Innovative Network for Next Generation Training and Sequencing of Virome

Informations projet

INEXTVIR

N° de convention de subvention: 813542

DOI

10.3030/813542

Projet clôturé

Date de signature de la CE 29 Janvier 2019

Date de début 1 Février 2019

Date de fin 31 Juillet 2023

Financé au titre de

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Coût total

€ 3 737 141,88

Contribution de l’UE

€ 3 737 141,88

Coordonné par

NACIONALNI INSTITUT ZA BIOLOGIJO
Slovenia

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

Other (1)

PhD dissertations and awarding of doctoral degrees

Each ESR will prepare a dissertation thesis concerning hishers research topic and will defend it as a part of hisher postgraduate study program

Documents, reports (7)

Viromes of environmental water samples

Viromes of sampled environmental determined during the course of the project analysed and published as a part of the scientific publication

Conceptual framework for assessing socio-economic impact of virome

The overall objective is to assess the perceived impacts of improved knowledge on perceived risks and benefits of the virome in agriculture This will enable how society defines perceived risks and benefits and will add information of direct relevance to the process of risk Analysis assessment management communication linked to the virome in agriculture

Publication of protocols and guidelines for the characterisation of plant viruses discovered with NGS for the scientific community and the plant health

On the basis of experiences gathered through the project and wide expertise of the involved institutions, guidelines for the characterisation of plant viruses discovered by NGS will be prepared.

Guidelines with protocols for plant virus detection through NGS technologies
Molecular, epidemiological and biological characterization on newly identified viruses

Viruses detected in the screening WP2 projects will be further characterised by individual respective labs and the data about their epidemiology or biology will be published in the form of reports or scientific papers

User-friendly graphical interface for plant virome data analysis

New methods for homology free machinelearning specifically tailored for virome classification and for virome microbiome interaction analysis will be designed and developed The resulting pipeline will be integrated within a userfriendly graphical system such as eg Galaxy providing a complete bioinformatics analysis workflow from raw sequencing reads

Systematic understanding of consumer perceptions of the risks and benefits of the virome in agriculture, and societal and priorities regarding associated policies

The overall objective is to understand the societal perceptions of existing and emerging risks in relation to the virome and link this to effective communication strategies This will deliver a validated communication strategy to engage stakeholders from policy industry enduser and society in general

Demonstrators, pilots, prototypes (1)

Virome data available on line for further analyses

Virome data collected by different partners on different crops formatted in standardized tabelaric form and published online for wider research community

Websites, patent fillings, videos etc. (1)

Project webpage

The project webpage as one of the main dissemination means of the project that will include project general information, dissemination material, information on projet events, achievements, news etc.

Publications

Peer reviewed articles (30)

Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests

Auteurs: Haegeman A, Foucart Y, De Jonghe K, Goedefroit T, Al Rwahnih M, Boonham N, Candresse T, Gaafar YZA, Hurtado-Gonzales OP, Kogej Zwitter Z, Kutnjak D, Lamovšek J, Lefebvre M, Malapi M, Mavrič Pleško I, Önder S, Reynard JS, Salavert Pamblanco F, Schumpp O, Stevens K, Pal C, Tamisier L, Ulubaş Serçe Ç, van Duivenbode I, Waite DW, Hu X, Ziebell H, Massart S
Publié dans: Plants, 2023, ISSN 2223-7747
Éditeur: Plants
DOI: 10.3390/plants12112139

Ecological Strategies for Resource Use by Three Bromovirusesin Anthropic and Wild Plant Communities

Auteurs: Bisola Babalola, Aurora Fraile Fernando García-Arenal, Michael McLeish
Publié dans: Viruses, Numéro Bimonthly, 2023, Page(s) 1779, ISSN 1999-4915
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v15081779

Genetic diferentiation and migration fluxes of viruses from melon crops and crops edge weeds

Auteurs: Ayoub Maachi, Livia Donaire, Yolanda Hernando and Miguel A. Aranda
Publié dans: Jorunal of Virology, 2022, Page(s) 1-19, ISSN 0022-538X
Éditeur: American Society for Microbiology
DOI: 10.1128/jvi.00421-22

Complete genome sequence of malva-associated soymovirus 1: a novel virus infecting common mallow

Auteurs: Ayoub Maachi; Yolanda Hernando; Miguel A. Aranda; Livia Donaire
Publié dans: Virus Genes, Numéro 6, 2022, Page(s) 372-375, ISSN 0920-8569
Éditeur: Kluwer Academic Publishers
DOI: 10.1007/s11262-022-01900-0

Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing.

