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.

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 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.

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.

Figure 1. Phylogenetic analysis of HIV gag gene (p24-p7) sequences (nt 1577–2040, HXB2) from HIV infected Nairobi residents.

This tree (neighbor-joining) was created by aligning the selected sequences with reference sequences from Los Alamos database shown in bold). The sequence F1.FR.96.MP411 was selected as the out group.

Figure 2. Neighbor-Joining Phylogenetic trees of the three most represented subtypes, A (Fig. 2A), D (Fig. 2B) and C (Fig. 2C), depicting geographical associations of the studied sample group with other global regions.

Reference Sequences from Los Alamaos Database have been indicated in bold. Out groups selected for Fig. 2A, B, and C were, respectively, A.EE.02.EST2002 394, NL.x.M12020, and IL.98.98IS002.