HIV infection is currently the single biggest epidemic globally. HIV is the etiologic agent for AIDS. HIV is divided into two types: HIV type 1 (HIV-1) and HIV type 2 (HIV-2). HIV-2 is rare and is mainly found in some parts of West Africa, though an increasing number of cases have been recognized in Europe, India, and the United States of America in recent times. HIV-1 accounts for most cases of AIDS. The strains of HIV-1 can be classified into four groups: the "major" group M, the "outlier" group O and the "new" group N and the most recent group P. These three groups may represent three separate introductions of SIVs into humans. This cross sectional study was carried out to determine the HIV-1 subtype diversity in Busia, Western Kenya. Briefly, patients were consented into the study based on pre-determined inclusion criteria. Viral RNA quantification was performed to select patients with virologic failure for drug resistance testing. HIV 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. One hundred and forty-six (146/915) patients were confirmed to have 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. We noted an increase in CRFs in the population compared to previous studies. Circulating HIV subtypes should be continually monitored in Busia in order to determine trends in transmission and map the circulating recombinant forms for epidemiological purposes.

Keywords: HIV-1, Busia County, Subtype Diversity, Reverse Transcriptase