Frequency of P/S(XX)P Duplication and FRFE, Absence of LYP in P6Gag of Indian Human Immunodeficiency Virus-1 Subtype C Isolates

Problem statement: The presence of a p6 domain at the C-terminus of the Gag polyprotein is a characteristic feature of HIV-1 and other primate lentiviruses. The p6Gag protein is considered as a major phosphoprotein in mature HIV-1 virions and is involved in the viral assembly and budding process. Sequence variation in the p6gag region in HIV-1 has been associated with changes in viral replication capacity and antiretroviral drug susceptibility. Approach: We examined sequence variation in the HIV-1 p6gag region using 38 isolates or infected Peripheral Blood Mononuclear Cells of HIV-1 subtype C and 20 additional Indian subtype C gag sequences from the Los Alamos database. Different patterns of insertions and deletions were observed in different motifs present in the p6 region. PTAP duplication was found in three strains. Results: We found PAP/TAP/LEPTAP/LPTVPTAP/ PAVPAAP like insertions at PTAP duplication site. KQE motif (84%) was observed as one of the most conserved motif in p6Gag while LYP motif was absolutely absent in Indian clade C sequences. Insertion of T/H/TT /PYRE/PYKE/EPKDRE was found instead of LYP motif. Conclusion: Further studies are needed to determine whether p6gag polymorphisms found in different motifs influence viral replication capacity, antiretroviral drug susceptibility, or other phenotypic properties of these strains.