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Moubset O, Filloux D, Fontes H, Julian C, Fernandez E, Galzi S, Blondin L, Chehida SB, Lett JM, Mesléard F, Kraberger S, Custer JM, Salywon A, Makings E, Marais A, Chiroleu F, Lefeuvre P, Martin DP, Candresse T, Varsani A, Ravigné V, Roumagnac P. Virome release of an invasive exotic plant species in southern France. Virus Evol 2024; 10:veae025. [PMID: 38566975 PMCID: PMC10986800 DOI: 10.1093/ve/veae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/27/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments can outcompete indigenous species and become invasive. We here propose the virome release hypothesis (VRH) as a virus-centered variant of the conventional ERH that is only focused on enemies. The VRH predicts that vertically transmitted plant-associated viruses (PAV, encompassing phytoviruses and mycoviruses) should be co-introduced during the dissemination of the IEPS, while horizontally transmitted PAV of IEPS should be left behind or should not be locally transmitted in the introduced area due to a maladaptation of local vectors. To document the VRH, virome richness and composition as well as PAV prevalence, co-infection, host range, and transmission modes were compared between indigenous plant species and an invasive grass, cane bluestem (Bothriochloa barbinodis), in both its introduced range (southern France) and one area of its native range (Sonoran Desert, Arizona, USA). Contrary to the VRH, we show that invasive populations of B. barbinodis in France were not associated with a lower PAV prevalence or richness than native populations of B. barbinodis from the USA. However, comparison of virome compositions and network analyses further revealed more diverse and complex plant-virus interactions in the French ecosystem, with a significant richness of mycoviruses. Setting mycoviruses apart, only one putatively vertically transmitted phytovirus (belonging to the Amalgaviridae family) and one putatively horizontally transmitted phytovirus (belonging to the Geminiviridae family) were identified from B. barbinodis plants in the introduced area. Collectively, these characteristics of the B. barbinodis-associated PAV community in southern France suggest that a virome release phase may have immediately followed the introduction of B. barbinodis to France in the 1960s or 1970s, and that, since then, the invasive populations of this IEPS have already transitioned out of this virome release phase, and have started interacting with several local mycoviruses and a few local plant viruses.
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Affiliation(s)
- Oumaima Moubset
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Denis Filloux
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Hugo Fontes
- Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc, Arles 13200, France
- Institut Méditerranéen de Biodiversité et Ecologie, UMR CNRS-IRD, Avignon Université, Aix-Marseille Université, IUT d’Avignon, Avignon 84911, France
| | - Charlotte Julian
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Emmanuel Fernandez
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Serge Galzi
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Laurence Blondin
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | | | | | - François Mesléard
- Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc, Arles 13200, France
- Institut Méditerranéen de Biodiversité et Ecologie, UMR CNRS-IRD, Avignon Université, Aix-Marseille Université, IUT d’Avignon, Avignon 84911, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew Salywon
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ 85008, USA
| | - Elizabeth Makings
- Vascular Plant Herbarium, School of Life Sciences, Arizona State University, 734 West Alameda Drive, Tempe Tempe, AZ 85282, USA
| | - Armelle Marais
- UMR BFP, University Bordeaux, INRAE, Villenave d’Ornon 33140, France
| | | | | | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Rd, Cape Town 7925, South Africa
| | - Thierry Candresse
- UMR BFP, University Bordeaux, INRAE, Villenave d’Ornon 33140, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7700, South Africa
| | - Virginie Ravigné
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Philippe Roumagnac
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
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Marais A, Gentit P, Brans Y, Renvoisé JP, Faure C, Saison A, Cousseau P, Castaing J, Chambon F, Pion A, Calado G, Lefebvre M, Garnier S, Latour F, Bresson K, Grasseau N, Candresse T. Comparative performance evaluation of double-stranded RNA high-throughput sequencing for the detection of viral infection in temperate fruit crops. Phytopathology 2024. [PMID: 38376958 DOI: 10.1094/phyto-12-23-0480-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
There 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.
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Affiliation(s)
| | - Pascal Gentit
- Anses Laboratoire de la sante des vegetaux, 205543, Angers, Pays de la Loire, France;
| | - Yoann Brans
- Centre technique interprofessionnel des fruits et legumes, 113950, LVBM - Virology and molecular laboratory, 28 route des Nebouts, Prigonrieux, France, 24130;
| | - Jean Philippe Renvoisé
- Anses Laboratoire de la sante des vegetaux, 205543, Unité de Quarantaine, Lempdes, Auvergne, France;
| | | | - Anne Saison
- Anses Laboratoire de la sante des vegetaux, 205543, Angers, Pays de la Loire, France;
| | - Pascaline Cousseau
- Anses Laboratoire de la sante des vegetaux, 205543, Angers, Pays de la Loire, France;
| | - Julie Castaing
- Centre technique interprofessionnel des fruits et legumes, 113950, LVBM - Virology and molecular laboratory, Prigonrieux, Île-de-France, France;
| | - Fabien Chambon
- Anses Laboratoire de la sante des vegetaux, 205543, Unité de Quarantaine, Lempdes, Auvergne, France;
| | - Angélique Pion
- Anses Laboratoire de la sante des vegetaux, 205543, Unité de Quarantaine, Lempdes, Auvergne, France;
| | - Grégory Calado
- Anses Laboratoire de la sante des vegetaux, 205543, Unité de Quarantaine, Lempdes, Auvergne, France;
| | | | - Soraya Garnier
- Anses Laboratoire de la sante des vegetaux, 205543, Unité de Quarantaine, Lempdes, Auvergne, France;
| | | | - Kevin Bresson
- Centre technique interprofessionnel des fruits et legumes, 113950, LVBM - Virology and molecular laboratory, Prigonrieux, Île-de-France, France;
| | - Nathalie Grasseau
- Centre technique interprofessionnel des fruits et legumes, 113950, LVBM - Virology and molecular laboratory, Prigonrieux, France;
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Schönegger D, Moubset O, Margaria P, Menzel W, Winter S, Roumagnac P, Marais A, Candresse T. Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community. J Virol 2023; 97:e0130023. [PMID: 37888981 PMCID: PMC10688312 DOI: 10.1128/jvi.01300-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities of varying complexity levels, up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 families and 61 genera of plant viruses. The results obtained confirm that the dsRNA-based approach provides a more complete representation of the RNA virome, in particular, for high complexity ones. However, for viromes of low to medium complexity, VANA appears a reasonable alternative and would be the preferred choice if analysis of DNA viruses is of importance. Several parameters impacting performance were identified as well as a direct relationship between the completeness of virome description and sample sequencing depth. The strategy, results, and tools used here should prove useful in a range of virome analysis efforts.
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Affiliation(s)
| | - Oumaima Moubset
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Paolo Margaria
- Plant Virus Department, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Wulf Menzel
- Plant Virus Department, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Stephan Winter
- Plant Virus Department, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d’Ornon, France
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Candresse T, Faure C, Calonnec A, Cartolaro P, Marais A. First report of Vitis cryptic virus (VCV) infecting mildew-resistant grapevine interspecific hybrids in France. Plant Dis 2023. [PMID: 37828707 DOI: 10.1094/pdis-09-23-1751-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Vitis cryptic virus (VCV), a deltapartitivirus identified in Japan in Vitis coignetiae (Nabeshima and Abe, 2021), is known from only two other countries. It was detected in China (Fan et al., 2022) and in Russia, including in a V. labrusca and the Saperavi Severnyi interspecific hybrid (Shvets et al., 2022). There is no information on VCV pathogenicity but deltapartitiviruses are generally not pathogenic. Fan et al. (2022) reported VCV graft transmission and chlorotic mottling symptoms developing on a graft-inoculated vine, in spite of the fact that cryptic viruses are not known to move cell-to-cell or be graft-transmissible. In fall 2022, a few plants of the Prior interspecific hybrid (https://www.vivc.de) showed unusual red blotch and leaf curl in Bordeaux (France), prompting the HTS analysis of two plants using total leaf RNA. Following host genome substraction, the ribodepleted RNASeq data was assembled de novo using CLC Genomics Workbench (Candresse et al., 2018) and contigs annotated by BlastX against the GenBank database. Rupestris stem pitting virus, grapevine pinot gris virus, hop stunt viroid and grapevine yellow speckle viroid 1 were identified. In addition, mycoviral contigs were identified, together with contigs for Rhopalosiphum padi virus and a divergent isolate of barley aphid RNA virus 10 (the later only in one plant), and the two genomic RNAs of VCV. The VCV RNA1 contigs were 1570 and 1574 nucleotides (nt) long, respectively, and 100% identical, showing 97.1% nt identity to a Japanese isolate (LC746759). They integrated 6480 and 4613 reads (0.2 and 0.4% of total substracted reads) for a coverage of 611 and 433x, respectively. The VCV RNA2 contigs were also 100% identical and shared 95.5% identity with a Japanese isolate (LC746761). They were 1518-1519 nt long, integrated 11338 and 9999 reads (0.4 and 0.9% of reads) for a coverage of 1109 and 972x, respectively. The Prior VCV RNAs were deposited in GenBank (OR474475-76). Specific RNA2 primers 5' TTACAGGTTTGATTGGAATCATG 3' and 5' ATAGTAGGTCCAATCACTAATC 3' (Tm 56°C) were used to confirm VCV presence in the original plants as well as in three other asymptomatic Prior vines. Amplicons 100% identical to the contigs were obtained from 4 of 5 plants. Two plants of Bronner, one of Prior parents, also tested positive. The rootstock (Fercal) of a VCV-infected Prior and two plants of another hybrid, Artaban, (sampled in the same plot as Prior) tested negative. BlastN datamining identified VCV reads in RNASeq data from a range of wild grapevines including V. acerifolia (SRX2885763), V. quinquangularis (SRX1496837), V. romanetii (SRR3938616), V. cinerea (SRR10135144), V. davidii (SRR3255926), V. amurensis (SRX13387918) and V. vinifera subsp. sylvestris (HAOE01029819, HAOE01001237). Although not experimentally verified, detection in wild Vitis, including V. amurensis, a Saperavi Severnyi, Bronner and Prior progenitor, suggests VCV might have been introduced in these hybrids through crosses aiming to develop powdery and downy mildew resistant varieties. To the best of our knowledge, this is the first report of VCV infection in grapevine in France. The symptoms that prompted this research have not recurred in 2023 and are not linked to VCV because the virus was also identified in symptomless Prior plants. The risk of introducing VCV in European grapevine through breeding efforts appears limited, but VCV may be present in fungal disease-resistant cultivars in a range of countries.
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Affiliation(s)
- Thierry Candresse
- INRA Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, INRA - Université de Bordeaux, CS20032, Villenave d'Ornon , France, 33882 cedex;
| | - Chantal Faure
- INRAE, 27057, UMR 1332 BFP, Paris, Aquitaine, France;
| | | | | | - Armelle Marais
- INRAE, 27057, UMR 1332 Biologie du Fruit et Pathologie, INRA - Université de Bordeaux, Paris, Aquitaine, France;
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Orfanidou CG, Katsiani A, Candresse T, Marais A, Gkremotsi T, Drogoudi P, Kazantzis K, Katis NI, Maliogka VI. Identification of divergent isolates of cherry latent virus 1 in Greek sweet cherry orchards. Arch Virol 2023; 168:243. [PMID: 37676309 PMCID: PMC10485082 DOI: 10.1007/s00705-023-05875-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023]
Abstract
In this study, samples collected from eight sweet cherry trees in northern Greece were analyzed by high-throughput sequencing for the presence of viruses. Bioinformatic analysis revealed the presence of divergent isolates of cherry latent virus 1 (CLV-1), a recently identified trichovirus in a sweet cherry accession imported into the USA from the Republic of Georgia. The complete genome sequences of seven CLV-1 isolates were determined, and phylogenetic analysis indicated that they belonged to a separate clade from the previously characterized Georgian isolate. A small-scale survey confirmed the presence of CLV-1 in 47 out of 151 sweet cherry samples tested, and partial sequencing of 15 isolates showed a high degree of nucleotide sequence similarity among them.
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Affiliation(s)
- Chrysoula G Orfanidou
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Asimina Katsiani
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, France
| | - Theodora Gkremotsi
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Pavlina Drogoudi
- Department of Deciduous Fruit trees, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization - 'DIMITRA', 38 R.R. Station, Naoussa, 59035, Greece
| | - Konstantinos Kazantzis
- Department of Deciduous Fruit trees, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization - 'DIMITRA', 38 R.R. Station, Naoussa, 59035, Greece
| | - Nikolaos I Katis
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Varvara I Maliogka
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece.
