title: Near full-length clones and reference sequences for subtype C isolates of HIV type 1 from three different continents.
abstract: Among the major circulating HIV-1 subtypes, subtype C is the most prevalent. To generate full-length subtype C clones and sequences, we selected 13 primary (PBMC-derived) isolates from Zambia, India, Tanzania, South Africa, Brazil, and China, which were identified as subtype C by partial sequence analysis. Near full-length viral genomes were amplified by using a long PCR technique, sequenced in their entirety, and phylogenetically analyzed. Amino acid sequence analysis revealed 10.2, 6.3, and 17.3% diversity in predicted Gag, Pol, and Env protein sequences. Ten of 13 viruses were nonmosaic subtype C genomes, while all three isolates from China represented B/C recombinants. One of them was composed primarily of subtype C sequences with three small subtype B portions in gag, pol, and nef genes. Two others exhibited these same mosaic regions, but contained two additional subtype B portions at the gag/pol overlap and in the accessory gene region, suggesting ongoing B/C recombination in China. All subtype C genomes contained a prematurely truncated second exon of rev, but other previously proposed subtype C signatures, including three potential NF-kappa B-binding sites in the viral promoter-enhancer regions, were found in only a subset of these genomes.
authors.affiliation: Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.
authors.forename: C M
authors.initials: CM
authors.lastname: Rodenburg
authors.forename: Y
authors.initials: Y
authors.lastname: Li
authors.forename: S A
authors.initials: SA
authors.lastname: Trask
authors.forename: Y
authors.initials: Y
authors.lastname: Chen
authors.forename: J
authors.initials: J
authors.lastname: Decker
authors.forename: D L
authors.initials: DL
authors.lastname: Robertson
authors.forename: M L
authors.initials: ML
authors.lastname: Kalish
authors.forename: G M
authors.initials: GM
authors.lastname: Shaw
authors.forename: S
authors.initials: S
authors.lastname: Allen
authors.forename: B H
authors.initials: BH
authors.lastname: Hahn
authors.forename: F
authors.initials: F
authors.lastname: Gao
mesh_terms: D000328:Adult; D001483:Base Sequence; D001938:Brazil; D002681:China; D005260:Female; D015686:Gene Products, env; D015683:Gene Products, gag / Q000235:genetics; D015684:Gene Products, pol / Q000235:genetics; D015694:Gene Products, rev; D016679:Genome, Viral; D015658:HIV Infections / Q000821:virology*; D016325:HIV Long Terminal Repeat / Q000235:genetics; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D007194:India; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment; D013019:South Africa; D013636:Tanzania; D054321:rev Gene Products, Human Immunodeficiency Virus
chemical_list: D015686:Gene Products, env; D015683:Gene Products, gag; D015684:Gene Products, pol; D015694:Gene Products, rev; D054321:rev Gene Products, Human Immunodeficiency Virus