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News and Announcements from INEXTVIR

12 March 2023

Web-based roundtable: Adoption and impact of high throughput sequencing in plant health: Seed testing, surveillance and certification

Within the Inextvir final network meeting and conference the round table on adoption and impact of high throughput sequencing in plant health: Seed testing, surveillance and certification has been held With Wilfred Jonkers (Bejo Zadem, The Netherlands), Kelvin Hughes (Plant Health, UK), Mike Rott (Food Inspection, Canada), Françoise Petter (EPPO, France) and INEXTVIR experts. https://youtu.be/XPYOCrXqqOQ

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Yolanda Hernando Saiz

30 January 2023

First Report of Ranunculus White Mottle Ophiovirus in Slovenia in Pepper with Yellow Leaf Curling Symptom and in Tomato

Rivarez MPS, Kogej Z, Jakoš N, Pecman A, Seljak G, Vučurović A, Ravnikar M, Mehle N, Kutnjak D. First Report of Ranunculus White Mottle Ophiovirus in Slovenia in Pepper with Yellow Leaf Curling Symptom and in Tomato. Plant Dis. 2022 May 22:PDIS08211624PDN. doi: 10.1094/PDIS-08-21-1624-PDN. We have reported the first detection of Ranunculus white mottle ophiovirus in Slovenia. The virus was detected in pepper and tomato. This report represent, globally, its first detection in tomato.

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Yolanda Hernando Saiz

30 January 2023

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

Rivarez, M. P. S., Pecman, A., Bačnik, K., Maksimović Carvalho Ferreira, O., Vučurović, A., Seljak, G., Mehle, N., Gutiérrez-Aguirre, I., Ravnikar, M., & Kutnjak, D. (2022). In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem. BioRxiv, 2022.06.30.498278. https://doi.org/10.1101/2022.06.30.498278 In this comprehensive virome study of tomato agroecosystems in Slovenia, we have investigated presence of viruses in tomatoes and weeds and discovered a high amount of virus diversity in these two sample types. Most strikingly, a high amount of previously unknown viruses were detected in wild plant species (“weeds”) that surrounded tomato farming sites.

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Yolanda Hernando Saiz

30 January 2023

THE EXPANDING MENAGERIE OF PRUNUS-INFECTING LUTEOVIRUSES

Khalili M, Candresse T, Koloniuk I, Safarova D, Brans Y, Faure C, Delmas M, Massart S, Aranda MA, Cagalayan 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, Sedlack J, Marais A. Phytopathology 2023 doi: 10.1094/PHYTO-06-22-0203-R. Members of the genus Luteovirus are responsible for economically destructive plant diseases worldwide. In Prunus trees, three luteoviruses had been characterized so far. Applying high-throughput sequencing to 350 Prunus samples and datamining allowed to identify five novel luteoviruses. The development of specific diagnostic tests allowed to demonstrate that peach-infecting luteoviruses have a high prevalence and a wide distribution in Europe, apparently without causing any significant symptoms.

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Yolanda Hernando Saiz

30 January 2023

Molecular characterization of a new Prunus-infecting cheravirus and complete genome sequence of stocky prune virus

M. Khalili, T. Candresse, Y. Brans, C. Faure, JM. Audergon, V. Decroocq, A. Marais. 2022 Viruses 14:2325. doi: 10.3390/v14112325. High-throughput sequencing allowed to identify three variants of a novel cheravirus, Alpine wild Prunus virus (AWPV), in three Prunus species, P. armeniaca (apricot), P. brigantina (wild apricot) and P. mahaleb (mahaleb or St Lucie cherry). A potential association of AWPV with symptoms could not be established so far due to mixed viral infections in the sampled trees. Moreover, the genome of stocky prune virus (StPV), a poorly known Prunus-infecting cheravirus, was determined. Phylogenetic analyses showed StPV and AWPV form a distinct cluster, away from other cheraviruses.

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Yolanda Hernando Saiz

29 January 2023

Genetic differentiation and migration fluxes of viruses from melon crops and crop edge weeds

Maachi, A. ; Donaire, L. ; Hernando, Y. ; Aranda, M.A. Journal of Virology, August 2021 | doi : 10.1128/jvi.00421-22 Weeds surrounding crops may act as alternative hosts, playing important epidemiological roles as virus reservoirs and impacting virus evolution. We used high-throughput sequencing to identify viruses in Spanish melon crops and plants belonging to three pluriannual weed species, Ecballium elaterium, Malva sylvestris, and Solanum nigrum, sampled at the edges of the crops.

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Yolanda Hernando Saiz

26 January 2023

Global advances in tomato virome research: current status and the impact of high-throughput sequencing

Rivarez MPS, Vučurović A, Mehle N, Ravnikar M and Kutnjak D (2021) Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing. Front. Microbiol. 12:671925. doi: 10.3389/fmicb.2021.671925 In this review paper we have collected the existing knowledge about the viruses infecting tomato, focusing on the viruses that caused important economic damage in tomato production in a past decade. We have also addressed how high-throughput sequencing technologies have contributed to discovery of novel viruses infecting tomato and evaluated the extent of post-discovery characterisation studies for such viruses.

