Abstract
We used genotypic and phenotypic assays to estimate the frequency of X4/DM viruses in 131 patients infected with non-subtype-B viruses at the time of primary HIV-1 infection (PHI). All patients were enrolled in the French PRIMO Cohort from 1996 to 2007. Most strains belonged to CRF02_AG (51.1%) and subtype A (14.5%). Sixteen viruses (12.2%) were classified as CXCR4 tropic ("X4 strains") by the combined criteria of amino acids 11 and 25 of the V3 loop (11/25) and net charge rules and/or the SVMgeno2pheno(10%) algorithm: 6 strains by the combined genotypic rule, 7 by the SVMgeno2pheno(10%) algorithm, and 3, clustering in subtype D, by both algorithms. However, only one strain (0.8%), belonging to subtype A, was defined as a dual-tropic (DM) virus by the phenotypic assay. The 67 CRF02_AG strains included 2 classified as X4 strains by the combined genotypic rule (3%) and 2 others classified as X4 strains by SVMgeno2pheno(10%) (3%), but none of these 4 strains was an X4 or DM strain according to the phenotypic assay. These results suggest that the cellular virus reservoir was established with X4 strains in very few non-subtype-B-infected patients at the time of PHI. Genotypic predictions can overestimate the proportion of non-subtype-B X4 viruses at PHI.
Publication types
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Research Support, Non-U.S. Gov't
MeSH terms
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Female
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France
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Genotype
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HIV Infections / virology*
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HIV-1 / classification
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HIV-1 / genetics
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HIV-1 / isolation & purification
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HIV-1 / physiology*
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Humans
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Male
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Molecular Sequence Data
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Phylogeny
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RNA, Viral / genetics
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Receptors, CXCR4 / metabolism*
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Receptors, HIV / metabolism*
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Sequence Analysis, DNA
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Virus Attachment*
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env Gene Products, Human Immunodeficiency Virus / genetics
Substances
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CXCR4 protein, human
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RNA, Viral
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Receptors, CXCR4
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Receptors, HIV
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env Gene Products, Human Immunodeficiency Virus
Associated data
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GENBANK/GU988902
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GENBANK/GU988903
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GENBANK/GU988904
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