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Methods Blood samples were collected from 212 HIV-1 seropositive subjects between 2007 and 2011. HIV-1 subtypes were determined using at least two or three viral genes, gag, pol, and env using maximum likelihood tree. Recombination events were identified using RIP ver 3 tools followed by breakpoints analysis in Simplot version 3.5.1 and fragment-specific phylogenetic analysis. Results When a single gene was used for subtype determination, the mean proportion of HIV-1C, B and A1 were 95.9%, 1.9% and 0.2% respectively while recombinants constituted 2.1%. The overall prevalence of URFs (BC/A1C) increased significantly to 10% when two (p<0.01) or three genes (p=0.02) were used. All the A1 and B strains, identified in the single-gene approach, were re-identified as URFs. Detailed analysis indicated that the B segment of the URF_BC probably originated from China/Thailand, while the A1 segments originated from eastern Africa. Among the four geographical regions examined, a high proportion of the recombinant strains based on the two-gene approach were identified in north-eastern (46.7%) and northern (18.5%) followed by southern India (5%), while central India appeared to have a concentrated subtype C epidemic (100%). Conclusion The rapid and continuous evolution of the HIV-1 epidemic in India was evidenced by the increase of recombinant strains. The use of multiple genes, rather than a single gene to identify HIV-1 subtypes can reduce the chances of false identification. These results warrant an urgent need for continued molecular surveillance to guide efficient disease intervention strategies and develop an effective subunit-based vaccine.

Emergence of unique recombinant forms (URFs) in Indian HIV-1 epidemic: data from nationwide clinical cohort between 2007 and 2011