The Relatedness of HIV Epidemics in the United States–Mexico Border Region

Abstract Phylogeography can improve the understanding of local and worldwide HIV epidemics, including the migration of subepidemics across national borders. We analyzed HIV-1 sequences sampled from Mexico and San Diego, California to determine the relatedness of these epidemics. We sampled the HIV epidemics in (1) Mexico by downloading all publicly available HIV-1 pol sequences from antiretroviral-naive individuals in GenBank (n = 100) and generating similar sequences from cohorts of injection drug users and female sex workers in Tijuana, Mexico (n = 27) and (2) in San Diego, California by pol sequencing well-characterized primary (n = 395) and chronic (n = 267) HIV infection cohorts. Estimates of population structure (FST), genetic distance cluster analysis, and a cladistic measure of migration events (Slatkin–Maddison test) were used to assess the relatedness of the epidemics. Both a test of population differentiation (FST = 0.06; p < 0.01) and a cladistic estimate of migration events (84 migrations, p ...