Rates and patterns of indels in HIV-1 gp120 within and among hosts

John Lawrence Palmer, The University of Western Ontario

Abstract

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 by applying a Poisson-based model to indel counts and time data.

Variable loop indel rates appeared higher within hosts than among hosts in subtype C. Our findings improve understanding of indel evolution in HIV-1 gp120 and enable the evaluation of models describing indels, which I present as work in progress.