Auteurs: Mark Paul Selda Rivarez; Mark Paul Selda Rivarez; Ana Vučurović; Ana Vučurović; Nataša Mehle; Maja Ravnikar; Maja Ravnikar; Denis Kutnjak
Publié dans: Frontiers in Microbiology, Numéro 1, 2021, ISSN 1664-302X
Éditeur: Frontiers Media
DOI: 10.3389/fmicb.2021.671925

Risk perception associated with an emerging agri-food risk in Europe: plant viruses in agriculture

Auteurs: Johny Hilaire; Sophie Tindale; Glyn Jones; Gabriela Pingarron-Cardenas; Katarina Bačnik; Mercy Ojo; Lynn J. Frewer
Publié dans: Agriculture & Food Security, Numéro 2, 2022, ISSN 2048-7010
Éditeur: BMC
DOI: 10.1186/s40066-022-00366-5

Carrot populations in France and Spain host a complex virome rich in previously uncharacterized viruses

Auteurs: Deborah Schönegger, Armelle Marais,Bisola Mercy Babalola, Chantal Faure,Marie Lefebvre, Laurence Svanella-Dumas, Sára Brázdová, Thierry Candresse
Publié dans: PLOS ONE, 2023, ISSN 1932-6203
Éditeur: Public Library of Science
DOI: 10.1371/journal.pone.0290108

Diversity of polerovirus-associated RNAs in the virome of wild and cultivated carrots

Auteurs: Deborah Schönegger, Bisola Mercy Babalola, Armelle Marais, Chantal Faure, Thierry Candresse
Publié dans: Plant Pathology, 2022, ISSN 1365-3059
Éditeur: Wiley & Sons
DOI: 10.1111/ppa.13623

A new flavi-like virus identified in populations of wild carrots

Auteurs: Deborah Schönegger, Armelle Marais, Chantal Faure, Thierry Candresse
Publié dans: Archives of Virology, 2022, ISSN 0304-8608
Éditeur: Springer Verlag
DOI: 10.1007/s00705-022-05544-1

Identification of two novel putative satellite RNAs with hammerhead structures in the virome of French and Spanish carrot samples

Auteurs: B. M. Babalola, D. Schönegger, C. Faure, A. Marais, A. Fraile, F. Garcia-Arenal & T. Candresse
Publié dans: Archives in virology, 2022, ISSN 0304-8608
Éditeur: Springer Verlag
DOI: 10.1007/s00705-022-05538-z

Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: Virus infections of melon, <i>Cucumis melo</i>, crops, and adjacent wild communities

Auteurs: Michael J McLeish; Adrián D Zamfir; Bisola M Babalola; Adrián Peláez; Aurora Fraile; Fernando García-Arenal
Publié dans: Virus evolution, Numéro 3, 2022, ISSN 2057-1577
Éditeur: Oxford University Press
DOI: 10.1093/ve/veac095

In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem

Auteurs: Mark Paul Selda Rivarez, Katarina Bačnik, Olivera Maksimović Carvalho Ferreira, Ana Vučurović, Gabrijel Seljak, Nataša Mehle, Ion Gutiérrez-Aguirre, Maja Ravnikar and Denis Kutnjak
Publié dans: MICROBIOME, 2023, ISSN 2049-2618
Éditeur: BMC, part of Springer Nature
DOI: 10.1186/s40168-023-01500-6

Complete genome sequence of almond luteovirus 1, a novel luteovirus species infecting almond

Auteurs: Khalili, M., Candresse, T., Faure, C. & Marais, A
Publié dans: Archives in Virology, Numéro 165, 2020, Page(s) 2123-2126, ISSN 0304-8608
Éditeur: Springer Verlag
DOI: 10.1007/s00705-020-04715-2

First Report of Ranunculus white mottle ophiovirus in Slovenia in Pepper with yellow leaf curling symptom and in Tomato

Auteurs: """Rivarez, Mark Paul Selda Kogej, Zala Jakos, Nejc Pecman, Anja Seljak, Gabrijel Vučurović, Ana Mehle, Natasa Ravnikar, Maja Kutnjak, Denis"""
Publié dans: Plant Disease, 2021, ISSN 0191-2917
Éditeur: American Phytopathological Society
DOI: 10.1094/pdis-08-21-1624-pdn

The Molecular Characterization of a New Prunus-Infecting Cheravirus and Complete Genome Sequence of Stocky Prune Virus

