title: Construction and characterization of an infectious molecular clone of HIV-1 subtype A of Indian origin.
abstract: India has the second highest number of HIV-1 infected people next to South Africa. The predominant proportion of HIV-1 circulating in India is of subtype C origin, with a small fraction made up of subtypes A and B. In this report, we describe the construction and characterization of the first full-length infectious molecular clone p1579A-1 HIV-1, from an HIV-1 subtype A infected person from India, using long PCR and successive ligation of the amplimers. Phylogenetic analysis of the sequence of the entire proviral DNA and LTR confirmed p1579A-1 to be an HIV-1 subtype A. Analysis of the env gene of p1579A-1 showed a conserved GPGQ motif and the absence of basic amino acids at positions 11 and 25 suggesting CCR5 coreceptor usage. Analysis of env N-linked glycosylation sites revealed fewer sites in the V1 region of envelope compared to other subtype A. Transcription factor binding site analysis of the LTR sequences identified conserved as well as unique transcription factor binding sites (TFBS) in p1579A-1. This infectious clone of HIV-1 can be useful to study the molecular mechanism of dominance of subtype C in India.
authors.affiliation: Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 426 Parran Hall, 130 DeSoto Street, PA 15261, USA.
authors.forename: Milka A
authors.initials: MA
authors.lastname: Rodriguez
authors.forename: Yue
authors.initials: Y
authors.lastname: Chen
authors.forename: Jodi K
authors.initials: JK
authors.lastname: Craigo
authors.forename: Ramdas
authors.initials: R
authors.lastname: Chatterjee
authors.forename: Deena
authors.initials: D
authors.lastname: Ratner
authors.forename: Masashi
authors.initials: M
authors.lastname: Tatsumi
authors.forename: Pratima
authors.initials: P
authors.lastname: Roy
authors.forename: Dhruba
authors.initials: D
authors.lastname: Neogi
authors.forename: Phalguni
authors.initials: P
authors.lastname: Gupta
mesh_terms: D000293:Adolescent; D000328:Adult; D000595:Amino Acid Sequence; D002460:Cell Line; D003001:Cloning, Molecular; D005260:Female; D015686:Gene Products, env / Q000737:chemistry / Q000235:genetics; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics / Q000472:pathogenicity*; D006801:Humans; D007194:India / Q000453:epidemiology; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D010802:Phylogeny
chemical_list: D015686:Gene Products, env