title: HIV-1 subtype diversity based on envelope C2V3 sequences from Kenyan patients on highly active antiretroviral therapy.
abstract: There is a continuous need to genetically characterize the HIV strains in circulation in order to assess interventions and inform vaccine discovery. We partially sequenced the envelope C2V3 gene from a total of 59 Kenyan patients on highly active antiretroviral treatment (HAART) and determined HIV subtypes using both the JPHMM subtyping tool and the phylogenetic method. HIV-1 subtype A1 was the predominant strain in circulation, representing 65.5% and 74.5% of all isolates as determined by JPHMM and phylogenetic methods, respectively. Subtypes C and D were the next most prevalent pure strains at 9.1% each by both methods. JPHMM identified 9.1% of the isolates as recombinant. Four isolates had short sequences not covering the entire C2V3 region and were thus not subtyped. From this study, subtype A viruses are still the predominant HIV-1 strains in local circulation in Kenya. Constant surveillance is needed to update molecular trends under continuing HAART scale-up.
authors.affiliation: 1 Center for Research in Therapeutic Sciences, Strathmore University , Nairobi, Kenya .
authors.forename: Rose C
authors.initials: RC
authors.lastname: Kitawi
authors.forename: Timothy
authors.initials: T
authors.lastname: Nzomo
authors.forename: Ruth S
authors.initials: RS
authors.lastname: Mwatelah
authors.forename: Rashid
authors.initials: R
authors.lastname: Aman
authors.forename: Maureen J
authors.initials: MJ
authors.lastname: Kimulwo
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Masankwa
authors.forename: Raphael M
authors.initials: RM
authors.lastname: Lwembe
authors.forename: Javan
authors.initials: J
authors.lastname: Okendo
authors.forename: Bernhards
authors.initials: B
authors.lastname: Ogutu
authors.forename: Washingtone
authors.initials: W
authors.lastname: Ochieng
mesh_terms: D000328:Adult; D000368:Aged; D023241:Antiretroviral Therapy, Highly Active; D016000:Cluster Analysis; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy* / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D007630:Kenya / Q000453:epidemiology; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D055815:Young Adult; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
chemical_list: D054299:env Gene Products, Human Immunodeficiency Virus