Viruses, Vol. 12, Pages 182: In Search of Covariates of HIV-1 Subtype B Spread in the United States —A Cautionary Tale of Large-Scale Bayesian Phylogeography

Viruses, Vol. 12, Pages 182: In Search of Covariates of HIV-1 Subtype B Spread in the United States—A Cautionary Tale of Large-Scale Bayesian Phylogeography Viruses doi: 10.3390/v12020182 Authors: Samuel L. Hong Simon Dellicour Bram Vrancken Marc A. Suchard Michael T. Pyne David R. Hillyard Philippe Lemey Guy Baele Infections with HIV-1 group M subtype B viruses account for the majority of the HIV epidemic in the Western world. Phylogeographic studies have placed the introduction of subtype B in the United States in New York around 1970, where it grew into a major source of spread. Currently, it is estimated that over one million people are living with HIV in the US and that most are infected with subtype B variants. Here, we aim to identify the drivers of HIV-1 subtype B dispersal in the United States by analyzing a collection of 23,588 pol sequences, collected for drug resistance testing from 45 states during 2004–2011. To this end, we introduce a workflow to reduce this large collection of data to more computationally-manageable sample sizes and apply the BEAST framework to test which covariates associate with the spread of HIV-1 across state borders. Our results show that we are able to consistently identify certain predictors of spread under reasonable run times across datasets of up to 10,000 sequences. However, the general lack of phylogenetic structure and the high uncertainty associated with HIV trees make it difficult to interpr...
Source: Viruses - Category: Virology Authors: Tags: Article Source Type: research