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Comparative performance evaluation of double-stranded RNA high-throughput sequencing for the detection of viral infection in temperate fruit crops

hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorMARAIS, Armelle
hal.structure.identifierLaboratoire de la santé des végétaux [LSV]
dc.contributor.authorGENTIT, Pascal
hal.structure.identifierCtifl - Centre de Lanxade [Ctifl - Centre de Lanxade ]
dc.contributor.authorBRANS, Yoann
hal.structure.identifierLaboratoire de la santé des végétaux [LSV]
dc.contributor.authorRENVOISÉ, Jean Philippe
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorFAURE, Chantal
hal.structure.identifierLaboratoire de la santé des végétaux [LSV]
dc.contributor.authorSAISON, Anne
hal.structure.identifierLaboratoire de la santé des végétaux [LSV]
dc.contributor.authorCOUSSEAU, Pascaline
hal.structure.identifierCtifl - Centre de Lanxade [Ctifl - Centre de Lanxade ]
dc.contributor.authorCASTAING, Julie
hal.structure.identifierLaboratoire de la santé des végétaux [LSV]
dc.contributor.authorCHAMBON, Fabien
hal.structure.identifierLaboratoire de la santé des végétaux [LSV]
dc.contributor.authorPION, Angélique
hal.structure.identifierLaboratoire de la santé des végétaux [LSV]
dc.contributor.authorCALADO, Grégory
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorLEFEBVRE, Marie
hal.structure.identifierLaboratoire de la santé des végétaux [LSV]
dc.contributor.authorGARNIER, Soraya
hal.structure.identifierCtifl - Centre de Lanxade [Ctifl - Centre de Lanxade ]
dc.contributor.authorLATOUR, Francois
hal.structure.identifierCtifl - Centre de Lanxade [Ctifl - Centre de Lanxade ]
dc.contributor.authorBRESSON, Kevin
hal.structure.identifierCtifl - Centre de Lanxade [Ctifl - Centre de Lanxade ]
dc.contributor.authorGRASSEAU, Nathalie
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorCANDRESSE, Thierry
dc.date.issued2024-02-20
dc.identifier.issn0031-949X
dc.description.abstractEnThere is limited information on the compared performance of currently used biological, serological and molecular assays with high-throughput sequencing (HTS) for viral indexing in temperate fruit crops. Here, using a range of samples of predetermined virological status, we compared two performance criteria (inclusivity and analytical sensitivity) of ELISA, molecular hybridization, RT-PCR and double-stranded RNA (dsRNA) HTS for the detection of a total of 14 viruses (10 genera) and four viroids (three genera). Using undiluted samples from individual plants, ELISA had the lowest performance, with an overall detection rate of 68.7%, followed by RT-PCR (82.5%) and HTS (90.7%, and 100% if considering only viruses). The lower performance of RT-PCR reflected the inability to amplify some isolates as a consequence of point mutations affecting primer-binding sites. In addition, HTS identified viruses that had not been identified by others assays in close to two-thirds of samples. Analysis of serial dilutions of fruit tree samples allowed to compare analytical sensitivity for various viruses. ELISA showed the lowest analytical sensitivity but RT-PCR showed higher analytical sensitivity than HTS for a majority of samples. Overall, these results confirm the superiority of HTS over biological indexing in terms of speed, and inclusivity and show that while absolute analytical sensitivity of RT-PCR tends to be higher than that of HTS, PCR inclusivity is affected by viral genetic diversity. Taken together these results make a strong case for the implementation of HTS-based approaches in fruit tree viral testing protocols supporting quarantine and certification programs.
dc.language.isoen
dc.publisherAmerican Phytopathological Society
dc.subject.enFruit tree
dc.subject.enPrunus
dc.subject.enMalus
dc.subject.enPyrus
dc.subject.envirus
dc.subject.enviroid
dc.subject.enIndexing
dc.subject.enHigh-throughput sequencing
dc.subject.endsRNA
dc.title.enComparative performance evaluation of double-stranded RNA high-throughput sequencing for the detection of viral infection in temperate fruit crops
dc.typeArticle de revue
dc.identifier.doi10.1094/PHYTO-12-23-0480-R
dc.subject.halSciences du Vivant [q-bio]
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale/Phytopathologie et phytopharmacie
bordeaux.journalPhytopathology
bordeaux.peerReviewedoui
hal.identifierhal-04530518
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-04530518v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Phytopathology&rft.date=2024-02-20&rft.eissn=0031-949X&rft.issn=0031-949X&rft.au=MARAIS,%20Armelle&GENTIT,%20Pascal&BRANS,%20Yoann&RENVOIS%C3%89,%20Jean%20Philippe&FAURE,%20Chantal&rft.genre=article


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