Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 May 30:14:1181562.
doi: 10.3389/fmicb.2023.1181562. eCollection 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  1 , Maryam Khalili  2   3 , Ayoub Maachi  4 , Mark Paul S Rivarez  5   6 , Johan Rollin  1   7 , Ferran Salavert  8 , Coline Temple  1 , Miguel A Aranda  9 , Neil Boonham  8 , Marleen Botermans  10 , Thierry Candresse  2 , Adrian Fox  8   11 , Yolanda Hernando  4 , Denis Kutnjak  5 , Armelle Marais  2 , Françoise Petter  11 , Maja Ravnikar  5 , Ilhem Selmi  1 , Rachid Tahzima  1   12 , Charlotte Trontin  13 , Thierry Wetzel  14 , Sebastien Massart  1   15
Affiliations

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 et al. Front Microbiol. .

Abstract

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. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties.

Keywords: Pest Risk Analysis (PRA); biological characterization; high throughput sequencing (HTS); plant health; plant viruses and viroids; regulatory agencies; virus disease.

PubMed Disclaimer

Conflict of interest statement

AF was employed by Fera Science Ltd. AyM and YH were employed by Abiopep S.L. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Percentage of newly identified Poaceae viruses for which data was developed for each characterization category, as defined by Hou et al. (2020).
Figure 2
Figure 2
Proposed framework following the discovery of a novel virus or viroid. Y means positive response (yes) and N means negative response (no). Multi-stakeholders are involved in green-highlighted actions, and researchers in white-highlighted actions. Actions belonging to each step are separated with a dotted line, and numbers in brackets correspond to subchapters in the text.
Figure 3
Figure 3
Pie chart diagram summarizing the data gaps to be filled in step 4 of the framework (adapted from Figure 2).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Adams I. P., Fox A., Boonham N., Massart S., De Jonghe K. (2018). The impact of high throughput sequencing on plant health diagnostics. Eur. J. Plant Pathol. 152, 909–919. doi: 10.1007/s10658-018-1570-0 - DOI
    1. Adams I. P., Skelton A., Macarthur R., Hodges T., Hinds H., Flint L., et al. . (2014). Carrot yellow leaf virus is associated with carrot internal necrosis. PLoS One 9:e109125. doi: 10.1371/journal.pone.0109125, PMID: - DOI - PMC - PubMed
    1. Aguilar E., Cutrona C., del Toro F. J., Vallarino J. G., Osorio S., Pérez-Bueno M. L., et al. . (2017). Virulence determines beneficial trade-offs in the response of virus-infected plants to drought via induction of salicylic acid. Plant Cell Environ. 40, 2909–2930. doi: 10.1111/pce.13028, PMID: - DOI - PubMed
    1. Al Rwahnih M., Daubert S., Úrbez-Torres J. R., Cordero F., Rowhani A. (2011). Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses. Arch. Virol. 156, 397–403. doi: 10.1007/s00705-010-0869-8, PMID: - DOI - PMC - PubMed
    1. Ammar E.-D., Khlifa E. A., Mahmoud A., Abol-Ela S. E., Peterschmitt M. (2007). Evidence for multiplication of the leafhopper-borne maize yellow stripe virus in its vector using ELISA and dot-blot hybridization. Arch. Virol. 152, 489–494. doi: 10.1007/s00705-006-0877-x, PMID: - DOI - PubMed