Background of virology

Question 1

What is the virome?

Answer 1

All the viruses a specific body part carries around (similar to microbiome for bacteria)

Question 2

What is the definition of a virus?

Answer 2

An infectious, obligate intracellular parasite, comprising genetic material (DNA/RNA), often surrounded by a protein coat, sometimes by a membrane

Question 3

Which two organic stages do viruses have?

Answer 3

1. Virion
2. Infected cell

Question 4

What is a virion?

Answer 4

An infectious viral particle

Question 5

True or false: viruses outnumber cellular life

Answer 5

True; viruses outnumber cellular life by at least 10:1 -> greatest biodiversity on earth

Question 6

What are the 5 general steps of the infectious viral cycle?

Answer 6

1. Attachment & entry
2. Translation
3. Genome replication
4. Assembly
5. Release

Question 7

What is a (virus-)susceptible cell?

Answer 7

A cell that has a functional receptor for a given virus -> only implies viral attachment

This cell may or may not be able to support viral replication

Question 8

What is a (virus-)resistant cell?

Answer 8

A cell without the entry receptor for a specific virus

This cell may or may not be competent to support viral replication

Question 9

What is a (virus-)permissive cell?

Answer 9

A cell that has the capacity to replicate virus

This cell may or may not be susceptible to the virus

Question 10

How can a virus-permissive cell be brought to produce virus, even when it does not have the required entry receptor?

Answer 10

It can be artificially transfected, after which the cellular machinery will produce virus

Question 11

Which two factors does a cell need to have in order for a virus to be able to infect and replicate in the cell?

Answer 11

1. Susceptibe -> right entry receptor
2. Permissive -> right cellular machinery for viral replication

Question 12

How is the infectious cycle often studied?

Answer 12

In cell cultures

Question 13

What is cytopathic effect (CPE)?

Answer 13

Viral effects on a cell -> can be used to identify the presence of virus

Question 14

How can viral infectivity be studied? (2 methods)

Answer 14

1. Plaque assays (for viruses that create plaques)
2. Endpoint dilution assays (for viruses that do not create plaques)

Question 15

True or false: all particles produced by a virus-infected cell are infectious

Answer 15

False; often a majority of the particles is non-infectious and defective

Question 16

How can the amount of infectious particles be measured in relation to the total number of particles?

Answer 16

Particle/PFU ratio -> total amount of particles/plaque forming units

Question 17

What are reasons for viral particles to be unsuccesfull in infecting another cell? (3)

Answer 17

1. Damaged particles
2. Mutations
3. Complexity of infectious cycle

Question 18

What is the eclipse period of the infectious cycle?

Answer 18

The period in which no (new) viral particles are detected -> intracellular production of viral particles

Question 19

What is the latent period?

Answer 19

The delay between intracellular viral particle production and release of particles

Question 20

What is MOI?

Answer 20

Multiplicity of infectious particles added per cell

= number of infected particles added per cell

Question 21

What are techniques that can be used to measure the presence of viral particles? (4)

Answer 21

1. Hemagglutination
2. Electron microscopy
3. Viral enzymes
4. Serology

Question 22

How can hemagluttination be used to measure viral particles?

Answer 22

Erythrocytes stick together when infected -> causes hemagluttination

So: hemagluttination shows presence of (infectious) viral particles

Question 23

How can viral enzyme activity be used to determine the presence and amount of viral particles?

Answer 23

Metabolism assays can determine the amount of enzyme, which can be extrapolated to the amount of viral particles

Question 24

How can serology be used to show the presence of viral particles?

Answer 24

Antibodies are used to label viral antigens -> titre can be determined

Question 25

How can PCR be used to determine the amount of viruses?

Answer 25

By limiting the amount of cycles, one can determine the original amount of virus present in a sample

Question 26

What is (+)-mRNA?

Answer 26

'Ribosome ready' mRNA -> can directly be translated to produce proteins

Question 27

What is (+)-DNA?

Answer 27

DNA of equivalent polarity to (+)-RNA

Question 28

What is Baltimore Classification group 1?

Answer 28

dsDNA -> can be directly transcribed into mRNA by RNA polymerase

Question 29

What is Baltimore Classification group 2?

Answer 29

(+)-ssDNA -> needs to be made into dsDNA before being transcribed

Question 30

What is Baltimore Classification group 3?

Answer 30

dsRNA -> have to copy the (-)-strand to produce a complementary (+)-RNA during replication Need to produce their own RNA-polymerase -> human cells are unable to copy RNA from RNA

Question 31

What is Baltimore Classification group 4?

Answer 31

(+)-ssRNA -> needs an (-)-ssRNA intermediate before mRNA is produced Needs a viral RNA polymerase to produce (+)- and (-)-RNA strands

Question 32

What is Baltimore Classification group 5?

Answer 32

(-)-ssRNA -> can directly be translated into (+)-ssRNA Needs a viral RNA polymerase to produce (+)-RNA

Question 33

What is Baltimore Classification group 6?

Answer 33

(+)RNA, which gets copied into (-)-DNA, after which a complementary strand is synthesized The dsDNA that gets synthesized is integrated into the host genome

Question 34

What is Baltimore Classification group 7?

Answer 34

Gapped dsDNA -> strands need to be completed before transcription can occur

Question 35

What is the virosphere?

Answer 35

All viruses on earth

Question 36

What is the advantage of DNA genomes over RNA genomes?

Answer 36

DNA genomes are stable, can be larger and are less prone to mutation

Question 37

What kind of viruses are most often dsDNA?

Answer 37

Bacteriophages

Question 38

How many of the novel (viral) diseases are zoonotic?

Answer 38

2/3

Question 39

Why are zoonoses from wildlife more common than from farm animals?

Answer 39

We have been co-evolving with our livestock for a long time -> our immune system is (somewhat) adapted to their pathogens This is not the case for wildlife

Question 40

What are 3 drivers for the emergence of novel infectious diseases?

Answer 40

1. 20-fold growth in wildlife trade over the last 50 years 2. Enormous amounts of land use of agriculture/animal husbandry 3. 10-fold growth in global trade over the last 50 years

Question 41

What is orthopathogenesis?

Answer 41

Pathogenesis in an animal reservoir

Question 42

What is neopathogenesis?

Answer 42

Pathogenesis of viruses in a new host

Question 43

Why would you want to study neopathogenesis (in humans) and compare it with the ortopathogenesis of a virus?

Answer 43

Differences between these provide clues about the mechanism for severe disease in humans

Question 44

What are the two possible strategies an organism can use to protect itself from infection?

Answer 44

1. Resistance: detection and elimination of the invading pathogen by the immune system 2. Tolerance: reduction of negative impacts of infection by tolerating the presence of the pathogen