paleovirology 1+2

Question 1

what is an integrated virus called

Answer 1

provirus

Question 2

endogenous viruses in vertebrates

Answer 2

endogenous retroviruses

Question 3

effects ERVs might have

Answer 3

shaped some aspects of immunity

seems to cause disease in some contexts- e.g. in sheep, there was talk of one contributing to ME but hard to separate cause and effect

Question 4

how do ERVs form their ‘fossil record’

Answer 4

different mutation rates to hosts, makes them easy to identify and can track down likely times of integration

Question 5

RELIK

Answer 5

endogenous lentiviral lineage in rabbits- unusual, they don’t normally integrate

Question 6

how has analyses of RELIK given us info about lentivirus infections?

Answer 6

present in rabbits and hares but not pikas- therefore know the age of the viral relic

Question 7

what did RELIK teach us about lentiviruses?

Answer 7

at least 12 million years old, older than current estimates

Question 8

other endogenous lentiviruses

Answer 8

pSIVgml, a transitional form in SIV evolution

Question 9

how old have analyses of the SIV lineage predicted the virus to be?

Answer 9

3.5my old

Question 10

what theories of origin are consistent with the age of SIV?

Answer 10

all of them, so can’t really discriminate- ancestral codivergence, ancestral transfer via a terrestrial route before Madagascan landmass split off, flying vector transfer

Question 11

ways to study paleovirology other than bioinformatics

Answer 11

reconstruction- adding virus bits that are lost, helps study encoded proteins etc and compare structure with extant viruses

Question 12

another example of genome invasion time being identified

Answer 12

SloEFV (foamy virus)- 40ish my old virus in sloths

can be aligned with timing of continent formation and separation of mammals by looking at coevolution between virus and mammal species

Question 13

why are non-retroviruses less likely to integrate into the genome?

Answer 13

genome integration is not an obligate step

Question 14

how can non-retroviral DNA get integrated into the genome?

Answer 14

non-homologous recombination of DNA viruses, mRNA interaction with cellular retroelements

Question 15

example of a primate non-retrovirus integration

Answer 15

bornavirus, integration around 40mya- human version makes mRNA

Question 16

how many types of virus (in terms of nucleic acid type) have been seen as EVEs?

Answer 16

all of them

Question 17

how can we tell if a viral element is functional?

Answer 17

simulating evolution under neutral circumstances and comparing to reality- e.g. in bornavirus, found no stop codons where under neutral evolution we would expect 15ish

Question 18

term for antiviral factors derived from viruses

Answer 18

EVE derived immunity (EDI)

Question 19

when do we think bornaviruses originated?

Answer 19

93mya, in the mesozoic

Question 20

when do we think circoviruses appeared?

Answer 20

68mya, mesozoic

Question 21

correlation between body mass and ERV acquisition

Answer 21

larger body mass tends to lower ERVs- possibly because less defence against insertional mutagenesis?

Question 22

correlation between body mass and age of ERVs

Answer 22

larger mass > older ERVs

Question 23

body size and retroviral activity

Answer 23

larger body size > lower retroviral activity