title: Low frequency of CXCR4-using viruses in patients at the time of primary non-subtype-B HIV-1 infection.
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.
authors.affiliation: Universitéé Paris Descartes, EA 3620, AP-HP, Laboratoire de Virologie, Hôpital Necker-Enfants Malades, Paris, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Frange
authors.forename: Marie-Laure
authors.initials: ML
authors.lastname: Chaix
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Raymond
authors.forename: Julie
authors.initials: J
authors.lastname: Galimand
authors.forename: Christiane
authors.initials: C
authors.lastname: Deveau
authors.forename: Laurence
authors.initials: L
authors.lastname: Meyer
authors.forename: Cécile
authors.initials: C
authors.lastname: Goujard
authors.forename: Christine
authors.initials: C
authors.lastname: Rouzioux
authors.forename: Jacques
authors.initials: J
authors.lastname: Izopet
mesh_terms: D005260:Female; D005602:France; D005838:Genotype; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology*; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D019718:Receptors, CXCR4 / Q000378:metabolism*; D015728:Receptors, HIV / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D053585:Virus Attachment; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: C527276:CXCR4 protein, human; D012367:RNA, Viral; D019718:Receptors, CXCR4; D015728:Receptors, HIV; D054299:env Gene Products, Human Immunodeficiency Virus