANT] -\> Up to 0.2 base changes per round of replication * Recombination of genomes upon co-infection * Deaminase hypermutation (APOBEC3G) leads to G to A hypermutation There are also other mechanisms: * Extensive glycan shield masking the antigens * Steric constraints reduce B cell recognition * Transient exposure of neutralizing epitopes reduces B cell recognition

Answer 174

1. Cytotoxic T cell approaches -\> Require supplying the intracellular HIV antigens for presentation as peptides on MHC class-I-peptide to the T cells 2. Antibody approaches -\> Require supplying envelope glycoproteins to the B cells * Antibodies may be directly neutralizing for the virus * Antibodies may be non-neutralizing but otherwise antiviral (e.g. they can still recruit other immune cells, even if they don't prevent viral entry) * Antibodies may also be transferred passively for prophylactic use

Answer 175

1. Recombinant subunit vaccines * Used to stimulate ANTIBODY responses * Genes for the HIV envelope glycoproteins are transfected into a cell that expresses them -\> This induces a response to them 2. Vectored vaccines * Used to stimulate CYTOTOXIC T CELL responses * Genes for internal HIV proteins are cloned into an adenovirus vector that expresses them -\> This induces a response in cytotoxic T cells 3. Nucleic acid vaccines * Used to stimulate ANTIBODY and CYTOTOXIC T CELL responses * HIV genes are cloned into a plasmid DNA vector or RNA vector, and the genetic material itself produces an immune response (Check this! * Conventional inactivated vaccines do not work for HIV-1 • Attenuated vaccines are too risky as may revert to virulence

Answer 176

Uses vector-driven expression of HIV-1 genes to elicit cytoplasmic antigen: * Viral vectors including poxvirus and adenovirus * Nucleic acid DNA and RNA vector-based vaccines

Answer 177

They appear to show the most promise of the various vaccine types.

Answer 178

* Use Env trimers to encourage B cell recognition of highly conserved neutralizing epitopes * Enhance Env stability for optimal B cell engagement and extended in vivo lifetime * Multimerize Env immunogens (eg. nanoparticles) to enhance B cell activation * Optimize immunization regimens and adjuvants for long-lived responses

Answer 179

* Reverse transcriptase * Protease * Integrase * Entry mechanisms

Answer 180

* Heterodimer of p51 and p66 subunits with 2 enzyme functions: reverse transcriptase and RNAse H * RNA template enters between ‘thumb’ and ‘fingers’ of enzyme and is reverse transcribed into DNA * RNAse H destroys RNA template after new DNA strand is synthesised

Answer 181

* Nucleoside RT inhibitors (NRTI) -\> These are essentially chain terminators that are close analogues to thymidine * Non-nucleoside RT inhibitors (NNRTI) -\> Active site inhibitors

Answer 182

* Chain terminator -\> AZT (a close analogue of thymidine) * Active site blocker -\> Nivirapine

Answer 183

* Integrase engages both ends of viral DNA, cleaving host cell DNA and subsequently splicing in proviral DNA * Inhibitors prevent strand transfer of viral DNA into host cell chromatin

Answer 184

Raltegravir

Answer 185

* It is an dimeric aspartyl protease * Cleaves immature precursor Gag/Pol polypeptides into mature functional peptides * Inhibition with small-molecule pseudosubstrate prevents maturation of virions into an infectious form

Answer 186

Saquinavir

Answer 187

* Maraviroc * It binds CCR5 (on the surface on T lymphocytes)

Answer 188

HIV has a very high mutation rate so it is to prevent the development of drug resistance.

Answer 189

Group 4 (single-stranded positive RNA)

Answer 190

SARS-CoV-2 virus

Answer 191

* The genome is made of postive single-strand RNA so it can be translated directly * It has 13 genes that are translated into a polyprotein * There are two proteases encoded, that in turn cleave the polyprotein into the other proteins

Answer 192

Spike protein on the surface

Answer 193

1. Virus binds to ACE2 on the surface of various human cells using spike proteins. This leads to internalisation via an endosome or fusion with the membrane (fusion involves a host membrane protease cleaving the spike protein to expose a fusion peptide). 2. Viral genome is released. 3. Host ribsosomes translate the genome (positive single-strand RNA) into the viral polyprotein 4. Polyprotein is then cleaved by proteases into the individual enzymes and proteins required for replication 5. Replication of the viral genome occurs using the RNA-dependent RNA polymerase to give genomic and sub-genomic (partial) RNA 6. Transcription and replication of this genomic RNA occurs 7. The subgenomic RNA is used to produce viral proteins in the endoplasmic reticulum 8. The viruses are assembled 9. The virus matures (undergoes cleavage so that it is infectious) 10. The virus is released from the vesicle it is carried in 11.