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Yolanda Hernando Saiz

23 January 2023

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

Johan Rollin*1,2, Wei Rong*1 and Sébastien Massart1. 1. University of Liège, Gembloux Agro-Bio Tech, Plant Pathology Laboratory, 5030, Gembloux, Belgium 2. DNAVision, 6041, Gosselies, Belgium. *These authors contributed equally to this work. https://doi.org/10.1101/2023.01.23.525161 Conclusions: Cross-contamination between samples when detecting viruses using HTS can be monitored and highlighted by Cont-ID (provided an alien control is present). Cont-ID is based on a flexible methodology relying on the output of bioinformatics analyses of the sequencing reads and considering the contamination pattern specific to each batch of samples. The Cont-ID method is adaptable so that each laboratory can optimise it before its validation and routine use.

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Yolanda Hernando Saiz

23 January 2023

Validation of high throughput sequencing as virus indexing test for Musa germplasm: performance criteria evaluation and contamination monitoring using an alien control

Wei Rong1*, Johan Rollin1,2*, Marwa Hanafi1, Nicolas Roux3, Sebastien Massart1. 1Laboratory of Plant Pathology – TERRA - Gembloux Agro-Bio Tech – University of Liège, 5030 Gembloux, Belgium. 2DNAVision, 6041 Gosselies, Belgium . 3Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France. *These authors contributed equally to this work. https://doi.org/10.1094/PHYTOFR-03-22-0030-FI Overall, HTS used displayed a better analytical sensitivity compared to RT-PCR and a better inclusivity. Repeatability and reproducibility of virus detection were both of 100%. The diagnostic sensitivity was very high but false positive results were observed. Finally, the results also underlined the need of expert judgement in the interpretation of the results. In conclusion, the HTS test with an alien control and completed by expert evaluation has fulfilled the criteria of virus indexing protocol for Musa germplasm.

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Yolanda Hernando Saiz

23 January 2023

HIGH THROUGHPUT SEQUENCING TECHNOLOGIES COMPLEMENTED BY GROWER’S PERCEPTION HIGHLIGHT THE IMPACT OF TOMATO VIROME IN DIVERSIFIED VEGETABLE FARMS

Coline Temple1, Arnaud G. Blouin2, Sophie Tindale 3, Stephan Steyer4, Kevin Marechal5, Sebastien Massart1*. https://doi.org/10.1101/2023.01.12.523758 To better understand the risks associated with plant viruses in diversified vegetable production systems, and to evaluate the impact of cultural practices on plant viruses, we developed a methodology that combine growers' perception, the presence of viral symptoms (visual inspection) and non-targeting detection of nearly all viruses present in the plants by high throughput sequencing technologies (HTS).

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Yolanda Hernando Saiz

23 January 2023

BIOLOGICAL AND GENETIC CHARACTERIZATION OF PHYSOSTEGIA CHLOROTIC MOTTLE VIRUS IN EUROPE BASED ON HOST RANGE, LOCATION, AND TIME

Coline Temple1, Arnaud G. Blouin1,9, Kris De Jonghe2, Yoika Foucart2, Marleen Botermans3, Marcel Westenberg3, Ruben Schoen3, Pascal Gentit4, Michèle Visage4, Eric Verdin5, Catherine Wipf-Scheibel5, Heiko Ziebell6, Yahya Z. A. Gaafar6, Amjad Zia6, Xiao-Hua Yan6, Katja R. Richert-Pöggeler6, Roswitha Ulrich7, Mark Paul S. Rivarez8, Denis Kutnjak8, Ana Vučurović8, Sébastien Massart1* https://doi.org/10.1094/PDIS-12-21-2800-RE We report here how prepublication datasharing resulted in an international collaboration across eight laboratories in five countries, enabling an in-depth characterization of Physostegia chlorotic mottle virus (PhCMoV). In this study, we highlight the first detection of the virus in six European countries and in seven new natural host plants. Our research established that PhCMoV is associated with severe symptoms and the additional 21 generated sequences allowed to study its phylogeny across time and geographic locations.

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Yolanda Hernando Saiz

23 January 2023

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

Hilaire, J., Tindale, S., Jones, G. et al. Agric & Food Secur 11, 21 (2022). https://doi.org/10.1186/s40066-022-00366-5 The research in this paper aims at exploring what the public think about plant viruses in agriculture in Europe. Plant viruses represent an emerging agricultural risk, resulting in agriculture yield losses estimated at $30 billion per year worldwide, and account for nearly 50% of emerging plant diseases globally, representing a threat to global food security. In Europe, plant viruses are responsible for significant economic damage in a range of crops including vegetables, grains, and ornamentals.

