Prediction of HIV Type 1 Subtype C Tropism by Genotypic Algorithms Built From Subtype B Viruses

被引:48
作者
Raymond, Stephanie [1 ,2 ,3 ]
Delobel, Pierre [1 ,2 ,4 ]
Mavigner, Maud [1 ]
Ferradini, Laurent [5 ]
Cazabat, Michelle [1 ,3 ]
Souyris, Corinne [1 ,3 ]
Sandres-Saune, Karine [1 ,2 ,3 ]
Pasquier, Christophe [1 ,2 ,3 ]
Marchou, Bruno [2 ,4 ]
Massip, Patrice [2 ,4 ]
Izopet, Jacques [1 ,2 ,3 ]
机构
[1] INSERM, U563, F-31300 Toulouse, France
[2] Univ Toulouse 3, Fac Med Toulouse Purpan, F-31300 Toulouse, France
[3] CHU Toulouse, Hop Purpan, Virol Lab, F-31300 Toulouse, France
[4] CHU Toulouse, Hop Purpan, Serv Malad Infect & Trop, F-31300 Toulouse, France
[5] Epictr, Paris, France
关键词
HIV envelope protein 120; V3; genotype; phenotype; CCR5; CXCR4; HIV-1 subtype C; ACTIVE ANTIRETROVIRAL THERAPY; DISEASE PROGRESSION; CORECEPTOR USAGE; SOUTH-AFRICA; MAJOR CORECEPTOR; SMALL-MOLECULE; V3; SEQUENCES; CXCR4; CCR5; PHENOTYPE;
D O I
10.1097/QAI.0b013e3181c8413b
中图分类号
R392 [医学免疫学]; Q939.91 [免疫学];
学科分类号
100102 ;
摘要
Background: Genotypic predictions of HIV-1 tropism could simplify CCR5 antagonist usage. However, the genotypic algorithms built from subtype B viruses could be inadequate for non-B subtypes. We therefore performed paired genotypic and phenotypic determination of subtype C tropism. Methods: We studied 52 patients recruited in Malawi and 21 patients recruited in France. We directly sequenced the V3 env region and performed a recombinant virus phenotypic entry assay in parallel. Results: The Malawi patients had 29% of CXCR4-using subtype C viruses compared with only 5% in the patients from France. For detecting CXCR4-using subtype C viruses, the genotypic rule combining the amino acids at positions 11/25 and the net charge of V3 was 93.3% sensitive and 96.4% specific. The Geno2pheno tool was 86.7% sensitive and 89.1% specific. The WebPSSM tool with the SI/NSI matrix was 80% sensitive and 98.2% specific in its subtype B version and 93.3% sensitive and 81.8% specific in its subtype C version. Conclusions: The genotypic determinants of coreceptor usage for HIV-1 subtype C were mainly in V3 and were globally similar to those previously reported for subtype B viruses. The main genotypic algorithms built from subtype B viruses perform well when applied to subtype C viruses.
引用
收藏
页码:167 / 175
页数:9
相关论文
共 35 条
  • [1] CC CKRS: A RANTES, MIP-1 alpha, MIP-1 beta receptor as a fusion cofactor for macrophage-tropic HIV-1
    Alkhatib, G
    Combadiere, C
    Broder, CC
    Feng, Y
    Kennedy, PE
    Murphy, PM
    Berger, EA
    [J]. SCIENCE, 1996, 272 (5270) : 1955 - 1958
  • [2] A small-molecule, nonpeptide CCR5 antagonist with highly potent and selective anti-HIV-1 activity
    Baba, M
    Nishimura, O
    Kanzaki, N
    Okamoto, M
    Sawada, H
    Iizawa, Y
    Shiraishi, M
    Aramaki, Y
    Okonogi, K
    Ogawa, Y
    Meguro, K
    Fujino, M
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 96 (10) : 5698 - 5703
  • [3] A new classification for HIV-1
    Berger, EA
    Doms, RW
    Fenyö, EM
    Korber, BTM
    Littman, DR
    Moore, JP
    Sattentau, QJ
    Schuitemaker, H
    Sodroski, J
    Weiss, RA
    [J]. NATURE, 1998, 391 (6664) : 240 - 240
  • [4] Envelope V3 amino acid sequence predicts HIV-1 phenotype (co-receptor usage and tropism for macrophages)
    Briggs, DR
    Tuffle, DL
    Sleasman, JW
    Goodenow, MM
    [J]. AIDS, 2000, 14 (18) : 2937 - 2939
  • [5] Absence of coreceptor switch with disease progression in human immunodeficiency virus infections in India
    Cecilia, D
    Kulkarni, SS
    Tripathy, SP
    Gangakhedkar, RR
    Paranjape, RS
    Gadkari, DA
    [J]. VIROLOGY, 2000, 271 (02) : 253 - 258
  • [6] Mapping of independent V3 envelope determinants of human immunodeficiency virus type 1 macrophage tropism and syncytium formation in lymphocytes
    Chesebro, B
    Wehrly, K
    Nishio, J
    Perryman, S
    [J]. JOURNAL OF VIROLOGY, 1996, 70 (12) : 9055 - 9059
  • [7] Genotypic and phenotypic characterization of viral isolates from HIV-1 subtype C-infected children with slow and rapid disease progression
    Choge, Isaac
    Cilliers, Tonie
    Walker, Polly
    Taylor, Natasha
    Phoswa, Mary
    Meyers, Tammy
    Viljoen, Johannes
    Violari, Avy
    Gray, Glenda
    Moore, Penny L.
    Papathanosopoulos, Maria
    Morris, Lynn
    [J]. AIDS RESEARCH AND HUMAN RETROVIRUSES, 2006, 22 (05) : 458 - 465
  • [8] The CCR5 and CXCR4 coreceptors are both used by human immunodeficiency virus type 1 primary isolates from subtype C
    Cilliers, T
    Nhlapo, J
    Coetzer, M
    Orlovic, D
    Ketas, T
    Olson, WC
    Moore, JP
    Trkola, A
    Morris, L
    [J]. JOURNAL OF VIROLOGY, 2003, 77 (07) : 4449 - 4456
  • [9] Genetic characteristics of the V3 region associated with CXCR4 usage in HIV-1 subtype C isolates
    Coetzer, Mia
    Cilliers, Tonie
    Ping, Li-Hua
    Swanstrom, Ronald
    Morris, Lynn
    [J]. VIROLOGY, 2006, 356 (1-2) : 95 - 105
  • [10] Emergence of X4 usage among HIV-1 subtype C: evidence for an evolving epidemic in South Africa
    Connell, Bridgette J.
    Michler, Katherine
    Capovilla, Alexio
    Venter, Willem D. F.
    Stevens, Wendy S.
    Papathanasopoulos, Maria A.
    [J]. AIDS, 2008, 22 (07) : 896 - 899