Genetic Analysis of HIV-1 Subtypes in Nairobi, Kenya

Abstract

BackgroundGenetic 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.ObjectiveIn this study we have analyzed the subtypes of Human Immunodeficiency Virus -1 (HIV-1) circulating in a diverse sample population of Nairobi, Kenya.Methodology69 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.ResultsBlood 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.ConclusionOur 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.

Clinicopathological and prognostic implications of genetic alterations in oral cancers

“…Samples with bands obtained at 150bp were considered positive. To determine the quality of amplification of the extracted tumor DNA, β-globin PCR was performed(20). …”

Molecular and Phylogeographic Analysis of Human Immuno-deficiency Virus Type 1 Strains Infecting Treatment-naive Patients from Kigali, Rwanda

“…The region is also characterized by a very heterogeneous epidemic. Uganda and Kenya show a predominance of subtype A and D [12], [13], [14]. In Burundi, the epidemic is largely due to subtype C [15] while subtype A and C predominate in Tanzania [16], [17].…”

Molecular Characterization of HIV Type 1 Among HIV-Infected Respondents in a Cohort Being Prepared for HIV Phase III Vaccine Clinical Trials, Western Kenya

“…3 Previous molecular epidemiological studies done in Kenya mostly used samples from Nairobi. [4][5][6][7][8][9] A few other studies also investigated southern, 10 northern, 11 and western Kenya, 12 as well as the coastal region. 13,14 All of these studies indicated that HIV-1 subtype A is the most common subtype in Kenya, but that subtypes C, D, G, and recombinant forms were also detected.…”

“…13,14 All of these studies indicated that HIV-1 subtype A is the most common subtype in Kenya, but that subtypes C, D, G, and recombinant forms were also detected. [4][5][6][7][8][9][10][11][12][13][14] The complexity of HIV-1 diversity creates major challenges for vaccine design and development strategies. More than one HIV-1 vaccine candidate based on HIV-1 subtype A has been evaluated in Kenya during Phase I and II clinical trials.…”