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

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 pr imary (PBMC-derived) isolates from Zambia, India, Tanzania, South Africa, B razil, and China, which were identified as subtype C by partial sequence an alysis. Near full-length viral genomes were amplified by using a long PCR t echnique, sequenced in their entirety, and phylogenetically analyzed. Amino acid sequence analysis revealed 10.2, 6.3, and 17.3% diversity in predicte d Gag, Pol, and Env protein sequences. Ten of 13 viruses were nonmosaic sub type C genomes, while all three isolates from China represented B/C recombi nants, One of them was composed primarily of subtype C sequences with three small subtype B portions in gag, pol, and aef 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 signa tures, including three potential NF-kappaB-binding sites in the viral promo ter-enhancer regions, were found in only a subset of these genomes.