title: Increased promoter diversity reveals a complex phylogeny of human immunodeficiency virus type 1 subtype C in India.
abstract: OBJECTIVE
  To evaluate human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) sequence diversity among distinct populations within India and to determine the prevalent subtype.
  
  
  METHODS
  Analysis of the 3'LTR was conducted from 28 HIV-1-positive samples: 1992-1993 (Pune, New Delhi) and 1995-1996 (Pune, Mumbai and Vellore). Genomic DNA was extracted from cocultivated peripheral blood mononuclear cells (PBMCs) and used for polymerase chain reaction (PCR) amplification and sequencing using dye terminator chemistry. Sequences were edited, aligned, and analyzed phylogenetically utilizing gap-stripped and bootstrapping parameters. Mobility shift assays were used to confirm binding activity.
  
  
  RESULTS
  All nucleotide sequences were HWV-1 subtype C based on phylogenetic analysis. The isolates from Pune/Delhi formed subclusters when analyzed separately, irrespective of time or sample source. However, no significant subclustering was observed with isolates from Mumbai or Vellore or with the entire sample set when analyzed collectively. Subtype-specific enhancer analysis revealed an expected third NF-kappaB site but also revealed six isolates with insertions and deletions not previously described, one of which resembles an AP-1 binding site.
  
  
  CONCLUSIONS
  The results confirm the prevalence of HIV-1C and suggest increasingly complex phylogeny of HIV-1C within India, such that the previously observed subclustering may no longer adequately reflect the diversity of isolates currently circulating throughout India.
authors.affiliation: Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA.
authors.forename: S
authors.initials: S
authors.lastname: Choudhury
authors.forename: M A
authors.initials: MA
authors.lastname: Montano
authors.forename: C
authors.initials: C
authors.lastname: Womack
authors.forename: J T
authors.initials: JT
authors.lastname: Blackard
authors.forename: J K
authors.initials: JK
authors.lastname: Maniar
authors.forename: D G
authors.initials: DG
authors.lastname: Saple
authors.forename: S
authors.initials: S
authors.lastname: Tripathy
authors.forename: S
authors.initials: S
authors.lastname: Sahni
authors.forename: S
authors.initials: S
authors.lastname: Shah
authors.forename: G P
authors.initials: GP
authors.lastname: Babu
authors.forename: M
authors.initials: M
authors.lastname: Essex
mesh_terms: D001483:Base Sequence; D003001:Cloning, Molecular; D004251:DNA Transposable Elements; D017353:Gene Deletion; D015658:HIV Infections / Q000453:epidemiology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D007194:India / Q000453:epidemiology; D008969:Molecular Sequence Data; D016328:NF-kappa B / Q000235:genetics; D009841:Oligonucleotides / Q000032:analysis; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics; D016415:Sequence Alignment; D020079:Terminal Repeat Sequences
chemical_list: D004251:DNA Transposable Elements; D016328:NF-kappa B; D009841:Oligonucleotides; D012367:RNA, Viral