Human immunodeficiency virus type 1 (HIV-1) subtype diversity in Busia, Western Kenya

HIV infection is currently the single biggest epidemic globally. HIV the etiologic agent for AIDS is divided into two types: HIV-1 and HIV-2. HIV-2 is rare and is mainly found in some parts of West Africa. HIV-1 accounts for most cases of AIDS reported globally. HIV-1 strains can be classified into four groups: The "major" group M, group O, group N and the most recent group P. All of which may represent separate introductions of SIVs into humans. This cross sectional study determined the HIV-1 subtype diversity in Busia, Western Kenya. Briefly, participants were consented into the study based on pre-determined inclusion criteria. Viral RNA quantification was performed to select participants with virologic failure for drug resistance testing. HIV drug resistance testing (DRT) was performed and sequences obtained were used to determine circulating HIV-1 subtypes using the REGA HIV-1 Subtyping Tool Version 3.0. Phylogenetic analysis was performed using MEGA software V7.0 to confirm the circulating HIV subtypes. Out of 915 participants screened, 146 participants had virologic failure although 140 were successfully sequenced. Subtype A1 was the most prevalent subtype present in 52.9% of the participants followed by subtype D (20.7%), CRF A1_D (7.1%) subtype C and subtype B (4.3%) and subtype A2 (3.6%). Sequences within the same subtype and CRF clustered close together on the phylogenetic tree. An increase in CRFs in the population compared to previous studies. Circulating HIV subtypes should be continually monitored in Busia to determine trends in transmission and map the circulating recombinant forms for epidemiological purposes.   Key words: HIV-1, Busia county, subtype diversity, reverse transcriptase.