A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing

Autor: St John, Elizabeth P., Simen, Birgitte B., Turenchalk, Gregory S., Braverman, Michael S., Abbate, Isabella, Aerssens, Jeroen, Bouchez, Olivier, Gabriel, Christian, Izopet, Jacques, Meixenberger, Karolin, Di Giallonardo, Francesca, Schlapbach, Ralph, Paredes, Roger, Sakwa, James, Schmitz-Agheguian, Gudrun G., Thielen, Alexander, Victor, Martin, Metzner, Karin J., Daeumer, Martin P., 454 HIV-1 Alpha Study Group
Přispěvatelé: 454 Life Sciences, Natl Inst Infect Dis L Spallanzani, Janssen Infect Dis Diagnost Bvba, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], GeT PlaGe, Genotoul, Institut National de la Recherche Agronomique (INRA), Blutzentrale Linz, Fac Med Toulouse - U563, Institut National de la Santé et de la Recherche Médicale (INSERM), Robert Koch Institute [Berlin] (RKI), Div Infect Dis & Hosp Epidemiol, University hospital of Zurich [Zurich], Funct Genom Ctr Zurich, University of Zurich, Institut de Recerca de la Sida (IrsiCaixa), Technol Innovat Agcy Natl Genom Platform, Roche Applied Science, Institute of Immunology and Genetics, École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), ProdInra, Archive Ouverte, GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, Institut National de la Recherche Agronomique ( INRA ), Institut National de la Santé et de la Recherche Médicale ( INSERM ), Robert Koch Institute ( RKI ), Institut de Recerca de la Sida ( IrsiCaixa )
Jazyk: angličtina
Rok vydání: 2016
Předmět:
0301 basic medicine
[SDV]Life Sciences [q-bio]
lcsh:Medicine
population
Drug resistance
law.invention
10234 Clinic for Infectious Diseases
immunodeficiency-virus
reverse-transcriptase inhibitor
minority variant
low-frequency
naive patient
mutation
protease
pcr
diversity
law
Amino Acids
Cooperative Behavior
lcsh:Science
Polymerase chain reaction
education.field_of_study
Multidisciplinary
High-Throughput Nucleotide Sequencing
Amplicon
3. Good health
[SDV] Life Sciences [q-bio]
Plasmids
Research Article
Population
610 Medicine & health
1100 General Agricultural and Biological Sciences
Biology
Tropism
Deep sequencing
03 medical and health sciences
1300 General Biochemistry
Genetics and Molecular Biology

Drug Resistance
Viral

Humans
education
Genotyping
1000 Multidisciplinary
[ SDV ] Life Sciences [q-bio]
lcsh:R
Reproducibility of Results
Molecular biology
Reverse transcriptase
030104 developmental biology
HIV-1
lcsh:Q
Follow-Up Studies
Zdroj: PLoS ONE
PLoS ONE, Public Library of Science, 2016, 11 (1), pp.Non Paginé. ⟨10.1371/journal.pone.0146687⟩
PLoS One
PLoS ONE, Vol 11, Iss 1, p e0146687 (2016)
Recercat. Dipósit de la Recerca de Catalunya
instname
PLoS ONE, 2016, 11 (1), pp.Non Paginé. ⟨10.1371/journal.pone.0146687⟩
Recercat: Dipósit de la Recerca de Catalunya
Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
PLoS ONE, Public Library of Science, 2016, 11 (1), pp.Non Paginé. 〈10.1371/journal.pone.0146687〉
Plos One 1 (11), Non Paginé. (2016)
Dipòsit Digital de Documents de la UAB
Universitat Autònoma de Barcelona
PLoS ONE, 11 (1)
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0146687⟩
Popis: Background Ultra deep sequencing is of increasing use not only in research but also in diagnostics. For implementation of ultra deep sequencing assays in clinical laboratories for routine diagnostics, intra- and inter-laboratory testing are of the utmost importance. Methods A multicenter study was conducted to validate an updated assay design for 454 Life Sciences’ GS FLX Titanium system targeting protease/reverse transcriptase (RTP) and env (V3) regions to identify HIV-1 drug-resistance mutations and determine co-receptor use with high sensitivity. The study included 30 HIV-1 subtype B and 6 subtype non-B samples with viral titers (VT) of 3,940–447,400 copies/mL, two dilution series (52,129–1,340 and 25,130–734 copies/mL), and triplicate samples. Amplicons spanning PR codons 10–99, RT codons 1–251 and the entire V3 region were generated using barcoded primers. Analysis was performed using the GS Amplicon Variant Analyzer and geno2pheno for tropism. For comparison, population sequencing was performed using the ViroSeq HIV-1 genotyping system. Results The median sequencing depth across the 11 sites was 1,829 reads per position for RTP (IQR 592–3,488) and 2,410 for V3 (IQR 786–3,695). 10 preselected drug resistant variants were measured across sites and showed high inter-laboratory correlation across all sites with data (P20% were missed, variants 2–10% were detected at most sites (even at low VT), and variants 1–2% were detected by some sites. All mutations detected by population sequencing were also detected by UDS. Conclusions This assay design results in an accurate and reproducible approach to analyze HIV-1 mutant spectra, even at variant frequencies well below those routinely detectable by population sequencing. ISSN:1932-6203
Databáze: OpenAIRE