Midterm #3: Viruses

Question 1

What is a virus?

Answer 1

• An infectious, obligate parasite containing RNA or DNA genetic material in complex with or surrounded by protein and/or lipid membrane
• They have an extracellular stage and an intracellular stage in their replication cycle
• Latin for poison
• They do not by themselves carry out any metabolic processes
• They are generally small (30-1000nm) compared to human cells and bacteria

Question 2

Size of virus

Answer 2

• ​A typical virus is ~100nm (1x10-7 m) in diameter
• A typical person is ~1m in size
• The Earth is ~10,000km (1x107 m) in diameter
• A virus in comparison to you, is similar in size as! you are in comparison to the planet Earth

Question 3

Viruses are all around us

Answer 3

• We are constantly breathing in, ingesting and coming into contact with billions of viruses (and bacteria)
• The vast majority of viruses we are constantly encountering and harbor are NOT pathogenic and may even perform beneficial biological functions in our bodies
  
  • Example of murine norovirus helping to maintain gut homeostasis when commensal bacteria are perturbed
• Our genome is ~30-40% retroviral in origin!
• Viruses are known to infect ALL living organisms
• They are found in every environment where organisms have been isolated: air, water, surfaces, sea, even in extreme environments…
• Large fraction of total biomass is due to viruses
• Total biomass of viruses in the oceans = ~75,000,000 blue whales or
  >10 gigatons. If you lined them up end-to-end, they would span tens of millions of light years; in fact they would reach far past the neighboring Andromeda galaxy.
• They are responsible for tremendous bacterial turn over and resulting recycling of gigatons of organic matter every year.
• Bacterial viruses (bacteriophages) are responsible for significant transfer of genetic material between bacteria

Question 4

How were the first viruses isolated?

Answer 4

• 1886 Mayer showed tobaco mosaic disease could be transmitted from an infected plant to an uninfected plant through liquid extracts
• 1892 Ivanovsky showed the extracts could be filtered removing bacteria and retain infectivity. 1898 Beijerink independently discovered the same and realized the infectious agent was far smaller than bacteria
• Infectivity did not increase in the extract alone (as bacteria would) instead, would require a host to replicate
• 1898 Loeftler and Frosch showed that foot-and-mouth diesease virus also passed through fine filters
• ~25nm FMDV protein capsid with RNA inside

Question 5

Pasteur

Answer 5

• Realized he could passage rabies through rabits and obtain an attenuated form of the infectious agent that provides protection from rabies
• 1885

Question 6

When was the first influenza vaccine available?

Answer 6

1936

Question 7

How could more material virus be made and propogated?

Answer 7

• Tissue culture, once the technology became available in the 1950’s
• Embryonated chicken eggs 1931
  
  • need host cell that is alive and replicating/carrying out metabolic processes

Question 8

Embryonated Chicken Eggs

Answer 8

• Eggs are still the primary source for influenza virus vaccines
• 2013 recombinant HA based vaccine available (Flublok)

Question 9

Extracellular and Intracellular Stages

Answer 9

• ​Extracellular Stage: Viruses are essentially inert until they encounter a host cell
• Intracellular Stage: virus hijacks the host cell and repurposes it to make more copies of the virus

Question 10

Stages of the viral infectious cycle

Answer 10

• Host cell recognition (attachement)
  
  • Specificity of virus and protein receptor. Determines what types of cells will be infected
• “Entry”
  
  • Signal to get into the cell. Some just transfer genome
• Genome delivery (uncoating)
  
  • Releases cargo and deliver genetic material
• Replicate components
  
  • copy genome
• Assembly
  
  • Pieces of genome and coat come together
• Maturation
  
  • Assembled but immature, is not infectious
• Egress
  
  • Tamiflu targets this so that virus can’t get out (neuramidase inhibitor)

Question 11

Eclipse Period

Answer 11

• Nothing at first because delivering gentic material and replicating
• In the burst phase, the cell lyses and lots of free virus pops out
• Not see this with bacteria
• Different replication kinetics than for bacteria since viruses assembly from pools of expressed components, rather than undergoing binary fission

Question 12

Suseptible, Resistant, Permissive

Answer 12

• A cell that is susceptible has the right receptor on its surface that the virus can bind to. Cell may not necessarily be capable of supporting viral replication.
• A cell that lacks the necessary receptor is resistant to infection by that virus
• A cell that can support the replication of virus once it is inside is called permissive. It may not necessarily be susceptible (e.g. one could inject viral genetic material and initiate replication w/o virus having to attach and enter).
• A cell that a virus can attach to (the key fits the lock) and that is capable of supporting replication of viral genetic material and protein production is both susceptible AND permissive.

Question 13

Notable examples where lack of receptor confers resistance

Answer 13

• Why we are not highly suseptible to avian influenza
• The sole individual cured from HIV/AIDS
  
  • Also had leukemia
  • Chemotherapy wiped out resivoirs of HIV by chance
  • Then introduced immune cells from donor that had mutation preventing virus entering cells (wrong receptor)
• “Tropism” of a virus in the body

Question 14

Not suseptible but permissive

Answer 14

• “Pseudotyping”: change the protein so that it fits the receptor
• Can introduce the viral genetic material and get the cell to replicate

Question 15

How are viruses classified?

Answer 15

• Nucleic acid type (RNA/DNA, +/- sense, single/double stranded) and its sequence
  
  • • is like mRNA and can start replication cycle immediately
  • • is the complementary strand
• Structure, symmetry and dimensions of protein capsid
• Contains membrane or not (enveloped vs non-enveloped or naked)

Question 16

Pieces associated with virus structure

Answer 16

• Nucleic acid encapsulated inside
  
  • nucleic acid may be protein-associated
• Attachment or Receptor Binding protein
• Membrane (acquired from host cell)
• Protein capsid (very robust)

Question 17

Key Step in infectious cycle

Answer 17

• need to produce mRNA in order to generate viral proteins for assembly of new particles
• Viruses also need to produce copies of it’s genetic material. Typically encode a polymerase enzyme
• Viruses with a particular nucleic acid organization do not necessarily share similar morphologies or even have the same number of genes

Question 18

Not every particle produced is necessarily infectious

Answer 18

• ​Particle/PFU can be >>1
  
  • Defective particles: lacking genetic material, lacking other components, improper assembly
• Virion: a complete, infectious particle

Question 19

How was it determined that nucleic acid carries the genetic information?

Answer 19

• Hershey Chase experiment on bacteriophage
• Radiolabel protein OR DNA, detect whether the progeny virus particles have radioactivity or not.
• The protein “body” of the phage remains outside the cell and does not pellet with the cell pellet
• In fact, this was the first demonstration that DNA carries genetic material in general, not just for viruses