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Rivarez MPS, Faure C, Svanella-Dumas L, Pecman A, Tušek-Žnidaric M, Schönegger D, De Jonghe K, Blouin A, Rasmussen DA, Massart S, Ravnikar M, Kutnjak D, Marais A, Candresse T. Diversity and Pathobiology of an Ilarvirus Unexpectedly Detected in Diverse Plants and Global Sequencing Data. Phytopathology 2023; 113:1729-1744. [PMID: 37399026 DOI: 10.1094/phyto-12-22-0465-v] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
High-throughput sequencing (HTS) and sequence mining tools revolutionized virus detection and discovery in recent years, and implementing them with classical plant virology techniques results in a powerful approach to characterize viruses. An example of a virus discovered through HTS is Solanum nigrum ilarvirus 1 (SnIV1) (Bromoviridae), which was recently reported in various solanaceous plants from France, Slovenia, Greece, and South Africa. It was likewise detected in grapevines (Vitaceae) and several Fabaceae and Rosaceae plant species. Such a diverse set of source organisms is atypical for ilarviruses, thus warranting further investigation. In this study, modern and classical virological tools were combined to accelerate the characterization of SnIV1. Through HTS-based virome surveys, mining of sequence read archive datasets, and a literature search, SnIV1 was further identified from diverse plant and non-plant sources globally. SnIV1 isolates showed relatively low variability compared with other phylogenetically related ilarviruses. Phylogenetic analyses showed a distinct basal clade of isolates from Europe, whereas the rest formed clades of mixed geographic origin. Furthermore, systemic infection of SnIV1 in Solanum villosum and its mechanical and graft transmissibility to solanaceous species were demonstrated. Near-identical SnIV1 genomes from the inoculum (S. villosum) and inoculated Nicotiana benthamiana were sequenced, thus partially fulfilling Koch's postulates. SnIV1 was shown to be seed-transmitted and potentially pollen-borne, has spherical virions, and possibly induces histopathological changes in infected N. benthamiana leaf tissues. Overall, this study provides information to better understand the diversity, global presence, and pathobiology of SnIV1; however, its possible emergence as a destructive pathogen remains uncertain. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Mark Paul Selda Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Chantal Faure
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Laurence Svanella-Dumas
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Anja Pecman
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Magda Tušek-Žnidaric
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Deborah Schönegger
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Merelbeke, 9820, Belgium
| | - Arnaud Blouin
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium
| | - David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, 27606, U.S.A
| | - Sebastien Massart
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Armelle Marais
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Thierry Candresse
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
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Schönegger D, Marais A, Babalola BM, Faure C, Lefebvre M, Svanella-Dumas L, Brázdová S, Candresse T. Carrot populations in France and Spain host a complex virome rich in previously uncharacterized viruses. PLoS One 2023; 18:e0290108. [PMID: 37585477 PMCID: PMC10431682 DOI: 10.1371/journal.pone.0290108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/01/2023] [Indexed: 08/18/2023] Open
Abstract
High-throughput sequencing (HTS) has proven a powerful tool to uncover the virome of cultivated and wild plants and offers the opportunity to study virus movements across the agroecological interface. The carrot model consisting of cultivated (Daucus carota ssp. sativus) and wild carrot (Daucus carota ssp. carota) populations, is particularly interesting with respect to comparisons of virus communities due to the low genetic barrier to virus flow since both population types belong to the same plant species. Using a highly purified double-stranded RNA-based HTS approach, we analyzed on a large scale the virome of 45 carrot populations including cultivated, wild and off-type carrots (carrots growing within the field and likely representing hybrids between cultivated and wild carrots) in France and six additional carrot populations from central Spain. Globally, we identified a very rich virome comprising 45 viruses of which 25 are novel or tentatively novel. Most of the identified novel viruses showed preferential associations with wild carrots, either occurring exclusively in wild populations or infecting only a small proportion of cultivated populations, indicating the role of wild carrots as reservoir of viral diversity. The carrot virome proved particularly rich in viruses involved in complex mutual interdependencies for aphid transmission such as poleroviruses, umbraviruses and associated satellites, which can be the basis for further investigations of synergistic or antagonistic virus-vector-host relationships.
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Affiliation(s)
- Deborah Schönegger
- INRAE &, UMR 1332 Biology du Fruit et Pathologie, Univ. Bordeaux, Villenave d’Ornon Cedex, France
| | - Armelle Marais
- INRAE &, UMR 1332 Biology du Fruit et Pathologie, Univ. Bordeaux, Villenave d’Ornon Cedex, France
| | - Bisola Mercy Babalola
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Madrid, Spain
| | - Chantal Faure
- INRAE &, UMR 1332 Biology du Fruit et Pathologie, Univ. Bordeaux, Villenave d’Ornon Cedex, France
| | - Marie Lefebvre
- INRAE &, UMR 1332 Biology du Fruit et Pathologie, Univ. Bordeaux, Villenave d’Ornon Cedex, France
| | - Laurence Svanella-Dumas
- INRAE &, UMR 1332 Biology du Fruit et Pathologie, Univ. Bordeaux, Villenave d’Ornon Cedex, France
| | - Sára Brázdová
- INRAE &, UMR 1332 Biology du Fruit et Pathologie, Univ. Bordeaux, Villenave d’Ornon Cedex, France
| | - Thierry Candresse
- INRAE &, UMR 1332 Biology du Fruit et Pathologie, Univ. Bordeaux, Villenave d’Ornon Cedex, France
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8
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Svanella-Dumas L, Tsarmpopoulos I, Marais A, Faure C, Theil S, Glasa M, Predajna L, Gaudin J, Tian S, Porcher L, Gentit P, De Oliveira ML, Krause-Sakate R, Candresse T. Molecular and Biological Characterization of Novel and Known Family Secoviridae Members Infecting Lettuce. Phytopathology 2023; 113:1595-1604. [PMID: 37081712 DOI: 10.1094/phyto-03-23-0095-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
High-throughput sequencing of two lettuces showing virus-like symptoms in France provided evidence of infection by members of the family Secoviridae. One plant (JG1) had a complex mixed infection that involved, among others, a novel waikavirus (lettuce waikavirus 1) and two isolates of a sequivirus related to lettuce mottle virus (LeMoV). The second lettuce plant (JG2) was singly infected by LeMoV. Complete genomic sequences were obtained for all four isolates and, in addition, near complete genome sequences were obtained for other LeMoV or LeMoV-related isolates (from French cultivated and wild lettuces and from a Brazilian cultivated lettuce) and for two isolates of another family Asteraceae-infecting sequivirus, dandelion yellow mosaic virus (DaYMV). Analysis of these genomic sequences allows the proposal of tentative genome organization for the various viruses and clarification of their phylogenetic relationships. Sequence and host range comparisons point to significant differences between the two sequivirus isolates identified in the JG1 plant and LeMoV isolates from France and Brazil, suggesting they belong to a novel species for which the name lettuce star mosaic virus is proposed.
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Affiliation(s)
- Laurence Svanella-Dumas
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Iason Tsarmpopoulos
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Armelle Marais
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Chantal Faure
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Miroslav Glasa
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic
| | - Lukas Predajna
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic
| | - Jonathan Gaudin
- INRAE, Bordeaux Sciences Agro, UMR Santé et Agroécologie du Vignoble, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Sixing Tian
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Laëtitia Porcher
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Pascal Gentit
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Milena Leite De Oliveira
- Laboratorio Central Multisuarios (LACEM), Faculdade de Ciências Agronômicas, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - Renate Krause-Sakate
- Department of Plant Protection, Faculdade de Ciências Agronômicas, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - Thierry Candresse
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
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9
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Diouf MB, Guyader S, Nopoly MM, Gaspard O, Filloux D, Candresse T, Marais A, Teycheney PY, Umber M. Molecular diversity of yam virus Y and identification of banana mild mosaic virus isolates infecting yam (Dioscorea spp.). Arch Virol 2023; 168:180. [PMID: 37311875 DOI: 10.1007/s00705-023-05809-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/02/2023] [Indexed: 06/15/2023]
Abstract
Two members of the family Betaflexiviridae associated with yam (Dioscorea spp.) have been described so far: yam latent virus (YLV) and yam virus Y (YVY). However, their geographical distribution and molecular diversity remain poorly documented. Using a nested RT-PCR assay, we detected YVY in D. alata, D. bulbifera, D. cayenensis, D. rotundata, and D. trifida in Guadeloupe, and in D. rotundata in Côte d'Ivoire, thus extending the known host range of this virus and geographical distribution. Using amplicon sequencing, we determined that the molecular diversity of YVY in the yam samples analyzed in this work ranged between 0.0 and 29.1% and that this diversity is partially geographically structured. We also identified three isolates of banana mild mosaic virus (BanMMV) infecting D. alata in Guadeloupe, providing the first evidence for BanMMV infection in yam.
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Affiliation(s)
- Mame Boucar Diouf
- INRAE, UR ASTRO, 97170, Petit‑Bourg, Guadeloupe, France
- CIRAD, UMR AGAP Institut, 97130, Capesterre Belle Eau, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 97130, Capesterre Belle Eau, France
| | | | | | | | - Denis Filloux
- CIRAD, UMR PHIM, 34090, Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
| | - Thierry Candresse
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Pierre-Yves Teycheney
- CIRAD, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France
- UMR PVBMT, Université de la Réunion, 97410, Saint-Pierre, La Réunion, France
| | - Marie Umber
- INRAE, UR ASTRO, 97170, Petit‑Bourg, Guadeloupe, France.
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10
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Fontdevila Pareta N, Khalili M, Maachi A, Rivarez MPS, Rollin J, Salavert F, Temple C, Aranda MA, Boonham N, Botermans M, Candresse T, Fox A, Hernando Y, Kutnjak D, Marais A, Petter F, Ravnikar M, Selmi I, Tahzima R, Trontin C, Wetzel T, Massart S. Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis. Front Microbiol 2023; 14:1181562. [PMID: 37323908 PMCID: PMC10265641 DOI: 10.3389/fmicb.2023.1181562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/25/2023] [Indexed: 06/17/2023] Open
Abstract
The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties.
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Affiliation(s)
| | - Maryam Khalili
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
- EGFV, Univ. Bordeaux, INRAE, ISVV, Villenave d’Ornon, France
| | | | - Mark Paul S. Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- College of Agriculture and Agri-Industries, Caraga State University, Butuan, Philippines
| | - Johan Rollin
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- DNAVision (Belgium), Charleroi, Belgium
| | - Ferran Salavert
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Coline Temple
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Miguel A. Aranda
- Department of Stress Biology and Plant Pathology, Center for Edaphology and Applied Biology of Segura, Spanish National Research Council (CSIC), Murcia, Spain
| | - Neil Boonham
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive Plants and Plant Health (NIVIP), Wageningen, Netherlands
| | | | - Adrian Fox
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
- Fera Science Ltd, York Biotech Campus, York, United Kingdom
| | | | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | | | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Ilhem Selmi
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Rachid Tahzima
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Plant Sciences Unit, Institute for Agricultural, Fisheries and Food Research (ILVO), Merelbeke, Belgium
| | - Charlotte Trontin
- European and Mediterranean Plant Protection Organization, Paris, France
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
| | - Sebastien Massart
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Bioversity International, Montpellier, France
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11
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Khalili M, Candresse T, Koloniuk I, Safarova D, Brans Y, Faure C, Delmas M, Massart S, Aranda MA, Caglayan K, Decroocq V, Drogoudi P, Glasa M, Pantelidis G, Navratil M, Latour F, Spak J, Pribylova J, Mihalik D, Palmisano F, Saponari A, Necas T, Sedlak J, Marais A. The Expanding Menagerie of Prunus-Infecting Luteoviruses. Phytopathology 2023; 113:345-354. [PMID: 35972890 DOI: 10.1094/phyto-06-22-0203-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Members of the genus Luteovirus are responsible for economically destructive plant diseases worldwide. Over the past few years, three luteoviruses infecting Prunus trees have been characterized. However, the biological properties, prevalence, and genetic diversity of those viruses have not yet been studied. High-throughput sequencing of samples of various wild, cultivated, and ornamental Prunus species enabled the identification of four novel species in the genus Luteovirus for which we obtained complete or nearly complete genomes. Additionally, we identified another new putative species recovered from Sequence Read Archive data. Furthermore, we conducted a survey on peach-infecting luteoviruses in eight European countries. Analyses of 350 leaf samples collected from germplasm, production orchards, and private gardens showed that peach-associated luteovirus (PaLV), nectarine stem pitting-associated virus (NSPaV), and a novel luteovirus, peach-associated luteovirus 2 (PaLV2), are present in all countries; the most prevalent virus was NSPaV, followed by PaLV. The genetic diversity of these viruses was also analyzed. Moreover, the biological indexing on GF305 peach indicator plants demonstrated that PaLV and PaLV2, like NSPaV, are transmitted by graft at relatively low rates. No clear viral symptoms have been observed in either graft-inoculated GF305 indicators or different peach tree varieties observed in an orchard. The data generated during this study provide a broader overview of the genetic diversity, geographical distribution, and prevalence of peach-infecting luteoviruses and suggest that these viruses are likely asymptomatic in peach under most circumstances.
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Affiliation(s)
- Maryam Khalili
- Université de Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | | | - Igor Koloniuk
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Dana Safarova
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Yoann Brans
- Laboratoire de Virologie et de Biologie Moléculaire, CTIFL, Prigonrieux, France
| | - Chantal Faure
- Université de Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | - Marine Delmas
- INRAE, Unité Expérimentale Arboricole, Toulenne, France
| | - Sébastien Massart
- Laboratory of Plant Pathology, TERRA, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Miguel A Aranda
- Department of Stress Biology and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura, CSIC, Murcia, Spain
| | - Kadriye Caglayan
- Department of Plant Protection, Hatay Mustafa Kemal University, Antakya, Hatay, Turkey
| | | | - Pavlina Drogoudi
- Department of Deciduous Fruit Trees, Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Naoussa, Greece
| | - Miroslav Glasa
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Bratislava, Slovakia
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Trnava, Slovakia
| | - George Pantelidis
- Department of Deciduous Fruit Trees, Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Naoussa, Greece
| | - Milan Navratil
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - François Latour
- Laboratoire de Virologie et de Biologie Moléculaire, CTIFL, Prigonrieux, France
| | - Josef Spak
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jaroslava Pribylova
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Daniel Mihalik
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Trnava, Slovakia
| | - Francesco Palmisano
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura "Basile Caramia", Locorotondo, Italy
| | - Antonella Saponari
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura "Basile Caramia", Locorotondo, Italy
| | - Tomas Necas
- Department of Fruit Science, Faculty of Horticulture, Mendel University, Lednice, Czech Republic
| | - Jiri Sedlak
- Vyzkumny A Slechtitelsky Ustav Ovocnarsky, Holovousy, Czech Republic
| | - Armelle Marais
- Université de Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
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12
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Tsarmpopoulos I, Marais A, Faure C, Theil S, Candresse T. A new potyvirus from hedge mustard (Sisymbrium officinale (L.) Scop.) sheds light on the evolutionary history of turnip mosaic virus. Arch Virol 2022; 168:14. [PMID: 36576617 DOI: 10.1007/s00705-022-05682-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/09/2022] [Indexed: 12/29/2022]
Abstract
A novel potyvirus was identified in symptomatic hedge mustard (Sisymbrium officinale (L.) Scop.) and wild radish (Raphanus raphanistrum L.) in France. The nearly complete genome sequence of hedge mustard mosaic virus (HMMV) was determined, demonstrating that it belongs to a sister species to turnip mosaic virus (TuMV). HMMV readily infected several other members of the family Brassicaceae, including turnip, shepherd's purse (Capsella bursa-pastoris), and arabidopsis. The identification of HMMV as a Brassicaceae-infecting virus closely related to TuMV leads us to question the current scenario of TuMV evolution and suggests a possible alternative one in which transition from a monocot-adapted ancestral lifestyle to a Brassicaceae-adapted one could have occurred earlier than previously recognized.Please check and confirm that the authors and their respective affiliations have been correctly identified and amend if necessary.all OK.