Answer 194

* The virus binds to ACE2 on the surface of various human cells using the S1 domain of spike proteins. * This leads to internalisation via an endosome or fusion with the membrane * In order for fusion to happen, the transmembrane serine protease cleaves the S1 domain out, exposing the fusion peptide on the S2 domain * This brings the virus closer to the membrane, leading to fusion of the two membranes

Answer 195

* When HeLa cells that do not usually present ACE2 are made to present it, the infectious susceptibility of the HeLa cells increased. * This was, however, not the case with mouse ACE2, suggesting it is not a great model for studying Covid-19.

Answer 196

* Neuropilin 1 is a host cell protein that has been shown to increase the rate of entry of Covid-19 into cells. * Its expression in the CNS could explain the spread of Covid to the CNS.

Answer 197

SARS-Cov-2 has a broader tissue tropism than SARS-CoV.

Answer 198

* Bronchi * Lungs * Conjunctiva (in eye) * Gut enterocytes * Other tissues

Answer 199

1. Covi-19 primarily infects the epithelial cells in the alveoli, but also the type 2 penumocytes and any macrophages present 2. Infection attracts macrophages 3. These macrophages secrete cytokines that attract more leukocytes, which in turn release even more cytokines -\> This leads to a cytokine storm that cause inflammation of the lungs 4. Scar tissue can form in the lungs due to the deposition of fibrin 5. Weakened blood vessels allow fluid to seep in and fill the alveoli, decreasing gas exchange

Answer 200

There are a number of phenomena seen in both mild and severe disease: * Decreased levels of lymphocytes (lymphopenia) * This leads to increased T cell activation * But this leads to exhaustion of the T cells, so there is lymphocyte dysfunction * Neutrophils are increased, but other granulocytes and monocytes are decreased * Increased production of cytokines and antibodies

Answer 201

ISG15 = Interferon-stimulated gene 15 * This a protein produced in cells upon stimulation by interferons * ISG15 acts to post-translationally modify host cell proteins in a manner that slows and inhibits the viral cell cycle (ISGylation) * Some mechanisms: * Increasing autophagic clearance of viral proteins * Modifiying host proteins used in viral budding and release

Answer 202

* ISG15 levels rise as would be normally expected during an infection. * However, coronaviruses have proteases that can remove the ISGylation of various host proteins * So the levels of ISGylated proteins are low compared to other infections

Answer 203

It downregulates MHC-I and MHC-II.

Answer 204

It leads to a shift to a pro-inflammatory state by increase pro-inflmmatory cytokines and decreasing anti-inflammatory cytokines.

Answer 205

* Viral protease (PLpro) * This is shown by experiments that introduce this protease into cells without actually infection them

Answer 206

* Decreased ISGylation of host proteins * Downregulation of MHC classes I and II * Triggering of an inflammatory state in macrophages (Lee, 2020)

Answer 207

Adenovirus vaccines: * An adenovirus is genetically engineered to contain the DNA for the Covid-19 spike protein * It inserts this DNA into the human genome, so the cells can produce the spike protein and an immune response can be mounted mRNA vaccines: * mRNA encoding the Covid-19 spike protein is contained within a lipid nanoparticle * This allows the mRNA to get inside cells, so the cells can produce the Covid-19 spike protein and an immune response can be mounted In other words, both vaccines try to get the body to produce the spike protein, just in different ways.

Answer 208

* \>90% of infections are asymptomatic * 5-10% get fever, headache, nausea, fatigue, and muscle pains and spasms. * 1% show paralysis

Answer 209

* Feco-oral route [IMPORTANT] * Inspiration of aerosol droplets

Answer 210

In the GI tract and blood.

Answer 211

A picornavirus (an RNA enterovirus inhabiting human gut)

Answer 212

* Single strand positive RNA * Baltimore group 4 [CHECK]

Answer 213

No, so the capsid proteins require low pH to penetrate the cytoplasm of the host cell (just like with influenza).

