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News and Announcements from INEXTVIR

21 August 2023

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

Deborah Schönegger, Armelle Marais, Bisola Mercy Babalola, Chantal Faure, Marie Lefebvre, Laurence Svanella-Dumas, Sára Brázdová, Thierry Candresse. https://doi.org/10.1371/journal.pone.0290108. Using a HTS approach, we analyzed the virome of 51 cultivated and wild carrot populations from France and central Spain. A rich virome comprising 45 viruses of which 25 are novel was identified. Most of the novel viruses showed preferential association with wild carrots, indicating the role of wild carrots as reservoir of viral diversity. The carrot virome proved rich in viruses involved in complex interactions such as poleroviruses, umbraviruses and associated satellites, which can be the basis for further investigations of virus-vector-host relationships

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Yolanda Hernando Saiz

01 August 2023

VIROME ANALYSIS OF IRRIGATION WATER SOURCES PROVIDES EXTENSIVE INSIGHTS INTO THE DIVERSITY AND DISTRIBUTION OF PLANT VIRUSES IN AGROECOSYSTEMS

Paper by OLIVERA MAKSIMOVIĆ, KATARINA BAČNIK, MARK PAUL SELDA RIVAREZ, ANA VUČUROVIĆ, NATAŠA MEHLE, MAJA RAVNIKAR, ION GUTIÉRREZ-AGUIRRE, DENIS KUTNJAK. BIORXIV 2023.06.20.545696; DOI: HTTPS://DOI.ORG/10.1101/2023.06.20.545696. Plant viruses pose a threat to agriculture and can remain infectious in water bodies. The presence of plant viruses in irrigation waters is understudied. In a large-scale virome analysis we detected nucleic acids from 20 virus families, including novel ones. Water source influenced virome composition. Water virome data provided insights into virus distribution. The study offers crucial perspectives on irrigation water viromes and highlights the potential of HTS-based surveillance for detecting plant disease outbreaks and studying virus diversity in ecosystems.

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Yolanda Hernando Saiz

30 July 2023

Round table: https://youtu.be/XPYOCrXqqOQ

Adoption and impact of high throughput sequencing in plant health: Seed testing, surveillance and certification With Wilfred Jonkers (Bejo Zadem, The Netherlands), Kelvin Hughes (Plant Health, UK), Mike Rott (Food Inspection, Canada), Françoise Petter (EPPO, France) and INEXTVIR experts

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Yolanda Hernando Saiz

24 July 2023

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

Nuria Fontdevila Pareta, Maryam Khalili, Ayoub Maachi, Mark Paul S. Rivarez, Johan Rollin, Ferran Salavert8, Coline Temple, Miguel A. Aranda, Neil Boonham8, Marleen Botermans, Thierry Candresse, Adrian Fox, Yolanda Hernando, Denis Kutnjak, Armelle Marais, Françoise Petter, Maja Ravnikar, Ilhem Selmi, Rachid Tahzima, Charlotte Trontin, Thierry Wetzel and Sebastien Massart. DOI 10.3389/fmicb.2023.1181562 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.

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Yolanda Hernando Saiz

03 July 2023

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

Deborah Schönegger, Armelle Marais, Chantal Faure, Thierry Candresse. https://doi.org/10.1007/s00705-022-05544-1. A new flavi-like virus was identified in the virome of wild carrots. It is tentatively named “carrot flavi-like virus 1” (CtFLV-1) and has a large genome of 21.8 kb with a single open reading frame encoding a large polyprotein with conserved RNA helicase and RNA-dependent RNA polymerase domains. CtFLV-1 is phylogenetically related to flavi-like viruses from arthropods, but is closest to a plant-associated virus, gentian Kobu-sho-associated virus (GKSaV), with which it could form the basis for a new genus of plant-associated viruses, for which the name “Koshovirus” is proposed

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Yolanda Hernando Saiz

02 July 2023

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

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. DOI.ORG/10.3389/FPLS.2023.1187920In this study we aimed towards filling some of the knowledge gaps in the epidemiology and diagnosis of ToBRFV, by studying the virus survival in water, the detection of the virus in environmental irrigation waters and the role of water-mediated transmission on its epidemiology.

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Yolanda Hernando Saiz

02 July 2023

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

Bisola Mercy Babalola, Chantal Faure, Armelle Marais, Aurora Fraile, Fernando Garcia‑Arenal, Thierry Candresse. https://doi.org/10.1007/s42161-022-01196-x Carrot torradovirus 1 (CaTV1) has been reported in carrot in the UK, France and Japan and in other Apiaceae in Germany and Greece. In June 2021, Illumina sequencing of five cultivated carrot populations from Segovia (Spain) revealed the presence of CaTV1 in four of them. Genomic contigs showed respectively 95% (RNA1) and 98% (RNA2) nucleotide identity with those of the reference isolate (KF533719-20). CaTV1 presence was confirmed using a two-step RT-PCR assay. To our knowledge, this is the first report of CaTV1 infection in carrots in Spain.

