Molecular surveillance of HIV-1 field strains in Nigeria in preparation for vaccine trials.

We conducted a national molecular epidemiologic survey of HIV-1 strains in Nigeria to determine the most prevalent subtype(s) for use in developing candidate vaccines. A total of 230 HIV-1-positive blood samples collected from 34 of the 36 Nigerian states were analyzed by our modified env gp41-based heteroduplex mobility assay (HMA) and/or gp41 sequencing and analysis. Overall, 103 (44.8%) were subtype A, 125 (54.3%) were subtype G, one (0.4%) was subtype C, and one (0.4%) was subtype J, and one (0.4%) was unclassifiable. To further characterize Nigerian viruses to aid in strain selection for candidate vaccines, one gp41 subtype G and five gp41 subtype A strains were selected for full envelope sequencing. The one subtype G sequence had consistent phylogenies throughout gp160, using programs to detect recombination. However, all five sequences that were primarily subtype A in gp41 were found to be recombinant viruses. Two of the five (40%) were A/G/J mosaics with common breakpoints. The remaining three gp160 recombinants all had their own unique break points: two A/? and one A/?/G, however, all five had the majority of their mosaic breakpoints occurring in gp41. None of the five were consistent with the circulating recombinant form (CRF)02_AG strain previously reported to be prevalent in West Africa. In conclusion, we showed a clear dominance and widespread distribution of gp41 subtypes A and G in fairly equal proportions, suggesting that vaccines designed for use in this geographic locale should incorporate the gene(s) of both subtypes. However, appreciating the magnitude of diversity of HIV-1 strains in Nigeria may require sequencing and analysis of longer gene regions for the identification of prevalent or emerging CRFs.