Genetic diversity of HIV-1 in Central province, Kenya-Pilot study

Abstract

Reports on emergence of new strains characterize HIV epidemic in Sub-SaharanAfrican countries. The distribution of these diversified strains is thought to followgeographic and population dynamics. These HIV variants have been reported to havedistinctively regionalized endemicity. In Kenya, studies on subtype distribution havebeen done in Western, Nyanza, North-Eastern, Rift Valley, Nairobi and CoastalProvinces. However, this information in Central Province is lacking. This work reportsgenetic diversities of HIV-1 circulating in the Central Province of Kenya. HIV positiveblood samples were collected from 8 health facilities in the province namely Nyeri,Maragua, Kiambu, Thika, Kerugoya, Kikuyu, Tumutumu and Kieni Mission hospital. Atotal of 96 samples were collected, 12 from each health facility. Part of the proviralHIV-1 env gene (gp41) was PCR amplified and directly sequenced. Subtypes weredetermined by sequence analysis using geographically diverse subtype referencesequences as well as sequences of known subtypes from Kenya. Sixty eight percent (68%) of the samples analysed were subtype A-1, 10% were subtype C, 12% subtype D,while the rest were circulating recombinant forms (CRFs) mainly between C, D, G andA. This analysis of HIV-1 strains demonstrated the predominance of HIV-1 subtype A-1. Understanding the genetic diversity of HIV-1 in this region is important inmonitoring the spread of infection and developing effective control strategies. This pilotstudy provides the basis for more expansive studies in determining HIV geneticdiversity in Central province of Kenya. It also sets the benchmark for future studies inviral phylogeography.