Molecular characterization of HIV type 1 among HIV-infected respondents in a cohort being prepared for HIV phase III vaccine clinical trials, Western Kenya

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dc.contributor.authorOyaro M.
dc.contributor.authorMbithi J.
dc.contributor.authorOyugi F.
dc.contributor.authorLaten A.
dc.contributor.authorAnzala O.
dc.contributor.authorEngelbrecht S.
dc.date.accessioned2011-05-15T16:03:20Z
dc.date.available2011-05-15T16:03:20Z
dc.date.issued2011
dc.description.abstractKenya is one of the sub-Saharan African countries affected by HIV-1 infection and AIDS. We investigated HIV-1 genetic diversity in 130 individuals from Busia, Bungoma, and Kakamega in western Kenya as part of an HIV-1 vaccine feasibility study in preparation for Phase III efficacy clinical trials. After RNA extraction the partial gag (484bp) and env (1297bp) regions were amplified and directly sequenced. Phylogenetic analysis was done using MEGA version 4 and recombinants were identified using the jpHMM tool and phylogenetic analysis. HIV-1 sequences were amplified from 122 of the 130 samples, 118 (90.8%) from the gag region and 78 (60 %) from the env region and 74 samples (56.9%) from both the gag and env regions. Of these sequenced on both regions, 51.4% were subtype A, 9.4% subtype D, 1.4% subtype C, 4.1% subtype G, and 33.7% were discordant and thus possible recombinants, including A1/C, A1/D, A1/A2, and A2/C. The jpHMM tool indicated a further two samples with CD and BD breakpoints within the env gene and one within the gag gene (A1C). An additional sample had an A1D breakpoint in the gag gene, but the envelope was not amplified. HIV-1 subtype diversity in western Kenya should be considered in vaccines designed for clinical trials in this region and this genetic diversity should be continuously monitored. © 2011, Mary Ann Liebert, Inc.
dc.description.versionArticle
dc.identifier.citationAIDS Research and Human Retroviruses
dc.identifier.citation27
dc.identifier.citation3
dc.identifier.issn8892229
dc.identifier.other10.1089/aid.2010.0061
dc.identifier.urihttp://hdl.handle.net/10019.1/12581
dc.subjectGag protein
dc.subjectHuman immunodeficiency virus vaccine
dc.subjectRNA
dc.subjectadult
dc.subjectarticle
dc.subjectclinical assessment
dc.subjectcohort analysis
dc.subjectdrug efficacy
dc.subjectenvelope gene
dc.subjectfeasibility study
dc.subjectfemale
dc.subjectgene amplification
dc.subjectgene sequence
dc.subjectgenetic variability
dc.subjecthuman
dc.subjectHuman immunodeficiency virus 1 infection
dc.subjectHuman immunodeficiency virus infected patient
dc.subjectKenya
dc.subjectmajor clinical study
dc.subjectmale
dc.subjectmolecular biology
dc.subjectnucleotide sequence
dc.subjectphase 3 clinical trial (topic)
dc.subjectphylogeny
dc.subjectpolymerase chain reaction
dc.subjectpriority journal
dc.subjectpromoter region
dc.subjectquestionnaire
dc.subjectrecombinant gene
dc.subjectRNA extraction
dc.titleMolecular characterization of HIV type 1 among HIV-infected respondents in a cohort being prepared for HIV phase III vaccine clinical trials, Western Kenya
dc.typeArticle
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