Genetic analysis of human immunodeficiency virus type I strains in Kenya: A comparison using phylogenetic analysis and a combinatorial melting assay

We surveyed human immunodeficiency virus (HIV) subtype distribution from pe ripheral blood mononuclear cells (PBMCs) collected in 1995 from 24 HIV-l-in fected Kenyan residents (specimens from predominantly male truck drivers an d female sex workers near Mombasa and Nairobi), Processed lysates from the PBMC samples were used for env amplification, directly sequenced, and analy zed by phylogenetic analysis. Envelope amplification products were also use d for analysis in a polymerase chain reaction (PCR)-based assay, called the combinatorial melting assay (COMA). Results of the two tests were compared for assignment of subtype for this Kenyan cohort. The COMA, a PCR capture technique with colorimetric signal detection, was used with HIV reference s ubtype strains as well as regional (East Africa) HIV strains for subtype id entification. Performance of the COMA was at 100% concordance (24 of 24) as compared with DNA sequencing analysis. Phylogenetic analysis showed 17 iso lates to be subtype A, 3 subtype D, and 4 subtype C viruses. This may repre sent an increase in subtype C presence in Kenya compared with previously do cumented reports, The COMA can offer advantages for rapid HIV-1 subtype scr eening of large populations, with the use of previously identified regional strains to enhance the identification of local strains. When more detailed genetic information is desired, DNA sequencing and analysis may be require d.