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, M. L. Kalish, G. M. Shaw, S. Allen, B. H. Hahn, F. Gao, S. Osmanov, L. Jacobs, J. Esparza, B. Galvao-Castro, Y. Shao, N. Samuel, S. Maayan, A. Bobkov, T. SmolskayaW. Makgoba, C. Williamson, S. M'Boup, F. 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 journalArticle

152 Citations (Scopus)

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 languageEnglish
Pages (from-to)161-168
Number of pages8
JournalAIDS Research and Human Retroviruses
Volume17
Issue number2
DOIs
Publication statusPublished - 2001

Fingerprint

HIV-1
China
Clone Cells
Genome
gag-pol Fusion Proteins
nef Genes
pol Genes
gag Genes
env Gene Products
Zambia
Tanzania
Viral Genome
Protein Sequence Analysis
South Africa
Genetic Promoter Regions
Genetic Recombination
Brazil
Sequence Analysis
India
Exons

ASJC Scopus subject areas

  • Immunology
  • Virology

Cite this

Rodenburg, C. M., Li, Y., Trask, S. A., Chen, Y., Decker, J., Robertson, D. L., ... Zolla-Pazner, S. (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), 161-168. https://doi.org/10.1089/08892220150217247

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 journalArticle

Rodenburg, CM, Li, Y, Trask, SA, Chen, Y, Decker, J, Robertson, DL, Kalish, ML, Shaw, GM, Allen, S, Hahn, BH, 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 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, vol. 17, no. 2, pp. 161-168. https://doi.org/10.1089/08892220150217247
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. / Near full-length clones and reference sequences for subtype C isolates of HIV type 1 from three different continents. In: AIDS Research and Human Retroviruses. 2001 ; Vol. 17, No. 2. pp. 161-168.
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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.",
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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

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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.

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