title: Short Communication: Phylogenetic and Molecular Characterization of Six Full-Length HIV-1 Genomes from India Reveals a Monophyletic Lineage of Indian Sub-Subtype A1.
abstract: Although HIV-1 epidemic in India is mainly driven by subtype C, subtype A has been reported for over two decades. This is the first comprehensive analysis of sequences of HIV-1 subtype A from India, based on the near full-length genome sequences of six different HIV-1 subtype A Indian isolates along with available partial gene sequences from India and global sequences. The phylogenetic analyses revealed the convergence of all Indian whole-genome sequences and majority of the partial gene sequences to a single node with the sequences most closely related to African sub-subtype A1. The presence of the signature motifs consistent with those observed in subtype A and CTL epitopes characterized specifically for subtype A1 were observed among the study sequences. Deletion of LY amino acid of LYPXnL motif of p6gag and one amino acid in V3 loop have been observed among the study isolates, which have also been observed in a few sequences from East Africa. Overall, the results are indicative of a monophyletic lineage or founder effect of the Indian epidemic due to sub-subtype A1 and supportive of a possible migration of subtype A1 into India from East Africa.
authors.affiliation: 1 Department of Immunology, National AIDS Research Institute (ICMR) , Pune, India .
authors.forename: Sudhanshu Shekhar
authors.initials: SS
authors.lastname: Pandey
authors.affiliation: 2 Bioinformatics Group, National Institute of Virology (ICMR) , Pune, India .
authors.forename: Sarah
authors.initials: S
authors.lastname: Cherian
authors.affiliation: 1 Department of Immunology, National AIDS Research Institute (ICMR) , Pune, India .
authors.forename: Madhuri
authors.initials: M
authors.lastname: Thakar
authors.affiliation: 1 Department of Immunology, National AIDS Research Institute (ICMR) , Pune, India .
authors.forename: Ramesh S
authors.initials: RS
authors.lastname: Paranjape
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D016679:Genome, Viral / Q000235:genetics*; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D007194:India / Q000453:epidemiology; D010802:Phylogeny; D017384:Sequence Deletion / Q000235:genetics