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Yolanda Hernando Saiz

02 July 2023

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

Sukhorukov, Grigorii, Maryam Khalili, Olivier Gascuel, Thierry Candresse, Armelle Marais-Colombel, and Macha Nikolski. "VirHunter: A deep learning-based method for detection of novel RNA viruses in plant sequencing data." Frontiers in Bioinformatics 2 (2022): 867111. High-throughput sequencing enables broad virus detection in various hosts. We propose a deep learning method called VirHunter to efficiently detect novel and known viruses in sequencing datasets, specifically trained for plant RNA viruses. VirHunter outperforms existing methods in detecting novel viruses in plant viromes, making it valuable for plant health diagnostics.

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Yolanda Hernando Saiz

20 June 2023

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

Deborah Schönegger, Bisola Mercy Babalola, Armelle Marais, Chantal Faure, Thierry Candresse. https://doi.org/10.1111/ppa.13623. Four self-replicating tombusvirus-like associated RNAs (tlaRNAs) were identified in the virome of wild and cultivated carrots including a new one, carrot red leaf virus-associated RNA 2 (CtRLVaRNA-2) and one recently described from South America, arracacha latent virus E-associated RNA (ALVEaRNA). The prevalence, preferential association with wild or cultivated carrots of these four agents were studied in France and Spain. ALVEaRNA and beet western yellows virus-associated RNA (BWYVaRNA) showed a degree of flexibility in the choice of their helper virus.

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Yolanda Hernando Saiz

15 May 2023

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

Bisola Mercy Babalola, Chantal Faure, Armelle Marais, Aurora Fraile, Fernando Garcia-Arenal, and Thierry Candresse. https://doi.org/10.1002/ndr2.1209. The Apium virus Y (ApVY) Potyvirus infects cultivated and wild Apiaceae species. It has been reported in Australia, Germany, Slovenia, New Zealand and the USA. In June 2021, ApVY was identified by Illumina sequencing of a wild carrot population sampled near Segovia (Spain). Presence of ApVY was confirmed by a specific two-step RT-PCR assay. This is the first reported natural ApVY infection in carrot and in Spain. Due to mixed infections, it was not possible to evaluate the pathogenicity of ApVY in carrot.

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Yolanda Hernando Saiz

02 April 2023

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

Paper by Adrián D. Zamfir, Bisola M. Babalola, Aurora Fraile, Michael J. McLeish and Fernando García-Arenal. HTTPS://DOI.ORG/10.1094/PHYTO-11-22-0439-V Distribution of tobamovirus infection in plant communities in a heterogeneous ecosystem showed large host ranges and limited genetic diversity, not depending on host or habitat. result underscore the relevance of the probability of virus-host encounters, rahter than of apdatation, in tobamovirus host ranges in nature.

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Yolanda Hernando Saiz

02 April 2023

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

Michael J McLeish, Adrián D. Zamfir, Bisola M. Babalola, Adrián Peláez, Aurora Fraile, Fernando García-Arenal https://doi.org/10.1093/ve/veac095 Comparison of the virome of melon crops and plants growing in adjacent edges uncovered a strong spatial structure of virus-plant interactions indicative of limited inoculum flow between plant communities. Most host plants showed no disease symptoms, which suggests non-antagonistic symbioses are common

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Yolanda Hernando Saiz

30 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. The complete round table can be followed here https://youtu.be/XPYOCrXqqOQ

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Yolanda Hernando Saiz

07 February 2023

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

Bisola Mercy Babalola, Deborah Schönegger, Chantal Faure, Armelle Marais, Aurora Fraile, Fernando Garcia-Arenal, and Thierry Candresse. https://doi.org/10.1007/s00705-022-05538-z. Carrot virome analysis by high-throughput sequencing revealed two RNA molecules with properties of satellite RNAs and are homologous to the satellite RNA of cereal yellow dwarf virus-RPV. Satellite 1 is 298 nt long, while satellite 2 is 368 nt long. Their positive and negative genome strands contain hammerhead ribozymes similar to those found in other self-cleaving satellite RNAs. While both satellites were detected in Spanish carrot populations, satellite 2 was also found in France. The most likely helper virus for these two satellites is the polerovirus carrot red leaf virus.

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Yolanda Hernando Saiz

05 February 2023

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

Mark Paul Selda Rivarez, Chantal Faure, Laurence Svanella-Dumas, Anja Pecman, Magda Tušek-Žnidaric, Deborah Schönegger, Kris De Jonghe, Arnaud Blouin, David Rasmussen, Sebastien Massart, Maja Ravnikar, Denis Kutnjak, Armelle Marais, Thierry Candresse. https://doi.org/10.1094/PHYTO-12-22-0465-V HTS virome surveys, mining of sequence read archives, and a literature search identified globally Solanum nigrum ilarvirus 1 (SnIV1) from diverse plant and non-plant sources. Its isolates showed relatively low variability. Systemic infection of SnIV1 in Solanum villosum and its mechanical and graft transmissibility to several solanaceous species were demonstrated, as well as its seed-transmission and potential pollen transmission. Overall, modern and classical virological approaches a better understanding of the diversity, global presence and pathobiology of SnIV1

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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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