Abstract
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 language | English |
|---|---|
| Pages (from-to) | 161-168 |
| Number of pages | 8 |
| Journal | AIDS Research and Human Retroviruses |
| Volume | 17 |
| Issue number | 2 |
| DOIs | |
| Publication status | Published - 2001 |
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ASJC Scopus subject areas
- Immunology
- Virology
Cite this
Near full-length clones and reference sequences for subtype C isolates of HIV type 1 from three different continents. / 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.; Gao, F.; Osmanov, S.; Jacobs, L.; Esparza, J.; Galvao-Castro, B.; Shao, Y.; Samuel, N.; Maayan, S.; Bobkov, A.; Smolskaya, T.; Makgoba, W.; Williamson, C.; M'Boup, S.; Mhalu, F.; Auewarakul, P.; Kaleebu, P.; Sempala, S.; Dietrich, U.; Von Briesen, H.; Nick, S.; Nubling, M.; Halbauer, J.; Hamouda, O.; Kücherer, C.; Riedl, R.; Wolf, H.; Hoelscher, M.; Holmes, H.; Beddows, S.; Giraldo, G.; Buonaguro, L.; Scarlatti, G.; Salminen, M.; Van der Groen, G.; Barré-Sinoussi, F.; Peeters, M.; Fenyö, E.; López Galíndez, C.; Lukashov, B.; Bradac, J.; Mullins, J.; Hahn, B.; Gao, F.; Abimiku, A.; Berman, P.; Birx, D.; Chappey, C.; Ferrari, G.; Kalish, M.; McCutchan, F.; Zolla-Pazner, S.
In: AIDS Research and Human Retroviruses, Vol. 17, No. 2, 2001, p. 161-168.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Near full-length clones and reference sequences for subtype C isolates of HIV type 1 from three different continents
AU - Rodenburg, C. M.
AU - Li, Y.
AU - Trask, S. A.
AU - Chen, Y.
AU - Decker, J.
AU - Robertson, D. L.
AU - Kalish, M. L.
AU - Shaw, G. M.
AU - Allen, S.
AU - Hahn, B. H.
AU - Gao, F.
AU - Osmanov, S.
AU - Jacobs, L.
AU - Esparza, J.
AU - Galvao-Castro, B.
AU - Shao, Y.
AU - Samuel, N.
AU - Maayan, S.
AU - Bobkov, A.
AU - Smolskaya, T.
AU - Makgoba, W.
AU - Williamson, C.
AU - M'Boup, S.
AU - Mhalu, F.
AU - Auewarakul, P.
AU - Kaleebu, P.
AU - Sempala, S.
AU - Dietrich, U.
AU - Von Briesen, H.
AU - Nick, S.
AU - Nubling, M.
AU - Halbauer, J.
AU - Hamouda, O.
AU - Kücherer, C.
AU - Riedl, R.
AU - Wolf, H.
AU - Hoelscher, M.
AU - Holmes, H.
AU - Beddows, S.
AU - Giraldo, G.
AU - Buonaguro, L.
AU - Scarlatti, G.
AU - Salminen, M.
AU - Van der Groen, G.
AU - Barré-Sinoussi, F.
AU - Peeters, M.
AU - Fenyö, E.
AU - López Galíndez, C.
AU - Lukashov, B.
AU - Bradac, J.
AU - Mullins, J.
AU - Hahn, B.
AU - Gao, F.
AU - Abimiku, A.
AU - Berman, P.
AU - Birx, D.
AU - Chappey, C.
AU - Ferrari, G.
AU - Kalish, M.
AU - McCutchan, F.
AU - Zolla-Pazner, S.
PY - 2001
Y1 - 2001
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=0035141859&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0035141859&partnerID=8YFLogxK
U2 - 10.1089/08892220150217247
DO - 10.1089/08892220150217247
M3 - Article
C2 - 11177395
AN - SCOPUS:0035141859
VL - 17
SP - 161
EP - 168
JO - AIDS Research and Human Retroviruses
JF - AIDS Research and Human Retroviruses
SN - 0889-2229
IS - 2
ER -