Auteurs: by Maryam Khalili, Thierry Candresse,Yoann Brans,Chantal Faure,Jean-Marc Audergon,Véronique Decroocq,Guillaume RochandArmelle Marais
Publié dans: Viruses, 2022, ISSN 1999-4915
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14112325

First report of Apium virus Y in wild carrot (Daucus carota ssp.carota) in Spain

Auteurs: B. M. Babalola1 C. Faure2 A. Marais2 A. Fraile1 F. Garcia-Arenal1 T. Candresse2
Publié dans: New Disease report, 2022, ISSN 2044-0588
Éditeur: John Wiley and sons
DOI: 10.1002/ndr2.12097

Evaluation of Methods and Processes for Robust Monitoring of SARS-CoV-2 in Wastewater

Auteurs: Olivera Maksimovic Carvalho Ferreira, Živa Lengar, Zala Kogej, Katarina Bačnik, Irena Bajde, Mojca Milavec, Anže Županič, Nataša Mehle, Denis Kutnjak, Maja Ravnikar & Ion Gutierrez-Aguirre
Publié dans: Food and Environmental Virology, 2022, ISSN 1867-0342
Éditeur: Springer
DOI: 10.1007/s12560-022-09533-0

Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis

Auteurs: Nuria Fontdevila Pareta, Maryam Khalili, Ayoub Maachi, Mark Paul S. Rivarez, Johan Rollin, Ferran Salavert, Coline Temple, Miguel A. Aranda, Neil Boonham, Marleen Botermans, Thierry Candresse, Adrian Fox, Yolanda Hernando, Denis Kutnjak, Armelle Marais, Françoise Petter, Maja Ravnikar, Ilhem Selmi1 Rachid Tahzima, Charlotte Trontin, Thierry Wetzel, Sebastien Massart
Publié dans: Frontiers in Microbiology, 2023, ISSN 1664-302X
Éditeur: Frontiers Media
DOI: 10.3389/fmicb.2023.1181562

The expanding menagerie of Prunus-infecting luteoviruses

Auteurs: Maryam Khalili, Thierry Candresse, Igor Koloniuk, Dana Safarova, Yoann Brans, Chantal Faure , Marine Delmas, Sébastien Massart, Miguel A. Aranda, Kadriye Cagalayan, …. And Armelle Marais 
Publié dans: Phytophatology, 2022, ISSN 0031-949X
Éditeur: American Phytopathological Society
DOI: 10.1094/phyto-06-22-0203-r

Cohombrillo-associated virus: a novel virus infecting Ecballium elaterium plants

Auteurs: Ayoub Maachi, Yolanda Hernando, Miguel A. Aranda and Livia Donaire
Publié dans: Archives in Virology, 2023, Page(s) 1-4, ISSN 0920-8569
Éditeur: Kluwer Academic Publishers
DOI: 10.1007/s00705-022-05669-3

First reports of Apple luteovirus 1, Apple rubodvirus 1 and Apple hammerhead viroid infecting apples in Belgium

Auteurs: N. Fontdevila Pareta, M. Lateur, S. Steyer, A.G. Blouin, S. Massart
Publié dans: New Disease report, 2022, ISSN 2044-0588
Éditeur: Wiley and sons
DOI: 10.1002/ndr2.12076

Tobamoviruses show broad host ranges and little genetic diversity in four habitat types of a heterogeneous ecosystem

Auteurs: Zamfir, A.D., Babalola, B.M., Fraile, A., McLeish, M.J., García-Arenal, F.
Publié dans: Phytopathology, 2023, ISSN 0031-949X
Éditeur: American Phytopathological Society
DOI: 10.1094/phyto-11-22-0439-v

Tomato brown rugose fruit virus in aqueous environments - survival and significance of water-mediated transmission

Auteurs: Nataša Mehle, Katarina Bačnik, Irena Bajde, Jakob Brodarič, Adrian Fox, Ion Gutiérrez-Aguirre, Miha Kitek, Denis Kutnjak, Yue Lin Loh, Olivera Maksimović Carvalho Ferreira, Maja Ravnikar, Elise Vogel, Christine Vos, Ana Vučurović
Publié dans: Frontiers in plant Science, 2023, ISSN 1664-462X
Éditeur: Frontiers Media S. A.
DOI: 10.3389/fpls.2023.1187920

VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data.

