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Rates And Patterns Of Indels In Hiv-1 Gp120 Within And Among Hosts, John Lawrence Palmer
Rates And Patterns Of Indels In Hiv-1 Gp120 Within And Among Hosts, John Lawrence Palmer
Electronic Thesis and Dissertation Repository
Insertions and deletions (indels) in the HIV-1 gp120 variable loops modulate sensitivity to neutralizing antibodies and are therefore implicated in HIV-1 immune escape. However, the rates and characteristics of variable loop indels have not been investigated within hosts. Here, I report a within-host phylogenetic analysis of gp120 variable loop indels, with mentions to my preceding study on these indels among hosts.
We processed longitudinally-sampled gp120 sequences collected from a public database (n = 11,265) and the Novitsky Lab (n=2,541). I generated time-scaled within-host phylogenies using BEAST, extracted indels by reconstructing ancestral sequences in Historian, and estimated variable loop indel rates …