title: Determination of gag and env subtypes of HIV-1 detected among injecting drug users (IDUs) in Manipur, India: evidence for intersubtype recombination.
abstract: The majority of HIV-1 transmission in Manipur, one of the northeastern states of India, is through the sharing of needles and syringes among the injecting drug users (IDUs). A total of 28 HIV seropositive samples were used to determine the HIV-1 subtypes with respect to both gag and envelope genes. The specific regions within gag and envelope genes were amplified from PBMC DNA by nested PCR using appropriate primers. These amplicons were used in heteroduplex mobility assay followed by DNA sequencing. Phylogenetic analysis of the nucleotide sequences of respective regions showed that 89% of samples (25/28) were infected with subtype C with respect to both gag and envelope genes; however, 11% of the samples (3/28) showed subtype discordance with respect to the envelope (C2-V3) and gag (p24-p7) genomic regions. Simplot analysis of the discordant samples showed the presence of intersubtype recombination between subtype C and Thai B; two samples were found to be subtype C in envelope but Thai B in gag, whereas, one sample was found to be subtype Thai B in envelope and 'C' in gag region.
authors.affiliation: National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Calcutta 700010, India.
authors.forename: Payel
authors.initials: P
authors.lastname: Bhanja
authors.forename: Satarupa
authors.initials: S
authors.lastname: Sengupta
authors.forename: N Yaima
authors.initials: NY
authors.lastname: Singh
authors.forename: Kamalesh
authors.initials: K
authors.lastname: Sarkar
authors.forename: Sujit Kumar
authors.initials: SK
authors.lastname: Bhattacharya
authors.forename: Sekhar
authors.initials: S
authors.lastname: Chakrabarti
mesh_terms: D000328:Adult; D004279:DNA, Viral / Q000032:analysis; D015686:Gene Products, env / Q000737:chemistry / Q000235:genetics; D015683:Gene Products, gag / Q000737:chemistry / Q000235:genetics; D015752:Genes, env / Q000235:genetics*; D015750:Genes, gag / Q000235:genetics*; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics; D020180:Heteroduplex Analysis; D006801:Humans; D007194:India; D008297:Male; D008969:Molecular Sequence Data; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D015819:Substance Abuse, Intravenous / Q000150:complications*
chemical_list: D004279:DNA, Viral; D015686:Gene Products, env; D015683:Gene Products, gag