Lecture 9- Viral evolutionary genetics

Question 1

2 scales in which viruses evolve

Answer 1

within and between hosts

Question 2

features of the HIV genome

Answer 2

single genome, with diversity generated by mutation and recombination
has structural genes, such as gag for capsid and env for envelope
has overlapping reading frames

Question 3

influenza A features

Answer 3

8 genomes, segmented, with each encoding genes in various numbers
genetic diversity can be generated through reassortment as well as mutation
not really much recombination

Question 4

what is the baltimore classification of viruses

Answer 4

way of classifying viruses based on their nucleic acid structure

Question 5

type I virus

Answer 5

mostly linear dsDNA virus
no segmentation

Question 6

genome size vs mutation rate correlation

Answer 6

smaller genome - higher mut rate

Question 7

mutation rate of RNA vs DNA

Answer 7

higher in RNA

Question 8

3 main types of infection

Answer 8

acute infection- e.g. flu, covid
latent persistent- bursts of infection but go dormant, e.g. herpes
chronic persistent- evolve within the host, e.g. HIV, hep B/C

Question 9

different selection pressures within- and between-hosts

Answer 9

within-host- want to maximise fitness within an infection, transmission is less important
between-host- transmission is highly important

Question 10

how evolution looks different at the different scales

Answer 10

within-host there are less bottlenecks and evolution seems faster and more linear, compared to a more highly branched between-host tree with a much slower (5x) evolutionary rate

Question 11

HIV gene which is under strong selection

Answer 11

env

Question 12

what is ‘toggling’

Answer 12

a lot of change at specific points which don’t necessarily lead to evolution, can be adaptation and reversion etc

Question 13

example of why it is useful to understand population-level evolution

Answer 13

understanding viral origins, looking at antigenic variation in flu for virus development

Question 14

what was phylogenetics used to discover about HIV

Answer 14

zoonotic spread to humans in about 1920 DRC, original zoonotic origin before in Cameroon

Question 15

example of a forensic application

Answer 15

looking at cases of potential purposeful infection- Florida dentist case, could determine the dentist as the original infecting party to patients
Banglazi hospital case- found clustering with a doctor and patients but there was common ancestors predating the doctor starting work, used to prove innocence