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A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1.

Publication ,  Journal Article
Gao, F; Robertson, DL; Carruthers, CD; Morrison, SG; Jian, B; Chen, Y; Barré-Sinoussi, F; Girard, M; Srinivasan, A; Abimiku, AG; Shaw, GM ...
Published in: J Virol
July 1998

Non-subtype B viruses cause the vast majority of new human immunodeficiency virus type 1 (HIV-1) infections worldwide and are thus the major focus of international vaccine efforts. Although their geographic dissemination is carefully monitored, their immunogenic and biological properties remain largely unknown, in part because well-characterized virological reference reagents are lacking. In particular, full-length clones and sequences are rare, since subtype classification is frequently based on small PCR-derived viral fragments. There are only five proviral clones available for viruses other than subtype B, and these represent only 3 of the 10 proposed (group M) sequence subtypes. This lack of reference sequences also confounds the identification and analysis of mosaic (recombinant) genomes, which appear to be arising with increasing frequency in areas where multiple sequence subtypes cocirculate. To generate a more representative panel of non-subtype B reference reagents, we have cloned (by long PCR or lambda phage techniques) and sequenced 10 near-full-length HIV-1 genomes (lacking less than 80 bp of long terminal repeat sequences) from primary isolates collected at major epicenters of the global AIDS pandemic. Detailed phylogenetic analyses identified six that represented nonrecombinant members of HIV-1 subtypes A (92UG037.1), C (92BR025. 8), D (84ZR085.1 and 94UG114.1), F (93BR020.1), and H (90CF056.1), the last two comprising the first full-length examples of these subtypes. Four others were found to be complex mosaics of subtypes A and C (92RW009.6), A and G (92NG083.2 and 92NG003.1), and B and F (93BR029.4), again emphasizing the impact of intersubtype recombination on global HIV-1 diversification. Although a number of clones had frameshift mutations or translational stop codons in major open reading frames, all the genomes contained a complete set of genes and three had intact genomic organizations without inactivating mutations. Reconstruction of one of these (94UG114.1) yielded replication-competent virus that grew to high titers in normal donor peripheral blood mononuclear cell cultures. This panel of non-subtype B reference genomes should prove valuable for structure-function studies of genetically diverse viral gene products, the generation of subtype-specific immunological reagents, and the production of DNA- and protein-based subunit vaccines directed against a broader spectrum of viruses.

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Published In

J Virol

DOI

ISSN

0022-538X

Publication Date

July 1998

Volume

72

Issue

7

Start / End Page

5680 / 5698

Location

United States

Related Subject Headings

  • Virology
  • Terminology as Topic
  • Repetitive Sequences, Nucleic Acid
  • Recombination, Genetic
  • Proviruses
  • Phylogeny
  • Molecular Sequence Data
  • Middle Aged
  • Male
  • Humans
 

Citation

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Gao, F., Robertson, D. L., Carruthers, C. D., Morrison, S. G., Jian, B., Chen, Y., … Hahn, B. H. (1998). A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1. J Virol, 72(7), 5680–5698. https://doi.org/10.1128/JVI.72.7.5680-5698.1998
Gao, F., D. L. Robertson, C. D. Carruthers, S. G. Morrison, B. Jian, Y. Chen, F. Barré-Sinoussi, et al. “A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1.J Virol 72, no. 7 (July 1998): 5680–98. https://doi.org/10.1128/JVI.72.7.5680-5698.1998.
Gao F, Robertson DL, Carruthers CD, Morrison SG, Jian B, Chen Y, et al. A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1. J Virol. 1998 Jul;72(7):5680–98.
Gao, F., et al. “A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1.J Virol, vol. 72, no. 7, July 1998, pp. 5680–98. Pubmed, doi:10.1128/JVI.72.7.5680-5698.1998.
Gao F, Robertson DL, Carruthers CD, Morrison SG, Jian B, Chen Y, Barré-Sinoussi F, Girard M, Srinivasan A, Abimiku AG, Shaw GM, Sharp PM, Hahn BH. A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1. J Virol. 1998 Jul;72(7):5680–5698.

Published In

J Virol

DOI

ISSN

0022-538X

Publication Date

July 1998

Volume

72

Issue

7

Start / End Page

5680 / 5698

Location

United States

Related Subject Headings

  • Virology
  • Terminology as Topic
  • Repetitive Sequences, Nucleic Acid
  • Recombination, Genetic
  • Proviruses
  • Phylogeny
  • Molecular Sequence Data
  • Middle Aged
  • Male
  • Humans