Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection.

ABSTRACT: Phylogenies of highly genetically variable viruses such as HIV-1 are potentially informative of epidemiological dynamics. Several studies have demonstrated the presence of clusters of highly related HIV-1 sequences, particularly among recently HIV-infected individuals, which have been used to argue for a high transmission rate during acute infection. Using a large set of HIV-1 subtype B pol sequences collected from men who have sex with men, we demonstrate that virus from recent infections tend to be phylogenetically clustered at a greater rate than virus from patients with chronic infection ('excess clustering') and also tend to cluster with other recent HIV infections rather than chronic, established infections ('excess co-clustering'), consistent with previous reports. To determine the

SUBMITTER: Volz EM 

PROVIDER: S-EPMC3386305 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature