Lecture 11- Viral Genetics

Question 1

Mutation Rates/Fidelity of replication for cellular DNA polymerases

Answer 1

SV40, papilloma, parvoviruses, lambda, phix174, m13
before proofreading: 10^-4 to -5
with proof reading: 10^-6 to -8
with post replicative mismatch repair: 10^-9 to -10
very high fidelity

Question 2

Mutation rates Viral dna polymerases

Answer 2

aden viruses, herpes, bacteriophage T4

with proof reading: 10^-5 to 10^-8

Question 3

RNA viral replicases

Answer 3

no proof reading, no mismatch repair (get influenza virus antigenic drift)
4x10^-4 to 10^-4
very high error rate

Question 4

Retroviruses

Answer 4

reverse transcriptase (DNA polymerase) and cellular RNA pol (hiv variation)
reverse transcribes RNA to make dna, cell rna pol makes more viral rna.  retroviral dana does not have any proofreading capability. very high mutation rate 
1x10^-4 approx

Question 5

Mutation rates- quasispecies

Answer 5

consider mutation rates in relation to genome size
E coli yields about 1 error every 1000 genome replications
RNA viruses have about 10000 nucleotides
error rate RNA replicases is 10^-4, so yields about 1 error with every genome replication. close to tolerable threshold; higher error rates would introduce lethal mutation with every replication event.
upper limit: if these viruses were larger, could no the sustained
whereas bacterial genomes and euk genomes are relatively static, rna viruses are a mixture of diverse genetic variants!

Question 6

mutation rates: Viral quasispecies

Answer 6

viral quasi species: RNA populations are composed of a diverse mixture of genetic variants that arise from high mutation rates
diversity and integrity of viral populations as function of replicase fidelity
excessively high error rate results in many possible viral sequences

Question 7

Recombination- DNA viruses vs RNA viruses

Answer 7

DNA viruses: homologous recombination
-cellular based enzymes
-virally-encoded enzymes
RNA viruses: 1) segmented genomes (reovirus 10 ds RNA seg, influenza A 8 ssRNA seg) cells wouldn’t have machinery to carry out recombination
two parental flu viruses infect the same cell. when sorting segments into new virions, cannot tell difference between two genomes. takes 8 segments picked at random from a larger pool and puts into a virus particle. get recombinant flu virus, antigenic SHIFT (dramatic, vs drift which is gradual. ex of shift is swine flu)
2) Intact genomes- copy choice recombination
Poliovirus replication and copy choice recombination
ss rna genome, replicated through an antigenome, used as template to make more genomes. three nascent chains (both on plus and minus)

Question 8

Poliovirus replication and copy choice recombination (cont)

Answer 8

actual recombination: genome with big allele and little allele together. Still dual infection. While replicating one minus strand, replicase dissociates from here and hold onto 3’ end and realigns with other genome at same seq of nuc that it did on first strand. no add or loss of nuc going forward. continues replication; get a mix of alleles