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

C. M. Rodenburg, Y. Li, S. A. Trask, Y. Chen, J. Decker, D. L. Robertson, G. M. Shaw, S. Allen, S. Osmanov, L. Jacobs, J. Esparza, B. Galvao-Castro, Y. Shao, N. Samuel, S. Maayan, A. Bobkov, T. Smolskaya, W. Makgoba, C. Williamson, S. M'BoupF. Mhalu, P. Auewarakul, P. Kaleebu, S. Sempala, U. Dietrich, H. Von Briesen, S. Nick, M. Nubling, J. Halbauer, O. Hamouda, C. Kücherer, R. Riedl, H. Wolf, M. Hoelscher, H. Holmes, S. Beddows, G. Giraldo, L. Buonaguro, G. Scarlatti, M. Salminen, G. Van der Groen, F. Barré-Sinoussi, M. Peeters, E. Fenyö, C. López Galíndez, B. Lukashov, J. Bradac, J. Mullins, B. Hahn, F. Gao, A. Abimiku, P. Berman, D. Birx, C. Chappey, G. Ferrari, M. Kalish, F. McCutchan, S. Zolla-Pazner

    Research output: Contribution to journalArticlepeer-review


    Among the major circulating HIV-1 subtypes, subtype C is the most prevalent. To generate full-length sub-type 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-κB-binding sites in the viral promoter-enhancer regions, were found in only a subset of these genomes.
    Original languageEnglish
    Pages (from-to)161-168
    Number of pages7
    JournalAIDS research and human retroviruses
    Issue number2
    Publication statusPublished - 2001


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