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Yolanda Hernando Saiz

22 January 2023

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

Fontdevila Pareta, N., Lateur, M., Steyer, S., Blouin, A.G. & Massart, S. (2022) First reports of Apple luteovirus 1, Apple rubodvirus 1 and Apple hammerhead viroid infecting apples in Belgium. New Dis Rep. 45, e12076. https://doi.org/10.1002/ndr2.12076 As part of a pilot study on germplasm collections, leaves were collected from six apple trees (Malus domestica) in the germplasm collection of the CRA-W in Belgium in June 2019 and June 2020. Double-stranded RNA (dsRNA) and total RNA were extracted from collected leaf tissue, and the extracted nucleic acids were submitted to high-throughput sequencing (HTS).

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Yolanda Hernando Saiz

08 December 2022

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

Maksimović, O., Lengar, Ž., Kogej, Z., Bačnik K., Bajde, I., Milavec, M., Županič, A., Mehle, N., Kutnjak, D., Ravnikar, M., Gutierrez-Aguirre, I., Food Environ. Virol. 2022 Dec.; 384-400. doi: 10.1007/s12560-022-09544-0 Water based epidemiology was employed as a tool for tracking the transmission dynamics of SARS-CoV-2 in a given area. In this paper, we describe the evaluation of the methods that are currently used in the Slovenian national wastewater monitoring scheme for SARS-CoV-2. Specifically we compared several methods for virus concentration, different RT-qPCR assays and tested the stability of the virus over time in different temperature regiments.

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Yolanda Hernando Saiz

29 November 2022

Importance of associated weeds and cropping systems in shaping the viromes of horticultural crops. Ayoub Maachi PhD Thesis

Metagenomics based on high throughput sequencing (HTS) has opened a new era of unbiased discovery and genomic characterization of viruses. As for other viruses from other kingdoms, metagenomic studies indicate that the diversity of plant viruses was until recently far underestimated. As potentially important components of unmanaged and cultivated ecosystems, there is a need to explore the diversity of the viruses associated with plant populations and to understand the drivers shaping their diversity in space and time.

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Yolanda Hernando Saiz

29 November 2022

Use of high throughput sequencing and two RNA input methods to identify viruses infecting tomato crops.

Maachi, A. ; Torre, C. ; Sempere, R.N. ; Hernando, Y. ; Aranda, M.A. ; Donaire, L. Microorganisms, May 2021| doi : 10.3390/microorganisms9051043 We used high-throughput sequencing to identify viruses on tomato samples showing virus-like symptoms. Samples were collected from crops in the Iberian Peninsula. Either total RNA or double-stranded RNA (dsRNA) were used as starting material to build the cDNA libraries. In total, seven virus species were identified, with pepino mosaic virus being the most abundant one.

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Yolanda Hernando Saiz

29 November 2022

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

Maachi, A. ; Hernando, Y. ; Aranda, M.A. ; Donaire, L. Virus Genes, April 2022 | doi: 10.1007/s11262-022-01900-0 In this work, a novel viral genomic sequence with a gene organization typical of members of the genus Soymovirus was identified using high-throughput sequencing data from common mallow. This species is a vigorous wild weed native to the Mediterranean region, commonly found in borders and edges of cultivated fields, making it a suitable reservoir for plant pests and pathogens.

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Yolanda Hernando Saiz

25 October 2022

Known and new viruses identified in the virome of crops scanned by INEXTVIR

By means of bioinformatics analysis of the virome high-throughput sequencing data, an integrated vision of the virome of each crop has being generated. That has allowed the identification of a total of 157 viral agents (virus, viroid and satellites), of which 48 (30.6%) represent novel viruses. The data listing for each crop addressed in INEXTVIR the known and novel viral agents identified, together with the country(ies) and year(s) in which the agent was identified.

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Yolanda Hernando Saiz

18 October 2022

Scanning the virome of Prunus : Identification and characterization of novel luteoviruses and Secoviridae members

M. Khalili. Thèse de doctorat en Science de la Vie et de la Santé, Mention Biologie Végétale, sous la direction de Armelle Marais, Université de Bordeaux, 2022, 178 p. The main objective of this thesis was to explore using advanced sequencing technology the composition of the virome (all the viruses present) of Prunus species (apricot, cherry, peach, plum, almond, and related wild or ornamental species). During this work, beyond known viruses, six novel viruses were discovered, significantly increasing the number of viruses known to infect Prunus. Diagnostic tests have been developed, allowing to detect them specifically. We have shown that some of the peach-infecting viruses have a very wide distribution in Europe, without causing any apparent symptoms. Overall, this exploration of the Prunus virome has enriched our knowledge of these viruses and provided new elements to assess the risks associated with these different agents. They open new research perspectives to account for their potential impact.

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Yolanda Hernando Saiz

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