Comparative Performance Evaluation of Double-Stranded RNA High-Throughput Sequencing for the Detection of Viral Infection in Temperate Fruit Crops

被引:1
作者
Marais, Armelle [1 ]
Gentit, Pascal [2 ]
Brans, Yoann [3 ]
Renvoise, Jean Philippe [4 ]
Faure, Chantal [1 ]
Saison, Anne [2 ]
Cousseau, Pascaline [2 ]
Castaing, Julie [3 ]
Chambon, Fabien [4 ]
Pion, Angelique [4 ]
Calado, Gregory [4 ]
Lefebvre, Marie [1 ]
Garnier, Soraya [4 ]
Latour, Francois [3 ]
Bresson, Kevin [3 ]
Grasseau, Nathalie [3 ]
Candresse, Thierry [1 ]
机构
[1] Univ Bordeaux, INRAE, UMR Biol Fruit & Pathol 1332, CS20032, F-33882 Villenave Dornon, France
[2] ANSES, Plant Hlth Lab, Unite Bacteriol Virol & Detect OGM, 7 Rue Jean Dixmeras, F-49044 Angers 01, France
[3] Ctr Lanxade, CTIFL, Lab virol fruitiere, F-24130 Prigonrieux, France
[4] ANSES, Unite Quarantaine, Plant Hlth Lab, F-63370 Lempdes, France
关键词
dsRNA; fruit tree; high-throughput sequencing; indexing; Malus; Prunus; Pyrus; viroid; virus; LATENT-RINGSPOT-VIRUS; RT-PCR; PLANT; DIAGNOSIS; TECHNOLOGIES; DIVERSITY; IMPACT; ASSAY;
D O I
10.1094/PHYTO-12-23-0480-R
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
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.
引用
收藏
页码:1701 / 1709
页数:9
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