Evaluating whole HIV-1 genome sequence for estimation of incidence and migration in a rural South African community.

ABSTRACT: Background: South Africa has the largest number of people living with HIV (PLWHIV) in the world, with HIV prevalence and transmission patterns varying greatly between provinces. Transmission between regions is still poorly understood, but phylodynamics of HIV-1 evolution can reveal how many infections are attributable to contacts outside a given community. We analysed whole genome HIV-1 genetic sequences to estimate incidence and the proportion of transmissions between communities in Hlabisa, a rural South African community. Methods: We separately analysed HIV-1 for gag, pol, and env genes sampled from 2,503 PLWHIV. We estimated time-scaled phylogenies by maximum likelihood under a molecular clock model. Phylodynamic models were fitted to time-scaled tree

SUBMITTER: Nascimento FF 

PROVIDER: S-EPMC10276198 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature