title: Genetic analysis of HIV-1 subtypes in Nairobi, Kenya.
abstract: 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, in 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 Human Immunodeficiency Virus -1 (HIV-1) circulating in a diverse sample population of Nairobi, Kenya.
  
  
  METHODS
  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 Polymerase 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 CRF01_AE, 2 subtype G and 1 subtype AC and 1 AG. Deeper phylogenetic analysis revealed HIV subtype A sequences to be highly divergent as compared to subtypes D and C.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biological and Biomedical Sciences, Aga Khan University Hospital, Karachi, Pakistan.
authors.forename: Suhail
authors.initials: S
authors.lastname: Khoja
authors.forename: Peter
authors.initials: P
authors.lastname: Ojwang
authors.forename: Saeed
authors.initials: S
authors.lastname: Khan
authors.forename: Nancy
authors.initials: N
authors.lastname: Okinda
authors.forename: Reena
authors.initials: R
authors.lastname: Harania
authors.forename: Syed
authors.initials: S
authors.lastname: Ali
mesh_terms: D000293:Adolescent; D000328:Adult; D004279:DNA, Viral / Q000235:genetics; D005260:Female; D016679:Genome, Viral; D015658:HIV Infections / Q000097:blood / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D007630:Kenya; D008297:Male; D008875:Middle Aged; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D055544:beta-Globins / Q000378:metabolism
chemical_list: D004279:DNA, Viral; D055544:beta-Globins
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