Auteurs: Grigorii Sukhorukov; Maryam Khalili; Olivier Gascuel; Thierry Candresse; Armelle Marais-Colombel; Macha Nikolski
Publié dans: Frontiers in bioinformatics, Numéro 4, 2022, ISSN 2673-7647
Éditeur: Frontiers Media SA
DOI: 10.3389/fbinf.2022.867111

Use of High-Throughput Sequencing and Two RNA Input Methods to Identify Viruses Infecting Tomato Crops

Auteurs: Ayoub Maachi; Covadonga Torre; Raquel Navarro Sempere; Yolanda Hernando; Miguel A. Aranda; Livia Donaire
Publié dans: Microorganisms, Vol 9, Iss 1043, p 1043 (2021), Numéro 2, 2021, Page(s) 1-17, ISSN 2076-2607
Éditeur: MDPI
DOI: 10.3390/microorganisms9051043

Validation of High-Throughput Sequencing as Virus Indexing Test for Musa Germplasm: Performance Criteria Evaluation and Contamination Monitoring Using an Alien Control

Auteurs: Wei Rong, Johan Rollin, Marwa Hanafi, Nicolas Roux, and Sebastien Massart
Publié dans: PhytoFrontiers, 2023, ISSN 2690-5442
Éditeur: APS publications
DOI: 10.1094/phytofr-03-22-0030-fi

First report of carrot torrado virus 1 (CaTV1) naturally infecting carrots in Spain

Auteurs: Bisola Mercy Babalola, Chantal Faure, Armelle Marais, Aurora Fraile, Fernando Garcia-Arenal & Thierry Candresse
Publié dans: Journal of plant pathology, 2022, ISSN 1125-4653
Éditeur: Societa Italiana di Patologia Vegetale
DOI: 10.1007/s42161-022-01196-x

High throughput sequencing technologies complemented by growers’ perceptions highlight the impact of tomato virome in diversified vegetable farms and a lack of awareness of emerging virus threats

Auteurs: Coline Temple; Arnaud G. Blouin; Sophie Tindale; Stephan Steyer; Kevin Marechal; Sebastien Massart
Publié dans: Frontiers in Sustainable Food Systems, 2023, ISSN 2571-581X
Éditeur: Frontiers
DOI: 10.3389/fsufs.2023.1139090

Diversity and pathobiology of an ilarvirus unexpectedly detected in diverse host plants and in global sequencing data

Auteurs:  Mark Paul Selda Rivarez, Chantal Faure, Laurence Svanella-Dumas, Anja Pecman, Magda Tušek-Žnidaric, Deborah Schönegger, Kris DeJonghe, Arnaud Blouin, Sebastien Massart, Maja Ravnikar, Denis Kutnjak, Armelle Marais, Thierry Candresse
Publié dans: Phytopathology, 2023, ISSN 0031-949X
Éditeur: American Phytopathological Society
DOI: 10.1094/phyto-12-22-0465-v

Biological and Genetic Characterization of Physostegia Chlorotic Mottle Virus in Europe Based on Host Range, Location, and Time

Auteurs: Coline Temple, Arnaud G. Blouin, Kris De Jonghe, Yoika Foucart, Marleen Botermans, Marcel Westenberg, Ruben Schoen, Pascal Gentit, Michèle Visage, Eric Verdin, Catherine Wipf-Scheibel, Heiko Ziebell, Yahya Z. A. Gaafar, Amjad Zia, Xiao-Hua Yan, Katja R. Richert-Pöggeler, Roswitha Ulrich, Mark Paul S. Rivarez, Denis Kutnjak, Ana Vučurović, and Sébastien Massart
Publié dans: Plant disease, 2022, ISSN 0191-2917
Éditeur: American Phytopathological Society
DOI: 10.1094/pdis-12-21-2800-re

Other (2)

Virome analysis of irrigation water sources provides extensive insights into the diversity and distribution of plant viruses in agroecosystems

Auteurs: Olivera Maksimović, Katarina Bačnik, Mark Paul Selda Rivarez, Ana Vučurović, Nataša Mehle, Maja Ravnikar, Ion Gutiérrez-Aguirre, Denis Kutnjak
Publié dans: 2023
Éditeur: BioRxiV
DOI: 10.1101/2023.06.20.545696

Cont-ID: Detection of samples cross-contamination in viral metagenomic data

Auteurs: Johan Rollin, Wei Rong, Sébastien Massart
Publié dans: 2023
Éditeur: bioRxiv
DOI: 10.1101/2023.01.23.525161