Phylogenetic analysis of the envelope HIV-1 type 1 isolates among Kenyan cohort

Abstract

Background: As the AIDS pandemic progresses, an increasingly broad range of genetic diversity continues to be reported within the main (M) group of HIV-1 viruses with viral subtype predominating in specific geographical areas.

Objective: Determine the genetic diversity and trends of HIV-1 subtypes among Kenyan individuals.

Methodology: One hundred and seventy six subjects (176) were recruited from five study sites in Nairobi and its environs. The viral DNA was extracted using Qiagen® MiniViral DNA isolation kit and target env–C2-V3 gene amplified by nested PCR. The amplified products were analysed by gel electrophoresis and visualized under UV light. The successfully amplified products were then labeled with a sequence dye in sequence PCR reaction using the Big Dye® sequence terminator kit (Applied Biosystem®) and the products purified by use of Qiagen purification kit before directly sequenced using an automated ABI 310 sequencer ( Applied Biosystem, Foster City CA). In RT gene (288bp) of viruses sequenced.

Results: Analysis of the sequences showed that a majority of them belonged to subtype A1: 73.9% (130/176), followed by C: 10.8% (19/176), D: 9.7% (17/176), G, AIC and A2 1.1% (2/176) each and 2.3% (4/176) were unique recombinants forms. As from previous studies conducted in other parts of Kenya, HIV-1 subtype A1 still remains the most predominant subtype while subtype C continues to show an increasing prevalence.

Conclusion: Continued surveillance of circulating subtypes of HIV-1 in Kenya is important in determining the evolution of the HIV/AIDS epidemic in Kenya.