Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses

Abstract

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 (2010-2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsid-less 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.

African army ants at the forefront of virome surveillance in a remote tropical forest

“…In July 2019, two sampling surveys were conducted in the Ogooué-Ivindo region (Northeast Gabon). Over 250 individual ants from 29 colonies were collected along roadsides between Mekambo and Mendemba villages, immediately stored in liquid nitrogen and further transferred to Montpellier (France) where they were stored at -80°C. Two-hundred and nine samples, including 145 samples containing only one ant and 64 samples each containing pools of 2 to 13 individual ants (Table 1 and Supplementary Table 1) were further processed using the virion-associated nucleic acid based (VANA) metagenomics approach 29 .…”

“…Each of the 209 collected samples was processed using the VANA viral metagenomics approach that is comprehensively detailed in François et al (2018) 30 . It is noteworthy that the VANA approach is suited to the detection of both DNA and RNA viruses, and includes several steps that aim at both removing host nucleic acids and maximizing the yield of virion-associated nucleic acids 29 . Briefly, ants were first ground using tissue homogenizer and sterile steel beads.…”

“…We have recently conducted a simulation experiment that has revealed that the accuracy of the BLASTx virus family and genus assignations are high, i.e. >97.9% and >90.6%, respectively, when contigs have lengths ≥200 nt 29 . We therefore selected contigs with lengths ≥200 nt and retained viral BLASTx assignations of these contigs wherever they yielded e-values < 0.001.…”

Assembly of plant virus agroinfectious clones using biological material or DNA synthesis

“…High-throughput sequencing advances have allowed discovering of an unprecedented number of plant viruses ( Dolja et al., 2020 ; Kutnjak et al., 2021 ; Moubset et al., 2022 ). Their biological characterization is now a major bottleneck that limits disease causality studies, evaluation of agronomical and ecological impact of infections, and implementation of virus control strategies ( Hou et al., 2020 ; Massart et al., 2017 ).…”

Translating virome analyses to support biosecurity, on-farm management, and crop breeding

“…Scientists and practitioners must consider pathogen risks and societal impacts to effectively address and mitigate these challenges. There are a wide range of new tools and frameworks for improving virome data analysis, virus discovery and diagnostics, and applications such as phytosanitary practices and regulation ( Massart et al., 2014 ; Massart et al., 2017 ; Massart et al., 2019 ; Maclot et al., 2020 ; Kumar et al., 2021 ; Moubset et al., 2022 ). Our goal in this paper is to synthesize current knowledge of virus discovery and state-of-the-art technologies, and the potential for translation of big data to benefit stakeholders, from national agencies to individual farmers.…”