Emergence of a unique recombinant form of HIV-1 from Manipur (India)

Abstract Background The AIDS epidemic in Manipur, India, manifests unique features, having co-circulation of B and C HIV-1 subtypes along with recombinant forms. Manipur has the highest incidence of HIV-1 infection compared to the other states of India, but limited information is available regarding the full-length sequence of HIV-1 recombinants. Objectives To characterize the near full-length genome of a novel recombinant HIV-1 strain from an injecting drug user of Manipur. Study design Viral RNA, extracted from the plasma of a male injecting drug user aged 35, was diagnosed with HIV-1 infection. Near full-length genome was amplified by polymerase chain reaction using primer walking approach. Phylogenetic relationships were determined with neighbor-joining trees. The recombination break points were detected using boot scan and Simplot analyses. Results This recombinant predominantly had subtype C genome and exhibited mosaic structures with subtype B insertions at three different positions of HIV-1 genome. Simplot analysis of near full-length genome sequence from the recombinant HIV-1 strain, MAN86 exhibited similarity with the sequence of C.IN.93.93IN905 in its subtype C backbone, while the subtype B insertions showed resemblance with the sequence of B.TH.99.99TH _C1416. Conclusions This study confirms the presence of a unique recombinant HIV-1 strain, emerging as a result of recombination between HIV-1 strains from India and Thailand.