Tomato Brown Rugose Fruit Virus Nextstrain Build Version 3: Rise of a Novel Clade
In the Netherlands, tomato brown rugose fruit virus (ToBRFV; genus Tobamovirus) was first identified in tomato crops in 2019. Since then, the National Plant Protection Organization (NPPO-NL) has performed surveys to track and trace this regulated virus aiming for its eradication. To gain more insigh...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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The American Phytopathological Society
2023-09-01
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| Series: | PhytoFrontiers |
| Subjects: | |
| Online Access: | https://apsjournals.apsnet.org/doi/10.1094/PHYTOFR-09-22-0090-A |
| _version_ | 1827095691994857472 |
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| author | Marleen Botermans Pier P. M. de Koning Carla Oplaat Aimee R. Fowkes Sam McGreig Anna Skelton Ian P. Adams Adrian Fox Kris De Jonghe Jill E. Demers Johanna W. Roenhorst Marcel Westenberg Bart T. L. H. van de Vossenberg |
| author_facet | Marleen Botermans Pier P. M. de Koning Carla Oplaat Aimee R. Fowkes Sam McGreig Anna Skelton Ian P. Adams Adrian Fox Kris De Jonghe Jill E. Demers Johanna W. Roenhorst Marcel Westenberg Bart T. L. H. van de Vossenberg |
| author_sort | Marleen Botermans |
| collection | DOAJ |
| description | In the Netherlands, tomato brown rugose fruit virus (ToBRFV; genus Tobamovirus) was first identified in tomato crops in 2019. Since then, the National Plant Protection Organization (NPPO-NL) has performed surveys to track and trace this regulated virus aiming for its eradication. To gain more insight in the epidemiology of ToBRFV, genomes were assembled from Illumina sequence data. Whole-genome phylogenetics was integrated with epidemiological metadata in a Nextstrain build. Two new clades were defined, one of which displayed a rapid increase in comparison to the previous version of the Nextstrain build. This rapid increase could be attributed to the unauthorized application of an isolate of ToBRFV as a cross-protection product. Further analysis of the test results of positive samples from tomato production sites suggests that both deliberate application and accidental introduction had occurred. This report introduces the inclusion of 61 new (near) complete ToBRFV genomes in version three of the Nextstrain build, available from https://nextstrain.nrcnvwa.nl/ToBRFV/20220412. [Figure: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license. |
| first_indexed | 2024-03-08T07:20:37Z |
| format | Article |
| id | doaj.art-a9437a6574084b3d8d1bed724466f82e |
| institution | Directory Open Access Journal |
| issn | 2690-5442 |
| language | English |
| last_indexed | 2025-03-20T07:03:55Z |
| publishDate | 2023-09-01 |
| publisher | The American Phytopathological Society |
| record_format | Article |
| series | PhytoFrontiers |
| spelling | doaj.art-a9437a6574084b3d8d1bed724466f82e2024-10-01T12:35:47ZengThe American Phytopathological SocietyPhytoFrontiers2690-54422023-09-013244244610.1094/PHYTOFR-09-22-0090-ATomato Brown Rugose Fruit Virus Nextstrain Build Version 3: Rise of a Novel CladeMarleen Botermans0Pier P. M. de Koning1Carla Oplaat2Aimee R. Fowkes3Sam McGreig4Anna Skelton5Ian P. Adams6Adrian Fox7Kris De Jonghe8Jill E. Demers9Johanna W. Roenhorst10Marcel Westenberg11Bart T. L. H. van de Vossenberg12Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), National Plant Protection Organization, Geertjesweg 15, 6706EA Wageningen, The NetherlandsNetherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), National Plant Protection Organization, Geertjesweg 15, 6706EA Wageningen, The NetherlandsNetherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), National Plant Protection Organization, Geertjesweg 15, 6706EA Wageningen, The NetherlandsFera Science Ltd, Sand Hutton, York, YO41 1LZ, United KingdomFera Science Ltd, Sand Hutton, York, YO41 1LZ, United KingdomFera Science Ltd, Sand Hutton, York, YO41 1LZ, United KingdomFera Science Ltd, Sand Hutton, York, YO41 1LZ, United KingdomFera Science Ltd, Sand Hutton, York, YO41 1LZ, United KingdomPlant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, 9820, BelgiumBayer Crop Science, St. Louis, MO, U.S.A.Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), National Plant Protection Organization, Geertjesweg 15, 6706EA Wageningen, The NetherlandsNetherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), National Plant Protection Organization, Geertjesweg 15, 6706EA Wageningen, The NetherlandsNetherlands Institute for Vectors, Invasive plants and Plant health (NIVIP), National Plant Protection Organization, Geertjesweg 15, 6706EA Wageningen, The NetherlandsIn the Netherlands, tomato brown rugose fruit virus (ToBRFV; genus Tobamovirus) was first identified in tomato crops in 2019. Since then, the National Plant Protection Organization (NPPO-NL) has performed surveys to track and trace this regulated virus aiming for its eradication. To gain more insight in the epidemiology of ToBRFV, genomes were assembled from Illumina sequence data. Whole-genome phylogenetics was integrated with epidemiological metadata in a Nextstrain build. Two new clades were defined, one of which displayed a rapid increase in comparison to the previous version of the Nextstrain build. This rapid increase could be attributed to the unauthorized application of an isolate of ToBRFV as a cross-protection product. Further analysis of the test results of positive samples from tomato production sites suggests that both deliberate application and accidental introduction had occurred. This report introduces the inclusion of 61 new (near) complete ToBRFV genomes in version three of the Nextstrain build, available from https://nextstrain.nrcnvwa.nl/ToBRFV/20220412. [Figure: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.https://apsjournals.apsnet.org/doi/10.1094/PHYTOFR-09-22-0090-Across-protectionepidemiologygenomicsplant virologytrack and trace |
| spellingShingle | Marleen Botermans Pier P. M. de Koning Carla Oplaat Aimee R. Fowkes Sam McGreig Anna Skelton Ian P. Adams Adrian Fox Kris De Jonghe Jill E. Demers Johanna W. Roenhorst Marcel Westenberg Bart T. L. H. van de Vossenberg Tomato Brown Rugose Fruit Virus Nextstrain Build Version 3: Rise of a Novel Clade PhytoFrontiers cross-protection epidemiology genomics plant virology track and trace |
| title | Tomato Brown Rugose Fruit Virus Nextstrain Build Version 3: Rise of a Novel Clade |
| title_full | Tomato Brown Rugose Fruit Virus Nextstrain Build Version 3: Rise of a Novel Clade |
| title_fullStr | Tomato Brown Rugose Fruit Virus Nextstrain Build Version 3: Rise of a Novel Clade |
| title_full_unstemmed | Tomato Brown Rugose Fruit Virus Nextstrain Build Version 3: Rise of a Novel Clade |
| title_short | Tomato Brown Rugose Fruit Virus Nextstrain Build Version 3: Rise of a Novel Clade |
| title_sort | tomato brown rugose fruit virus nextstrain build version 3 rise of a novel clade |
| topic | cross-protection epidemiology genomics plant virology track and trace |
| url | https://apsjournals.apsnet.org/doi/10.1094/PHYTOFR-09-22-0090-A |
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