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Affiliation(s)
- Iason Tsarmpopoulos
- Univ. Bordeaux, INRAE, UMR BFP, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Chantal Faure
- Univ. Bordeaux, INRAE, UMR BFP, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- Univ. Bordeaux, INRAE, UMR BFP, CS 20032, 33882, Villenave d'Ornon Cedex, France
- INRAE, UMRF, Aurillac, France
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR BFP, CS 20032, 33882, Villenave d'Ornon Cedex, France.
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13
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Candresse T, Svanella-Dumas L, Marais A, Depasse F, Faure C, Lefebvre M. Identification of Seven Additional Genome Segments of Grapevine-Associated Jivivirus 1. Viruses 2022; 15:39. [PMID: 36680079 PMCID: PMC9862270 DOI: 10.3390/v15010039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
Jiviruses are a group of recently described viruses characterized with a tripartite genome and having affinities with Virgaviridae (RNA1 and 2) and Flaviviridae (RNA3). Using a combination of high-throughput sequencing, datamining and RT-PCR approaches, we demonstrate here that in grapevine samples infected by grapevine-associated jivivirus 1 (GaJV-1) up to 7 additional molecules can be consistently detected with conserved 5' and 3' non-coding regions in common with the three previously identified GaJV-1 genomic RNAs. RNA4, RNA5, RNA6, RNA7, RNA8 and RNA10, together with a recombinant RNArec7-8, are all members of a family sharing a previously non recognized conserved protein domain, while RNA9 is part of a distinct family characterized by another conserved motif. Datamining of pecan (Carya illinoinensis) public transcriptomic data allowed the identification of two further jiviviruses and the identification of supplementary genomic RNAs with homologies to those of GaJV-1. Taken together, these results reshape our vision of the divided genome of jiviviruses and raise novel questions about the function(s) of the proteins encoded by jiviviruses supplementary RNAs.
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Affiliation(s)
- Thierry Candresse
- INRAE, UMR BFP, University of Bordeaux, CS20032, CEDEX, 33882 Villenave d’Ornon, France
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14
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Moubset O, François S, Maclot F, Palanga E, Julian C, Claude L, Fernandez E, Rott P, Daugrois JH, Antoine-Lorquin A, Bernardo P, Blouin AG, Temple C, Kraberger S, Fontenele RS, Harkins GW, Ma Y, Marais A, Candresse T, Chéhida SB, Lefeuvre P, Lett JM, Varsani A, Massart S, Ogliastro M, Martin DP, Filloux D, Roumagnac P. Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses. Phytopathology 2022; 112:2253-2272. [PMID: 35722889 DOI: 10.1094/phyto-03-22-0096-rvw] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Oumaima Moubset
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - François Maclot
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Essowè Palanga
- Institut Togolais de Recherche Agronomique (ITRA-CRASS), B.P. 129, Kara, Togo
| | - Charlotte Julian
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Lisa Claude
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Rott
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Jean-Heinrich Daugrois
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | | | - Arnaud G Blouin
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
- Plant Protection Department, Agroscope, 1260, Nyon, Switzerland
| | - Coline Temple
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Gordon W Harkins
- South African Medical Research Council Capacity Development Unit, South African National Bioinformatics, Institute, University of the Western Cape, South Africa
| | - Yuxin Ma
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | | | | | | | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Sébastien Massart
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | | | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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15
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Svanella-Dumas L, Faure C, Marais A, Candresse T. First report of ash shoestring-associated virus (ASaV) infecting European ash (Fraxinus excelsior L.) in France. Plant Dis 2022; 107. [PMID: 36302726 DOI: 10.1094/pdis-09-22-2272-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ash shoestring-associated virus (ASaV) is a recently described Emaravirus with five genome segments identified in Germany and Switzerland from European ash (Fraxinus excelsior) or South European flowering ash (F. ornus) trees with chlorotic spots or mosaics and leaf curling or leaf shoestring symptoms [1]. In summer 2021 several European ash trees with severe leaf mosaic and deformation were observed 50 km south east of Bordeaux (France). Double stranded RNAs were purified from the leaves of one of the trees (2021-432) and analyzed by Illumina high throughput sequencing (HTS, 2x150 nt) as described [2]. Following quality trimming, reads were assembled de novo (CLC Genomics Workbench 21, Qiagen) and contigs annotated by BlastX analysis. Contigs homologous to ASaV genomic RNAs 2 to 5 were identified. For ASaV RNA2, four contigs were identified which could be manually assembled to yield a single scaffold while a single contig was obtained for RNAs 3, 4 and 5. The RNA2 scaffold assembled 1,206 reads for an average coverage of 58.2x, while the corresponding values for RNAs 3 to 5 were respectively 21,381 reads (1,529x), 18,146 reads (1,266x) and 1,234 reads (97.4x). While no contig was identified for ASaV RNA1 (or for other viruses), mapping of reads on an RNA1 reference (OU466880) allowed to identify 25 reads for this genomic segment (average coverage 0.4x). In total, ASaV reads represented 3.9% of the ca. 1 million reads obtained from the ash sample. The RNAs 2 to 5 scaffolds for isolate 2021-432 have been deposited in GenBank (OP501824-7). They show between 94.6% and 97.6% nucleotide identity with the corresponding RNAs of a reference isolate (OU466881-4). In order to validate the presence of ASaV in the original tree, PCR primers were designed based on RNAs 1 and 3 sequences. Primers ASaV1-F (5'-ATTATTCACAGTATGAAAGGG-3') and ASaV1-R (5'-GGTGTGGAGAATATCAAACC-3') amplify a 286 nt RNA1 fragment, while primers ASaV3-F (5'-GCTATACCCAGCTGAGGTGC-3') and ASaV3-R (5'-GTGTGCAATTCTATCAGCCTC-3') amplify a 322 nt RNA3 fragment. Amplicons of the expected size were obtained and directly sequenced. The RNA3 amplicon sequence was identical to the corresponding region of the HTS contig, while the RNA1 amplicon was 97.5% identical to the OU466880 reference sequence. The same primer pairs and a third one, ASaV4-F (5'- GAGGTTGCTTTGATGTCAGG -3') and ASaV4-R (5'- TGCCTCTCCGATGGTGATG -3'), amplifying a 411 nt RNA4 fragment, were used to test a European ash (2022-91) showing similar mosaic and shoestring symptoms collected in spring 2022 about 170 km south of Bordeaux. Again, amplifications were positive and the sequences of the amplicons showed 94.3 to 96.5% nt identity with the corresponding regions of the reference ASaV isolate and 93.9 to 94.3% identity with the French 2021-432 isolate. The PCR amplicon sequences for the two French isolates have been deposited in GenBank (OP501828-32). To our knowledge, these results represent the first report of a natural infection of ASaV in European ash in France. Identification of the virus in two ash populations about 150 km apart suggests the virus maybe widespread. The finding of ASaV in an ash tree with severe leaf symptoms and in which no other virus was identified by HTS supports its role as the causal agent of the symptoms observed. Ash trees in Europe are already threatened by the invasive ash dieback agent [3] and ASaV represents a further potential threat that deserves to be evaluated.
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Affiliation(s)
| | | | - Armelle Marais
- INRA Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, INRA - Université de Bordeaux, 71 avenue E. Bourlaux CS20032, Villenave d'Ornon , France, 33882;
| | - Thierry Candresse
- INRA Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, INRA - Université de Bordeaux, CS20032, Villenave d'Ornon , France, 33882 cedex;
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Sikkema KJ, Rabie S, King A, Watt MH, Mulawa MI, Andersen LS, Wilson PA, Marais A, Ndwandwa E, Majokweni S, Orrell C, Joska JA. ImpACT+, a coping intervention to improve clinical outcomes for women living with HIV and sexual trauma in South Africa: study protocol for a randomized controlled trial. Trials 2022; 23:680. [PMID: 35982485 PMCID: PMC9386207 DOI: 10.1186/s13063-022-06655-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background Addressing sexual trauma in the context of HIV care is essential to improve clinical outcomes and mental health among women in South Africa. Women living with HIV (WLH) report disproportionately high levels of sexual trauma and have higher rates of posttraumatic stress disorder. Adherence to antiretroviral therapy (ART) may be difficult for traumatized women, as sexual trauma compounds the stress associated with managing HIV and is often comorbid with other mental health disorders, further compromising care engagement and adherence. ART initiation represents a unique window of opportunity for intervention to enhance motivation, increase care engagement, and address the negative effects of trauma on avoidant coping behaviors. Mental health interventions delivered by non-specialists in low- and middle-income countries have potential to treat depression, trauma, and effects of intimate partner violence among WLH. This study will examine the effectiveness of Improving AIDS Care after Trauma (ImpACT +), a task-shared, trauma-focused coping intervention, to promote viral suppression among WLH initiating ART in a South African clinic setting. Methods This study will be conducted in Khayelitsha, a peri-urban settlement situated near Cape Town, South Africa. Using a hybrid type 1 effectiveness-implementation design, we will randomize 350 WLH initiating ART to the ImpACT + experimental condition or the control condition (three weekly sessions of adapted problem-solving therapy) to examine the effectiveness of ImpACT + on viral suppression, ART adherence, and the degree to which mental health outcomes mediate intervention effects. ImpACT + participants will receive six once-a-week coping intervention sessions and six monthly maintenance sessions over the follow-up period. We will conduct mental health and bio-behavioral assessments at baseline, 4, 8, and 12 months, with care engagement data extracted from medical records. We will explore scalability using the Consolidated Framework for Implementation Research (CFIR). Discussion This trial is expected to yield important new information on psychologically informed intervention models that benefit the mental health and clinical outcomes of WLH with histories of sexual trauma. The proposed ImpACT + intervention, with its focus on building coping skills to address traumatic stress and engagement in HIV care and treatment, could have widespread impact on the health and wellbeing of individuals and communities in sub-Saharan Africa. Trial registration Clinicaltrials.gov NCT04793217. Retrospectively registered on 11 March 2021.
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Affiliation(s)
- K J Sikkema
- Department of Sociomedical Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - S Rabie
- Department of Psychiatry and Mental Health, HIV Mental Health Research Unit, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - A King
- Department of Sociomedical Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - M H Watt
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - M I Mulawa
- Duke University School of Nursing and Duke Global Health Institute, Durham, NC, USA
| | - L S Andersen
- Department of Psychiatry and Mental Health, HIV Mental Health Research Unit, Neuroscience Institute, University of Cape Town, Cape Town, South Africa.,Present Address, University of Copenhagen, Copenhagen, Denmark
| | - P A Wilson
- Department of Psychology, University of California, Los Angeles, USA
| | - A Marais
- Department of Psychiatry and Mental Health, HIV Mental Health Research Unit, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - E Ndwandwa
- Department of Psychiatry and Mental Health, HIV Mental Health Research Unit, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - S Majokweni
- Department of Psychiatry and Mental Health, HIV Mental Health Research Unit, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - C Orrell
- Desmond Tutu HIV Foundation, University of Cape Town Medical School, Cape Town, South Africa
| | - J A Joska
- Department of Psychiatry and Mental Health, HIV Mental Health Research Unit, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
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Schönegger D, Marais A, Faure C, Candresse T. A new flavi-like virus identified in populations of wild carrots. Arch Virol 2022; 167:2407-2409. [PMID: 35962825 DOI: 10.1007/s00705-022-05544-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/13/2022] [Indexed: 11/24/2022]
Abstract
We report the discovery of a new flavi-like virus identified in wild carrots (Daucus carota subsp. carota), using a double-stranded (ds)RNA high-throughput sequencing (HTS) approach. The new virus, tentatively named "carrot flavi-like virus 1" (CtFLV-1), has a large genome of 21.8 kb that harbours a single open reading frame encoding a 7,078-aa polyprotein with conserved RNA helicase (Hel) and RNA-dependent RNA polymerase (RdRp) domains. The new virus is phylogenetically related to recently described flavi-like viruses from arthropods, but its closest relative is a plant-associated virus, gentian Kobu-sho-associated virus (GKSaV). A pairwise comparison showed that these two viruses share 38.4% amino acid (aa) sequence identity in their polyproteins and 73% and 47.8% aa sequence identity in their conserved RdRp and Hel domains, respectively. Based on their similar genome organization and phylogenetic relationship, GKSaV and CtFLV-1 could form the basis for a new genus of plant-associated viruses, possibly within the family Flaviviridae, for which the name "Koshovirus" is proposed.
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Affiliation(s)
- Deborah Schönegger
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Chantal Faure
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France.
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Candresse T, Faure C, Marais A. First report of grapevine red globe virus (GRGV) and grapevine rupestris vein feathering virus (GRVFV) infecting grapevine (Vitis vinifera L.) in Portugal. Plant Dis 2022; 107:974. [PMID: 35939753 DOI: 10.1094/pdis-06-22-1326-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Grapevine Red globe virus (GRGV) and grapevine rupestris vein feathering virus (GRVFV) are relatively recently described grape viruses that respectively belong to the genera Maculavirus and Marafivirus in the family Tymoviridae [1]. Owing to their rather recent description, still limited information on their biology, on their molecular variability and on their geographic distribution is available. Both viruses are apparently completely or largely asymptomatic in European grapevine and have likely been overlooked in a wide range of situations (Martelli, 2014). According to sequences in GenBank, GRGV has been identified in Asia (Iran, Japan, China), the Americas (USA, Brazil) and Europe (Spain, France, Slovenia, Hungary, Czech Republic and Germany). GRVFV has been reported from the same countries but also in Oceania (New Zealand, Australia) and from a range of other countries including India, Pakistan and South Korea for Asia, Canada for North America and Switzerland, Slovakia, Italy and Russia for Europe. Evidence for the presence of GRGV and GRVFV in grapevine plants from northern Portugal (variety(ies) unknown) was obtained through the bioinformatic analysis [2] of RNASeq Illumina data obtained from phloem scrapings from five grapevine samples collected in different plots in 2016 [3]. Following grapevine genome substraction, contigs assembly and Blast-based contigs annotation using CLC Genomics Workbench, two plants, #4 and #5b, yielded contigs representing near complete GRGV genomes. The plant #4 contig integrated 474 reads (0.15% of reads for an average coverage of 10.1x) while the corresponding values for the contig for plant #5b are 2185 reads (2.4% of total reads) for a coverage of 47.2x. The two GRGV contigs show 91.4% nucleotide (nt) identity and the closest GRGV full genome sequence in GenBank, MZ451067 from Canada, shares respectively 98.9% and 91.6% nt identity with them. The near complete genome contigs have been deposited in GenBank (ON603917 and ON603918). Simultaneously, two near full length genomic contigs for GRVFV were identified from plant #5b and have also been deposited in GenBank (ON603919 and ON603920). These contigs show 84.4% nt identity to each other and were respectively assembled from 4643 (5.2% of total reads) and 5326 reads (6.0% of total reads) for respective average coverages of 102.3x and 117.3x. The closest full GRVFV genome in GenBank is MZ027155 from the USA, with 84.3-85.3% nt identity. Confirmation of the presence of GRVG and GRVFV in the doubly infected plant #5b was achieved by specific RT-PCR assays. A published assay [4] was used for GRGV and primers GRVFV-Cp-F 5'AAYCCTGTCACHCTCCACTG3' and GRVFV-Cp-R 5'TTCATGGTGGTGCCDGTGAG3' (Tm 55°C) were used for GRVFV. The obtained 447nt GRGV amplicon showed a single difference with the HTS contig while the 218 nt GRVFV amplicon showed 3 mutations as compared to one of the HTS contigs. The different grapevines had initially been sampled because they showed relatively poor and stunted growth but besides GRVFV and/or GRGV the HTS analysis indicated that they were also infected by hop stunt viroid, grapevine yellow speckle viroid 1, grapevine rupestris stem pitting virus, plus respectively a novel nepovirus (plant #4) and grapevine leafroll-associated virus 2 and grapevine Pinot gris virus (plant #5b) so that the results reported here do not shed novel light on the potential pathogenicity of GRGV or GRVFV. To the best of our knowledge, this is the first report of GRGV and GRVFV in Portugal.
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Affiliation(s)
- Thierry Candresse
- INRA Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, INRA - Université de Bordeaux, CS20032, Villenave d'Ornon , France, 33882 cedex;
| | | | - Armelle Marais
- INRA Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, INRA - Université de Bordeaux, 71 avenue E. Bourlaux CS20032, Villenave d'Ornon , France, 33882;
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Massé D, Filloux D, Candresse T, Massart S, Marais A, Verdin E, Cassam N, Fernandez E, Roumagnac P, Teycheney PY, Lefeuvre P, Lett JM. Identification of a novel vitivirus from pineapple in Reunion Island. Arch Virol 2022; 167:2355-2357. [PMID: 35857149 DOI: 10.1007/s00705-022-05512-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/11/2022] [Indexed: 11/29/2022]
Abstract
We report the complete genome sequence of a novel member of the genus Vitivirus (family Betaflexiviridae, subfamily Trivirinae) infecting pineapple. The complete genome sequence of this virus was obtained from total RNA extracted from pineapple leaf samples collected in Reunion Island, using a combination of high-throughput sequencing technologies. The viral genome is 6,757 nt long, excluding the poly(A) tail, and shares all the hallmarks of vitiviruses. Phylogenetic analysis performed on the replication-associated protein and capsid protein gene sequences unambiguously place this new virus, for which we propose the name "pineapple virus A", in the genus Vitivirus.
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Affiliation(s)
- Delphine Massé
- ANSES, LSV RAPT, 97410, Saint Pierre, La Réunion, France.,Université de La Réunion, UMR PVBMT, 97410, Saint Pierre, La Réunion, France
| | - Denis Filloux
- UMR PHIM, CIRAD, Campus International de Baillarguet, 34398, Montpellier Cedex-5, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Massart
- Plant Pathology Laboratory, TERRA, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgique
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Eric Verdin
- INRAE, UR407 Unité de Pathologie Végétale, CS 60094, 84140, Montfavet, France
| | | | - Emmanuel Fernandez
- UMR PHIM, CIRAD, Campus International de Baillarguet, 34398, Montpellier Cedex-5, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
| | - Philippe Roumagnac
- UMR PHIM, CIRAD, Campus International de Baillarguet, 34398, Montpellier Cedex-5, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
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Diouf MB, Gaspard O, Marais A, Filloux D, Gomez RM, Faure C, Roumagnac P, Candresse T, Theil S, Contreras S, Teycheney PY, Umber M. Molecular characterization of Cordyline virus 1 isolates infecting yam (Dioscorea spp). Arch Virol 2022; 167:2275-2280. [PMID: 35842549 DOI: 10.1007/s00705-022-05535-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/04/2022] [Indexed: 11/02/2022]
Abstract
Cordyline virus 1 (CoV1) is a velarivirus that has so far only been reported in ornamental Ti plants (Cordyline fruticosa). Using high-throughput sequencing, we identified CoV1 infection in yam accessions from Vanuatu. Using a specific RT-PCR assay, we found that CoV1 is also present and highly prevalent in Dioscorea alata, D. cayenensis, and D. trifida in Guadeloupe. Phylogenetic analysis showed that CoV1 isolates infecting yam in Guadeloupe display a low level of molecular diversity. These data provide insights into the transmission of CoV1 in yam in Guadeloupe.
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Affiliation(s)
- Mame Boucar Diouf
- INRAE, UR ASTRO, 97170, Petit‑Bourg, Guadeloupe, France.,CIRAD, UMR AGAP Institut, 97130, Capesterre Belle Eau, France.,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 97130, Capesterre Belle Eau, France
| | | | - Armelle Marais
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090, Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
| | | | - Chantal Faure
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090, Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
| | - Thierry Candresse
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Sandy Contreras
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Pierre-Yves Teycheney
- CIRAD, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France.,UMR PVBMT, Université de la Réunion, 97410, Saint-Pierre, La Réunion, France
| | - Marie Umber
- INRAE, UR ASTRO, 97170, Petit‑Bourg, Guadeloupe, France.
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Svanella-Dumas L, Vitry C, Valade R, Robin N, Thibord JB, Marais A, Candresse T. First report of barley virus G infecting winter barley (Hordeum vulgare L.) in France. Plant Dis 2022; 107:591. [PMID: 35771104 DOI: 10.1094/pdis-06-22-1294-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As part of a cereals virome project high throughput sequencing (HTS)-based viral indexing was performed on plants with symptoms of barley yellow dwarf disease collected in June (2017-2020) in the main French cereals production areas. Total RNAs from 32 individual plants were purified (RNeasy Plant Mini Kit, Qiagen, Courtaboeuf, France) and Illumina sequenced (2x150 nt) following ribodepletion (Genewiz-Azenta, Leipzig, Germany). Following quality trimming, reads for each sample were de novo assembled (CLC Genomics Workbench 21, Qiagen) [1] and contigs annotated by BlastX analysis. In four winter barley samples collected in 2018 (18-58, 18-325 and 18-326) and 2019 (19-30A), besides contigs representing diverse viruses such as barley yellow dwarf viruses-PAV and PAS, Hordeum vulgare endornavirus, cereal yellow dwarf virus-RPV (18-326), wheat dwarf virus (18-325 and 18-326) and a novel Polerovirus (18-58 and 18-326), large contigs with high identity to barley virus G (BVG) were identified. BVG, a tentative Polerovirus, was initially reported in barley in South Korea in 2016 [2] and has so far been identified in a few other hosts including wheat, oat, maize, proso and foxtail millets as well as switchgrass. It has been reported from the USA and Australia [3] and, in Europe, from the Netherlands, Germany, Hungary and Greece [4]. Large BVG scaffolds representing near complete genomes could be reconstructed for each sample, integrating a total of 128.339, 7.188, 8.078 and 20.073 reads, for samples 19-30A, 18-58, 18325 and 18-326 respectively. Given that between 17.2 and 20.5 million reads had been obtained per sample, these values translate into between 0.04% (18-58 and 18-325) and 0.6% (19-30A) of total reads, and to average coverages of between 158x (18-58) and 2866x (19-30A) for the genomic scaffolds. The four assembled sequences (5584-5610 nt) have been deposited in GenBank (ON419453-ON419456). They are nearly identical (98.4 to 99.5% nt identity) and share between 97.7% and 98.5% nt identity with a barley reference isolate from the South Korea (NC_029906). To confirm the presence of BVG, a primer pair was designed based on available BVG sequences. Primers BVG-F(5'-CTAGCCCAACGAGTTGCGGG-3') and BVG-R(5'-GGTACAGAAGCTCTACGGTTC-3') amplifying a 394 nt were used in a two-step RT-PCR on new RNA extracts obtained from the 18-325 and 18-326 infected plants. The amplicons were directly sequenced and showed respectively 99.2% (ON419457, 18-325) and 100% (18-326) nt identity with the corresponding de novo scaffolds. The four analyzed samples have been collected respectively in 2018 (18-58, 18-325, 18-326) and 2019 (19-30A) in three different regions of France (Auvergne-Rhône-Alpes, Occitanie and Centre-Val de Loire), indicating a wide distribution and a persistence over time of BVG in France. To our knowledge, this represents the first report of a natural infection of BVG in cultivated winter barley in France. Presence of BVG may have been overlooked in a range of situation, as indicated by its retrospective discovery in a 34 years old Australian sample [3], possibly explaining its broad distribution in France. While the mixed infection status of the analyzed plants precludes any conclusion on its pathogenicity in French cereals, BVG has been reported to be associated with a range of symptoms in various hosts so that further studies to evaluate its prevalence and impact in France and to begin to understand its epidemiology are clearly warranted by the present results.
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Affiliation(s)
| | - Cindy Vitry
- Arvalis Experimental Research Station Boigneville, 173484, Boigneville, Île-de-France, France;
| | - Romain Valade
- Arvalis Experimental Research Station Boigneville, 173484, Boigneville, Île-de-France, France;
| | - Nathalie Robin
- Arvalis Institut du Vegetal, 105107, Paris, Île-de-France, France;
| | | | - Armelle Marais
- INRA, UMR GDPP, IBVM, 71 avenue E. Bourlaux, Bordeaux, France, 33270;
| | - Thierry Candresse
- INRA Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, INRA - Université de Bordeaux, CS20032, Villenave d'Ornon , France, 33882 cedex;
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Svanella-Dumas L, Candresse T, Lefebvre M, Lluch J, Valiere S, Larignon P, Marais A. First Report of Grapevine Virus L Infecting Grapevine in Southeast France. Plant Dis 2022; 106:PDIS10212310PDN. [PMID: 34978867 DOI: 10.1094/pdis-10-21-2310-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- L Svanella-Dumas
- Univ. Bordeaux, INRAE, UMR BFP, CS 20032, 33882 Villenave d'Ornon, France
| | - T Candresse
- Univ. Bordeaux, INRAE, UMR BFP, CS 20032, 33882 Villenave d'Ornon, France
| | - M Lefebvre
- Univ. Bordeaux, INRAE, UMR BFP, CS 20032, 33882 Villenave d'Ornon, France
| | - J Lluch
- INRAE, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France
| | - S Valiere
- INRAE, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France
| | | | - A Marais
- Univ. Bordeaux, INRAE, UMR BFP, CS 20032, 33882 Villenave d'Ornon, France
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Ayed C, Hamdi I, Najar A, Marais A, Faure C, Candresse T, Dridi BAM. First Report of Garlic virus A, Garlic virus B, and Garlic virus C on Garlic ( Allium sativum) in Tunisia. Plant Dis 2022; 106:1312. [PMID: 34668406 DOI: 10.1094/pdis-08-21-1706-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- C Ayed
- Laboratoire Agrobiodiversité et Ecotoxicologie, Institut Supérieur Agronomique de Chott Mariem, Université de Sousse, Sousse, 4042, Tunisia
| | - I Hamdi
- Laboratoire de Protection des Végétaux, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, El Menzah, 1004, Tunisia
| | - A Najar
- Laboratoire de Protection des Végétaux, Institut National de la Recherche Agronomique de Tunisie, Université de Carthage, El Menzah, 1004, Tunisia
| | - A Marais
- Université Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, CS20032, Villenave d'Ornon Cedex, 33882, France
| | - C Faure
- Université Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, CS20032, Villenave d'Ornon Cedex, 33882, France
| | - T Candresse
- Université Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, CS20032, Villenave d'Ornon Cedex, 33882, France
| | - B Al-Mohandes Dridi
- Laboratoire Agrobiodiversité et Ecotoxicologie, Institut Supérieur Agronomique de Chott Mariem, Université de Sousse, Sousse, 4042, Tunisia
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Umber M, Filloux D, Svanella-Dumas L, Bonheur L, Acina-Mambole I, Gomez RM, Faure C, Anzala F, Pavis C, Roumagnac P, Marais A, Theil S, Candresse T, Teycheney PY. Host range and molecular variability of the sadwavirus dioscorea mosaic associated virus. Arch Virol 2022; 167:917-922. [PMID: 35107668 DOI: 10.1007/s00705-022-05379-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/20/2022] [Indexed: 11/02/2022]
Abstract
Dioscorea mosaic associated virus (DMaV) is a member of the genus Sadwavirus, family Secoviridae, that is associated with mosaic symptoms in Dioscorea rotundata in Brazil. The genome of a DMaV isolate detected in D. trifida in Guadeloupe was sequenced by high-throughput sequencing. Using an RT-PCR-based detection assay, we found that DMaV infects D. alata, D. bulbifera, D. cayenensis-rotundata, D. esculenta, and D. trifida accessions conserved in Guadeloupe and Côte d'Ivoire and displays a very high level of molecular diversity in a relatively small region of the genome targeted by the assay. We also provide evidence that DMaV is also present in D. rotundata in Benin and in D. alata in Nigeria.
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Affiliation(s)
- Marie Umber
- INRAE, UR1321 ASTRO Agrosystèmes tropicaux, 97170, Petit-Bourg, Guadeloupe, France
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090, Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Laurence Svanella-Dumas
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Lydiane Bonheur
- CIRAD, UMR AGAP Institut, Station de Neufchâteau, Sainte-Marie, 97130, Capesterre Belle-Eau, France.,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 97130, Capesterre Belle-Eau, France
| | - Isabelle Acina-Mambole
- CIRAD, UMR AGAP Institut, Station de Neufchâteau, Sainte-Marie, 97130, Capesterre Belle-Eau, France.,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 97130, Capesterre Belle-Eau, France
| | - Rose-Marie Gomez
- INRAE, UR1321 ASTRO Agrosystèmes tropicaux, 97170, Petit-Bourg, Guadeloupe, France
| | - Chantal Faure
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Fabiola Anzala
- INRAE, UR1321 ASTRO Agrosystèmes tropicaux, 97170, Petit-Bourg, Guadeloupe, France
| | - Claudie Pavis
- INRAE, UR1321 ASTRO Agrosystèmes tropicaux, 97170, Petit-Bourg, Guadeloupe, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090, Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Pierre-Yves Teycheney
- CIRAD, UMR PVBMY, F-97410, Saint Pierre, La Réunion, France. .,UMR PVBMT, Université de la Réunion, F-97410, Saint Pierre, La Réunion, France.
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25
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Fournier P, Pellan L, Barroso-Bergadà D, Bohan DA, Candresse T, Delmotte F, Dufour MC, Lauvergeat V, Le Marrec C, Marais A, Martins G, Masneuf-Pomarède I, Rey P, Sherman D, This P, Frioux C, Labarthe S, Vacher C. The functional microbiome of grapevine throughout plant evolutionary history and lifetime. ADV ECOL RES 2022. [DOI: 10.1016/bs.aecr.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Marais A, Murolo S, Faure C, Brans Y, Larue C, Maclot F, Massart S, Chiumenti M, Minafra A, Romanazzi G, Lefebvre M, Barreneche T, Robin C, Petit RJ, Candresse T. Sixty Years from the First Disease Description, a Novel Badnavirus Associated with Chestnut Mosaic Disease. Phytopathology 2021; 111:1051-1058. [PMID: 33084526 DOI: 10.1094/phyto-09-20-0420-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Although chestnut mosaic disease (ChMD) was described several decades ago, its etiology is still not clear. Using classical approaches and high-throughput sequencing (HTS) techniques, we identified a novel Badnavirus that is a strong etiological candidate for ChMD. Two disease sources from Italy and France were submitted to HTS-based viral indexing. Total RNAs were extracted, ribodepleted, and sequenced on an Illumina NextSeq500 (2 × 150 nt or 2 × 75 nt). In each source, we identified a single contig of ≈7.2 kb that corresponds to a complete circular viral genome and shares homologies with various badnaviruses. The genomes of the two isolates have an average nucleotide identity of 90.5%, with a typical badnaviral genome organization comprising three open reading frames. Phylogenetic analyses and sequence comparisons showed that this virus is a novel species; we propose the name Chestnut mosaic virus (ChMV). Using a newly developed molecular detection test, we systematically detected the virus in symptomatic graft-inoculated indicator plants (chestnut and American oak) as well in chestnut trees presenting typical ChMD symptoms in the field (100 and 87% in France and Italy surveys, respectively). Datamining of publicly available chestnut sequence read archive transcriptomic data allowed the reconstruction of two additional complete ChMV genomes from two Castanea mollissima sources from the United States as well as ChMV detection in C. dentata from the United States. Preliminary epidemiological studies performed in France and central eastern Italy showed that ChMV has a high incidence in some commercial orchards and low within-orchard genetic diversity.
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Affiliation(s)
- Armelle Marais
- University of Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | - Sergio Murolo
- Department Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Chantal Faure
- University of Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | - Yoann Brans
- Laboratoire de Virologie et de Biologie Moléculaire, Centre Technique Interprofessionnel des Fruits et Légumes, Prigonrieux, France
| | - Clément Larue
- University of Bordeaux, INRAE, UMR Biogeco, Cestas, France
- INVENIO, Maison Jeannette, Douville, France
| | - François Maclot
- Plant Pathology Laboratory, TERRA-Gembloux Agro-BioTech, University of Liège, Belgium
| | - Sébastien Massart
- Plant Pathology Laboratory, TERRA-Gembloux Agro-BioTech, University of Liège, Belgium
| | - Michela Chiumenti
- National Research Council of Italy Institute for Sustainable Plant Protection, Bari, Italy
| | - Angelantonio Minafra
- National Research Council of Italy Institute for Sustainable Plant Protection, Bari, Italy
| | - Gianfranco Romanazzi
- Department Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Marie Lefebvre
- University of Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | | | - Cécile Robin
- University of Bordeaux, INRAE, UMR Biogeco, Cestas, France
| | - Rémy J Petit
- University of Bordeaux, INRAE, UMR Biogeco, Cestas, France
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27
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Kwibuka Y, Bisimwa E, Blouin AG, Bragard C, Candresse T, Faure C, Filloux D, Lett JM, Maclot F, Marais A, Ravelomanantsoa S, Shakir S, Vanderschuren H, Massart S. Novel Ampeloviruses Infecting Cassava in Central Africa and the South-West Indian Ocean Islands. Viruses 2021; 13:v13061030. [PMID: 34072594 PMCID: PMC8226816 DOI: 10.3390/v13061030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 11/30/2022] Open
Abstract
Cassava is one of the most important staple crops in Africa and its production is seriously damaged by viral diseases. In this study, we identify for the first time and characterize the genome organization of novel ampeloviruses infecting cassava plants in diverse geographical locations using three high-throughput sequencing protocols [Virion-Associated Nucleotide Acid (VANA), dsRNA and total RNA], and we provide a first analysis of the diversity of these agents and of the evolutionary forces acting on them. Thirteen new Closteroviridae isolates were characterized in field-grown cassava plants from the Democratic Republic of Congo (DR Congo), Madagascar, Mayotte, and Reunion islands. The analysis of the sequences of the corresponding contigs (ranging between 10,417 and 13,752 nucleotides in length) revealed seven open reading frames. The replication-associated polyproteins have three expected functional domains: methyltransferase, helicase, and RNA-dependent RNA polymerase (RdRp). Additional open reading frames code for a small transmembrane protein, a heat-shock protein 70 homolog (HSP70h), a heat shock protein 90 homolog (HSP90h), and a major and a minor coat protein (CP and CPd respectively). Defective genomic variants were also identified in some cassava accessions originating from Madagascar and Reunion. The isolates were found to belong to two species tentatively named Manihot esculenta-associated virus 1 and 2 (MEaV-1 and MEaV-2). Phylogenetic analyses showed that MEaV-1 and MEaV-2 belong to the genus Ampelovirus, in particular to its subgroup II. MEaV-1 was found in all of the countries of study, while MEaV-2 was only detected in Madagascar and Mayotte. Recombination analysis provided evidence of intraspecies recombination occurring between the isolates from Madagascar and Mayotte. No clear association with visual symptoms in the cassava host could be identified.
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Affiliation(s)
- Yves Kwibuka
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium; (A.G.B.); (F.M.)
- Faculté des Sciences Agronomiques, Université Catholique de Bukavu, BP 285 Bukavu, Democratic Republic of the Congo;
- Correspondence: (Y.K.); (S.M.)
| | - Espoir Bisimwa
- Faculté des Sciences Agronomiques, Université Catholique de Bukavu, BP 285 Bukavu, Democratic Republic of the Congo;
| | - Arnaud G. Blouin
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium; (A.G.B.); (F.M.)
| | - Claude Bragard
- Earth and Life Institute, Applied Microbiology-Phytopathology, UCLouvain, 1348 Louvain-la-Neuve, Belgium;
| | - Thierry Candresse
- Université Bordeaux, INRAE, UMR BFP, CS20032, CEDEX, 33882 Villenave d’Ornon, France; (T.C.); (C.F.); (A.M.)
| | - Chantal Faure
- Université Bordeaux, INRAE, UMR BFP, CS20032, CEDEX, 33882 Villenave d’Ornon, France; (T.C.); (C.F.); (A.M.)
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France;
- PHIM Plant Health Institute, Université Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34000 Montpellier, France
| | - Jean-Michel Lett
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, Saint-Pierre, F-97410 Ile de la Reunion, France;
| | - François Maclot
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium; (A.G.B.); (F.M.)
| | - Armelle Marais
- Université Bordeaux, INRAE, UMR BFP, CS20032, CEDEX, 33882 Villenave d’Ornon, France; (T.C.); (C.F.); (A.M.)
| | | | - Sara Shakir
- Plant Genetics Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium; (S.S.); (H.V.)
| | - Hervé Vanderschuren
- Plant Genetics Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium; (S.S.); (H.V.)
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, Biosystems Department, KU Leuven, 3000 Leuven, Belgium
| | - Sébastien Massart
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium; (A.G.B.); (F.M.)
- Correspondence: (Y.K.); (S.M.)
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28
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Ma Y, Fort T, Marais A, Lefebvre M, Theil S, Vacher C, Candresse T. Leaf-associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems. Plant Environ Interact 2021; 2:87-99. [PMID: 37284285 PMCID: PMC10168098 DOI: 10.1002/pei3.10043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 06/08/2023]
Abstract
Plants are colonized by diverse fungal and viral communities that influence their growth and survival as well as ecosystem functioning. Viruses interact with both plants and the fungi they host. Our understanding of plant-fungi-virus interactions is very limited, especially in wild plants. Combining metagenomic and culturomic approaches, we assessed the richness, diversity, and composition of leaf-associated fungal and viral communities from pools of herbaceous wild plants representative of four sites corresponding to cultivated or natural ecosystems. We identified 161 fungal families and 18 viral families comprising 249 RNA-dependent RNA polymerase-based operational taxonomic units (RdRp OTUs) from leaves. Fungal culturomics captured 12.3% of the fungal diversity recovered with metagenomic approaches and, unexpectedly, retrieved viral OTUs that were almost entirely different from those recovered by leaf metagenomics. Ecosystem management had a significant influence on both leaf mycobiome and virome, with a higher fungal community richness in natural ecosystems and a higher viral family richness in cultivated ecosystems, suggesting that leaf-associated fungal and viral communities are under the influence of different ecological drivers. Both the leaf-associated fungal and viral community compositions showed a strong site-specificity. Further research is needed to confirm these trends and unravel the factors structuring plant-fungi-virus interactions in wild plant populations.
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Affiliation(s)
- Yuxin Ma
- Univ. BordeauxINRAEUMR 1332 BFPVillenave d’Ornon cedexFrance
| | | | - Armelle Marais
- Univ. BordeauxINRAEUMR 1332 BFPVillenave d’Ornon cedexFrance
| | - Marie Lefebvre
- Univ. BordeauxINRAEUMR 1332 BFPVillenave d’Ornon cedexFrance
| | - Sébastien Theil
- Univ. BordeauxINRAEUMR 1332 BFPVillenave d’Ornon cedexFrance
- Present address:
INRA UMRF20, côte de ReyneAurillac15000France
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29
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Svanella-Dumas L, Marais A, Faure C, Lefebvre M, Gaudin J, Candresse T. First report of lettuce necrotic leaf curl virus infecting cultivated lettuce in France. Plant Dis 2020; 105:1233. [PMID: 33349003 DOI: 10.1094/pdis-11-20-2348-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lettuce necrotic leaf curl virus (LNLCV, genus Torradovirus, family Secoviridae) has a bipartite single-stranded RNA genome and has so far only been reported in the Netherlands in open field lettuce (Verbeek et al. 2014). It was the first Torradovirus described from non-tomato host and, contrary to whitefly-transmitted tomato torradoviruses, aphids are its natural vectors (Verbeek et al. 2017). In October 2019, a symptomatic lettuce (JG3, cv. "Tregoney") was collected in an open field in southwestern France. Symptoms included stunted and deformed leaves with light necrosis and yellow spotting along minor veins of older leaves. Double-stranded RNAs were purified from JG3 leaves as described (Marais et al. 2018) and a cDNA library prepared and analyzed by Illumina NovaSeq sequencing. Analysis of sequence data identified two nearly fully assembled RNAs integrating respectively 28.9% and 60.9% of the sequencing reads and sharing respectively 85.5% and 83.3% nucleotide (nt) identity with the RNAs 1 and 2 of the LNLCV reference isolate, (NC_035214 and NC_035219, respectively). To confirm the presence of LNLCV in the original JG3 plant, it was used to mechanically inoculate indicator Nicotiana benthamiana, Chenopodium quinoa and C. amaranticolor plants. Only N. benthamiana developed symptoms, in the form of smaller and yellowed leaves. All inoculated plants were tested one month post-inoculation for the presence of LNLCV. Total RNAs were extracted according to Foissac et al. (2005) and used for RT-PCR tests with primers designed from the alignment between NC_035214 and our RNA1 sequence (LNLCV-S 5'-ATATTTTCCAAGTTGGAGGCTC-3' and LNLCV-R 5'-AGTRACAAAGGGACTAACTG-3'). LNLCV was detected in 3 out of 4 inoculated N. benthamiana plants. The full length RNA1 sequence (7577 nt) and the near complete RNA2 (5286 nt, lacking 3 nt at the 5' end as compared to NC_035219) could be assembled from the JG3 sequencing data and have been deposited in GenBank (MW172270 and MW172271, respectively). The lettuce JG3 isolate RNA1 shows 86.5% nt identity with the reference isolate while the taxonomically informative protease-polymerase regions share 96.8% aa identity. JG3 RNA2 shares 84.8% nt identity with NC_035219 while the movement protein and capsid subunits share respectively 92.5% and 98.3% aa identity. The smaller upstream ORF that slightly overlaps with the large MP-CP1/2/3 ORF is also conserved and shows 94.8% aa identity with the reference isolate. To our knowledge, this represents the first report of a natural infection of LNLCV in cultivated lettuce in France and anywhere outside the Netherlands. Since no other viruses were detected in the sequence dataset, LNLCV is most likely responsible for the mild necrosis and leaf deformation symptoms observed on the JG3 plant that appear to be similar to those initially described for LNLCV (Verbeek et al. 2014). While the pathogenicity of LNLCV in lettuce appears to be firmly established, further studies are needed to establish its distribution and prevalence, to understand why this pathogenic and aphid-transmitted virus is not more widely reported and whether it has the potential to increase in impact as a potential emerging agent on field lettuce crops.
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Affiliation(s)
| | - Armelle Marais
- INRA, UMR GDPP, IBVM, 71 avenue E. Bourlaux, Bordeaux, France, 33270;
| | | | - Marie Lefebvre
- INRA Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, INRA - Université de Bordeaux, 71, av. Edouard Bourlaux, Villenave d'Ornon Cedex, France, CS 20032 -33882;
| | - Jonathan Gaudin
- INRA Bordeaux University, UMR SAVE, Villenave d'Ornon Cedex, France;
| | - Thierry Candresse
- INRA Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, INRA - Université de Bordeaux, CS20032, Villenave d'Ornon , France, 33882 cedex;
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Abstract
Chayote (Sechium edule (Jacq.) Sw.) is a vigorous perennial and climbing cucurbits, native to Mesoamerica, and cultivated for alimentary purposes in the American continent, Australia, New Zealand, South Europe, Asia and Africa. During spring 2019, some chayote plants showing bright yellow vein banding rings and lines were observed in a private garden in South Italy (Campania region). Symptoms coalesced in some leaves, covering almost the whole foliar area. Double-stranded RNAs were extracted from symptomatic leaves of a single chayote plant and reverse-transcribed, randomly amplified, and submitted to Illumina sequencing (Marais et al., 2018). Reads were assembled using CLC Genomics Workbench 11.1 (http://www.clcbio.com). Contigs were then annotated by Blastn and Blastx comparison with the Genbank database, which allowed the identification of eight contigs of between 380 and 980 nucleotides sharing significant identity with alfalfa mosaic virus (AMV) genomic RNAs. No other viral contigs were identified. Mapping of reads on AMV genomic RNAs identified 4,209 AMV reads (1.26% of total reads) and allowed the scaffolding of the contigs into three scaffolds corresponding to the three AMV genomic RNAs. To complete the sequence of the AMV chayote isolate genome (named See-1), primers were designed from the contig sequences and used to amplify RACE PCR products spanning the 5' and 3' terminal regions of the three genomic RNAs using the SMARTer™ RACE cDNA Amplification Kit (Clontech, China). All amplicons were cloned into the pGEM-T vector (Promega, USA) and sequenced (three clones for each amplicon) by Microsynth Seqlab (Microsynth AG, Switzerland). Finally, the complete genomic sequences of the three RNAs were assembled by MacVector 17.5 (MacVector Inc., USA). The RNA1, RNA2 and RNA3 of See-1 are 3,643, 2,593 and 2,037 nt respectively (GenBank accession Nos. MT093209 to MT093211), and share the highest nt sequence identity with the RNA1 and RNA3 of AMV isolate (HZ) from tobacco (99.5% for RNA1, HQ316635; 98.7% for RNA3, HQ316637) and with the RNA2 of isolate AMV-Gym from Gynostemma pentaphyllum (98.1%, MH332898), both from China. AMV isolate See-1 was classified as belonging to subgroup I based on the presence of a BamH I and two AvaII sites in the CP ORF (Parrella et al., 2000). Reverse transcription polymerase chain reaction, using primers targeting the CP gene (Parrella et al., 2000), confirmed AMV infection in three symptomatic cayote plants including that used for Illumina sequencing, with 100% of nt sequence identity of amplicons. Three plants each of Chenopodium amaranticolor, Nicotiana benthamiana and Solanum lycopersicon were mechanically inoculated with sap from isolate See-1 infected plant, leading to the appearance of typical AMV symptoms in all three hosts ten days post-inoculation (Jaspars & Bos, 1980). This note describes the first detection of AMV in cayote in Italy and, to the best of our knowledge, in the world. In some areas of Southern Italy, climatic conditions are favorable enough to allow chayote development in the wild. Further studies would be desirable to determine the distribution and incidence of AMV in chayote and to understand the possibility that this species may play a role in AMV epidemiology, representing a threat to other susceptible crops.
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Affiliation(s)
- Giuseppe Parrella
- Istituto per la Protezione Sostenibile delle Piante del CNR, Via Università 133, Portici (NA), Italy, 80055;
| | - Elisa Troiano
- Istituto per la Protezione Sostenibile delle Piante del CNR, 80055 Portici (NA), Italy, Italy;
| | - Chantal Faure
- INRAE, Univ. Bordeaux, UMR BFP, CS 20032, 33882 Villenave d'Ornon CEDEX, France, France;
| | - Armelle Marais
- INRAE, Univ. Bordeaux, UMR BFP, CS 20032, 33882 Villenave d'Ornon CEDEX, France, France;
| | - Thierry Candresse
- INRAE, Univ. Bordeaux, UMR BFP, CS 20032, 33882 Villenave d'Ornon CEDEX, France, France;
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31
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Umber M, Filloux D, Gélabale S, Gomez RM, Marais A, Gallet S, Gamiette F, Pavis C, Teycheney PY. Molecular Viral Diagnosis and Sanitation of Yam Genetic Resources: Implications for Safe Yam Germplasm Exchange. Viruses 2020; 12:v12101101. [PMID: 33003342 PMCID: PMC7650539 DOI: 10.3390/v12101101] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 01/25/2023] Open
Abstract
Yam (Dioscorea spp.) is an important crop in tropical and subtropical regions. Many viruses have been recently identified in yam, hampering genetic conservation and safe international exchanges of yam germplasm. We report on the implementation of reliable and cost-effective PCR-based detection tools targeting eight different yam-infecting viruses. Viral indexing of the in vitro yam collection maintained by the Biological Resources Center for Tropical Plants (BRC-TP) in Guadeloupe (French West Indies) unveiled a high prevalence of potyviruses, badnaviruses, Dioscorea mosaic associated virus (DMaV) and yam asymptomatic virus 1 (YaV1) and a high level of coinfections. Infected yam accessions were subjected to a combination of thermotherapy and meristem culture. Sanitation levels were monitored using PCR-based and high-throughput sequencing-based diagnosis, confirming the efficacy and reliability of PCR-based detection tools. Sanitation rates were highly variable depending on viruses. Sixteen accessions were successfully sanitized, paving the way to safe yam germplasm exchanges and the implementation of clean seed production programs worldwide.
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Affiliation(s)
- Marie Umber
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
- Correspondence: ; Tel.: +590-590-25-59-29
| | - Denis Filloux
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche—Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France;
- Biologie et Génétique des Interactions Plante-Parasite, Univ. Montpellier, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Institut National de Recherche pour l’Agriculture, Montpellier SupAgro, F-34060 Montpellier, France
| | - Suzia Gélabale
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Rose-Marie Gomez
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Armelle Marais
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Université de Bordeaux, Unité Mixte de Recherche Biologie du Fruit et Pathologie, F-33882 Villenave d’Ornon, France;
| | - Séverine Gallet
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Franciane Gamiette
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Claudie Pavis
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Pierre-Yves Teycheney
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-97130 Capesterre Belle-Eau, France;
- Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Univ. Montpellier, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Institut Agro, F-97130 Capesterre Belle-Eau, France
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Marais A, Umber M, Filloux D, Gomez RM, Faure C, Pavis C, Julian C, Roumagnac P, Acina-Mambole I, Bonheur L, Theil S, Contreras S, Candresse T, Teycheney PY. Yam asymptomatic virus 1, a novel virus infecting yams (Dioscorea spp.) with significant prevalence in a germplasm collection. Arch Virol 2020; 165:2653-2657. [PMID: 32852617 DOI: 10.1007/s00705-020-04787-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/26/2020] [Indexed: 02/05/2023]
Abstract
A novel virus infecting yams (Dioscorea spp.), tentatively named "yam asymptomatic virus 1" (YaV1), was characterized and sequenced from an asymptomatic D. alata plant from Vanuatu. Sequence comparisons and phylogenetic analysis showed that YaV1 is a novel ampelovirus and has the smallest genome among "subgroup 1" members. RT-PCR-based screening of a yam germplasm collection conserved in Guadeloupe showed that YaV1 is prevalent in D. alata, D. bulbifera, D. cayennensis subsp. rotundata, D. esculenta and D. trifida accessions but causes no apparent symptoms. Additional phylogenetic analysis revealed a low variability of YaV1 in Guadeloupe in a limited part of the genome, and suggested the occurrence of plant-to-plant transmission.
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Affiliation(s)
- Armelle Marais
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | - Marie Umber
- INRAE, UR ASTRO, 97170, Petit-Bourg, Guadeloupe, France
| | - Denis Filloux
- CIRAD, UMR BGPI, Montpellier, France.,BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Chantal Faure
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | - Claudie Pavis
- INRAE, UR ASTRO, 97170, Petit-Bourg, Guadeloupe, France
| | - Charlotte Julian
- CIRAD, UMR BGPI, Montpellier, France.,BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR BGPI, Montpellier, France.,BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Isabelle Acina-Mambole
- CIRAD, UMR AGAP, Station de Neufchâteau, Sainte-Marie, 97130, Capesterre Belle-Eau, Guadeloupe, France.,AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre Belle-Eau, Guadeloupe, France
| | | | - Sébastien Theil
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France.,INRAE, UMRF, Aurillac, France
| | - Sandy Contreras
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | | | - Pierre-Yves Teycheney
- CIRAD, UMR AGAP, Station de Neufchâteau, Sainte-Marie, 97130, Capesterre Belle-Eau, Guadeloupe, France. .,AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre Belle-Eau, Guadeloupe, France.
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Khalili M, Candresse T, Faure C, Marais A. Complete genome sequence of almond luteovirus 1, a novel luteovirus infecting almond. Arch Virol 2020; 165:2123-2126. [PMID: 32617763 DOI: 10.1007/s00705-020-04715-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 05/23/2020] [Indexed: 11/27/2022]
Abstract
In this study, we report the complete genome sequence of a novel luteovirus detected in almond using high-throughput sequencing. The genome of the new luteovirus comprises 5,047 nucleotides, and its genomic organization is similar to that of the recently described nectarine stem pitting associated virus (NSPaV), with only four open reading frames, encoding replication-related proteins, the coat protein (CP), and a CP readthrough protein involved in the aphid transmission of luteovirids. Phylogenic and pairwise distance analyses showed that this virus shares 79% and 57.8% amino acid identity in the P1-P2 fusion protein and the P3-P5 protein, respectively, with the most closely related luteovirus, NSPaV, suggesting that it represents a novel species, for which the name "Almond associated luteovirus 1" is proposed. To our knowledge, this is the first report of an almond-infecting luteovirus.
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Affiliation(s)
- Maryam Khalili
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | | | - Chantal Faure
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | - Armelle Marais
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France.
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Marais A, Šafářová D, Navrátil M, Faure C, Cornaggia D, Brans Y, Suchá J, Candresse T. Complete genome sequence of cherry virus T, a novel cherry-infecting tepovirus. Arch Virol 2020; 165:1711-1714. [PMID: 32409875 DOI: 10.1007/s00705-020-04656-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/12/2020] [Indexed: 10/24/2022]
Abstract
Double-stranded RNA and total RNA purified from sour cherry leaves (Prunus cerasus, cv. Amarelka Chvalkovicka) was analyzed by high-throughput sequencing. BLAST annotation identified contigs with homology to several already known cherry-infecting viruses (prune dwarf virus, prunus necrotic ringspot virus, prunus virus F, little cherry virus 1) as well as contigs with sequences more distantly related to those of members of the family Betaflexiviridae and in particular to prunus virus T of the genus Tepovirus. The full genome sequence of a putative virus (6,847 nucleotides [nt]; GenBank no. MT090966) was assembled and completed at the genome ends. The genome has a typical tepovirus organization, containing three overlapping open reading frames (ORFs), encoding a replication-associated protein, a movement protein and a capsid protein, respectively. Both its genome organization and its phylogenetic relationships show that the virus belongs to the genus Tepovirus, but considering the species demarcation criteria for the family Betaflexiviridae, it appears to represent a novel virus species, and we propose the name "cherry virus T" (ChVT) for this virus.
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Affiliation(s)
- A Marais
- INRAE, University of Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | - D Šafářová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, 783 71, Olomouc-Holice, Czech Republic
| | - M Navrátil
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, 783 71, Olomouc-Holice, Czech Republic
| | - C Faure
- INRAE, University of Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | - D Cornaggia
- Laboratoire de Virologie et de Biologie moléculaire, CTIFL, 28 Route des Nébouts, 24130, Prigonrieux, France
| | - Y Brans
- Laboratoire de Virologie et de Biologie moléculaire, CTIFL, 28 Route des Nébouts, 24130, Prigonrieux, France
| | - J Suchá
- Research Institute of Pomology in Holovousy Ltd, Holovousy 129, 508 01, Hořice, Czech Republic
| | - T Candresse
- INRAE, University of Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France.
