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Virus detection by high-throughput sequencing of small RNAs: large scale performance testing of sequence analysis strategies
hal.structure.identifier | Université de Liège | |
dc.contributor.author | MASSART, Sébastien | |
hal.structure.identifier | National Research Council of Italy | Consiglio Nazionale delle Ricerche [CNR] | |
dc.contributor.author | CHIUMENTI, Michela | |
hal.structure.identifier | Plant Sciences Unit | |
dc.contributor.author | DE JONGHE, Kris | |
hal.structure.identifier | Fera Science Limited | |
dc.contributor.author | GLOVER, Rachel | |
hal.structure.identifier | Plant Sciences Unit | |
dc.contributor.author | HAEGEMAN, Annelies | |
hal.structure.identifier | Biology Centre of the Czech Academy of Sciences [BIOLOGY CENTRE CAS] | |
dc.contributor.author | KOLONIUK, Igor | |
hal.structure.identifier | Crop research institute | |
dc.contributor.author | KOMÍNEK, Petr | |
hal.structure.identifier | International Potato Center [Lima] [CIP] | |
dc.contributor.author | KREUZE, Jan | |
hal.structure.identifier | Department of Biotechnology and Systems Biology | |
dc.contributor.author | KUTNJAK, Denis | |
hal.structure.identifier | Aristotle University of Thessaloniki | |
dc.contributor.author | LOTOS, Leonidas | |
hal.structure.identifier | Université de Liège | |
dc.contributor.author | MACLOT, François | |
hal.structure.identifier | Aristotle University of Thessaloniki | |
dc.contributor.author | MALIOGKA, Varvara | |
hal.structure.identifier | Agricultural Research Council [ARC] | |
dc.contributor.author | MAREE, Hans J. | |
hal.structure.identifier | Life Sciences Department | |
dc.contributor.author | OLIVIER, Thibaut | |
hal.structure.identifier | Instituto Valenciano de Investigaciones Agrarias - Institut Valencià d'Investigacions Agraries - Valencian Institute for agricultural Research [IVIA] | |
dc.contributor.author | OLMOS, Antonio | |
hal.structure.identifier | Biologie et Génétique des Interactions Plante-Parasite [UMR BGPI] | |
hal.structure.identifier | Department of Environmental Sciences | |
dc.contributor.author | POOGGIN, Mikhail M. | |
hal.structure.identifier | Agroscope | |
dc.contributor.author | REYNARD, Jean-Sébastien | |
hal.structure.identifier | Instituto Valenciano de Investigaciones Agrarias - Institut Valencià d'Investigacions Agraries - Valencian Institute for agricultural Research [IVIA] | |
dc.contributor.author | RUIZ-GARCIA, Ana B. | |
hal.structure.identifier | Palacky University Olomouc | |
dc.contributor.author | SAFAROVA, Dana | |
hal.structure.identifier | Université de Bâle = University of Basel = Basel Universität [Unibas] | |
dc.contributor.author | SCHNEEBERGER, Pierre H. H. | |
hal.structure.identifier | Agricultural Research Organization | |
dc.contributor.author | SELA, Noa | |
hal.structure.identifier | Department of Environmental Sciences, Botany | |
dc.contributor.author | TURCO, Silvia | |
hal.structure.identifier | Natural Resources Institute Finland [LUKE] | |
dc.contributor.author | VAINIO, Eeva J. | |
hal.structure.identifier | National Agricultural Research and Innovation Center [NARIC] | |
dc.contributor.author | VARALLYAY, Eva | |
hal.structure.identifier | Unité de Pathologie Végétale [PV] | |
dc.contributor.author | VERDIN, Eric | |
hal.structure.identifier | National Plant Protection Organization [NPPO] | |
dc.contributor.author | WESTENBERG, Marcel | |
hal.structure.identifier | Université de Liège | |
dc.contributor.author | BROSTAUX, Yves | |
hal.structure.identifier | Biologie du fruit et pathologie [BFP] | |
dc.contributor.author | CANDRESSE, Thierry | |
dc.date.issued | 2019 | |
dc.identifier.issn | 0031-949X | |
dc.description.abstractEn | Recent developments in high-throughput sequencing (HTS), also called next-generation sequencing (NGS), technologies and bioinformatics have drastically changed research on viral pathogens and spurred growing interest in the field of virus diagnostics. However, the reliability of HTS-based virus detection protocols must be evaluated before adopting them for diagnostics. Many different bioinformatics algorithms aimed at detecting viruses in HTS data have been reported, but little attention has been paid so far to their sensitivity and reliability for diagnostic purposes. We therefore compared the ability of 21 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 12 plant viruses through a double-blind large scale performance test ten datasets of 21-24 nt small (s)RNA sequences from three different infected plants. The sensitivity of virus detection ranged between 35 and 100% among participants, with a marked negative effect when sequence depth decreased. The false positive detection rate was very low and mainly related to the identification of host genome-integrated viral sequences or misinterpretation of the results. Reproducibility was high (91.6%). This work revealed the key influence of bioinformatics strategies for the sensitive detection of viruses in HTS sRNA datasets and, more specifically (i) the difficulty to detect viral agents when they are novel and/or their sRNA abundance is low, (ii) the influence of key parameters at both assembly and annotation steps, (iii) the importance of completeness of reference sequence databases and (iv) the significant level of scientific expertise needed when interpreting pipelines results. Overall, this work underlines key parameters and proposes recommendations for reliable sRNA-based detection of known and unknown viruses. | |
dc.language.iso | en | |
dc.publisher | American Phytopathological Society | |
dc.subject | Techniques | |
dc.subject | Virology | |
dc.title.en | Virus detection by high-throughput sequencing of small RNAs: large scale performance testing of sequence analysis strategies | |
dc.type | Article de revue | |
dc.identifier.doi | 10.1094/PHYTO-02-18-0067-R | |
dc.subject.hal | Sciences du Vivant [q-bio]/Biologie végétale/Phytopathologie et phytopharmacie | |
dc.subject.hal | Sciences du Vivant [q-bio]/Microbiologie et Parasitologie/Virologie | |
dc.description.sponsorshipEurope | Diversification for Tobacco Growing Farms by the alternative crop Stevia rebaudiana Bertoni | |
bordeaux.journal | Phytopathology | |
bordeaux.page | 488-497 | |
bordeaux.volume | 109 | |
bordeaux.issue | 3 | |
bordeaux.peerReviewed | oui | |
hal.identifier | hal-02627121 | |
hal.version | 1 | |
hal.popular | non | |
hal.audience | Internationale | |
hal.origin.link | https://hal.archives-ouvertes.fr//hal-02627121v1 | |
bordeaux.COinS | ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Phytopathology&rft.date=2019&rft.volume=109&rft.issue=3&rft.spage=488-497&rft.epage=488-497&rft.eissn=0031-949X&rft.issn=0031-949X&rft.au=MASSART,%20S%C3%A9bastien&CHIUMENTI,%20Michela&DE%20JONGHE,%20Kris&GLOVER,%20Rachel&HAEGEMAN,%20Annelies&rft.genre=article |
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