DOI: 10.1101/494344Dec 12, 2018Paper

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

BioRxiv : the Preprint Server for Biology
John Palmer, Art F Y Poon

Abstract

The transmission and pathogenesis of human immunodeficiency virus type 1 (HIV-1) is disproportionately influenced by evolution in the five variable regions of the virus surface envelope glycoprotein (gp120). Insertions and deletions (indels) are a significant source of evolutionary change in these regions. However, the influx of indels relative to nucleotide substitutions has not yet been quantified through a comparative analysis of HIV-1 sequence data. 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. In brief, our method employs maximum likelihood to reconstruct phylogenies scaled in time and fits a Poisson model to the observed distribution of indels between closely related pairs of sequences in the tree (cherries). The rate estimates ranged from 3.0e-5 to 1.5e-3 indels/nt/year and varied significantly among variable regions and subtypes. Indel rates were significantly lower in the region encoding variable loop V3, and also lower for HIV-1 subtype ...Continue Reading

Related Concepts

Base Sequence
Blood Circulation
Biological Evolution
Gene Deletion
Glycoproteins
HIV-1
Nucleotides
Recombinant Proteins
Research
Trees (plant)

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