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

被引:155
|
作者
Rodenburg, CM
Li, YY
Trask, SA
Chen, YL
Decker, J
Robertson, DL
Kalish, ML
Shaw, GM
Allen, S
Hahn, BH
Gao, F
机构
[1] Univ Alabama, Dept Med, Birmingham, AL 35294 USA
[2] Univ Alabama, Howard Hughes Med Inst, Birmingham, AL 35294 USA
[3] Univ Oxford, Dept Zool, Oxford OX1 3P3, England
[4] CDC, Div AIDS STD & TB Lab Res, Atlanta, GA 30333 USA
[5] Univ Alabama, Dept Epidemiol & Int Hlth, Birmingham, AL 35294 USA
[6] Univ Alabama, Dept Microbiol, Birmingham, AL 35294 USA
关键词
D O I
10.1089/08892220150217247
中图分类号
R392 [医学免疫学]; Q939.91 [免疫学];
学科分类号
100102 ;
摘要
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 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 signatures, including three potential NF-kappaB-binding sites in the viral promoter-enhancer regions, were found in only a subset of these genomes.
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页码:161 / 168
页数:8
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