Genetic subtypes of HIV type 1 based on the vpu/env sequences in the Republic of Congo

To investigate the HIV-1 subtypes prevalent in the Republic of Congo, we isolated 28 HIV-1 strains from Congolese AIDS patients in 1996 and 1997, and analyzed them phylogenetically. Phylogenetic analysis based on part of the 5' tat-env (vpu) and env sequences revealed that only 13 (46.4%) of the 28 isolates belonged to the same subtype in the vpu tree as in the env tree; the remaining 15 (53.6%) strains showed discordant subtypes between vpu and env with 6 different profiles; that is, 1 A/A (vpu/env), 1 D/D, 5 G/G, 4 H/H, 2 unclassified (U)/U, 9 G/A, 2 G/H, 1 G/J, 1 H/G, 1 U/A, and 1 U/J. Thus, 9 of the 15 discordant HIV-1s were of the G/A (vpu/env) type, and did not form any subcluster within the subtype G lineage in the vpu-based phylogenetic tree. In addition, CRF02_AG (IbNG), which is a G/A (vpu/env) type, was not found in the Republic of Congo. These data suggest that the majority of HIV-1 subtypes circulating in the Republic of Congo have mosaic structures and may have been derived from independent recombinational events.