دورية أكاديمية
Comparative Performance Evaluation of Double-Stranded RNA High-Throughput Sequencing for the Detection of Viral Infection in Temperate Fruit Crops.
| العنوان: | Comparative Performance Evaluation of Double-Stranded RNA High-Throughput Sequencing for the Detection of Viral Infection in Temperate Fruit Crops. |
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| المؤلفون: | Marais A; INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France., Gentit P; ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France., Brans Y; CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France., Renvoisé JP; ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France., Faure C; INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France., Saison A; ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France., Cousseau P; ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France., Castaing J; CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France., Chambon F; ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France., Pion A; ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France., Calado G; ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France., Lefebvre M; INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France., Garnier S; ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France., Latour F; CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France., Bresson K; CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France., Grasseau N; CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France., Candresse T; INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France. |
| المصدر: | Phytopathology [Phytopathology] 2024 Jul; Vol. 114 (7), pp. 1701-1709. Date of Electronic Publication: 2024 Jun 10. |
| نوع المنشور: | Journal Article; Comparative Study |
| اللغة: | English |
| بيانات الدورية: | Publisher: American Phytopathological Society] Country of Publication: United States NLM ID: 9427222 Publication Model: Print-Electronic Cited Medium: Print ISSN: 0031-949X (Print) Linking ISSN: 0031949X NLM ISO Abbreviation: Phytopathology Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: [St. Paul, Minn., etc., American Phytopathological Society] |
| مواضيع طبية MeSH: | High-Throughput Nucleotide Sequencing* , Plant Diseases*/virology , Crops, Agricultural*/virology , Plant Viruses*/genetics , Plant Viruses*/isolation & purification , RNA, Double-Stranded*/genetics , Fruit*/virology , RNA, Viral*/genetics, Enzyme-Linked Immunosorbent Assay ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Viroids/genetics ; Viroids/isolation & purification |
| مستخلص: | There is limited information on the compared performances of 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 enzyme-linked immunosorbent assay (ELISA), molecular hybridization, reverse transcription (RT)-PCR, and double-stranded RNA (dsRNA) HTS for the detection of a total of 14 viruses (10 genera) and four viroids (three genera). When undiluted samples from individual plants were used, ELISA had the lowest performance, with an overall detection rate of 68.7%, followed by RT-PCR (82.5%) and HTS (90.7%; 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 other assays in nearly two-thirds of the samples. Analysis of serial dilutions of fruit tree samples allowed comparison of analytical sensitivities for various viruses. ELISA showed the lowest analytical sensitivity, but RT-PCR showed higher analytical sensitivity than HTS for most of the samples. Overall, these results confirm the superiority of HTS over biological indexing in terms of speed and inclusivity and show that while the 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. Competing Interests: The author(s) declare no conflict of interest. |
| فهرسة مساهمة: | Keywords: Malus; Prunus; Pyrus; dsRNA; fruit tree; high-throughput sequencing; indexing; viroid; virus |
| المشرفين على المادة: | 0 (RNA, Double-Stranded) 0 (RNA, Viral) |
| تواريخ الأحداث: | Date Created: 20240220 Date Completed: 20240719 Latest Revision: 20240719 |
| رمز التحديث: | 20240719 |
| DOI: | 10.1094/PHYTO-12-23-0480-R |
| PMID: | 38376958 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 0031-949X |
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| DOI: | 10.1094/PHYTO-12-23-0480-R |