Frontiers in Virology (Apr 2024)
Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities
- Justine Charon,
- Ingrida Olendraite,
- Marco Forgia,
- Li Chuin Chong,
- Luke S. Hillary,
- Simon Roux,
- Anne Kupczok,
- Humberto Debat,
- Humberto Debat,
- Shoichi Sakaguchi,
- Rachid Tahzima,
- Rachid Tahzima,
- So Nakagawa,
- Artem Babaian,
- Artem Babaian,
- Aare Abroi,
- Nicolas Bejerman,
- Nicolas Bejerman,
- Karima Ben Mansour,
- Karima Ben Mansour,
- Katherine Brown,
- Anamarija Butkovic,
- Amelia Cervera,
- Florian Charriat,
- Guowei Chen,
- Yuto Chiba,
- Yuto Chiba,
- Lander De Coninck,
- Tatiana Demina,
- Guillermo Dominguez-Huerta,
- Jeremy Dubrulle,
- Serafin Gutierrez,
- Serafin Gutierrez,
- Erin Harvey,
- Fhilmar Raj Jayaraj Mallika,
- Dimitris Karapliafis,
- Shen Jean Lim,
- Sunitha Manjari Kasibhatla,
- Sunitha Manjari Kasibhatla,
- Jonathon C. O. Mifsud,
- Yosuke Nishimura,
- Ayda Susana Ortiz-Baez,
- Milica Raco,
- Ricardo Rivero,
- Sabrina Sadiq,
- Shahram Saghaei,
- James Emmanuel San,
- James Emmanuel San,
- Hisham Mohammed Shaikh,
- Hisham Mohammed Shaikh,
- Ella Tali Sieradzki,
- Matthew B. Sullivan,
- Yanni Sun,
- Michelle Wille,
- Yuri I. Wolf,
- Nikita Zrelovs,
- Uri Neri
Affiliations
- Justine Charon
- Fruit Biology and Pathology Unit, University of Bordeaux, INRAE, Bordeaux, France
- Ingrida Olendraite
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
- Marco Forgia
- Istituto per la Protezione Sostenibile Delle Piante, CNR, Torino, Italy
- Li Chuin Chong
- Institute for Experimental Virology, TWINCORE Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Luke S. Hillary
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Anne Kupczok
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
- Humberto Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE, CIAP, INTA), Córdoba, Argentina
- Humberto Debat
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Córdoba, Argentina
- Shoichi Sakaguchi
- 0Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
- Rachid Tahzima
- 1University of Liège, Gembloux AgroBioTech - TERRA, Gembloux, Belgium
- Rachid Tahzima
- 2Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit – Virology, Ghent, Belgium
- So Nakagawa
- 3Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- Artem Babaian
- 4Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Artem Babaian
- 5The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Aare Abroi
- 6Institute of Technology, University of Tartu, Tartu, Estonia
- Nicolas Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE, CIAP, INTA), Córdoba, Argentina
- Nicolas Bejerman
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Córdoba, Argentina
- Karima Ben Mansour
- 7Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Crop Research Institute, Prague, Czechia
- Karima Ben Mansour
- 8Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources Czech University of Life Sciences, Prague, Czechia
- Katherine Brown
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
- Anamarija Butkovic
- 9Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS, Paris, France
- Amelia Cervera
- 0Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat Politècnica de València (UPV), València, Spain
- Florian Charriat
- 1ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, France
- Guowei Chen
- 2Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Yuto Chiba
- 3School of Agriculture, Meiji University, Kawasaki, Japan
- Yuto Chiba
- 4Research Centre for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Lander De Coninck
- 5KU Leuven, Department of Microbiology, Immunology, and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
- Tatiana Demina
- 6Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
- Guillermo Dominguez-Huerta
- 7Department of Oceanography and Global Change, Centro Oceanográfico de Málaga (IEO-CSIC), Fuengirola, Spain
- Jeremy Dubrulle
- 8Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Serafin Gutierrez
- 1ASTRE, CIRAD, INRAE, University of Montpellier, Montpellier, France
- Serafin Gutierrez
- 9Department of Virology, Montpellier University Hospital, Montpellier, France
- Erin Harvey
- 0Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- Fhilmar Raj Jayaraj Mallika
- 1Molecular Virology Laboratory, ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu, India
- Dimitris Karapliafis
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
- Shen Jean Lim
- 2College of Marine Science, University of South Florida, St Petersburg, FL, United States
- Sunitha Manjari Kasibhatla
- 3Bioinformatics Centre, SP Pune University, Pune, India
- Sunitha Manjari Kasibhatla
- 4High Performance Computing (HPC)-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, India
- Jonathon C. O. Mifsud
- 0Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- Yosuke Nishimura
- 4Research Centre for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Ayda Susana Ortiz-Baez
- 0Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- Milica Raco
- 5Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Ricardo Rivero
- 6Paul G. Allen School for Global Health, Washington State University, Pullman, WA, United States
- Sabrina Sadiq
- 0Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
- Shahram Saghaei
- 7Bioinformatics/High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany
- James Emmanuel San
- 8KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), UKZN, Durban, South Africa
- James Emmanuel San
- 9School of Laboratory Medicine and Medical Sciences, University of KwaZulu–Natal, Durban, South Africa
- Hisham Mohammed Shaikh
- 0Research Department, Flanders Marine Institute (VLIZ), InnovOcean Site, Ostend, Belgium
- Hisham Mohammed Shaikh
- 1Department of Microbiology and Biochemistry, Faculty of Sciences, Ghent University, Ghent, Belgium
- Ella Tali Sieradzki
- 2Laboratoire Ampère, École Centrale de Lyon, Écully, France
- Matthew B. Sullivan
- 3Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, and Center of Microbiome Science, Ohio State University, Columbus, OH, United States
- Yanni Sun
- 2Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Michelle Wille
- 4Centre for Pathogen Genomics, Department of Microbiology and Immunology, University of Melbourne, at the Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Yuri I. Wolf
- 5National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
- Nikita Zrelovs
- 6Latvian Biomedical Research and Study Centre, Riga, Latvia
- Uri Neri
- 7The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
- DOI
- https://doi.org/10.3389/fviro.2024.1371958
- Journal volume & issue
-
Vol. 4
Abstract
Improved RNA virus understanding is critical to studying animal and plant health, and environmental processes. However, the continuous and rapid RNA virus evolution makes their identification and characterization challenging. While recent sequence-based advances have led to extensive RNA virus discovery, there is growing variation in how RNA viruses are identified, analyzed, characterized, and reported. To this end, an RdRp Summit was organized and a hybrid meeting took place in Valencia, Spain in May 2023 to convene leading experts with emphasis on early career researchers (ECRs) across diverse scientific communities. Here we synthesize key insights and recommendations and offer these as a first effort to establish a consensus framework for advancing RNA virus discovery. First, we need interoperability through standardized methodologies, data-sharing protocols, metadata provision and interdisciplinary collaborations and offer specific examples as starting points. Second, as an emergent field, we recognize the need to incorporate cutting-edge technologies and knowledge early and often to improve omic-based viral detection and annotation as novel capabilities reveal new biology. Third, we underscore the significance of ECRs in fostering international partnerships to promote inclusivity and equity in virus discovery efforts. The proposed consensus framework serves as a roadmap for the scientific community to collectively contribute to the tremendous challenge of unveiling the RNA virosphere.
Keywords
- RNA virus discovery
- viral metagenomics
- RNA-dependent RNA polymerase
- viral genome annotation
- metagenomic metadata standards
- virus evolution and diversity
