Analysis of HIV-1 gp120 quasispecies suggests high prevalence of intra-subtype recombination

IE Kiwelu, V Novitsky, L Margolin, J Baca, R Manongi, N Sam, J Shao, MF MacLane, SH Kapiga, and M Essex
Publication year: 

Recombination between viruses of the same HIV-1 subtype has been understudied primarily due to the lack of reference sequences, as well as appropriate bio-informatics tools. The introduction of recombination detection program (RDP3) made the detection of HIV-1 intra-subtype recombination feasible. Methods: This study determined the prevalence and patterns of HIV-1 intra-subtype recombinants among female bar and hotel workers in Moshi, Tanzania. The HIV-1 env gp120 V1-C5 quasispecies from 45 subjects classified as pure HIV-1 subtypes A1, C, or D were analyzed for recombination events by RDP3. Results: HIV-1 quasispecies with evidence for recombination were found in 89% of subjects infected with pure HIV-1 subtypes A, C, and D. Recombinant viruses were observed at both the baseline and the 12 month visits in 88% of the subjects; in 12% of subjects recombination was identified only at the later time point. Two major patterns were observed: 70% of subjects had unique recombination breakpoints without dominance of any particular variant, while in 30% of subjects a specific recombinant variant dominated in the pool of viral quasispecies. Conclusion: A large proportion of female bar and hotel workers were infected with intra-subtype recombinant viruses. These results suggest that HIV-1 co- and super-infections are common in this population, and occur more frequently than previously thought. Intra-subtype recombination contributes to the increased viral diversity which poses a challenge to HIV-1 vaccine design.