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The impact of high throughput sequencing on plant health diagnostics

European Journal of Plant Pathology volume 152, pages 909–919 (2018)Cite this article

Abstract

High throughput sequencing informed diagnostics is revolutionising plant pathology. The application of this technology is most advanced in plant virology, where it is already becoming a front-line diagnostic tool and it is envisaged that for other types of pathogen and pests this will be the case in the near future. However, there are implications to deploying this technology due to a number of technical and scientific challenges. Firstly, interpretation of data and the assessment of plant health risk against a limited baseline of existing knowledge of the presence of pathogens in a given geographic region. Secondly, evidence of causality and the separation of pathogenic from commensal organisms in the sequence data, thirdly, the tension between the generation of a rapid sequence result with the necessary but laborious epidemiological characterisation in support of plant health risk assessment. Finally, the validation and accreditation of methods based on this rapidly evolving technology. These in turn present challenges for plant health policy and regulation. This review discusses the development of this technology, its application in plant health diagnostics, and explores the implications of applying this technology in the plant health setting.

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References

  • Abdelfattah, A., Li Destri Nicosia, M. G., Cacciola, S. O., Droby, S., & Schena, L. (2015). Metabarcoding analysis of fungal diversity in the Phyllosphere and Carposphere of olive (Olea europaea). PLoS One, 10, e0131069.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Adams, I. P., Glover, R. H., Monger, W. A., et al. (2009). Next-generation sequencing and metagenomic analysis: A universal diagnostic tool in plant virology. Molecular Plant Pathology, 10, 537–545.

    Article  CAS  PubMed  Google Scholar 

  • Adams, I. P., Glover, R. H., Monger, W. A., et al. (2011). Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant pathology. In F. J. De Bruijn (Ed.), Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats (pp. 63–71). New York: Wiley.

    Chapter  Google Scholar 

  • Adams, I. P., Miano, D. W., Kinyua, Z. M., Wangai, A., Kimani, E., Phiri, N., Reeder, R., Harju, V., Glover, R., Hany, U., Souza-Richards, R., Deb Nath, P., Nixon, T., Fox, A., Barnes, A., Smith, J., Skelton, A., Thwaites, R., Mumford, R., & Boonham, N. (2013). Use of next-generation sequencing for the identification and characterization of Maize chlorotic mottle virus and sugarcane mosaic virus causing maize lethal necrosis in Kenya. Plant Pathology, 62, 741–749.

    Article  CAS  Google Scholar 

  • Adams IP, Harju VA, Hodges T, Hany U, Skelton A, Rai S, Deka MK, Smith J, Fox A, Uzayisenga B, Ngaboyisonga C, Uwumukiza B, Rutikanga A, Rutherford M, Ricthis B, Phiri N, Boonham N, (2014a). First report of maize lethal necrosis disease in Rwanda. New Disease Reports 29. 22.

