Search

Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Plant virus ecology began to be explored at the end of the 19 th century. Since then, major advances have revealed complex virus-host-vector interactions in a variety of environments. These advances have been accelerated by development of new technologies for virus detection and characterization, the latest of which being high-throughput sequencing (HTS). HTS technologies have proved to be effective for non-targeted characterization of all or nearly all viruses present in a sample without requiring prior information about virus identity, as would be needed for virus-targeted tests. Phytoviromic studies have thus made important advances, including characterization of the complex interactions between phytovirus dynamics and the structure of multi-species host communities, and documentation of the effects of anthropogenic ecosystem simplification on plant virus emergence and diversity. However, such studies must overcome challenges at every stage, from plant sampling to bioinformatics analysis. This review summarizes major advances in plant virus ecology, in association with technological developments, and presents key considerations for use of HTS in the study of the ecology of phytovirus communities.

Résumé: L'écologie des virus végétaux a commencé à être explorée à la fin du xix e siècle. Depuis lors, des avancées majeures ont mis en évidence de complexes interactions virus-hôte-vecteur dans des environnements variés. Ces progrès ont été accélérés par de nouvelles technologies de détection et de caractérisation des virus, dont la dernière en date est le séquençage à haut débit (HTS). Les technologies HTS permettent, pour la première fois, de caractériser sans information préalable le virome, c'est-à-dire l'ensemble des virus présents dans un échantillon. Ces travaux de phytoviromique basés sur les technologies HTS ont récemment produit d'importants résultats. À titre d'exemples, on peut citer la mise en évidence des influences réciproques entre la dynamique des phytovirus et la structure des communautés hôtes multi-espèces ou des effets de la simplification des écosystèmes causés par les activités humaines sur la biodiversité et l'émergence de nouveaux virus dans les cultures. Cependant, pour être efficaces, les études de phytoviromique doivent surmonter des défis à chaque étape de la procédure, depuis l'échantillonnage des plantes jusqu'aux analyses bio-informatiques. Cette revue résume tout d'abord les progrès historiques majeurs de l'écologie des virus végétaux réalisés en association avec les développements technologiques, puis précise les éléments clés à considérer pour tenter de se projeter à court terme vers des études sans a priori d'écologie des communautés virales. Plant virus ecology began to be explored at the end of the 19th century. Since then, major advances have revealed complex virus–host–vector interactions in a variety of environments. These advances have been accelerated by development of new technologies for virus detection and characterization, the latest of which being high-throughput sequencing (HTS). HTS technologies have proved to be effective for non-targeted characterization of all or nearly all viruses present in a sample without requiring prior information about virus identity, as would be needed for virus-targeted tests. Phytoviromic studies have thus made important advances, including characterization of the complex interactions between phytovirus dynamics and the structure of multi-species host communities, and documentation of the effects of anthropogenic ecosystem simplification on plant virus emergence and diversity. However, such studies must overcome challenges at every stage, from plant sampling to bioinformatics analysis. This review summarizes major advances in plant virus ecology, in association with technological developments, and presents key considerations for use of HTS in the study of the ecology of phytovirus communities. [ABSTRACT FROM AUTHOR]