Answer 214

CD155 (a tissue-restricted receptor)

Answer 215

* Poliovirus binds to the CD155 glycoprotein on human cells, which binds at “canyons” on the poliovirus capsid. * The virus enters by endocytosis, as with influenza, and crossing the membrane requires an acidic pH. * Release of RNA from the virion is triggered by the binding to CD155 -\> This is mediated by various uncoating intermediates, such as VP4-containing particles.

Answer 216

* First infects the **oropharyngeal and intestinal mucosa**, which itself does not cause many symptoms. * In some cases, it spreads to the **lymphoid tissues**, including Peyer’s patches and tonsils. * Unlike influenza, **viremia** can also occur, in a small number of cases resulting in spread to other tissue types. * Spread to the **CNS** rarely happens, either via the blood-brain barrier (perhaps via infected phagocytes) or retrograde transport in peripheral axons.

Answer 217

Proposed to be determined by an appropriate intracellular signal that is required for successful replication of the virus, which may be mediated via the IFN-I receptor.

Answer 218

* Poliovirus’ RNA is replicated and translated in the cytosol of the host cell. * It is a positive single-stranded RNA (Baltimore group 4), so it can be directly translated (without a need for prior transcription). * Ribosomes bind to the internal ribosomal entry site (IRES) on the 5’ non-coding region of the RNA, and require initiation and cellular factors. * Post-translational processing involved viral proteases. * RNA replication occurs on the surface of vesicles, using RNA-dependent RNA polymerase. * New poliovirus virions are released primarily upon eventual lysis of the host cell, not by budding.

Answer 219

By cell lysis.

Answer 220

It makes use of the ribosomes for translation.

Answer 221

Viral proteases are required.

Answer 222

* Inhibition of cell protein synthesis (by cleavage of eukaryotic translation initiation factor eIF4G by viral protein 2A). * Inhibition of cell transcription by all three classes of RNA polymerases. * Cytoskeletal changes, cell rounding and detachment from substratum. * Cell lysis. Lots of the pathogenesis of polio also results from apoptosis of cells.

Answer 223

* Via the blood-brain barrier (perhaps via infected phagocytes) * Retrograde transport in peripheral axons

Answer 224

The cases in which the CNS is affected appear to be random and not related to factors such as age (Mueller, 2005).

Answer 225

* Some people may experience some minor symptoms, including GI issues, sore throat, fever and other symptoms similar to influenza -\> Many symptoms are due to host cell apoptosis. * In few cases, the CNS is affected: * Usually, the condition is not paralytic, leading to just aseptic meningitis * In rare cases it can extent to paralytic meningitis, where apoptosis of motor neurons leads to (usually temporary) paralysis.

Answer 226

Motor neurons

Answer 227

* Poliovirus can trigger (via viral proteases 2A and 3C) or suppress (via viral protease 3A) host cell apoptosis depending on the conditions. * Similarly, CD155 could be involved in apoptosis signalling, either when poliovirus binds or due to other molecular interaction with the CD155.

Answer 228

Using iron lungs.

Answer 229

* Around 40% of those surviving paralysis may develop additional symptoms 15–40 years later * This “post-polio syndrome” includes new progressive muscle weakness, severe fatigue and pain in the muscles and joints

Answer 230

A virus with high antigenic conservatism.

Answer 231

* High antigenic variation. * Parasite infects red blood cells that do not express MHC molecules -\> So the parasite becomes “invisible” to the immune system Current vaccines therefore target the pre-erythrocyte stage of the parasite. The goal is opsonisation of the invading parasites. However, since some parasites will have invaded the liver within minutes of infection, T cell mediated immunity is also very important.

Answer 232

* All RNA viruses need viral RNA polymerases; negative-strand viruses need to carry theirs in the virion. * Retroviruses need reverse transcriptase and integrase (important drug targets).

Answer 233

Viral factors: * Releasing enzymes to degrade host metabolic precursors * Releasing proteins that inhibit the synthesis of important host factors, proteins, DNA and/or RNA. * Triggering of necrosis * Triggering of apoptosis * Stimulating growth, leading to cancers Host factors: * Excessive release of antibodies, interferons and pro-inflammatory cytokines, activation of the complement system, or hyperactivity of cytotoxic T cells. * Molecular mimicry

Answer 234

* Virus replication sometimes restricted by local production of Type I α/β interferons. * Virus-infected cells cleared by immune system, chiefly CD8+ lymphocytes (see 32.3.2). * Free virus cleared by antibody + complement. * Re-infection prevented by plasma IgG and secretory IgA.