Genetic Diversity of HIV Type 1 along the Coastal Strip of Kenya

Abstract

A study on the genetic diversity of HIV-1 subtypes present along the coastal strip of Kenya, i.e., Kilifi, Mombasa, Msambweni, and Malindi districts, was carried out. DNA sequences for regions encoding a portion of the env-gp41 region of the virus were generated by PCR and sequenced directly. Eighty six samples that were successfully sequenced were analyzed. From the analysis, 86% (74) were subtype A1, 5% (4) were subtype C, 8% (7) were subtype D, and 1% (1) was subtype G. This study shows that HIV-1 subtype A1 is the most dominant subtype in circulation in this region.

HIV-1 Subtype Diversity Based on Envelope C2V3 Sequences from Kenyan Patients on Highly Active Antiretroviral Therapy

“…[8][9][10][11] In two previous studies in Northern Kenya, we reported 50-57% of all HIV-1 in that region as subtype A, followed by subtypes C and D at 27-39% and 9-11%, respectively. 8,10 This pattern appeared to be influenced by cross-border population dynamics as we observed.…”

“…We later reported a different pattern at the Kenyan coast where the prevalence of subtype A1 was much higher at over 85%. 9 These rates may continue to vary as the evolutionary forces of host immunity and antiretroviral pressure exert influence. 5,12,13 Indeed, slow rates of evolution of subtype B in the western setting were found to track with the escalation of antiretroviral treatment (ART), while an increase in evolutionary rates of HIV-1C was associated with declining prevalence among Ethiopians.…”

Prevalence of Transmitted Drug Resistance Mutations in HIV-1-Infected Drug-Naive Patients from Urban and Suburban Regions of Kenya

“…This is consistent with previous reports on HIV subtypes in Kenya, where subtype A has been shown to be the most common HIV subtype. [20][21][22][23] The second most common viral subtype was D with a prevalence of 22%. This is also consistent with previous studies, where subtype D has been reported to be the second most prevalent subtype in Kenya (www.hiv.lanl.gov/).…”

HIV Type 1 Subtype Surveillance in Central Kenya

“…[12][13][14] Little is known about circulating subtypes of HIV-1 in rural areas, which are the home to many of the infected people. In this study, we sought to determine the circulating subtypes of HIV-1 in eight districts of central Kenya in which HIV-1 prevalence has been known to be high.…”

“…Peripheral blood mononuclear cells (PBMCs) were extracted from whole blood by density gradient centrifugation using Ficoll-Paque Plus (Pharmacia) and Proviral DNA extracted using DNAzol (Gibco BRL) and ethanol precipitation as previously described. 12,13 A segment of the env gp41 (corresponding to nucleotide 7850-8310 of HIV-1 HXB2 ) was amplified with primers, gp40F1 5'-TCTTAGGAGCAGCAGGAAGCACTATGGG-3¢ and gp41R1 5'-AACGACAAAGGTGAGTATCCCTGCCTAA-3' in the first round and gp46F2 5'-ACAATTATTGTCTGGTA TAGTGCAACAGCA-3' and gp47R2 5'-TTAAACCTAT CAAGCCTCCTACTATCATTA-3' for nesting. Amplification was done with one cycle of 95°C for 10 min and 35 cycles of 95°C for 30 s, 55°C for 30 s, and 72°C for 1 min, with a final extension of 72°C for 10 min.…”