Virology

Question 1

What is a virus? How big is it?

Answer 1

Smallest infectious agent (genetic element, surrounded by protein coat, that cannot replicate independently of a living [host] cell). Size: 20-300nm

Question 2

What are the five properties of viruses?

Answer 2

Contains DNA/RNA, undergoes replication within cells (not binary fission), they are obligate intercellular parasites (can only replicate within cells), they are small, and they have a simple structure

Question 3

How many viruses are there per litre of seawater?

Are they alive or dead?

What do they infect?

Answer 3

10¹¹ viruses per litre

Neither

Animals, plants, fungi, protozoa, bacteria, and other viruses

Question 4

What are the two (or three) elements that make up a virus?

Answer 4

Nucleic acid (ss/ds DNA/RNA), protein coat (capsid - protects genetic material and allows for entry into cell), viral envelope (derived from cell membrane as virus leaves cells)

Question 5

What is the name of the proteins that attach to either the capsid or the viral enveope? What are they for? What happens if they are lost?

Answer 5

Viral attachment proteins (VAPs) - for recognizing and binding to cells. If they are lost, virus is non-infectious.

Question 6

What is a bacteriophage? What do they typically look like? Where are the attachment proteins

Answer 6

A virus that infects bacteria (VAPs at bottom of tail)

Question 7

What is the combination of the genetic material and capsid (protein coat) called? If that is all there is, what else is it called?

And if it has a viral envelope?

Answer 7

Nucleocapsid (non-enveloped/naked virus)

Enveloped virus

Question 8

In an enveloped virus, how much of the envelope comes from the host cell? Which bits come from the virus?

Answer 8

90% (viral attachment proteins from virus)

Question 9

What is a ‘virion’?

Answer 9

Complete virus particle

Question 10

What proteins are encoded by viral genetic material?

Answer 10

Structural proteins (capsid and VAPs) and non-structural proteins (polymerases, proteins vs host defences, neuraminidases [cleave glycosidic bonds & liberate viruses from cell])

Question 11

What is the capsid?

What is a capsomere?

Answer 11

Protein shell that surrounds viral genome (composed of a number of protein molecules–capsomeres–that are arranged in precise and repetitive pattern around genetic material)

Question 12

What forms can the capsid take? [3]

Answer 12

Helical, icosahedral, complex

Question 13

What is the viral envelope? Where does it come from?

Answer 13

Bilayer phospholipid membrane derived 90% from host cell

Question 14

Give examples of enveloped and naked viruses

Which is more stable and less susceptible to environmental conditions? Why?

Answer 14

Enveloped (Hep B, Hep C, HIV, Coronavirus), naked (Hep A, poliovirus, rotavirus)

Naked are more stable (because VAPs are attached to capsid - with enveloped viruses, VAPs are attached to envelope, and can be more easily removed by, for example, a detergent)

Question 15

Why is icosahedron a common shape for viruses?

How many faces? And edges (interface between 2 faces)? And vertices (a point where 5 faces meet)?

How many folds of symmetry are there?

Answer 15

Permits greatest number of capsomeres to be stably packed

20 faces, 30 edges, 12 vertices

Five fold

Question 16

How many proteins are contained within the capsomere that sits on each vertice of the icosahedron? What is it known as?

How many proteins are contained within capsomere that sits in between these points? What is it known as?

Which of these has a constant number in all viruses?

Answer 16

Five (penton) [12 pentons, one on each vertice]

Six (hexon) [varied numbers]

Question 17

Rod-shaped viruses (eg: tobacco mosaic virus) have what kind of symmetry? What is its length determined by? And its width?

Answer 17

Helical symmetry (Length: determined by length of nucleic acid, Width: determined by size and packaging of protein subunits)

Question 18

Viruses: what are the criteria for classifying viruses? [3]

Answer 18

Nucleic acid (DNA/RNA, ss/ds, linear/circular/single molecule/segmented, negative/positive polarity [if ss])

Capsid symmetry (icosahedral, helical, complex)

Presence/absence of lipid envelope

Question 19

Classifying viruses. When it comes to nucleic acid, what do you need to take into account?

Answer 19

DNA/RNA, ss/ds, linear/circular/single molecule/segmented, negative/positive polarity [if ss]

Question 20

What is coronovirus most famous for causing?

When do they become dangerous?

Answer 20

The common cold (respiratory infections that are typically mild - restricted to upper respiratory tract)

When they spread to the lower respiratory tract (eg: SARS)

Question 21

What is the definition of coronaviruses? [genetic material, polarity, symmetry, envelope status]

Symptoms?

Transmission?

Answer 21

Single stranded RNA, positive polarity, helical symmetry, enveloped

Runny nose, headache, cough, sore throat, fever, general unwell [can cause lower respiratory problems such as pneumonia or bronchitis]

Close person/person contact, via respiratory droplets via cough/sneeze, touching contaminated surface/object

Question 22

What was the first dangerous human coronovirus?

What about MERS?

Novel 2019 coronovirus?

Answer 22

SARS (Severe Acute Respiratory SYndrome) in 2003 - 8000 infected, 10% died, and hasn’t been seen since 2004.

Middle East Respiratory Syndrome (2012): 2494 confirmed cases to nov 2019, and 30% died, originated in camels

Originated in bats (linked to Wuhan live animal market) before becoming person-to-person - far more confirmed cases (but only 2% deaths so far)

Question 23

What are the phases of viral replication? [5]

Answer 23

Recognition and attachment (adsorption) of virus to host cell (via viral attachment proteins)

Entry/penetration/injection of virion (and uncoating)

Synthesis of viral nucleic acid and protein components by host cell machinery

Assembly of capsids and packaging of viral genomes into new virions

Release/lysis/budding of mature virions from host cell

Question 24

What is the name of the phase in between viral uncoating inside cells and the assembly/packaging of new virions?

