Lookup NU author(s): Professor Neil Boonham
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© 2017, American Phytopathological Society. All rights reserved. In 2013, a novel virus named Carrot torradovirus 1 (CaTV1) was identified in the U.K. using next generation sequencing (NGS) in asymptomatic carrots (Daucus carota) during an investigation of the causes of root internal necrosis (†). It was recognized as a new member of the genus Torradovirus, an emerging group of viruses in the family Secoviridae affecting a range of crops worldwide. Epidemiological studies carried out in the U.K. in 2014 and 2015 indicated levels of infection up to 26.7 and 64.5%, respectively. Experiments also suggested that CaTV1 may be transmitted by the aphid species Myzus persicae and Cavariella aegopodii (†). So far, CaTV1 has only been described in the U.K. and its presence elsewhere in the world remains to be investigated. In October 2016, a total of 312 asymptomatic and symptomatic leaf samples with reddening, chlorosis, or necrosis were collected from several carrot fields in Aquitaine, in the southwest of France. Total RNAs were extracted using the Nucleospin RNA plant kit (Macherey-Nagel) and eluted in 40 µl of RNase-free water. Sample extracts were tested using a qPCR designed to amplify the cytochrome oxidase (COX) mRNA, used as a measure of the quality of the extraction, and subsequently used as template for RT-qPCR assays for the detection of CaTV1 RNA1 and RNA2 using two pairs of specific primers (†). Samples were also tested for known viruses affecting carrots: Carrot red leaf virus (CRLV), Carrot red leaf associated virus (CRLaV), and Carrot mottle virus (CMoV). The results obtained showed a CaTV1 infection level of 26.7% (16 out of 60 samples) in one of the fields sampled, which was characterized by year-round carrot cultivation and absence of insect control. CaTV1 was not detected in the four other locations sampled. To confirm these results, four of the CaTV1-positive samples were tested by two-step RT-PCR assays using Torradovirus generic primers specific for each of the genomic RNAs (†). After gel electrophoresis, RT-PCR products of 370 (RNA1) and 514 bp (RNA2) were obtained for each of the samples. The identity of CaTV1 was further established by the direct sequencing of representative RT-PCR amplicons (accession nos. KY636379 and KY636380), finally confirming the presence of CaTV1 in the RT-qPCR positive samples. Comparison of the sequences obtained with the CaTV1 U.K. sequences (KF533719 and KF533720) indicated 81 and 97.4% nucleotide (nt) and amino acid (aa) identity, respectively, in the amplified partial polymerase fragment (RNA1) and 85% (nt) and 48.7% (aa) identity, respectively, in the partial coat protein region (RNA2), demonstrating that the French CaTV1 isolate analyzed is significantly different from the U.K. isolate. The evaluation of a possible contribution of CaTV1 to symptom development in France was not possible because of the simultaneous presence in every CaTV1-positive plant of viruses associated with carrot mottle dwarf disease (CRLV, CRLaV, and CMoV). This is the first report of the virus in France and outside the U.K. Further studies are needed in order to establish the prevalence, transmission route, and impact of this virus in the field.
Author(s): Rozado-Aguirre Z, Marais A, Svanella-Dumas L, Faure C, Latour F, Villeneuve F, Dickinson M, Fox A, Boonham N, Candresse T
Publication type: Article
Publication status: Published
Journal: Plant Disease
Print publication date: 01/07/2017
Acceptance date: 02/04/2016
ISSN (print): 0191-2917
Publisher: American Phytopathological Society
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