The Tat and C2-V3 envelope genes in the molecular epidemiology of human immunodeficiency virus-1

In this study HIV-1 proviral DNA sequences derived from 201 clones of the C2-V3 env region and the first exon of tat were obtained from six HIV-1-infected heterosexual couples. These molecular data were used to confirm the epidemiological relationships. The ability of the molecular data to draw such conclusions was also tested. A bootstrap parsimony analysis of the C2-V3 sequences showed one couple failed to cluster and only two couples clustered in more than 70% of the replicates. The rapid diversification of the C2-V3 region and the length of time that elapsed since the infection event may have limited the certainty of the conclusions that can be reached to infer epidemiological relatedness from this region. Using data from the tat region, all couples clustered, four of them in more than 80% of bootstrap replicates. A single clone from the tat region did not cluster with others from that patient or with those from that patient's partner, indicating that multiple clones are necessary to firmly establish phylogenetic linkage. Nevertheless, the tat region was much more useful in establishing epidemiological relationships among this group than the commonly used C2-V3.