Section: Infections
Topic: Agricultural sciences, Applied biological sciences, Genetics/genomics

Implications of high throughput sequencing of plant viruses in biosecurity – a decade of progress?

Fox, Adrian1 orcid  ; Botermans, Marleen2 orcid ; Ziebell, Heiko3 orcid ; Fowkes, Aimee R.1 orcid ; Fontdevila Pareta, Nuria4, 5 orcid ; Massart, Sebastien4 orcid ; Rodoni, Brendan6, 7 orcid ; Chooi , Kar Mun8 orcid ; Kreuze, Jan9 orcid ; Kumar, P. Lava10 orcid ; Cuellar, Wilmer J.11 orcid ; Carvajal-Yepes, Monica11 orcid ; MacDiarmid , Robin M.8, 12 orcid 
1Fera Science Ltd, York Biotechnology Campus, Sand Hutton, York, YO41, United Kingdom
2Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Netherlands Food and Consumer Product Safety Authority, Wageningen, The Netherlands
3Julius Kühn-Institut, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
4Laboratory of Phytopathology, TERRA, Gembloux Agro-Bio Tech, Liège University, 5030 Gembloux, Belgium
5Agroscope, Route de Duillier 60, 1260 Nyon, Switzerland
6Agriculture Victoria, AgriBio Centre, Bundoora VIC Australia
7School of Applied Systems Biology, La Trobe University, Bundoora VIC Australia
8The New Zealand Institute for Plant & Food Research Limited, New Zealand
9International Potato Center (CIP), Apartado 1558, Lima, Peru
10International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria
11International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, 763537, Colombia
12School of Biological Sciences, University of Auckland, New Zealand

Corresponding author(s): Fox, Adrian (adrian.fox@fera.co.uk)

10.24072/pcjournal.572 - Peer Community Journal, Volume 5 (2025), article no. e71

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In the 15 years since High Throughput Sequencing (HTS) was first used for the detection and identification of plant viruses, the technology has matured and is now being used in frontline plant biosecurity applications. Anticipating the challenges this new approach was starting to reveal, recommendations were made a decade ago to streamline the application of these technologies. The recommendations were (1) for countries to increase baseline surveillance, (2) to address nomenclature for “data inferred” new viral sequence to differentiate from characterised viruses, and (3) to increase the focus on fundamental biological research to deal with the deluge of new discoveries. Here, we review the progress made on these recommendations in the intervening decade and discuss the anticipated future challenges posed by the broader adoption of HTS in routine biosecurity applications, especially as we move towards a potential asymptote in the rate of virus discovery. The three initial recommendations are still relevant, however, the decade of discovery and development has led to a change in approaches and ways of thinking. A fourth recommendation is made here, to reduce the biosecurity risks through equal inclusion and access to research and technology, locally and globally. This equality will create increased consonance between community members, researchers, risk analysts, biosecurity authorities, and policy makers at national and international levels and a step change reduction of biosecurity incursions of phytopathogenic viruses.

Published online:
DOI: 10.24072/pcjournal.572
Type: Opinion / perspective
Keywords: High Throughput Sequencing, Plant Health, Biosecurity, Plant Virus, High Throughput Sequencing, Plant Health, Biosecurity, Plant Virus

Fox, Adrian  1 ; Botermans, Marleen  2 ; Ziebell, Heiko  3 ; Fowkes, Aimee R.  1 ; Fontdevila Pareta, Nuria  4 , 5 ; Massart, Sebastien  4 ; Rodoni, Brendan   6 , 7 ; Chooi , Kar Mun  8 ; Kreuze, Jan  9 ; Kumar, P. Lava  10 ; Cuellar, Wilmer J.  11 ; Carvajal-Yepes, Monica  11 ; MacDiarmid , Robin M.  8 , 12

1 Fera Science Ltd, York Biotechnology Campus, Sand Hutton, York, YO41, United Kingdom
2 Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Netherlands Food and Consumer Product Safety Authority, Wageningen, The Netherlands
3 Julius Kühn-Institut, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
4 Laboratory of Phytopathology, TERRA, Gembloux Agro-Bio Tech, Liège University, 5030 Gembloux, Belgium
5 Agroscope, Route de Duillier 60, 1260 Nyon, Switzerland
6 Agriculture Victoria, AgriBio Centre, Bundoora VIC Australia
7 School of Applied Systems Biology, La Trobe University, Bundoora VIC Australia
8 The New Zealand Institute for Plant & Food Research Limited, New Zealand
9 International Potato Center (CIP), Apartado 1558, Lima, Peru
10 International Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, Nigeria
11 International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, 763537, Colombia
12 School of Biological Sciences, University of Auckland, New Zealand
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
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Fox, A.; Botermans, M.; Ziebell, H.; Fowkes, A. R.; Fontdevila Pareta, N.; Massart, S.; Rodoni, B.; Chooi , K. M.; Kreuze, J.; Kumar, P. L.; Cuellar, W. J.; Carvajal-Yepes, M.; MacDiarmid , R. M. Implications of high throughput sequencing of plant viruses in biosecurity – a decade of progress?. Peer Community Journal, Volume 5 (2025), article  no. e71. https://doi.org/10.24072/pcjournal.572

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.infections.100239

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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