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273 Predominance of HIV-1 Subtype A and a High Proportion of Intersubtype Recombinants among Infected Pregnant Women in Western Kenya
C. Yang*1, M. Li1, Y.-P. Shi1,2, R. Newman1, J. Otieno3, A. Misore3, J. Ayisi2, B. Nahlen1, and R. B. Lal1
1CDC, Atlanta, GA, USA; 2CDC/KEMRI; and 3New Nyanza Provincial Hosp, Kisumu, Kenya
Background: The high genetic variation in HIV-1 continues to complicate the effective vaccine development. To better understand the extent of genetic variation and contribution of intersubtype recombinants, a detailed analysis of 2 HIV-1 genomic regions (p24 and gp41) was conducted in women attending an antenatal clinic in western Kenya.
Methods: HIV-1-infected women between the ages of 14 and 40 years (median age, 22) were enrolled for a prospective study of mother-infant HIV-1 transmission in Kisumu, Kenya. Specimens obtained from 284 women at delivery were used for amplification and sequence analysis of gag p24 and env gp41. Selected specimens with discordant subtypes on p24 and gp41 were further tested for possible recombinants using a 2.1-kb fragment (nt1237-3370, HXB2) spanning gag-polregion.
Results: Phylogenetic analysis of nucleotide sequences in gp41 region revealed that 197 (69%) were subtype A, 57 (20%) subtype D, 19 (7%) subtype C, 6 (2%) subtype G, 4 (1%) unclassifiable, and 1 (0.4%) subtype B. Likewise, subtype A was the predominant subtype (67%), followed by subtype D (23%), subtype C (7%), subtypes G (2%), and unclassifiable (1%) based on the p24 region. More importantly, parallel analyses of p24 and gp41 genes indicated that 75 (26%) had discordant subtypes. The major discordant gag and env subtypes represented as D and A (33%), A and D (27%), C and A (12%), A and C (8%), and D and C (4%). Further analysis of selected specimens in the gag-pol region revealed that more than 50% of the discordant specimens were intersubtype recombinants with breakpoints identifiable within this region.
Conclusions: These data provide evidence of high genetic diversity with subtype A as the predominant subtype in western Kenya. We also find a high proportion of potential intersubtype recombinants in this region. This information will assist vaccine development efforts, including preparing this area in western Kenya as a vaccine testing site.
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