Genetic analysis of HIV-1 subtypes in Nairobi, Kenya

Suhail Khoja, Peter Ojwang, Saeed Khan, Nancy Okinda, Reena Harania, Syed Ali

Research output: Contribution to journalArticlepeer-review

25 Citations (Scopus)


Background: Genetic analysis of A viral infection helps in following its spread in a given population, in tracking the routes of infection and, where applicable, vaccine design. Additionally, sequence analysis of the viral genome provides information about patterns of genetic divergence that may have occurred during viral evolution. Objective: In this study we have analyzed the subtypes of Humans Immunodeficiency Virus-1 (HIV-1) circulating in a diverse sample population of Nairobi, Kenya. Methodology: 69 blood samples were collected from a diverse subject population :attending the Aga Khan University Hospital in Nairobi, Kenya. Total DNA was extracted from peripheral blood mononuclear cells (PBMCs), and used in a Plolymerase Chain Reaction (PCR) to amplify the HIV gag gene. The PCR amplimers were partially sequenced, and alignment and phylogenetic analysis of these sequences was performed using the Los Alamos HIV Database, Results: Blood samples from 69 HIV-1 infected subjects from varying ethnic backgrounds were analyzed. Sequence alignment and phylogenetic analysis showed 39 isolates to be subtype A, 13 subtype D, 7 subtype C, 3 subtype AD and CRF01Æ, 2 subtype G and 1 subme AC and 1 AG. Deeper phylogenetic analysis revealed HIV subtype A sequences to be highly divergent compared to subtypes D and C. Conclusion: Our analysis indicates that HIV-1 subtypes in the Nairobi province of Kenya are dominated by a genetically diverse clade A. Additionally, the prevalence of highly divergent, complex, subtypes, intersubtypes, and the recombinant forms indicates viral mixing in Kenyan population, possibly as a result of dual infections.

Original languageEnglish
Article numbere3191
JournalPLoS ONE
Issue number9
Publication statusPublished - Sep 11 2008

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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