Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes.

ABSTRACT: The transmission fitness and pathogenesis of HIV-1 is disproportionately influenced by evolution in the five variable regions (V1-V5) of the surface envelope glycoprotein (gp120). Insertions and deletions (indels) are a significant source of evolutionary change in these regions. However, the rate and composition of indels has not yet been quantified through a large-scale comparative analysis of HIV-1 sequences. Here, we develop and report results from a phylogenetic method to estimate indel rates for the gp120 variable regions across five major subtypes and two circulating recombinant forms (CRFs) of HIV-1 group M. We processed over 26,000 published HIV-1 gp120 sequences, from which we extracted 6,605 sequences for phylogenetic analysis. We reconstructed time-scaled phylogenies by maximum

SUBMITTER: Palmer J 

PROVIDER: S-EPMC6642732 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature