This page has only limited features, please log in for full access.

Dr. Thierry Candresse
INRAE and Université de Bordeaux, Equipe de Virologie, UMR 1332 Biologie du Fruit et Pathologie, 71 avenue E. Bourlaux, CS 20032, 33882 Villenave d'Ornon Cedex, France

Basic Info


Research Keywords & Expertise

0 Diagnostics
0 Metagenomics
0 Virus
0 Mycovirus
0 genome

Fingerprints

Virus
genome
viroid
Diagnostics
Metagenomics
Mycovirus

Honors and Awards

The user has no records in this section


Career Timeline

The user has no records in this section.


Short Biography

The user biography is not available.
Following
Followers
Co Authors
The list of users this user is following is empty.
Following: 0 users

Feed

Research article
Published: 28 July 2021 in Phytopathology®
Reads 0
Downloads 0

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.

ACS Style

Armelle Marais; Sergio Murolo; Chantal Faure; Yoann Brans; Clément Larue; François Maclot; Sébastien Massart; Michela Chiumenti; Angelantonio Minafra; Gianfranco Romanazzi; Marie Lefebvre; Teresa Barreneche; Cécile Robin; Rémy J. Petit; Thierry Candresse. Sixty Years from the First Disease Description, a Novel Badnavirus Associated with Chestnut Mosaic Disease. Phytopathology® 2021, 1 -09.

AMA Style

Armelle Marais, Sergio Murolo, Chantal Faure, Yoann Brans, Clément Larue, François Maclot, Sébastien Massart, Michela Chiumenti, Angelantonio Minafra, Gianfranco Romanazzi, Marie Lefebvre, Teresa Barreneche, Cécile Robin, Rémy J. Petit, Thierry Candresse. Sixty Years from the First Disease Description, a Novel Badnavirus Associated with Chestnut Mosaic Disease. Phytopathology®. 2021; ():1-09.

Chicago/Turabian Style

Armelle Marais; Sergio Murolo; Chantal Faure; Yoann Brans; Clément Larue; François Maclot; Sébastien Massart; Michela Chiumenti; Angelantonio Minafra; Gianfranco Romanazzi; Marie Lefebvre; Teresa Barreneche; Cécile Robin; Rémy J. Petit; Thierry Candresse. 2021. "Sixty Years from the First Disease Description, a Novel Badnavirus Associated with Chestnut Mosaic Disease." Phytopathology® , no. : 1-09.

Brief report
Published: 20 June 2021 in Archives of Virology
Reads 0
Downloads 0

A novel geminivirus was identified in France and Spain in asymptomatic plants of white clover (Trifolium repens) and shrub medick (Medicago arborea). Its genome has the hallmarks of a capulavirus, and its relationship to other capulaviruses was confirmed by phylogenetic analysis. White clover isolates formed a tight cluster in the phylogenetic tree, while shrub medick isolates formed two distinct, more divergent groups with sequence identity values close to the species cutoff. These three groups have likely participated in recombination events involving alfalfa leaf curl virus and French bean severe leaf curl virus. The name "trifolium virus 1" (TrV1) is proposed for this new Capulavirus. Three TrV1 genotypes (TrV1-A, TrV1-B, and TrV1-C) were clearly distinguished.

ACS Style

Yuxin Ma; Laurence Svanella-Dumas; Charlotte Julian; Serge Galzi; Emmanuel Fernandez; Michel Yvon; Elodie Pirolles; Marie Lefebvre; Denis Filloux; Philippe Roumagnac; Thierry Candresse. Genome characterization and diversity of trifolium virus 1: identification of a novel legume-infecting capulavirus. Archives of Virology 2021, 166, 2573 -2578.

AMA Style

Yuxin Ma, Laurence Svanella-Dumas, Charlotte Julian, Serge Galzi, Emmanuel Fernandez, Michel Yvon, Elodie Pirolles, Marie Lefebvre, Denis Filloux, Philippe Roumagnac, Thierry Candresse. Genome characterization and diversity of trifolium virus 1: identification of a novel legume-infecting capulavirus. Archives of Virology. 2021; 166 (9):2573-2578.

Chicago/Turabian Style

Yuxin Ma; Laurence Svanella-Dumas; Charlotte Julian; Serge Galzi; Emmanuel Fernandez; Michel Yvon; Elodie Pirolles; Marie Lefebvre; Denis Filloux; Philippe Roumagnac; Thierry Candresse. 2021. "Genome characterization and diversity of trifolium virus 1: identification of a novel legume-infecting capulavirus." Archives of Virology 166, no. 9: 2573-2578.

Journal article
Published: 29 May 2021 in Viruses
Reads 0
Downloads 0

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.

ACS Style

Yves Kwibuka; Espoir Bisimwa; Arnaud Blouin; Claude Bragard; Thierry Candresse; Chantal Faure; Denis Filloux; Jean-Michel Lett; François Maclot; Armelle Marais; Santatra Ravelomanantsoa; Sara Shakir; Hervé Vanderschuren; Sébastien Massart. Novel Ampeloviruses Infecting Cassava in Central Africa and the South-West Indian Ocean Islands. Viruses 2021, 13, 1030 .

AMA Style

Yves Kwibuka, Espoir Bisimwa, Arnaud Blouin, Claude Bragard, Thierry Candresse, Chantal Faure, Denis Filloux, Jean-Michel Lett, François Maclot, Armelle Marais, Santatra Ravelomanantsoa, Sara Shakir, Hervé Vanderschuren, Sébastien Massart. Novel Ampeloviruses Infecting Cassava in Central Africa and the South-West Indian Ocean Islands. Viruses. 2021; 13 (6):1030.

Chicago/Turabian Style

Yves Kwibuka; Espoir Bisimwa; Arnaud Blouin; Claude Bragard; Thierry Candresse; Chantal Faure; Denis Filloux; Jean-Michel Lett; François Maclot; Armelle Marais; Santatra Ravelomanantsoa; Sara Shakir; Hervé Vanderschuren; Sébastien Massart. 2021. "Novel Ampeloviruses Infecting Cassava in Central Africa and the South-West Indian Ocean Islands." Viruses 13, no. 6: 1030.

Journal article
Published: 03 May 2021 in Plants
Reads 0
Downloads 0

A RT–PCR assay developed to amplify the full coat protein (CP) gene of apple stem pitting virus (ASPV) was evaluated using 180 Greek apple and pear samples and showed a broad detection range. This method was used to investigate the presence of ASPV in quince in Greece and showed a high incidence of 52%. The sequences of 14 isolates from various hosts with a distinct RFLP profile were determined. ASPV population genetics and the factors driving ASPV evolution were analyzed using the Greek ASPV sequences, novel sequences from Brazilian apple trees and Chinese botanical Pyrus species, and homologous sequences retrieved from GenBank. Fourteen variant types of Greek, Brazilian and botanical isolates, which differ in CP gene length and presence of indels, were identified. In addition, these analyses showed high intra- and inter-group variation among isolates from different countries and hosts, indicating the significant variability present in ASPV. Recombination events were detected in four isolates originating from Greek pear and quince and two from Brazilian apples. In a phylogenetic analysis, there was a tendency for isolates to cluster together based on CP gene length, the isolation host, and the detection method applied. Although there was no strict clustering based on geographical origin, most isolates from a given country tended to regroup in specific clusters. Interestingly, it was found that the phylogeny was correlated to the type, position, and pattern of indels, which represent hallmarks of specific lineages and indicate their possible role in virus diversification, rather than the CP size itself. Evidence of recombination between isolates from botanical and cultivated species and the clustering of isolates from botanical species and isolates from cultivated species suggest the existence of a possible undetermined transmission mechanism allowing the exchange of ASPV isolates between the cultivated and wild/ornamental hosts.

ACS Style

Matthaios Mathioudakis; Varvara Maliogka; Thierry Candresse; Osmar Nickel; Thor Fajardo; Daria Budzyńska; Beata Hasiów-Jaroszewska; Nikolaos Katis. Molecular Characterization of the Coat Protein Gene of Greek Apple Stem Pitting Virus Isolates: Evolution through Deletions, Insertions, and Recombination Events. Plants 2021, 10, 917 .

AMA Style

Matthaios Mathioudakis, Varvara Maliogka, Thierry Candresse, Osmar Nickel, Thor Fajardo, Daria Budzyńska, Beata Hasiów-Jaroszewska, Nikolaos Katis. Molecular Characterization of the Coat Protein Gene of Greek Apple Stem Pitting Virus Isolates: Evolution through Deletions, Insertions, and Recombination Events. Plants. 2021; 10 (5):917.

Chicago/Turabian Style

Matthaios Mathioudakis; Varvara Maliogka; Thierry Candresse; Osmar Nickel; Thor Fajardo; Daria Budzyńska; Beata Hasiów-Jaroszewska; Nikolaos Katis. 2021. "Molecular Characterization of the Coat Protein Gene of Greek Apple Stem Pitting Virus Isolates: Evolution through Deletions, Insertions, and Recombination Events." Plants 10, no. 5: 917.

Review
Published: 14 April 2021 in Microorganisms
Reads 0
Downloads 0

High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus detection and virome characterization. We start from sample preparation and nucleic acid extraction as appropriate to the chosen HTS strategy, which is followed by basic data analysis requirements, an extensive overview of the in-depth data processing options, and taxonomic classification of viral sequences detected. By presenting the bioinformatic tools and a detailed overview of the consecutive steps that can be used to implement a well-structured HTS data analysis in an easy and accessible way, this paper is targeted at both beginners and expert scientists engaging in HTS plant virome projects.

ACS Style

Denis Kutnjak; Lucie Tamisier; Ian Adams; Neil Boonham; Thierry Candresse; Michela Chiumenti; Kris De Jonghe; Jan Kreuze; Marie Lefebvre; Gonçalo Silva; Martha Malapi-Wight; Paolo Margaria; Irena Mavrič Pleško; Sam McGreig; Laura Miozzi; Benoit Remenant; Jean-Sebastien Reynard; Johan Rollin; Mike Rott; Olivier Schumpp; Sébastien Massart; Annelies Haegeman. A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses. Microorganisms 2021, 9, 841 .

AMA Style

Denis Kutnjak, Lucie Tamisier, Ian Adams, Neil Boonham, Thierry Candresse, Michela Chiumenti, Kris De Jonghe, Jan Kreuze, Marie Lefebvre, Gonçalo Silva, Martha Malapi-Wight, Paolo Margaria, Irena Mavrič Pleško, Sam McGreig, Laura Miozzi, Benoit Remenant, Jean-Sebastien Reynard, Johan Rollin, Mike Rott, Olivier Schumpp, Sébastien Massart, Annelies Haegeman. A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses. Microorganisms. 2021; 9 (4):841.

Chicago/Turabian Style

Denis Kutnjak; Lucie Tamisier; Ian Adams; Neil Boonham; Thierry Candresse; Michela Chiumenti; Kris De Jonghe; Jan Kreuze; Marie Lefebvre; Gonçalo Silva; Martha Malapi-Wight; Paolo Margaria; Irena Mavrič Pleško; Sam McGreig; Laura Miozzi; Benoit Remenant; Jean-Sebastien Reynard; Johan Rollin; Mike Rott; Olivier Schumpp; Sébastien Massart; Annelies Haegeman. 2021. "A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses." Microorganisms 9, no. 4: 841.

Journal article
Published: 12 April 2021 in Plants
Reads 0
Downloads 0

In recent years, high throughput sequencing (HTS) has brought new possibilities to the study of the diversity and complexity of plant viromes. Mixed infection of a single plant with several viruses is frequently observed in such studies. We analyzed the virome of 10 tomato and sweet pepper samples from Slovakia, all showing the presence of potato virus Y (PVY) infection. Most datasets allow the determination of the nearly complete sequence of a single-variant PVY genome, belonging to one of the PVY recombinant strains (N-Wi, NTNa, or NTNb). However, in three to-mato samples (T1, T40, and T62) the presence of N-type and O-type sequences spanning the same genome region was documented, indicative of mixed infections involving different PVY strains variants, hampering the automated assembly of PVY genomes present in the sample. The N- and O-type in silico data were further confirmed by specific RT-PCR assays targeting UTR-P1 and NIa genomic parts. Although full genomes could not be de novo assembled directly in this situation, their deep coverage by relatively long paired reads allowed their manual re-assembly using very stringent mapping parameters. These results highlight the complexity of PVY infection of some host plants and the challenges that can be met when trying to precisely identify the PVY isolates involved in mixed infection.

ACS Style

Miroslav Glasa; Richard Hančinský; Katarína Šoltys; Lukáš Predajňa; Jana Tomašechová; Pavol Hauptvogel; Michaela Mrkvová; Daniel Mihálik; Thierry Candresse. Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains. Plants 2021, 10, 753 .

AMA Style

Miroslav Glasa, Richard Hančinský, Katarína Šoltys, Lukáš Predajňa, Jana Tomašechová, Pavol Hauptvogel, Michaela Mrkvová, Daniel Mihálik, Thierry Candresse. Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains. Plants. 2021; 10 (4):753.

Chicago/Turabian Style

Miroslav Glasa; Richard Hančinský; Katarína Šoltys; Lukáš Predajňa; Jana Tomašechová; Pavol Hauptvogel; Michaela Mrkvová; Daniel Mihálik; Thierry Candresse. 2021. "Molecular Characterization of Potato Virus Y (PVY) Using High-Throughput Sequencing: Constraints on Full Genome Reconstructions Imposed by Mixed Infection Involving Recombinant PVY Strains." Plants 10, no. 4: 753.

Research article
Published: 01 April 2021 in Plant Disease
Reads 0
Downloads 0

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.

ACS Style

Laurence Svanella-Dumas; Armelle Marais; Chantal Faure; Marie Lefebvre; Jonathan Gaudin; Thierry Candresse. First Report of Lettuce Necrotic Leaf Curl Virus Infecting Cultivated Lettuce in France. Plant Disease 2021, 105, 1233 .

AMA Style

Laurence Svanella-Dumas, Armelle Marais, Chantal Faure, Marie Lefebvre, Jonathan Gaudin, Thierry Candresse. First Report of Lettuce Necrotic Leaf Curl Virus Infecting Cultivated Lettuce in France. Plant Disease. 2021; 105 (4):1233.

Chicago/Turabian Style

Laurence Svanella-Dumas; Armelle Marais; Chantal Faure; Marie Lefebvre; Jonathan Gaudin; Thierry Candresse. 2021. "First Report of Lettuce Necrotic Leaf Curl Virus Infecting Cultivated Lettuce in France." Plant Disease 105, no. 4: 1233.

Research article
Published: 25 March 2021 in Plant-Environment Interactions
Reads 0
Downloads 0

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.

ACS Style

Yuxin Ma; Tania Fort; Armelle Marais; Marie Lefebvre; Sébastien Theil; Corinne Vacher; Thierry Candresse. Leaf‐associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems. Plant-Environment Interactions 2021, 2, 87 -99.

AMA Style

Yuxin Ma, Tania Fort, Armelle Marais, Marie Lefebvre, Sébastien Theil, Corinne Vacher, Thierry Candresse. Leaf‐associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems. Plant-Environment Interactions. 2021; 2 (2):87-99.

Chicago/Turabian Style

Yuxin Ma; Tania Fort; Armelle Marais; Marie Lefebvre; Sébastien Theil; Corinne Vacher; Thierry Candresse. 2021. "Leaf‐associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems." Plant-Environment Interactions 2, no. 2: 87-99.

Research article
Published: 01 March 2021 in Plant Disease
Reads 0
Downloads 0

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.

ACS Style

Giuseppe Parrella; Elisa Troiano; Miss Chantal Faure; Armelle Marais; Thierry Candresse. First Report of Alfalfa Mosaic Virus in Chayote in Italy. Plant Disease 2021, 105, 698 -698.

AMA Style

Giuseppe Parrella, Elisa Troiano, Miss Chantal Faure, Armelle Marais, Thierry Candresse. First Report of Alfalfa Mosaic Virus in Chayote in Italy. Plant Disease. 2021; 105 (3):698-698.

Chicago/Turabian Style

Giuseppe Parrella; Elisa Troiano; Miss Chantal Faure; Armelle Marais; Thierry Candresse. 2021. "First Report of Alfalfa Mosaic Virus in Chayote in Italy." Plant Disease 105, no. 3: 698-698.

Communication
Published: 27 February 2021 in Viruses
Reads 0
Downloads 0

Neofusicoccum parvum is a fungal plant-pathogen belonging to the family Botryosphaeriaceae, and is considered one of the most aggressive causal agents of the grapevine trunk disease (GTD) Botryosphaeria dieback. In this study, the mycovirome of a single strain of N. parvum (COLB) was characterized by high throughput sequencing analysis of total RNA and subsequent bioinformatic analyses. Contig annotations, genome completions, and phylogenetic analyses allowed us to describe six novel mycoviruses belonging to four different viral families. The virome is composed of two victoriviruses in the family Totiviridae, one alphaendornavirus in the family Endornaviridae, two mitoviruses in the family Mitoviridae, and one narnavirus belonging to the family Narnaviridae. The presence of the co-infecting viruses was confirmed by sequencing the RT-PCR products generated from total nucleic acids extracted from COLB. This study shows that the mycovirome of a single N. parvum strain is highly diverse and distinct from that previously described in N. parvum strains isolated from grapevines.

ACS Style

Armelle Marais; Chantal Faure; Gwenaëlle Comont; Thierry Candresse; Elodie Stempien; Marie-France Corio-Costet. Characterization of the Mycovirome of the Phytopathogenic Fungus, Neofusicoccum parvum. Viruses 2021, 13, 375 .

AMA Style

Armelle Marais, Chantal Faure, Gwenaëlle Comont, Thierry Candresse, Elodie Stempien, Marie-France Corio-Costet. Characterization of the Mycovirome of the Phytopathogenic Fungus, Neofusicoccum parvum. Viruses. 2021; 13 (3):375.

Chicago/Turabian Style

Armelle Marais; Chantal Faure; Gwenaëlle Comont; Thierry Candresse; Elodie Stempien; Marie-France Corio-Costet. 2021. "Characterization of the Mycovirome of the Phytopathogenic Fungus, Neofusicoccum parvum." Viruses 13, no. 3: 375.

Journal article
Published: 20 November 2020 in Agronomy
Reads 0
Downloads 0

Pomegranate is an important crop in the Mediterranean Basin that can be affected by a range of pathogens. With the aim to better understand the impact of viral diseases on pomegranate, two leaf samples from Turkey showing virus-like symptoms such as chlorotic spots and oak-leaf patterns were subjected to high throughput sequencing (HTS). Data analysis indicated the presence of passiflora edulis symptomless virus (PeSV: genus Roymovirus, Potyviridae family) in these two pomegranate samples, consistent with the observation by electron microscopy of flexuous filamentous viral particles 760 to 780 nm long. Further analysis of HTS reads revealed the presence of five PeSV variants in one of the samples and another single variant in the other. PeSV occurrence was also identified from publicly available SRA pomegranate RNA-Seq transcriptomic data from India and China. The genome of these PeSV-pomegranate variants share 78.0–86.8% nucleotide identity with that of the reference isolate from passionfruit (MH379332). The presence of PeSV in pomegranate was confirmed by specific RT-PCR assays targeting either the coat protein (CP) or Nla-Pro genes in 37 cultivated and one ornamental pomegranate out of 133 samples collected from the Eastern Mediterranean region of Turkey. To our knowledge, this is the first application of HTS to assess virus occurrence in pomegranate and the first recognition of pomegranate as a new host for PeSV.

ACS Style

Kadriye Caglayan; Mona Gazel; Vahid Roumi; Hamide Deniz Kocabag; Bahar Tunç; Jean Sebastien Reynard; Ana Belén Ruiz-García; Antonio Olmos; Thierry Candresse. Identification of Pomegranate as a New Host of Passiflora Edulis Symptomless Virus (PeSV) and Analysis of PeSV Diversity. Agronomy 2020, 10, 1821 .

AMA Style

Kadriye Caglayan, Mona Gazel, Vahid Roumi, Hamide Deniz Kocabag, Bahar Tunç, Jean Sebastien Reynard, Ana Belén Ruiz-García, Antonio Olmos, Thierry Candresse. Identification of Pomegranate as a New Host of Passiflora Edulis Symptomless Virus (PeSV) and Analysis of PeSV Diversity. Agronomy. 2020; 10 (11):1821.

Chicago/Turabian Style

Kadriye Caglayan; Mona Gazel; Vahid Roumi; Hamide Deniz Kocabag; Bahar Tunç; Jean Sebastien Reynard; Ana Belén Ruiz-García; Antonio Olmos; Thierry Candresse. 2020. "Identification of Pomegranate as a New Host of Passiflora Edulis Symptomless Virus (PeSV) and Analysis of PeSV Diversity." Agronomy 10, no. 11: 1821.

Research article
Published: 01 November 2020 in Plant Disease
Reads 0
Downloads 0

Apple chlorotic leaf spot virus (ACLSV), apple stem grooving virus (ASGV) and apple stem pitting virus (ASPV) cause significant losses to Brazilian (BR) apple production. Looking beyond these latent viruses, high-throughput sequencing (HTS) of three samples (Vacaria, RS, Brazil), each one of a different apple cultivar, was performed on the Illumina HiSeq X Ten platform (USA), cv. Braeburn and the BGISEQ-500 platform (China), cvs. Royal Gala and Mishima. Total nucleic acids (TNA) extracts were enriched for ds-RNA (Valverde et al. 1990) to prepare cDNA for HTS sequencing libraries using TrueSeq Stranded mRNA kit (Illumina, USA). CLC Genomics Workbench v. 8.5.1 (CLC Bio, Qiagen, USA) was used for quality trimming and de novo contig assembly of the reads. All contigs were annotated by BLASTn and BLASTx (http://www.ncbi.nlm.nih.gov/blast) against the nr or protein GenBank databases using a cut-off e-value of 10-4. Multiple nearly complete genome contigs corresponding to ACLSV, ASGV, and ASPV, were obtained from all three cvs showing respectively 78-95% (ACLSV; MK929793-96), 80-98.5% (ASGV; MK923757, MK929791-92) and 75-87% (ASPV; MK923753-56) nucleotide (nt) identities to sequences available in GenBank; reads mapping to respective reference genomes are contained in Supplementary Table 1. In addition, long contigs were obtained for apple rubbery wood virus 1 (ARWV 1; cv. Mishima), apple rubbery wood virus 2 (ARWV 2; cv. Royal Gala); and citrus concave gum-associated virus (CCGaV; cvs. Royal Gala and Mishima). The three viruses are related to the order Bunyavirales, family Phenuiviridae. Total reads mapped to the reference genomes were respectively 1958 (ARWV 1; cv. Mishima) and 905 (ARWV 2, cv. Royal Gala), corresponding to average genome coverages of 19.3x and 8.6x, respectively. The two viruses represented 0.004% of total reads for each of the apple samples. In the case of CCGaV a higher representation in the sequencing reads was observed with 50,835 mapped reads (0.24% of total reads, average coverage 541.7x) and 32,099 mapped reads (0.07% of total reads, average coverage 342.1x), respectively in cvs.Royal Gala and Mishima. Using the nearly complete assembled contigs for the various genomic RNAs of the BR isolates of ARWV 1 (MK936225-27) and 2 (MK936228-30) were shown to be closely related to those available in the GenBank with 95-96%, 94-96% and 95.8-98.7% nt identities with the L, M and S segments of ARWV 1 and 96-97%, 96.9-97.2% and 97.2-97.7% nt identities with the L, Ma and Sa segments of ARWV 2, respectively. Citrus concave gum-associated virus (CCGaV), recently described in citrus, is phylogenetically related to phlebo‐like viruses (Navarro et al. 2018), and possibly associated with an apple decline (Wright et al. 2018). Based on the long contigs assembled, the RNAs 1 (MK940540-41) and 2 (MK940542-43) of the two BR isolates had nt identities of 97-99% with the homologous sequences available in GenBank.To validate the HTS-based results in apples, RT-PCR assays were performed on TNA of three resampled original source plants using primers based on the HTS contigs (Supplementary Table 2). ARWV 1 S (MN652009) and ARWV2 Sa (MN652010) RT-PCR amplicons from cv. Braeburn showed 98.4% and 99.6% nt identities with sequences obtained by HTS (MK936225 and MK936228), respectively). The CCGaV RNA 2 (MN631048) RT-PCR amplicon from cv. Royal Gala showed 94.8% nt identity with the sequence obtained by HTS (MK940542). To determine prevalence of ARWV 1 and 2 and CCGaV, TNA from additional twelve apple cvs. was confirmed by RT-PCR using specific primers (Supplementary Table 2). Amplicons of the expected sizes were detected, respectively in nine, one and two of the analysed plants. Based on our knowledge, this is the first report of the occurrence of ARWV 1, ARWV 2 and CCGaV infecting apples in Brazil. Apple rubbery wood disease (ARWD) first described almost a century ago, damaged apple orchards in the 1970’s-1990’s in Brazil. Recently Rott et al. (2018) reported ARWV 1 and ARWV 2 in ARWD-affected apple plants in Germany. These results confirmed Wright et al. (2018) findings and highlight the presence of ARWV 1 and 2 and CCGaV in BR apple materials, suggesting the need to consider them in certification programs. Additional studies on the prevalence and possible effects of these viruses on apples in this region are necessary.

ACS Style

O. Nickel; T. V. M. Fajardo; T. Candresse. First Report on Detection of Three Bunya-Like Viruses in Apples in Brazil. Plant Disease 2020, 104, 3088 -3088.

AMA Style

O. Nickel, T. V. M. Fajardo, T. Candresse. First Report on Detection of Three Bunya-Like Viruses in Apples in Brazil. Plant Disease. 2020; 104 (11):3088-3088.

Chicago/Turabian Style

O. Nickel; T. V. M. Fajardo; T. Candresse. 2020. "First Report on Detection of Three Bunya-Like Viruses in Apples in Brazil." Plant Disease 104, no. 11: 3088-3088.

Review article
Published: 16 October 2020 in Frontiers in Microbiology
Reads 0
Downloads 0

The ecology of plant viruses began to be explored at the end of the 19th century. Since then, major advances have revealed mechanisms of virus-host-vector interactions in various environments. These advances have been accelerated by new technlogies for virus detection and characterization, most recently including high throughput sequencing (HTS). HTS allows investigators, for the first time, to characterize all or nearly all viruses in a sample without a priori information about which viruses might be present. This powerful approach has spurred new investigation of the viral metagenome (virome). The rich virome datasets accumulated illuminate important ecological phenomena such as virus spread among host reservoirs (wild and domestic), effects of ecosystem simplification caused by human activities (and agriculture) on the biodiversity and the emergence of new viruses in crops. To be effective, however, HTS-based virome studies must successfully navigate challenges and pitfalls at each procedural step, from plant sampling to library preparation and bioinformatic analyses. This review summarizes major advances in plant virus ecology associated with technological developments, and then presents important considerations and best practices for HTS use in virome studies.

ACS Style

François Maclot; Thierry Candresse; Denis Filloux; Carolyn M. Malmstrom; Philippe Roumagnac; René Van Der Vlugt; Sébastien Massart. Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales. Frontiers in Microbiology 2020, 11, 578064 .

AMA Style

François Maclot, Thierry Candresse, Denis Filloux, Carolyn M. Malmstrom, Philippe Roumagnac, René Van Der Vlugt, Sébastien Massart. Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales. Frontiers in Microbiology. 2020; 11 ():578064.

Chicago/Turabian Style

François Maclot; Thierry Candresse; Denis Filloux; Carolyn M. Malmstrom; Philippe Roumagnac; René Van Der Vlugt; Sébastien Massart. 2020. "Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales." Frontiers in Microbiology 11, no. : 578064.

Preprint content
Published: 05 October 2020
Reads 0
Downloads 0

The full-length genome of a novel Emaravirus has been identified and characterized from sycamore maple (Acer pseudoplatanus) - a tree species of significant importance in urban and forest areas - showing leaf mottle symptoms. RNA-Seq was performed using RNA preparations from a symptomatic and a symptomless maple tree. Purified double-stranded cDNA from each sample were used for RNA-Seq analysis on the Illumina HiSeq2500system and 14-198 MB data/sample of 100 bp-long paired-end sequence reads were generated. The sequence assembly and analysis revealed the presence of six RNA segments in the symptomatic sample (RNA1: 7,075 nt-long encoding the viral replicase; RNA2: 2,289 nt-long encoding the glycoprotein precursor; RNA3: 1,525 nt-long encoding the nucleocapsid protein; RNA4: 1,533 nt-long encoding the putative movement protein; RNA5: 1,825 nt-long encoding a hypothetical protein P5; RNA6: 1,179 nt-long encoding a hypothetical protein P6). Two independent HTS sequencing runs from the same symptomatic maple tree detected the same genome segments. For one of these sequencing runs the cDNA library was prepared using a primer targeting the conserved genome terminal region, known to be shared between emaraviruses genome segments and a high amount of sequence data was generated. We suggest, therefore, that the six identified genome segments represent the complete genome of a novel emaravirus from maple, which we tentatively name maple mottle-associated virus (MaMaV). RT-PCR assays were performed on symptomatic and non-symptomatic leaves of A. pseudoplatanus trees coming growing on two different locations in Berlin. MaMaV was only detected from symptomatic trees and all six RNAs were generally simultaneously detected. Non-symptomatic samples were consistently negative for MaMaV. These results suggest that MaMaV might be the symptom inducing virus in the sampled trees. In the present state of the art, this is the first time an Emaravirus is described from maple and is fully genetically characterized.

ACS Style

Artemis Rumbou; Thierry Candresse; Susanne Von Bargen; Carmen Buettner. A novel emaravirus identified in maple with leaf mottle symptoms by deep sequencing. 2020, 1 .

AMA Style

Artemis Rumbou, Thierry Candresse, Susanne Von Bargen, Carmen Buettner. A novel emaravirus identified in maple with leaf mottle symptoms by deep sequencing. . 2020; ():1.

Chicago/Turabian Style

Artemis Rumbou; Thierry Candresse; Susanne Von Bargen; Carmen Buettner. 2020. "A novel emaravirus identified in maple with leaf mottle symptoms by deep sequencing." , no. : 1.

Annotated sequence record
Published: 29 September 2020 in Archives of Virology
Reads 0
Downloads 0

We report the genome sequence of a putative new foveavirus infecting non-cultivated Vitis vinifera, tentatively named “grapevine foveavirus A” (GFVA). This virus was identified by high-throughput sequencing analysis of a European wild Vitis collected in Switzerland. Phylogenetic analysis revealed that this virus clustered with known grapevine virus T (GVT) isolates but was clearly distinct from any of them. If considering the International Committee of Taxonomy of Viruses (ICTV)-suggested foveavirus species demarcation criterion based on sequence similarity in the replicase gene/protein, this virus should be considered a member of a new species closely related to GVT. On the other hand, comparison of capsid gene/protein sequences using the same criteria indicates that GFVA is at the border of species demarcation. Whether this virus represents a highly divergent GVT isolate or a member of a distinct but closely related species is discussed.

ACS Style

Jean-Sébastien Reynard; Justine Brodard; Eric Remoliff; Marie Lefebvre; Olivier Schumpp; Thierry Candresse. A novel foveavirus identified in wild grapevine (Vitis vinifera subsp. sylvestris). Archives of Virology 2020, 165, 2999 -3002.

AMA Style

Jean-Sébastien Reynard, Justine Brodard, Eric Remoliff, Marie Lefebvre, Olivier Schumpp, Thierry Candresse. A novel foveavirus identified in wild grapevine (Vitis vinifera subsp. sylvestris). Archives of Virology. 2020; 165 (12):2999-3002.

Chicago/Turabian Style

Jean-Sébastien Reynard; Justine Brodard; Eric Remoliff; Marie Lefebvre; Olivier Schumpp; Thierry Candresse. 2020. "A novel foveavirus identified in wild grapevine (Vitis vinifera subsp. sylvestris)." Archives of Virology 165, no. 12: 2999-3002.

Journal article
Published: 27 September 2020 in Plants
Reads 0
Downloads 0

Genome organization and phylogenetic relationships of olive leaf yellowing-associated virus (OLYaV) with other members of the Closteroviridae family were determined. The complete coding sequence of OLYaV was obtained by high throughput sequencing of total RNA from a 35-year-old olive tree (cv. Zarzaleña) from Brazil, showing olive leaf yellowing disease and deformations in the wood. This represents the first report of OLYaV in this country. A genomic sequence of 16,700 nt containing 11 open reading frames (ORFs) was recovered, representing the complete virus coding capacity. The knowledge of the nucleotide sequence of the genome including the gene that codes the coat protein will facilitate the development of diagnostic tests, which are limited so far to PCR-based methods targeting the HSP70h gene. Interestingly, a thaumatin-like protein (ORF2), previously reported in other unassigned viruses in the Closteroviridae family, persimmon virus B and actidinia virus 1, was identified in the OLYaV genome. Phylogenetic analysis of shared proteins (ORF1a, ORF1b, HSP70h, HSP90h and CP) with all members of the Closteroviridae family provides new insight into the taxonomic position of these three closteroviruses and suggests they could represent a new genus in the family.

ACS Style

Ana Belén Ruiz-García; Thierry Candresse; Celia Canales; Félix Morán; Carlos Machado De Oliveira; Edson Bertolini; Antonio Olmos. Molecular Characterization of the Complete Coding Sequence of Olive Leaf Yellowing-Associated Virus. Plants 2020, 9, 1272 .

AMA Style

Ana Belén Ruiz-García, Thierry Candresse, Celia Canales, Félix Morán, Carlos Machado De Oliveira, Edson Bertolini, Antonio Olmos. Molecular Characterization of the Complete Coding Sequence of Olive Leaf Yellowing-Associated Virus. Plants. 2020; 9 (10):1272.

Chicago/Turabian Style

Ana Belén Ruiz-García; Thierry Candresse; Celia Canales; Félix Morán; Carlos Machado De Oliveira; Edson Bertolini; Antonio Olmos. 2020. "Molecular Characterization of the Complete Coding Sequence of Olive Leaf Yellowing-Associated Virus." Plants 9, no. 10: 1272.

Brief report
Published: 27 August 2020 in Archives of Virology
Reads 0
Downloads 0

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.

ACS Style

Armelle Marais; Marie Umber; Denis Filloux; Rose-Marie Gomez; Chantal Faure; Claudie Pavis; Charlotte Julian; Philippe Roumagnac; Isabelle Acina-Mambole; Lydiane Bonheur; Sébastien Theil; Sandy Contreras; Thierry Candresse; Pierre-Yves Teycheney. Yam asymptomatic virus 1, a novel virus infecting yams (Dioscorea spp.) with significant prevalence in a germplasm collection. Archives of Virology 2020, 165, 1 -5.

AMA Style

Armelle Marais, Marie Umber, Denis Filloux, Rose-Marie Gomez, Chantal Faure, Claudie Pavis, Charlotte Julian, Philippe Roumagnac, Isabelle Acina-Mambole, Lydiane Bonheur, Sébastien Theil, Sandy Contreras, Thierry Candresse, Pierre-Yves Teycheney. Yam asymptomatic virus 1, a novel virus infecting yams (Dioscorea spp.) with significant prevalence in a germplasm collection. Archives of Virology. 2020; 165 (11):1-5.

Chicago/Turabian Style

Armelle Marais; Marie Umber; Denis Filloux; Rose-Marie Gomez; Chantal Faure; Claudie Pavis; Charlotte Julian; Philippe Roumagnac; Isabelle Acina-Mambole; Lydiane Bonheur; Sébastien Theil; Sandy Contreras; Thierry Candresse; Pierre-Yves Teycheney. 2020. "Yam asymptomatic virus 1, a novel virus infecting yams (Dioscorea spp.) with significant prevalence in a germplasm collection." Archives of Virology 165, no. 11: 1-5.

Annotated sequence record
Published: 02 July 2020 in Archives of Virology
Reads 0
Downloads 0

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.

ACS Style

Maryam Khalili; Thierry Candresse; Chantal Faure; Armelle Marais. Complete genome sequence of almond luteovirus 1, a novel luteovirus infecting almond. Archives of Virology 2020, 165, 2123 -2126.

AMA Style

Maryam Khalili, Thierry Candresse, Chantal Faure, Armelle Marais. Complete genome sequence of almond luteovirus 1, a novel luteovirus infecting almond. Archives of Virology. 2020; 165 (9):2123-2126.

Chicago/Turabian Style

Maryam Khalili; Thierry Candresse; Chantal Faure; Armelle Marais. 2020. "Complete genome sequence of almond luteovirus 1, a novel luteovirus infecting almond." Archives of Virology 165, no. 9: 2123-2126.

Journal article
Published: 01 July 2020 in Journal of General Virology
Reads 0
Downloads 0

The family Alphaflexiviridae includes viruses with flexuous filamentous virions that are 470–800 nm in length and 12–13 nm in diameter. Alphaflexiviruses have a single-stranded, positive-sense RNA genome of 5.5–9 kb. They infect plants and plant-infecting fungi. They share a distinct lineage of alphavirus-like replication proteins that is unusual in lacking any recognized protease domain. With a single exception, cell-to-cell and long-distance movement is facilitated by triple gene block proteins in plant-infecting genera. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Alphaflexiviridae, which is available at www.ictv.global/report/alphaflexiviridae.

ACS Style

Jan F. Kreuze; Anna Maria Vaira; Wulf Menzel; Thierry Candresse; Sergey K. Zavriev; John Hammond; Ki Hyun Ryu; ICTV Report Consortium. ICTV Virus Taxonomy Profile: Alphaflexiviridae. Journal of General Virology 2020, 101, 699 -700.

AMA Style

Jan F. Kreuze, Anna Maria Vaira, Wulf Menzel, Thierry Candresse, Sergey K. Zavriev, John Hammond, Ki Hyun Ryu, ICTV Report Consortium. ICTV Virus Taxonomy Profile: Alphaflexiviridae. Journal of General Virology. 2020; 101 (7):699-700.

Chicago/Turabian Style

Jan F. Kreuze; Anna Maria Vaira; Wulf Menzel; Thierry Candresse; Sergey K. Zavriev; John Hammond; Ki Hyun Ryu; ICTV Report Consortium. 2020. "ICTV Virus Taxonomy Profile: Alphaflexiviridae." Journal of General Virology 101, no. 7: 699-700.

Research article
Published: 26 June 2020 in PLOS ONE
Reads 0
Downloads 0

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.

ACS Style

Artemis Rumbou; Thierry Candresse; Armelle Marais; Laurence Svanella-Dumas; Maria Landgraf; Susanne Von Bargen; Carmen Büttner. Unravelling the virome in birch: RNA-Seq reveals a complex of known and novel viruses. PLOS ONE 2020, 15, e0221834 .

AMA Style

Artemis Rumbou, Thierry Candresse, Armelle Marais, Laurence Svanella-Dumas, Maria Landgraf, Susanne Von Bargen, Carmen Büttner. Unravelling the virome in birch: RNA-Seq reveals a complex of known and novel viruses. PLOS ONE. 2020; 15 (6):e0221834.

Chicago/Turabian Style

Artemis Rumbou; Thierry Candresse; Armelle Marais; Laurence Svanella-Dumas; Maria Landgraf; Susanne Von Bargen; Carmen Büttner. 2020. "Unravelling the virome in birch: RNA-Seq reveals a complex of known and novel viruses." PLOS ONE 15, no. 6: e0221834.