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Candresse T, Marais A, Faure C, Lefebvre M, Lacombe T, Boursiquot JM. Complete genome sequence of a novel grapevine-infecting member of the genus Polerovirus, grapevine polerovirus 1. Arch Virol 2020; 165:1683-1685. [PMID: 32372367 DOI: 10.1007/s00705-020-04640-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/28/2020] [Indexed: 10/24/2022]
Abstract
Double-stranded RNAs and total RNAs purified from grapevine (Vitis vinifera) phloem scrapings of two varieties held in the INRAE (France) grapevine germplasm collection were analyzed by high-throughput sequencing. BLAST annotation revealed contigs with homology to Polerovirus genus members. The full genome sequence of one isolate (KT) was determined (5651 nucleotides [nt]), and a partial sequence representing about half of the genome was assembled for a second isolate (KS) that was found to share 95% nt sequence identity with the KT isolate. The genome has a typical polerovirus organization, containing six open reading frames (ORFs) as well as a putative additional ORF3a. Based on genome organization and phylogenetic relationships, the new virus belongs to the genus Polerovirus but, similar to the recently described persimmon polerovirus 1, is characterized by a highly divergent coat-protein/readthrough domain. Considering the species demarcation criteria for the family Luteoviridae, these two isolates, together with a closely related sequence recently deposited in the GenBank database (LC507098), represent a new Polerovirus species for which the name "Grapevine polerovirus 1" is proposed.
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Affiliation(s)
- T Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, 72 Avenue Edouard Bourlaux, CS20032, 33882, Villenave d'Ornon cedex, France.
| | - A Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, 72 Avenue Edouard Bourlaux, CS20032, 33882, Villenave d'Ornon cedex, France
| | - C Faure
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, 72 Avenue Edouard Bourlaux, CS20032, 33882, Villenave d'Ornon cedex, France
| | - M Lefebvre
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, 72 Avenue Edouard Bourlaux, CS20032, 33882, Villenave d'Ornon cedex, France
| | - T Lacombe
- UMR AGAP, INRAE, Montpellier SupAgro, TA A-108/03 Avenue Agropolis, 34398, Montpellier Cedex 5, France
- Centre de Ressources Biologiques de la Vigne, INRAE, 34340, Marseillan-Plage, France
| | - J M Boursiquot
- UMR AGAP, INRAE, Montpellier SupAgro, TA A-108/03 Avenue Agropolis, 34398, Montpellier Cedex 5, France
- Centre de Ressources Biologiques de la Vigne, INRAE, 34340, Marseillan-Plage, France
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Rumbou A, Candresse T, Marais A, Svanella-Dumas L, Landgraf M, von Bargen S, Büttner C. Unravelling the virome in birch: RNA-Seq reveals a complex of known and novel viruses. PLoS One 2020; 15:e0221834. [PMID: 32589631 PMCID: PMC7319284 DOI: 10.1371/journal.pone.0221834] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 06/10/2020] [Indexed: 12/22/2022] Open
Abstract
To unravel the virome in birch trees of German and Finnish origin exhibiting symptoms of birch leaf-roll disease (BRLD), high-throughput sequencing (HTS) was employed. In total five viruses, among which three were so far unknown, were detected by RNAseq. One to five virus variants were identified in the transcriptome of individual trees. The novel viruses were genetically—fully or partially—characterized, belonging to the genera Carlavirus, Idaeovirus and Capillovirus and are tentatively named birch carlavirus, birch idaeovirus, and birch capillovirus, respectively. The recently discovered birch leafroll-associated virus was systematically detected by HTS in symptomatic seedlings but not in symptomless ones. The new carlavirus was detected only in one of the three symptomatic seedlings. The novel putative Capillovirus was detected in all seedlings—irrespective of their BLRD status—while the Idaeovirus was identified in a plant without leaf symptoms at the time of sampling. Further efforts are needed to complete Koch’s postulates and to clarify the possible association of the detected viruses with the BLR disease. Our study elucidates the viral population in single birch seedlings and provides a comprehensive overview for the diversities of the viral communities they harbor, to date.
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Affiliation(s)
- Artemis Rumbou
- Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
- * E-mail:
| | - Thierry Candresse
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS, Villenave d’Ornon, Bordeaux, France
| | - Armelle Marais
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS, Villenave d’Ornon, Bordeaux, France
| | - Laurence Svanella-Dumas
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS, Villenave d’Ornon, Bordeaux, France
| | - Maria Landgraf
- Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Susanne von Bargen
- Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Carmen Büttner
- Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
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Ma Y, Marais A, Lefebvre M, Faure C, Candresse T. Metagenomic analysis of virome cross-talk between cultivated Solanum lycopersicum and wild Solanum nigrum. Virology 2019; 540:38-44. [PMID: 31734382 DOI: 10.1016/j.virol.2019.11.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 02/03/2023]
Abstract
Wild plants and weeds growing close to crops constitute a potential reservoir for future epidemies or for the emergence of novel viruses but the frequency and directionality of viral flow between cultivated and wild plants remains poorly documented in many cases. Here, we studied the diversity of viral populations between tomato (Solanum lycopersicum) and neighboring european black nightshade (Solanum nigrum) using high throughput sequencing (HTS) based metagenomics. A large variability in virome richness with only 17.9% shared Operational Taxonomy Units between tomato and nightshade, but this richness could not be linked to a particular host or to local conditions. A detailed population analysis based on assembled contigs for potato virus Y (PVY), broad wilt bean virus 1 and a new ilarvirus tentatively named Solanum nigrum ilarvirus 1 provides information on the circulation of these viruses between these two Solanum species and enriches our knowledge of the tomato virome.
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Affiliation(s)
- Yuxin Ma
- UMR 1332 BFP, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- UMR 1332 BFP, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Marie Lefebvre
- UMR 1332 BFP, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Chantal Faure
- UMR 1332 BFP, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Thierry Candresse
- UMR 1332 BFP, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France.
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Marais A, Leuschner M. The sore throat: a clinical approach to tonsillopharyngitis. S Afr Fam Pract (2004) 2019. [DOI: 10.4102/safp.v61i4.4957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Acute sore throat is a common complaint encountered by medical practitioners and health care workers routinely. The disease is mostly caused by viral infections of the upper respiratory tract and is usually self-limiting. Symptoms rarely exceed two weeks, irrespective of the cause. Group A beta-haemolytic streptococci accounts for the majority of bacterial instances of tonsillopharyngitis. Clinical examination is not always adequate to diagnose bacterial infections, resulting in the irrational and over-prescribing of antibiotics, especially in upper respiratory tract infections, contributing to communal antimicrobial bacterial resistance. A few scoring systems are available to assist physicians in deciding on the aetiology without resorting to unnecessary laboratory investigations. This article briefly reviews the scoring systems and antimicrobial management of streptococcal throat infections.
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Marais A, Faure C, Theil S, Candresse T. Characterization of the virome of shallots affected by the shallot mild yellow stripe disease in France. PLoS One 2019; 14:e0219024. [PMID: 31339882 PMCID: PMC6655591 DOI: 10.1371/journal.pone.0219024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/09/2019] [Indexed: 11/19/2022] Open
Abstract
To elucidate the etiology of a new disease of shallot in France, double-stranded RNAs from asymptomatic and symptomatic shallot plants were analyzed using high-throughput sequencing (HTS). Annotation of contigs, molecular characterization and phylogenetic analyses revealed the presence in symptomatic plants of a virus complex consisting of shallot virus X (ShVX, Allexivirus), shallot latent virus (SLV, Carlavirus) and two novel viruses belonging to the genera Carlavirus and Potyvirus, for which the names of shallot virus S (ShVS) and shallot mild yellow stripe associated virus (SMYSaV), are proposed. Complete or near complete genomic sequences were obtained for all these agents, revealing divergent isolates of ShVX and SLV. Trials to fulfill Koch's postulates were pursued but failed to reproduce the symptoms on inoculated shallots, even though the plants were proved to be infected by the four viruses detected by HTS. Replanting of bulbs from SMYSaV-inoculated shallot plants resulted in infected plants, showing that the virus can perpetuate the infection over seasons. A survey analyzing 351 shallot samples over a four years period strongly suggests an association of SMYSaV with the disease symptoms. An analysis of SMYSaV diversity indicates the existence of two clusters of isolates, one of which is largely predominant in the field over years.
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Affiliation(s)
- Armelle Marais
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Chantal Faure
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Sébastien Theil
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d’Ornon, France
| | - Thierry Candresse
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Villenave d’Ornon, France
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Abstract
Haemostasis and thrombosis rely on three components namely the vascular endothelial wall, blood platelets and the coagulation cascade. Non-physiologic excessive thrombosis occurs when haemostatic processes are dysfunctional, causing undue clot formation or reduced clot lysis. Antithrombotic agents including antiplatelet, anticoagulation and fibrinolytic agents are essential for the prophylaxis and pharmacological management of venous thromboembolism and arterial thrombosis. Anticoagulation treatment options have expanded steadily over the past few decades, providing a greater number of agents. Anticoagulants that directly target the enzymatic activity of thrombin and factor Xa have recently been developed to address the inadequacies of traditional vitamin K antagonists. Appropriate use of these agents requires knowledge of their individual characteristics, risks, and benefits.
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Affiliation(s)
- A Marais
- Department of Pharmacology & Therapeutics, School of Medicine, Sefako Makghato Health Sciences University, South Africa
- Department of Pharmacology, School of Medicine, Faculty of Health Sciences, University of Pretoria, South Africa
| | - E Osuch
- Department of Pharmacology & Therapeutics, School of Medicine, Sefako Makghato Health Sciences University, South Africa
| | - V Steenkamp
- Department of Pharmacology, School of Medicine, Faculty of Health Sciences, University of Pretoria, South Africa
| | - L Ledwaba
- Department of Pharmacology & Therapeutics, School of Medicine, Sefako Makghato Health Sciences University, South Africa
- Department of Pharmacology, School of Medicine, Faculty of Health Sciences, University of Pretoria, South Africa
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Scussel S, Candresse T, Marais A, Claverie S, Hoareau M, Azali HA, Verdin E, Tepfer M, Filloux D, Fernandez E, Roumagnac P, Robène I, Lefeuvre P, Jourda C, Roux-Cuvelier M, Lett JM. High-throughput sequencing of complete genomes of ipomoviruses associated with an epidemic of cassava brown streak disease in the Comoros Archipelago. Arch Virol 2019; 164:2193-2196. [PMID: 31123961 DOI: 10.1007/s00705-019-04228-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/05/2019] [Indexed: 11/26/2022]
Abstract
Using high-throughput sequencing of small interfering RNAs (siRNAs), virion-associated nucleic acid (VANA), and double stranded RNAs (dsRNAs), we have determined the complete genome sequences of Comorian isolates of two ipomoviruses, cassava brown streak virus (CBSV) and a divergent isolate of Ugandan cassava brown streak virus (UCBSV-KM) representing a new strain of this virus. While the large ORF of CBSV shares the highest nucleotide sequence identity (95.9%) with a Tanzanian isolate of CBSV, the large UCBSV-KM ORF shares the highest nucleotide sequence identity (77.5%) with a Malawian isolate of UCBSV. This low value is near the species demarcation threshold for the family Potyviridae (<76%). Phylogenetic analysis confirms that UCBSV-KM represents a new lineage that is genetically distinct from the currently described UCBSV strains.
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Affiliation(s)
- Sarah Scussel
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Sohini Claverie
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
- Université de La Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Murielle Hoareau
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | | | - Eric Verdin
- INRA, UR407 Unité de Pathologie Végétale, CS 60094, 84140, Montfavet, France
| | - Mark Tepfer
- INRA, UR407 Unité de Pathologie Végétale, CS 60094, 84140, Montfavet, France
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Saclay Plant Sciences (SPS), Université Paris-Saclay, 78026, Versailles, France
| | - Denis Filloux
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398, Montpellier Cedex-5, France
| | - Emmanuel Fernandez
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398, Montpellier Cedex-5, France
| | - Philippe Roumagnac
- CIRAD, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398, Montpellier Cedex-5, France
| | - Isabelle Robène
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Cyril Jourda
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Michel Roux-Cuvelier
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Jean-Michel Lett
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France.
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Marais A, Osuch E, Steenkamp V, Ledwaba L. Important pharmacogenomic aspects in the management of HIV/AIDS. S Afr Fam Pract (2004) 2019. [DOI: 10.4102/safp.v61i1.5047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
In managing HIV/AIDS with highly active antiretroviral agents, the historical therapeutic aim remains to maintain the plasma concentrations at a level above the half maximal inhibitory concentration (IC50) required for 50% inhibition in viral replication. Concentration dependent toxicity is often observed in patients with elevated drug exposure and high peak plasma levels in lieu of accurately calculated drug dosages. Similarly low plasma concentrations are frequently witnessed in individuals receiving adequate dosage regimens. Pharmacogenetic variations in drug metabolizing enzymes may contribute to this phenomenon. Over the last decade, knowledge about the role of pharmacogenetics in the treatment and prediction of ARV plasma levels have increased significantly. However, the extent of these genetic variations remain largely unknown in the South African population, which has sparked a renewed enthusiasm for local pharmacogenetic studies.
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Elbeaino T, Marais A, Faure C, Trioano E, Candresse T, Parrella G. High-Throughput Sequencing Reveals Cyclamen persicum Mill. as a Natural Host for Fig Mosaic Virus. Viruses 2018; 10:E684. [PMID: 30513865 PMCID: PMC6316199 DOI: 10.3390/v10120684] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 11/16/2022] Open
Abstract
In a search for viral infections, double-stranded RNA (dsRNA) were recovered from a diseased cyclamen (Cyclamen persicum Mill.) accession (Cic) and analyzed by high-throughput sequencing (HTS) technology. Analysis of the HTS data showed the presence of Fig mosaic emaravirus (FMV) in this accession. The complete sequences of six FMV-Cic RNA genomic segments were determined from the HTS data and using Sanger sequencing. All FMV-Cic RNA segments are similar in size to those of FMV from fig (FMV-Gr10), with the exception of RNA-6 that is one nucleotide longer. The occurrence of FMV in cyclamen was investigated through a small-scale survey, from which four plants (out of 18 tested) were found RT-PCR positive. To study sequence variations of cyclamen isolates of FMV, RT-PCR products generated through the amplification of the partially RNA-dependent RNA polymerase (RdRp, RNA-1), glycoprotein (GP, RNA-2), and nucleocapsid (NCP, RNA-3) genes were explored. The nucleotide sequence identities for cyclamen isolates ranged between 86% and 99% in RNA-1, 93% and 99% in RNA-2, and 98% and 99% in RNA-3, while lower identity levels were observed with the sequences of fig isolates. Based on the phylogenetic tree obtained with a 304-nt fragment of RNA3, all FMV isolates from cyclamens were assigned to a single cluster close to fig isolates from the Mediterranean. FMV was graft-transmitted to healthy cyclamens eliciting symptoms similar to those observed in the Cic accession, thus suggesting a causal role of FMV in the symptoms that prompted the investigation. This is the first report of FMV in a non-fig host, Cyclamen persicum, a finding that may help in the control of the mosaic and mosaic-like diseases of fig and cyclamen, respectively.
