title: Novel HIV-1 long terminal repeat (LTR) sequences of subtype B and mosaic intersubtype B/C recombinants in North India.
abstract: Although the HIV-1 epidemic in India is mainly due to subtype C, other subtypes have also been reported from different parts of India. HIV-1 LTR sequence analysis from six HIV-1 infected individuals from North India was carried out to determine the nature and extent of variations. Four out of six samples formed a unique phylogenetic cluster which was close to subtype B. The other two samples (A3 and S3) turned out to be novel mosaic recombinants showing resemblance to subtypes B, B/C-India and B/C-Myanmar gene segments. All four subtype B LTR samples and the two B/C recombinants showed conserved as well as unique polymorphisms in all of the putative transcription factor binding sites (TFBS). These changes may potentially alter basal as well as Tat-mediated HIV-1 LTR promoter activation. The two recombinants possessed three copies of the NF-kappaB TFBS as seen with the majority of subtype C and recombinant B/C isolates reported earlier, but the other four non-recombinant B-LTRs showed only two copies of the NF-kappaB site. This is the first study to show a dominance of unique subtype B-LTRs and strongly suggests that this region could also be a hot spot for the formation of highly complex inter subtype B/C recombinants.
authors.affiliation: Division of Virology, National Institute of Immunology, JNU Campus, New Delhi, India.
authors.forename: Ujjwal
authors.initials: U
authors.lastname: Neogi
authors.forename: Vikas
authors.initials: V
authors.lastname: Sood
authors.forename: Nidhi
authors.initials: N
authors.lastname: Goel
authors.forename: Ajay
authors.initials: A
authors.lastname: Wanchu
authors.forename: Akhil C
authors.initials: AC
authors.lastname: Banerjea
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D005838:Genotype; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D016325:HIV Long Terminal Repeat / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics* / Q000302:isolation & purification*; D006801:Humans; D007194:India / Q000453:epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D017385:Sequence Homology