title: Genetic characterization of HIV type 1 Tat exon 1 from a southern Indian clinical cohort: identification of unique epidemiological signature residues.
abstract: The trans-activator of transcription (Tat) of HIV-1 plays an important role in viral infection and pathogenesis. We examined the genetic characteristics of exon 1 of the tat gene derived from 102 seropositive subjects from southern India. Database-derived Indian (n=105) and global (n=413) HIV-1C sequences were also used for viral epidemiological signature pattern analysis in the Tat open reading frame (ORF). We identified HIV-1C as the most predominant genetic subtype (99%) and the presence of a novel A1C recombinant strain in one study participant. After examining all the available HIV-1C Indian sequences from primary clinical isolates and database-derived sequences, we found a high level of sequence conservation (92.6 ± 12%) within Tat amino acid residues. Furthermore, signature pattern analysis identified five amino acid positions in Tat that contained signature residues unique for Indian HIV-1C consisting of 21A, 24N, 29K, 40K, and 60Q. Our data have direct relevance for subunit-based Tat HIV-1 vaccine development.
authors.affiliation: Clinical Virology, Department of Microbiology, St. John's Medical College, St. John's National Academy of Health Sciences, Bangalore, India. ujjwalneogi@gmail.com
authors.forename: Ujjwal
authors.initials: U
authors.lastname: Neogi
authors.forename: Soham
authors.initials: S
authors.lastname: Gupta
authors.forename: Pravat Nalini
authors.initials: PN
authors.lastname: Sahoo
authors.forename: Anita
authors.initials: A
authors.lastname: Shet
authors.forename: Shwetha D
authors.initials: SD
authors.lastname: Rao
authors.forename: Udaykumar
authors.initials: U
authors.lastname: Ranga
authors.forename: Vinayaka R
authors.initials: VR
authors.lastname: Prasad
mesh_terms: D016915:AIDS Vaccines / Q000235:genetics*; D000328:Adult; D000595:Amino Acid Sequence; D004279:DNA, Viral; D015195:Drug Design; D005091:Exons / Q000235:genetics; D005260:Female; D015756:Genes, tat / Q000235:genetics*; D006679:HIV Seropositivity / Q000453:epidemiology* / Q000235:genetics; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D007194:India / Q000453:epidemiology; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny
chemical_list: D016915:AIDS Vaccines; D004279:DNA, Viral