Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions

Understanding of pandemics depends on characterization of pathogen collections from well-defined and demographically diverse cohorts. Since its emergence in Congo almost a century ago, HIV-1 has geographically spread and genetically diversified into distinct viral subtypes. Phylogenetic analysis can be used to reconstruct the ancestry of the virus to inform on the origin and distribution of subtypes.

We sequenced two 3.6 kb amplicons of HIV-1 genomes from 3,197 participants in a clinical trial with consistent and uniform sampling at sites across 35 countries and analyzed our data with another 2,632 genomes that comprehensively reflects the HIV-1 genetic diversity. We used maximum likelihood phylogenetic analysis coupled with geographical information to infer the state of ancestors.

The majority of our sequenced genomes (n=2,501) were either pure subtypes (A-D, F, G) or CRF01_AE. The diversity and distribution of subtypes across geographical regions differed; United States showed t...