Evolution

Question 1

What is the origin of viruses? Name and explain the different theories

Answer 1

1. regressive evolution: viruses are derived from intracellular parasites, loss of almost aöö genes not required for basic replication
2. cellular origin: viruses are developed from parts of the cell and developed the capacity for autonomous replication
3. coevulution with host: viruses developed from self replicating molecules in parallel to the evolution of their hosts

Question 2

define living organisms. Why are viruses thus not included?

Answer 2

all living organism contain probably 34 ribosomal protein genes which are still shared by archaeal (archis), bacterial and eucaryotic organisms –> viruses do not encode for ribosomal proteins

Question 3

Are prokaryotic and eukaryotic more infected by RNA or DNA viruses?

Answer 3

prokaryotic: almost exclusively DNA
eukaryotic: more RNA than DNA viruses

Question 4

Explain the evolution model for euk. RNA viruses?

Answer 4

• commen gene / enzyme for all RNA viruses: RdRp
• +RNA developed fropm cellular RT-coding introns
• dsRNA viruses developed from + RNA viruses
• -RNNA viruses developed from dsRNA viruses

Question 5

define evolution of viruses

Answer 5

constant change of a virus population under selection pressure

Question 6

define mutation

Answer 6

inheritable, stable change of the genetic information

Question 7

name types of mutation

Answer 7

1. point mutation
2. recombination: deletion, duplication, insertion, reassortment

Question 8

Name mechanism of virus evolution

Answer 8

1. mutation
2. recombination
3. reassortment
4. integration of cellular genes

Question 9

why are phenotypic mixing and complementation not a mechanism of virus evolution?

Answer 9

they are not a stable change –> no mutation

Question 10

define homologous recombination

Answer 10

recombination partners show significant sequence homologies
e.g: two poliovirus genomes

Question 11

define non-homologous recombination

Answer 11

recombination partners show no significant sequence homologies
e.g.: viral genome and cellular mRNA

Question 12

What role do polymerases play in evolution? Give examples

Answer 12

polymerases have error rates
RNA Polymerases have also no proof reading function

bacterial DNA polymerases: Taq has no proofreading, Pfu has one

Question 13

what is a quasi species?

Answer 13

RNA viruses as populations of genetic variants

Question 14

Name selection pressures viruses experience

Answer 14

• environment (virostatika)
• competition pressure
• counteraction of host (immune response)

Question 15

How do bottle neck experiments work?

Answer 15

1. slightly diverse population needed
2. very strong selection. e.g. by neutralizing monoclonal antibodies or antivirals in cell culture supernatants
3. massive reduction of hgeterogeneity in population

Question 16

what are the consequences of Evolution of viruses? name viral examples

Answer 16

• change in host range: HIV, Influenza, SARS
• increase/ decrease of virulence: Influenza, Polio
• immune escape: Lentiviruses, HCV, Influenza

Question 17

Where do HIV-1 and HIV-2 originate from?

Answer 17

HIV-1: chimpanzees
HIV-2: white collared monkey

Question 18

How many independent transmission of HIV-1 to humans are there?

Answer 18

3

Question 19

what mediates the change of host range in parvo viruses infecting animals?

Answer 19

mediated by a few amino acid changes in capsid protein
–> Adaption to transferrin receptor of host species

Question 20

which type of recombination is important for segmented genomes of RNA viruses?

Answer 20

reassortment

Question 21

How does reassortment work in influenza?

Answer 21

1. infection of one cell with two viruses
2. genome segments of the two different viruses randomly packed into one new virion

Question 22

What is the molecular basis of genetic/antigenic drift vs shift? What is the consequence?

Answer 22

drift: point mutations –> slow, minor changes of properties and antigenicity

shift: reassortment –> very rapid, massive change of properties and antigenicity

Question 23

Can genetic reassortment happen between avian and human influenza A in swine?

Answer 23

yes

Question 24

characterize avian influenza infection

Answer 24

• highly virulent
• most influenza viruses are not virulant for poultry and replicate only locally in the gut

Question 25

What can cause massive enhancement of virulence in influenza A? Why?

Answer 25

mutation at HA cleavage site because HA cleavage is a prerequisite for infectivity --> fusion peptide exposed by cleavage--> usually extracellular cleavage (local restriction since protease only occurs locally) but a locally restricted mutation (poly basic cleavage site in HA) can lead to intracellular cleavage by furin and thus systemic spread --> released viruses are infectious without further activation steps

Question 26

What decides between local or systemic virus spread / low or high virulence in influenza A infection in humans?

Answer 26

HA- cleavage

Question 27

What was the rabbit pox experiment in australia and why was it not effective? Why were prior lab experiments missleading?

Answer 27

release of myxomatosis virus to control the population of rabbits --> first efficient killing of rabbits but later adaption between host and viurs --> mortality rate much lower prior experiments misleading because higher survival rate when ambient temperature is higher

Question 28

How does attenuation of viruses in cell culture work? e.g poliovirus live vaccine strains

Answer 28

- passaging of viruses on cultured cells (especially cells derived from non host species) may lead to attenuated virus variants with decreased virulence - inefficient replication or receptor binding

Question 29

What is the problem with live vaccine polio straions? What is the consequence?

Answer 29

reversion of poliovirus 3 to wildtype --> only killed SALK vaccine is used now

Question 29

What are risk factors for reappearance of polio?

Answer 29

- wt virus in patient samples at research labs - vaccine production - chronically infected persons - live vaccines

Question 30

Which strategies can be used to prevent reversion to virulence in live attenuated polio vaccine?

Answer 30

- Cre element in 5' UTR - stable mutation in stem V - mutations lowering the error rate for 3Dpol and lowering the propensity for template switching

Question 31

Which biotypes of BVDV are there?

Answer 31

non cytopathic and cytopathic

Question 32

explain two different forms of infection in BVDV

Answer 32

1. infection of non pregnant animals --> acute, mostly clinically inapparent 2. diaplacentar infection: a. misscariage if infected too early b. persisten infection if infected in stage of gastation

Question 33

what is required for replication and packaging of BVDV genome?

Answer 33

NS2-3 cleavage for replication, no cleavage for packaging

Question 34

What makes BVDV cytopathic?

Answer 34

RNA recombination: cellular insertions in the viral RNA genome: - ubiquitin - NEDD8 - GATE-16 --> substrates for cellular proteases --> altered, deregulated cleavage --> upregulation of replication --> cytopathogenicity

Question 35

name two models of RNA recombination. Which dependent on viral replication?

Answer 35

1. template switching of RdRp during viral RNA replication 2. breakage (RNase) and ligation (ligase) of viral RNA genome independently from viral replication

Question 36

What does RNA recombination look like in BVDV?

Answer 36

- insertions - duplications - deletions mostly non homologous

Question 37

What does RNA recombination look like in feline coronavirus? What is the consequence?

Answer 37

non homologous via deletions --> mutant kills cat, prior infection without massive symptoms

Question 38

Define immune escape. Which viruses use this strategy?

Answer 38

= escape from the immune response of the host --> Lentiviruses (HIV), HCV

Question 39

Name mechanisms of virus evolution

Answer 39

1. genetic variability: change of virulence, adaptation 2. correction of lethal mutations --> genome conservation, repair of viral genomes, genetic stability 3. generation of novel viruses

Question 40

Name examples for generation of novel viruses

Answer 40

1. alphaviruses 2. dengue virus

Question 41

What are essential steps in RNA replication for RNA recombination?

Answer 41

1. discontinous transcription 2. cap snatching