title: Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use.
abstract: The coreceptor used by HIV-1 must be determined before a CCR5 antagonist, part of the arsenal of antiretroviral drugs, is prescribed because viruses that enter cells using the CXCR4 coreceptor are responsible for treatment failure. HIV-1 tropism is also correlated with disease progression and so must be determined for virological studies. Tropism can be determined by next-generation sequencing (NGS), but not all of these new technologies have been fully validated for use in clinical practice. The Illumina NGS technology is used in many laboratories but its ability to predict HIV-1 tropism has not been evaluated while the 454 GS-Junior (Roche) is used for routine diagnosis. The genotypic prediction of HIV-1 tropism is based on sequencing the V3 region and interpreting the results with an appropriate algorithm. We compared the performances of the MiSeq (Illumina) and 454 GS-Junior (Roche) systems with a reference phenotypic assay. We used clinical samples for the NGS tropism predictions and assessed their ability to quantify CXCR4-using variants. The data show that the Illumina platform can be used to detect minor CXCR4-using variants in clinical practice but technical optimization are needed to improve quantification.
authors.affiliation: INSERM, U1043, Toulouse, F-31300, France.|Université Toulouse III Paul-Sabatier, Faculté de Médecine Toulouse-Purpan, Toulouse, F-31300, France.|CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Raymond
authors.affiliation: CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Nicot
authors.affiliation: CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Jeanne
authors.affiliation: CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Delfour
authors.affiliation: CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300, France.
authors.forename: Romain
authors.initials: R
authors.lastname: Carcenac
authors.affiliation: CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300, France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Lefebvre
authors.affiliation: INSERM, U1043, Toulouse, F-31300, France.|CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300, France.
authors.forename: Michelle
authors.initials: M
authors.lastname: Cazabat
authors.affiliation: INSERM, U1043, Toulouse, F-31300, France.|Université Toulouse III Paul-Sabatier, Faculté de Médecine Toulouse-Purpan, Toulouse, F-31300, France.|CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300, France.
authors.forename: Karine
authors.initials: K
authors.lastname: Sauné
authors.affiliation: INSERM, U1043, Toulouse, F-31300, France.|Université Toulouse III Paul-Sabatier, Faculté de Médecine Toulouse-Purpan, Toulouse, F-31300, France.|CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, F-31300, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Delobel
authors.affiliation: INSERM, U1043, Toulouse, F-31300, France.|Université Toulouse III Paul-Sabatier, Faculté de Médecine Toulouse-Purpan, Toulouse, F-31300, France.|CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300, France.
authors.forename: Jacques
authors.initials: J
authors.lastname: Izopet
mesh_terms: D001483:Base Sequence; D015658:HIV Infections / Q000097:blood / Q000821:virology; D015497:HIV-1 / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009154:Mutation / Q000235:genetics; D010641:Phenotype; D019718:Receptors, CXCR4 / Q000235:genetics; D015728:Receptors, HIV / Q000235:genetics*; D056189:Viral Tropism
chemical_list: C527276:CXCR4 protein, human; D019718:Receptors, CXCR4; D015728:Receptors, HIV