Virology

Question 1

2 theories of how viruses fit into the tree of life?

Answer 1

1. RNA world theory: life arose with the viruses
2. Reductionist theory: viruses came after cellular life, they are reduced versions of cellular organisms
   * mimiviruses and megaviruses may be the missing link

Question 2

What are Ribozymes?

Answer 2

• RNAs that can catalyze specific reactions (similar to enzymes)
• ribozymes (produced in lab) can catalyze their own synthesis
• natural fans: cleave RNA, viral replication, tRNA biosynthesis

Question 3

Examples of DNA viruses?

Answer 3

• herpes, smallpox, mimivirus

DNA -> RNA -> protein

Question 4

Examples of RNA viruses?

Answer 4

• Rhino, influenza, SARS

RNA-> protein

Question 5

Examples of Retroviruses?

Answer 5

• HIV

RNA -> DNA (through reverse transcriptase) -> RNA -> protein

Question 6

Pros and cons of a DNA virus

Answer 6

pros: lower mutation rate, more stable (can carry more genes), no dsRNA phase
cons: lower mutation rate, slower replication

Question 7

Pros and cons of RNA virus

Answer 7

pros: fast replication rate, high mutation rate
cons: high mutation rate, limited sequence space (less stable), dsRNA phase, degrades faster, humans don’t have dsRNA (easy to identify)

Question 8

What happens frequently in reverse transcriptase?

Answer 8

• 1 mutation per virus, much more common in retrovirus

Question 9

What are some challenges in developing HIV vaccines?

Answer 9

• high mutation rate
• integration into host genome
• infects immune privileged region of host
• targets immune system
• multiple serotypes
• costs and time involved in development
• vaccine safety concerns

Question 10

What is the diversity in HIV strains

Answer 10

• 25-30% in circulating HIV strains

- mutation rate is - 1 base change per genome

Question 11

What effects can a mutation have on a virus?

Answer 11

• not all mutations are advantageous: some hinder the virus, some prevent virus replication, and some are silent ( have no effect)
• Some allow a competitive advantage, and some allow escape from antiviral drugs

Question 12

antiretroviral drug classes

Answer 12

• reverse transcriptase inhibitors (NRTIs)
• Fusion/entry inhibitors
• Integrase inhibitors
• Protease inhibitors

Question 13

Difference b/t nucleosides and nucleotides?

Answer 13

• nucleosides: sugar+ base
  3 phosphorylation events required for activity

-nucleotide: sugar+base+phosphate, 2 phosphorylation events required for activity

Question 14

Nucleoside analogs??

Answer 14

prevent adding of next nucleoside on to the chain looks like nucleoside but doesn’t have site to bind to next nucleoside so it is a chain terminator

Question 15

3TC (Epivir/Iamivudine)

Answer 15

• FDA approved 1995
• reverse transcriptase inhibitor
• nucleoside analog: mimics cytidine -> acts as a chain terminator

Question 16

DLV (Rescriptor/delavirdine)

Answer 16

• FDA approved 1997
• Reverse transcriptase inhibitor (non-nucleoside)
• binds RT catalytic site, blocking polymerase fxn

Question 17

Reverse transcriptase mutations?

Answer 17

• only takes 1 or 2 mutations of virus to make reverse transcriptase drugs ineffective

Question 18

DRV (darunavir/Prezista)

Answer 18

• FDA approved 2006
  protease inhibitor: binds the active site preventing the processing of viral protein precursors
• compete with the natural substrate

Question 19

EVG (Elvitegravir)

Answer 19

• FDA approved 2014

- Allosteric integrase inhibitor (prevents functional multimers from forming (dimers of dimers= tetramer)

Question 20

MVC (Selzentry/maraviroc)

Answer 20

• FDA approved 2007
• entry inhibitor (receptor antagonist)
  drug binds receptor (CCR5), preventing HIV from binding
• mutant bind receptor in a different conformation

Question 21

T20 (Fuzeon/entuvirtide)

Answer 21

• FDA approved 2003
• HIV fusion inhibitor
• mimics viral protein to displace it in the fusion complex (binds p41 and prevents formation of the entry pore)

