Implications of high throughput sequencing of plant viruses in biosecurity – a decade of progress?
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, recommendat...
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2025-07-01
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| author | Fox, Adrian Botermans, Marleen Ziebell, Heiko Fowkes, Aimee R. Fontdevila Pareta, Nuria Massart, Sebastien Rodoni, Brendan Chooi , Kar Mun Kreuze, Jan Kumar, P. Lava Cuellar, Wilmer J. Carvajal-Yepes, Monica MacDiarmid , Robin M. |
| author_facet | Fox, Adrian Botermans, Marleen Ziebell, Heiko Fowkes, Aimee R. Fontdevila Pareta, Nuria Massart, Sebastien Rodoni, Brendan Chooi , Kar Mun Kreuze, Jan Kumar, P. Lava Cuellar, Wilmer J. Carvajal-Yepes, Monica MacDiarmid , Robin M. |
| author_sort | Fox, Adrian |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-791bab7811854b3e85dea02fbb75aa28 |
| institution | Kabale University |
| issn | 2804-3871 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Peer Community In |
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| spelling | doaj-art-791bab7811854b3e85dea02fbb75aa282025-08-20T03:58:13ZengPeer Community InPeer Community Journal2804-38712025-07-01510.24072/pcjournal.57210.24072/pcjournal.572Implications of high throughput sequencing of plant viruses in biosecurity – a decade of progress? Fox, Adrian0https://orcid.org/0000-0003-1280-1836Botermans, Marleen1https://orcid.org/0000-0002-7761-3855Ziebell, Heiko2https://orcid.org/0000-0003-0059-1595Fowkes, Aimee R.3https://orcid.org/0000-0001-7918-441XFontdevila Pareta, Nuria4https://orcid.org/0000-0001-5694-3727Massart, Sebastien5https://orcid.org/0000-0002-7153-737XRodoni, Brendan 6https://orcid.org/0009-0007-8506-700XChooi , Kar Mun7https://orcid.org/0000-0003-2511-7224Kreuze, Jan8https://orcid.org/0000-0002-6116-9200Kumar, P. Lava9https://orcid.org/0000-0003-4388-6510Cuellar, Wilmer J.10https://orcid.org/0000-0003-4702-3237Carvajal-Yepes, Monica11https://orcid.org/0000-0003-2709-7909MacDiarmid , Robin M.12https://orcid.org/0000-0002-7057-2018Fera Science Ltd, York Biotechnology Campus, Sand Hutton, York, YO41, United Kingdom Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), Netherlands Food and Consumer Product Safety Authority, Wageningen, The NetherlandsJulius Kühn-Institut, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, GermanyFera Science Ltd, York Biotechnology Campus, Sand Hutton, York, YO41, United Kingdom Laboratory of Phytopathology, TERRA, Gembloux Agro-Bio Tech, Liège University, 5030 Gembloux, Belgium; Agroscope, Route de Duillier 60, 1260 Nyon, SwitzerlandLaboratory of Phytopathology, TERRA, Gembloux Agro-Bio Tech, Liège University, 5030 Gembloux, BelgiumAgriculture Victoria, AgriBio Centre, Bundoora VIC Australia; School of Applied Systems Biology, La Trobe University, Bundoora VIC AustraliaThe New Zealand Institute for Plant & Food Research Limited, New ZealandInternational Potato Center (CIP), Apartado 1558, Lima, PeruInternational Institute of Tropical Agriculture (IITA), Oyo Road, Ibadan, NigeriaInternational Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, 763537, Colombia International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, 763537, Colombia The New Zealand Institute for Plant & Food Research Limited, New Zealand; School of Biological Sciences, University of Auckland, New ZealandIn 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.https://peercommunityjournal.org/articles/10.24072/pcjournal.572/High Throughput SequencingPlant HealthBiosecurityPlant VirusHigh Throughput SequencingPlant HealthBiosecurityPlant Virus |
| spellingShingle | Fox, Adrian Botermans, Marleen Ziebell, Heiko Fowkes, Aimee R. Fontdevila Pareta, Nuria Massart, Sebastien Rodoni, Brendan Chooi , Kar Mun Kreuze, Jan Kumar, P. Lava Cuellar, Wilmer J. Carvajal-Yepes, Monica MacDiarmid , Robin M. Implications of high throughput sequencing of plant viruses in biosecurity – a decade of progress? Peer Community Journal High Throughput Sequencing Plant Health Biosecurity Plant Virus High Throughput Sequencing Plant Health Biosecurity Plant Virus |
| title | Implications of high throughput sequencing of plant viruses in biosecurity – a decade of progress?
|
| title_full | Implications of high throughput sequencing of plant viruses in biosecurity – a decade of progress?
|
| title_fullStr | Implications of high throughput sequencing of plant viruses in biosecurity – a decade of progress?
|
| title_full_unstemmed | Implications of high throughput sequencing of plant viruses in biosecurity – a decade of progress?
|
| title_short | Implications of high throughput sequencing of plant viruses in biosecurity – a decade of progress?
|
| title_sort | implications of high throughput sequencing of plant viruses in biosecurity a decade of progress |
| topic | High Throughput Sequencing Plant Health Biosecurity Plant Virus High Throughput Sequencing Plant Health Biosecurity Plant Virus |
| url | https://peercommunityjournal.org/articles/10.24072/pcjournal.572/ |
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