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Affiliation(s)
- Toufic Elbeaino
- Mediterranean Agronomic Institute of Bari (CIHEAM-IAMB), Via Ceglie 9, 70010 Valenzano, Italy.
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université Bordeaux, CS 20032, 33882 Villenave d'Ornon CEDEX, France.
| | - Chantal Faure
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université Bordeaux, CS 20032, 33882 Villenave d'Ornon CEDEX, France.
| | - Elisa Trioano
- Institute for Sustainable Plant Protection, National Research Council (CNR), Via Università 133, 80055 Portici, Italy.
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université Bordeaux, CS 20032, 33882 Villenave d'Ornon CEDEX, France.
| | - Giuseppe Parrella
- Institute for Sustainable Plant Protection, National Research Council (CNR), Via Università 133, 80055 Portici, Italy.
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Nourinejhad Zarghani S, Hily JM, Glasa M, Marais A, Wetzel T, Faure C, Vigne E, Velt A, Lemaire O, Boursiquot JM, Okic A, Ruiz-Garcia AB, Olmos A, Lacombe T, Candresse T. Grapevine virus T diversity as revealed by full-length genome sequences assembled from high-throughput sequence data. PLoS One 2018; 13:e0206010. [PMID: 30376573 PMCID: PMC6207325 DOI: 10.1371/journal.pone.0206010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/04/2018] [Indexed: 12/13/2022] Open
Abstract
RNASeq or double-stranded RNA based approaches allowed the reconstruction of a total of 9 full-length or near full-length genomes of the recently discovered grapevine virus T (GVT). In addition, datamining of publicly available grapevine RNASeq transcriptome data allowed the reconstruction of a further 14 GVT genomes from five grapevine sources. Together with four GVT sequences available in Genbank, these novel sequences were used to analyse GVT diversity. GVT shows a very limited amount of indels variation but a high level of nucleotide and aminoacid polymorphism. This level is comparable to that shown in the closely related grapevine rupestris stem pitting-associated virus (GRSPaV). Further analyses showed that GVT mostly evolves under conservative selection pressure and that recombination has contributed to its evolutionary history. Phylogenetic analyses allow to identify at least seven clearly separated groups of GVT isolates. Analysis of the only reported PCR GVT-specific detection primer pair indicates that it is likely to fail to amplify some GVT isolates. Taken together these results point at the distinctiveness of GVT but also at the many points it shares with GRSPaV. They constitute the first pan-genomic analysis of the diversity of this novel virus.
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Affiliation(s)
- Shaheen Nourinejhad Zarghani
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
- Department of Plant Protection, College of Abouraihan, University of Tehran, Tehran, Iran
| | | | - Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Armelle Marais
- Equipe de Virologie, UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
| | - Chantal Faure
- Equipe de Virologie, UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | | | - Amandine Velt
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Olivier Lemaire
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Jean Michel Boursiquot
- UMR 1334 AGAP, INRA, Montpellier SupAgro, Montpellier, France
- Centre de Ressources Biologiques de la Vigne, INRA, Marseillan-Plage, France
| | - Arnela Okic
- University of Sarajevo, Faculty of Agriculture and Food Science, Sarajevo, Bosnia and Herzegovina
| | | | - Antonio Olmos
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Thierry Lacombe
- UMR 1334 AGAP, INRA, Montpellier SupAgro, Montpellier, France
- Centre de Ressources Biologiques de la Vigne, INRA, Marseillan-Plage, France
| | - Thierry Candresse
- Equipe de Virologie, UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
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Svanella-Dumas L, Τsarmpopoulos Ι, Marais A, Theil S, Faure C, Gaudin J, Candresse T. Complete genome sequence of lettuce chordovirus 1 isolated from cultivated lettuce in France. Arch Virol 2018; 163:2543-2545. [PMID: 29730706 DOI: 10.1007/s00705-018-3858-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/27/2018] [Indexed: 10/17/2022]
Abstract
Double-stranded RNAs purified from cultivated (Lactuca sativa) or wild (L. serriola) lettuce from southwest France were analyzed by high-throughput sequencing. For both samples, BLAST annotation revealed contigs with homology to Betaflexiviridae family members. The full genome sequence of the isolate from cultivated lettuce (JG1) was completed (8,536 nucleotides [nt], excluding the poly(A) tail). The sequence of the 3' half of the genome (4,800 nt) of a wild lettuce isolate (P22) was determined and found to share 95.1% nt sequence identity with the JG1 isolate. The JG1 genome contains four open reading frames, encoding a replicase, a movement protein, a capsid protein, and a protein of unknown function, respectively. Based on genome organization and phylogenetic relationships, the lettuce virus is most closely related to the recently described carrot chordoviruses 1 and 2 in the family Betaflexiviridae. Considering the species demarcation criteria in this family, the two lettuce viruses represent isolates of a new chordovirus species for which the name "lettuce chordovirus 1" (LeCV1) is proposed.
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Affiliation(s)
- Laurence Svanella-Dumas
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Ιason Τsarmpopoulos
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Chantal Faure
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Jonathan Gaudin
- UMR 1065, Santé et Agroécologie du Vignoble, INRA, Bordeaux Sciences Agro, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Thierry Candresse
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France.
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Hily JM, Candresse T, Garcia S, Vigne E, Tannière M, Komar V, Barnabé G, Alliaume A, Gilg S, Hommay G, Beuve M, Marais A, Lemaire O. High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member. Front Microbiol 2018; 9:1782. [PMID: 30210456 PMCID: PMC6123372 DOI: 10.3389/fmicb.2018.01782] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/16/2018] [Indexed: 12/20/2022] Open
Abstract
In the past decade, high-throughput sequencing (HTS) has had a major impact on virus diversity studies as well as on diagnosis, providing an unbiased and more comprehensive view of the virome of a wide range of organisms. Rather than the serological and molecular-based methods, with their more "reductionist" view focusing on one or a few known agents, HTS-based approaches are able to give a "holistic snapshot" of the complex phytobiome of a sample of interest. In grapevine for example, HTS is powerful enough to allow for the assembly of complete genomes of the various viral species or variants infecting a sample of known or novel virus species. In the present study, a total RNAseq-based approach was used to determine the full genome sequences of various grapevine fanleaf virus (GFLV) isolates and to analyze the eventual presence of other viral agents. From four RNAseq datasets, a few complete grapevine-infecting virus and viroid genomes were de-novo assembled: (a) three GFLV genomes, 11 grapevine rupestris stem-pitting associated virus (GRSPaV) and six viroids. In addition, a novel viral genome was detected in all four datasets, consisting of a single-stranded, positive-sense RNA molecule of 6033 nucleotides. This genome displays an organization similar to Tymoviridae family members in the Tymovirales order. Nonetheless, the new virus shows enough differences to be considered as a new species defining a new genus. Detection of this new agent in the original grapevines proved very erratic and was only consistent at the end of the growing season. This virus was never detected in the spring period, raising the possibility that it might not be a grapevine-infecting virus, but rather a virus infecting a grapevine-associated organism that may be transiently present on grapevine samples at some periods of the year. Indeed, the Tymoviridae family comprises isometric viruses infecting a wide range of hosts in different kingdoms (Plantae, Fungi, and Animalia). The present work highlights the fact that even though HTS technologies produce invaluable data for the description of the sanitary status of a plant, in-depth biological studies are necessary before assigning a new virus to a particular host in such metagenomic approaches.
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Affiliation(s)
- Jean-Michel Hily
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon, Bordeaux, France
| | - Shahinez Garcia
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Emmanuelle Vigne
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Mélanie Tannière
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Véronique Komar
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Guillaume Barnabé
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Antoine Alliaume
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Sophie Gilg
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Gérard Hommay
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Monique Beuve
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon, Bordeaux, France
| | - Olivier Lemaire
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
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Svanella-Dumas L, Marais A, Faure C, Theil S, Lefebvre M, Candresse T. Genome characterization of a divergent isolate of the mycovirus Botrytis virus F from a grapevine metagenome. Arch Virol 2018; 163:3181-3183. [PMID: 30074093 DOI: 10.1007/s00705-018-3975-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022]
Abstract
As part of a grapevine metagenome study, total RNA extracted from grapevine phloem scrapings was analyzed by Illumina sequencing. For one 420A rootstock sample, reads mapping against a reference database and BLAST annotation of contigs identified the presence of a divergent isolate of Botrytis virus F (BVF). The full genome sequence of this isolate (IVC-5-77) was determined (6,828 nucleotides [nt], excluding the poly(A) tail) and shown to be collinear with that of the BVF reference isolate, with the two open reading frames encoding a replication-associated protein (REP) and a coat protein (CP). The IVC-5-77 isolate, however, is very divergent, showing only 81.3-81.6% nucleotide sequence identity to the two other sequenced BVF isolates. The internal non-coding region was also found to be highly variable between BVF isolates. Analysis of the RNASeq reads demonstrated that close to 20% of them belong to Botrytis cinerea, the putative host of the IVC-5-77 isolate. These results extend our knowledge of the diversity and variability of BVF and demonstrate its detectability, together with that of its B. cinerea host, in total RNA RNASeq data from grapevine phloem scrapings.
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Affiliation(s)
- Laurence Svanella-Dumas
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Chantal Faure
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Marie Lefebvre
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France.
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Verdin E, Marais A, Wipf-Scheibel C, Faure C, Pelletier B, David P, Svanella-Dumas L, Poisblaud C, Lecoq H, Candresse T. Biological and Genetic Characterization of New and Known Necroviruses Causing an Emerging Systemic Necrosis Disease of Corn Salad (Valerianella locusta) in France. Phytopathology 2018; 108:1002-1010. [PMID: 29490195 DOI: 10.1094/phyto-08-17-0284-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
An emerging systemic necrosis disease of corn salad was first observed in the Nantes region of France in the late 2000s. Classical virology and high-throughput sequencing approaches demonstrated that the disease is associated with four different necroviruses: tobacco necrosis virus A (TNVA), tobacco necrosis virus D (TNVD), olive mild mosaic virus (OMMV), and a novel recombinant Alphanecrovirus for which the name corn salad necrosis virus (CSNV) is proposed. Satellite tobacco necrosis virus was also frequently observed. Koch's postulates were completed for all four agents, each one alone being able to cause systemic necrosis of varying severity in corn salad. OMMV was the most frequently observed virus and causes the most severe symptoms. TNVA was the second, both in terms of prevalence and symptom severity while TNVD and CSNV were only rarely observed and caused the less severe symptoms. The emergence of this systemic disease may have been favored by the short and repeated cropping cycles used for corn salad, possibly allowing the selection of necrovirus isolates with an improved ability to systemically invade this specialty crop.
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Affiliation(s)
- E Verdin
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - A Marais
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - C Wipf-Scheibel
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - C Faure
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - B Pelletier
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - P David
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - L Svanella-Dumas
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - C Poisblaud
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - H Lecoq
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
| | - T Candresse
- First, third, and ninth authors: Unité de Pathologie Végétale, INRA, Domaine Saint Maurice, 67, allée des chênes, CS 60094, F84143 Montfavet Cedex, France; second, fourth, seventh, and tenth authors: Equipe de Virologie, UMR 1332 BFP, INRA, University of Bordeaux, 71 Avenue Edouard Bourleaux, CS20032, F33882 Villenave d'Ornon Cedex, France; fifth author: Comité Départemental de Développement Maraîcher (CDDM), Maisons des maraîchers, La métairie neuve, F44860 Pont St Martin, France; and sixth and eighth authors: HM.CLAUSE, 1 Chemin du Moulin des Ronzières, 49800 La Bohalle, France
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Katsiani A, Maliogka VI, Katis N, Svanella-Dumas L, Olmos A, Ruiz-García AB, Marais A, Faure C, Theil S, Lotos L, Candresse T. High-Throughput Sequencing Reveals Further Diversity of Little Cherry Virus 1 with Implications for Diagnostics. Viruses 2018; 10:E385. [PMID: 30037079 PMCID: PMC6070981 DOI: 10.3390/v10070385] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/11/2018] [Accepted: 07/19/2018] [Indexed: 12/21/2022] Open
Abstract
Little cherry virus 1 (LChV1, Velarivirus, Closteroviridae) is a widespread pathogen of sweet or sour cherry and other Prunus species, which exhibits high genetic diversity and lacks a putative efficient transmission vector. Thus far, four distinct phylogenetic clusters of LChV1 have been described, including isolates from different Prunus species. The recent application of high throughput sequencing (HTS) technologies in fruit tree virology has facilitated the acquisition of new viral genomes and the study of virus diversity. In the present work, several new LChV1 isolates from different countries were fully sequenced using different HTS approaches. Our results reveal the presence of further genetic diversity within the LChV1 species. Interestingly, mixed infections of the same sweet cherry tree with different LChV1 variants were identified for the first time. Taken together, the high intra-host and intra-species diversities of LChV1 might affect its pathogenicity and have clear implications for its accurate diagnostics.
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Affiliation(s)
- Asimina Katsiani
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Varvara I Maliogka
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Nikolaos Katis
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Laurence Svanella-Dumas
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Naquera km 4.5, Moncada, 46113 Valencia, Spain.
| | - Ana B Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Naquera km 4.5, Moncada, 46113 Valencia, Spain.
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Chantal Faure
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Sébastien Theil
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Leonidas Lotos
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
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