Question 22

Vacc-4x

Answer 22

therapeutic vaccine
in clinical trials 9phase 2)
peptide vaccine -> dropped viral load but didn’t slow CD4 T cell decline

Question 23

SB-728T gene therapy

Answer 23

in phase 1/2 trials
modifies a CD4 T cell CCR5 receptor, making it non-functional, prevents HIV entry
- harvest patient T cells, make mutation and replicate, and put back into pt
- this mutation occurs naturally and confers HIV resistance
- expensive and time consuming

Question 24

Interleukin

Answer 24

IL-7: trial abandoned b/c IL-7 increased the number of CD4+ T cells but that increased viral load too

IL-2: increased number of CD4+ T cells but didn’t significantly decrease clinical events or death, even when combined with antiretrovirals

Question 25

Chloroquine

Answer 25

- antimalarial - drops pH in vacuoles - disrupts Env protein gp120, inhibits maturation - drops viral load, doesn't affect T cells so doesn't stop T cells from decreasing

Question 26

What can be done to prevent escape mutants?

Answer 26

``` - combo drugs Atripla (3) Complera (4) Stribild (4) Triumeq (3) Combivir (4) ```

Question 27

Difference b/t viral and human evolution

Answer 27

- humans: complicated, multiple polymerases, error prone, and non-error prone sites, at most 1 mistake/ 100 million, proofreading and correcting machinery, and we only have a couple kids in a lifetime - viruses: often 1 mistake per genome, no proofreading, often whole populations knocked out, billions of genomes made per day

Question 28

Potential effects of viruses on human evolution

Answer 28

- immune system diversity - ABO blood system (decreased A allele frequency after smallpox epidemic) - endogenous retroviruses (1% of genome) - cell surface mutations (ex: CCR5)

Question 29

What does it mean that viruses are a part of us?

Answer 29

- they are a part of our regulation of host gene expression - they take part in placental formation - reason why there is immunosuppression during pregnancy - promoters, enhancers and proteins can be coopted by the host for its own purposes (placenta formation) - can be fixed or mobile, and no human endogenous retroviruses (ERVs) are capable of replication

Question 30

What are endogenous retroviruses (ERVs) associated with in humans?

Answer 30

- MS - schizophrenia - cancer - autoimmune diseases - amayotrophic lateral sclerosis (ALS)

Question 31

Mutation in humans that allow them to be resistant to HIV infection?

Answer 31

-mutation prevents an HIV corrector from being made by the cell, and therefore HIV can't infect people with this mutation (CCR5 delta 32 mutation) -> positive selection for this mutation

Question 32

Hypothesis for why mutation has been selected in specific regions (Europe, Asia, North Africa)?

Answer 32

- either plague (bacteria) or smallpox (virus)

Question 33

How can humans drive viral evolution?

Answer 33

- each infection is a population - zoonosis: virus mutating to be able to pass from one species to another - humans as an enviro: immune system and viral recombination - antiviral drugs: promote resistance and mutations

Question 34

difference b/t epidemic and pandemic?

Answer 34

- epidemic: greater than expected incidence "outbreak" ex: SARS, Dengue - pandemic: spread over a large geographical area (b/t continents) ex: HIV, smallpox, H1N1 (seasonal flu not a pandemic)

Question 35

Why do viruses start epidemics and then pandemics?

Answer 35

- increased virulence (severity of disease or ability to spread) - intro into novel setting - changes in host susceptibility to the infectious agent - changes in host exposure to the infectious agent

Question 36

Transmission modes of viruses?

Answer 36

- iatrogenic (blood transfusion) - vertical - vector borne - droplet - fecal-oral - sexually

Question 37

Zoonosis?

Answer 37

- disease that can pass from another species to humans or humans to another species - often diseases are adapted to their host and more deadly when they jump hosts (ex: Ebola) - Many viruses can pass from animal reservoir to humans, but have difficulties transmitting human to human - issues: domestication, deforestation, bush meat

Question 38

BSL-4 viruses

Answer 38

- aerosol viruses - severe/fatal viruses w/ no vaccines or other txs: - bolivian and argentine hemorrhagic fevers - marburg virus - ebola virus - lassa virus - crimean-congo hemorrhagic fever - small pox