Answer 24

Eclipse phase

Question 25

What do viral attachment proteins attach to? Give examples: influenza, HIV, polioviruses

Why do animals not get certain human viruses and vice versa?

Answer 25

Features/receptors of the appropriate host cell (Influenza: sialic residues on epithelial surfaces of respiratory tract, HIV: CD4 and CCR5 receptors on specific immune cells, Polio: CD155 “poliovirus receptor” on immune cells)

Because they do not have the specific cell features that the viral attachment proteins bind to

Question 26

What does the growth curve of a virus usually look like?

What is the latent period? What is the burst size?

Answer 26

Latent: eclipse phase + maturation, Burst Size: number of virions released

Question 27

What are the first steps of viral replication?

Answer 27

Synthesis of mRNA (has to be first +ssRNA don’t need to do anything, but other types may need to be processed), viral proteins, and nucleic acids

Question 28

David Baltimore: what are the six categories of viruses (based on nucleic acids), and how do they create the viral mRNA? Which genotype did it miss?

Answer 28

Gapped DNA of Hepadnaviridae

Question 29

David Baltimore’s 6 (7) categories:

What does + sense RNA have to do?

What about - sense RNA?

Answer 29

+RNA: already mRNA (nothing needed)

-RNA (opposite strand): RNA replicase (viral enzyme) provides mRNA (and can then be translated)

Question 30

Which is the most common variety of virus?

Answer 30

dsDNA

Question 31

dsDNA viruses: what needs to happen for replication?

What can be infected with dsDNA viruses?

Give an example of a dsDNA virus

Answer 31

Not much: host cell machinery transcribes and translates viral proteins, and DNA polymerase copies the genome of the virus

Prokaryotes, archaea, eukaryotes (protozoa, animals, not plants)

Herpes simplex

Question 32

ssDNA viruses: what needs to happen for viral replication?

What can be infected by ssDNA viruses?

Give examples of viruses

Answer 32

Cell doesn’t recognize ssDNA to replicate it, so first it will convert it into dsDNA via DNA polymerase. Then it can be replicated, and mRNA can be created by host cell RNA polymerases (and proteins made at ribosomes)

Prokaryotes, archaea, and all eukaryotes

Parvovirus B19 (“slapped cheek syndrome” - infants)

Question 33

ssRNA+ viruses: what needs to happen during replication?

What can they infect?

Give virus examples

Answer 33

RNA+ can just be used as mRNA (by host ribosomes). Host doesn’t have RNA replicase, but this is made from viral mRNA, and can then be copied.

Prokaryotes, not archaea, and eukaryotes (protozoa, animals, plants)

Norovirus, zika virus

Question 34

ssRNA- viruses: what needs to happen during replication?

What can be infected?

Give examples of viruses

Answer 34

RNA replicase contained with capsid - this converts it to ssRNA+, which can then be read and translated by host cell machinery (and is also used to replicate genome).

Eukaryotes (plants, protozoa, humans), not archaea, not bacteria

Influenza

Question 35

dsRNA viruses: what needs to happen during replication?

What can be infected?

Give examples of viruses

Answer 35

RNA replicase contained within capsid (which can copy the genome, and create mRNA to be used by host cell machinery to create proteins)

prokaryotes, not archaea, and eukaryotes (plants, protozoa, animals)

Rotavirus

Question 36

ssRNA+ retroviruses: what needs to happen for them to replicate?

What can be infected?

Give example of virus

Answer 36

Enzyme reverse transcriptase converts RNA into dsDNA and integrates it into host genome(viral enzyme: integrase). After this point, cell machinery does the rest.

Eukaryotes (animals, plants, protozoa), not archaea, not prokaryotes

HIV

Question 37

Gapped dsDNA viruses: what is needed for replication?

What can be infected?

Give virus example

Answer 37

Host DNA polymerases fills in gaps. RNA polymerases create mRNA, and then viral reverse transcriptase converts this into gapped DNA to also be included in new virions

Eukaryotes (humans, not plants or protozoa), not bacteria, not archaea

Hepatitis B

Question 38

Why is mRNA placed at the centre of the Baltimore system?

Answer 38

Because mRNA must be made (first) from all viral genomes

Question 39

Bacteriophages: draw out the progression of the typical virus. Also, what are the name of the two different cycles they can be on?

Answer 39

Question 40

What do you call a bacteriophage in the lysogenic cycle that has inserted into the host genome?

What might eventually happen to it?

Answer 40

Prophage

It may leave the host chromosome and enter the lytic cycle

Question 41

What is lysogeny?

Answer 41

Ability of some viruses to enter into host genome (called ‘temperate viruses’ - they can then infect other cells either through the lytic cycle, where they burst out a la aliens, or the lysogenic cycle, where they are just replicated over and over again as part of the host)

Question 42

Quantitation of viruses:

What is a titre?

What is a plaque assay?

Answer 42

T: number of infectious units per volume of fluid

PA: analagous to bacterial colony counts - a monolayer of host cells is infected with the virus at varying dilutions and covered with a semi-solid medium (to prevent virus from spreading too much. Plaque is formed when virus infects a cell within fixed cell monolayer: virus infected lyses and spreads infection to adjacent cells where the infection-to-lysis cycle repeats. The infected cell area will create a plaque (an area of infection surrounded by uninfected cells) which can be seen.