Notes 20100708 CS 798 Danill's talk -- HIV Evolution
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What's unique about HIV evolution?
- extremely fast evolution
- lateral gene transfer
- graphical representation representing the flow of genetic material to current sequences
- represents flow of information
- all nodes have at most two parents and have at most two children
- genes may be combined
- the phylogeny is not a tree: it's a directed acyclic graph
Common problem
- reconstruction of phylogeny probably impossible
- too many people for instance contain too many unique strains
Solve a subproblem instead
- describe which HIV is a substrain and which is a CRF
HIV history
- HIV uses RNA as its genomic material; each coat contains two copies of the genome -- this is similar to the homologous chromosomes we see in eukaryotes if not for the use of RNA instead of DNA
- this allows for added speed in evolution: more recombinations
- Not only that: if two strains of the HIV infect a single cell, then the offspring of those two strains will have one of six combinations of these two genomes
- CRF = circulating recombinant forms
