| Prediction of HIV type 1 subtype C tropism by genotypic algorithms built from subtype B viruses. | |
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MedLine Citation:
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PMID: 19996764 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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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. |
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Authors:
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Stéphanie Raymond; Pierre Delobel; Maud Mavigner; Laurent Ferradini; Michelle Cazabat; Corinne Souyris; Karine Sandres-Sauné; Christophe Pasquier; Bruno Marchou; Patrice Massip; Jacques Izopet |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: Journal of acquired immune deficiency syndromes (1999) Volume: 53 ISSN: 1944-7884 ISO Abbreviation: J. Acquir. Immune Defic. Syndr. Publication Date: 2010 Feb |
Date Detail:
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Created Date: 2010-01-28 Completed Date: 2010-02-17 Revised Date: 2011-09-06 |
Medline Journal Info:
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Nlm Unique ID: 100892005 Medline TA: J Acquir Immune Defic Syndr Country: United States |
Other Details:
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Languages: eng Pagination: 167-75 Citation Subset: IM; X |
Affiliation:
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INSERM, U563, Toulouse, F-31300 France. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Algorithms Amino Acid Sequence France / epidemiology Gene Expression Regulation, Viral Genotype HIV Envelope Protein gp120 / chemistry, genetics, metabolism HIV Infections / epidemiology, virology* HIV-1 / classification*, genetics* Humans Malawi / epidemiology Molecular Sequence Data Peptide Fragments / chemistry, genetics, metabolism Receptors, CCR5 Sensitivity and Specificity Viral Tropism / genetics* Virus Internalization |
| Chemical | |
Reg. No./Substance:
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0/HIV Envelope Protein gp120; 0/HIV envelope protein gp120 (305-321); 0/Peptide Fragments; 0/Receptors, CCR5 |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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