Near full-length clones and reference sequences for subtype C isolates of HIV type 1 from three different continents.

Other Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Rodenburg, CM; Li, Y; Trask, SA; Chen, Y; Decker, J; Robertson, DL; Kalish, ML; Shaw, GM; Allen, S; Hahn, BH; Gao, F; UNAIDS and NIAID Networks for HIV Isolation and Characterization,

Published Date

  • January 20, 2001

Published In

Volume / Issue

  • 17 / 2

Start / End Page

  • 161 - 168

PubMed ID

  • 11177395

International Standard Serial Number (ISSN)

  • 0889-2229

Digital Object Identifier (DOI)

  • 10.1089/08892220150217247


  • eng

Conference Location

  • United States