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

Rodenburg, C.M. et al. (2001) Near full-length clones and reference sequences for subtype C isolates of HIV type 1 from three different continents. AIDS Research and Human Retroviruses, 17(2), pp. 161-168. (doi:10.1089/08892220150217247) (PMID:11177395)

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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.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Robertson, Professor David
Authors: Rodenburg, C.M., Li, Y., Trask, S.A., Chen, Y., Decker, J., Robertson, D.L., Kalish, M.L., Shaw, G.M., Allen, S., Hahn, B.H., and Gao, F.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:AIDS Research and Human Retroviruses
Publisher:Mary Ann Liebert
ISSN:0889-2229
ISSN (Online):1931-8405

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