title: Position-specific automated processing of V3 env ultra-deep pyrosequencing data for predicting HIV-1 tropism.
abstract: HIV-1 coreceptor usage must be accurately determined before starting CCR5 antagonist-based treatment as the presence of undetected minor CXCR4-using variants can cause subsequent virological failure. Ultra-deep pyrosequencing of HIV-1 V3 env allows to detect low levels of CXCR4-using variants that current genotypic approaches miss. However, the computation of the mass of sequence data and the need to identify true minor variants while excluding artifactual sequences generated during amplification and ultra-deep pyrosequencing is rate-limiting. Arbitrary fixed cut-offs below which minor variants are discarded are currently used but the errors generated during ultra-deep pyrosequencing are sequence-dependant rather than random. We have developed an automated processing of HIV-1 V3 env ultra-deep pyrosequencing data that uses biological filters to discard artifactual or non-functional V3 sequences followed by statistical filters to determine position-specific sensitivity thresholds, rather than arbitrary fixed cut-offs. It allows to retain authentic sequences with point mutations at V3 positions of interest and discard artifactual ones with accurate sensitivity thresholds.
authors.affiliation: Laboratoire de Virologie, Hôpital Purpan, Toulouse, F-31300 France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Jeanne
authors.affiliation: Laboratoire de Virologie, Hôpital Purpan, Toulouse, F-31300 France.
authors.forename: Adrien
authors.initials: A
authors.lastname: Saliou
authors.affiliation: Laboratoire de Virologie, Hôpital Purpan, Toulouse, F-31300 France.
authors.forename: Romain
authors.initials: R
authors.lastname: Carcenac
authors.affiliation: Laboratoire de Virologie, Hôpital Purpan, Toulouse, F-31300 France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Lefebvre
authors.affiliation: Laboratoire de Virologie, Hôpital Purpan, Toulouse, F-31300 France.|INSERM, UMR1043, Toulouse, F-31300 France.
authors.forename: Martine
authors.initials: M
authors.lastname: Dubois
authors.affiliation: Laboratoire de Virologie, Hôpital Purpan, Toulouse, F-31300 France.|INSERM, UMR1043, Toulouse, F-31300 France.
authors.forename: Michelle
authors.initials: M
authors.lastname: Cazabat
authors.affiliation: Laboratoire de Virologie, Hôpital Purpan, Toulouse, F-31300 France.|INSERM, UMR1043, Toulouse, F-31300 France.
authors.forename: Florence
authors.initials: F
authors.lastname: Nicot
authors.affiliation: INSERM, UMR1043, Toulouse, F-31300 France.
authors.forename: Claire
authors.initials: C
authors.lastname: Loiseau
authors.affiliation: Laboratoire de Virologie, Hôpital Purpan, Toulouse, F-31300 France.|INSERM, UMR1043, Toulouse, F-31300 France.|Université Toulouse III Paul Sabatier, Toulouse, F-31000 France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Raymond
authors.affiliation: Laboratoire de Virologie, Hôpital Purpan, Toulouse, F-31300 France.|INSERM, UMR1043, Toulouse, F-31300 France.|Université Toulouse III Paul Sabatier, Toulouse, F-31000 France.
authors.forename: Jacques
authors.initials: J
authors.lastname: Izopet
authors.affiliation: INSERM, UMR1043, Toulouse, F-31300 France.|Université Toulouse III Paul Sabatier, Toulouse, F-31000 France.|Service des Maladies Infectieuses et Tropicales, Hôpital Purpan, Toulouse, F-31300 France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Delobel
mesh_terms: D000595:Amino Acid Sequence; D003510:Cyclohexanes / Q000494:pharmacology; D005838:Genotype; D015699:HIV Envelope Protein gp120 / Q000235:genetics* / Q000378:metabolism; D023581:HIV Fusion Inhibitors / Q000494:pharmacology; D015658:HIV Infections / Q000188:drug therapy / Q000378:metabolism / Q000821:virology; D015497:HIV-1 / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D054884:Host-Pathogen Interactions / Q000187:drug effects; D006801:Humans; D000077592:Maraviroc; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000235:genetics* / Q000378:metabolism; D010641:Phenotype; D017354:Point Mutation; D019713:Receptors, CCR5 / Q000378:metabolism; D019718:Receptors, CXCR4 / Q000378:metabolism; D015203:Reproducibility of Results; D014230:Triazoles / Q000494:pharmacology; D056189:Viral Tropism / Q000187:drug effects / Q000235:genetics / Q000502:physiology
chemical_list: C584933:CCR5 protein, human; C527276:CXCR4 protein, human; D003510:Cyclohexanes; D015699:HIV Envelope Protein gp120; D023581:HIV Fusion Inhibitors; C059762:HIV envelope protein gp120 (305-321); D010446:Peptide Fragments; D019713:Receptors, CCR5; D019718:Receptors, CXCR4; D014230:Triazoles; D000077592:Maraviroc