  • Adams, I. P., Skelton, A., Macarthur, R., Hodges, T., Hinds, H., Flint, L., Nath, P. D., Boonham, N., & Fox, A. (2014b). Carrot yellow leaf virus is associated with carrot internal necrosis. PLoS One, 9, e109125.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Afshinnekoo, E., Meydan, C., Chowdhury, S., Jaroudi, D., Boyer, C., Bernstein, N., Maritz, J. M., Reeves, D., Gandara, J., Chhangawala, S., Ahsanuddin, S., Simmons, A., Nessel, T., Sundaresh, B., Pereira, E., Jorgensen, E., Kolokotronis, S. O., Kirchberger, N., Garcia, I., Gandara, D., Dhanraj, S., Nawrin, T., Saletore, Y., Alexander, N., Vijay, P., Hénaff, E. M., Zumbo, P., Walsh, M., O’Mullan, G. D., Tighe, S., Dudley, J. T., Dunaif, A., Ennis, S., O’Halloran, E., Magalhaes, T. R., Boone, B., Jones, A. L., Muth, T. R., Paolantonio, K. S., Alter, E., Schadt, E. E., Garbarino, J., Prill, R. J., Carlton, J. M., Levy, S., & Mason, C. E. (2015a). Geospatial resolution of human and bacterial diversity with city-scale metagenomics. Cell Systems, 1, 72–87.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Afshinnekoo, E., Meydan, C., Chowdhury, S., Jaroudi, D., Boyer, C., Bernstein, N., Maritz, J. M., Reeves, D., Gandara, J., Chhangawala, S., Ahsanuddin, S., Simmons, A., Nessel, T., Sundaresh, B., Pereira, E., Jorgensen, E., Kolokotronis, S. O., Kirchberger, N., Garcia, I., Gandara, D., Dhanraj, S., Nawrin, T., Saletore, Y., Alexander, N., Vijay, P., Hénaff, E. M., Zumbo, P., Walsh, M., O’Mullan, G. D., Tighe, S., Dudley, J. T., Dunaif, A., Ennis, S., O’Halloran, E., Magalhaes, T. R., Boone, B., Jones, A. L., Muth, T. R., Paolantonio, K. S., Alter, E., Schadt, E. E., Garbarino, J., Prill, R. J., Carlton, J. M., Levy, S., & Mason, C. E. (2015b). Erratum: Geospatial resolution of human and bacterial diversity with City-scale metagenomics. Cell Systems, 1, 97–97.e3.

    Article  CAS  PubMed  Google Scholar 

  • Ahmed, M., Sapp, M., Prior, T., Karssen, G., & Back, M. (2015). Nematode taxonomy: From morphology to metabarcoding. SOIL Discuss., 2015, 1175–1220.

    Article  Google Scholar 

  • Al Rwahnih, M., Daubert, S., Golino, D., & Rowhani, A. (2009). Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Virology, 387, 395–401.

    Article  CAS  PubMed  Google Scholar 

  • Al Rwahnih, M., Daubert, S., Golino, D., Islas, C., & Rowhani, A. (2015). Comparison of next-generation sequencing versus biological indexing for the optimal detection of viral pathogens in grapevine. Phytopathology, 105, 758–763.

    Article  CAS  PubMed  Google Scholar 

  • An, J. H., Noh, Y. H., Kim, Y. E., Lee, H. I., & Cha, J. S. (2015). Development of PCR and TaqMan PCR assays to detect Pseudomonas coronafaciens, a causal agent of halo blight of oats. Plant Pathology Journal, 31, 25–32.

    Article  CAS  PubMed  Google Scholar 

  • Anderson, P. K., Cunningham, A. A., Patel, N. G., Morales, F. J., Epstein, P. R., & Daszak, P. (2004). Emerging infectious diseases of plants: Pathogen pollution, climate change and agrotechnology drivers. Trends in Ecology & Evolution, 19, 535–544.

    Article  Google Scholar 

  • Baker, R. H. A., Anderson, H., Bishop, S., Macleod, A., Parkinson, N., & Tuffen, M. G. (2014). The UK Plant health risk register: A tool for prioritizing actions. EPPO Bulletin, 44, 187–194.

    Article  Google Scholar 

  • Barba, M., Czosnek, H., & Hadidi, A. (2014). Historical perspective, development and applications of next-generation sequencing in plant virology. Viruses, 6, 106–136.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bonants, P. J. M., Gent-Pelzer, M. P. E., Leeuwen, G. C. M., & Lee, T. J. (2015). A real-time TaqMan PCR assay to discriminate between pathotype 1 (D1) and non-pathotype 1 (D1) isolates of Synchytrium endobioticum. European Journal of Plant Pathology, 143, 495–506.

    Article  CAS  Google Scholar 

  • Buée, M., Reich, M., Murat, C., et al. (2009). 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytologist, 184, 449–456.

    Article  CAS  PubMed  Google Scholar 

  • Bühlmann, A., Pothier, J., Tomlinson, J., et al. (2013a). Genomics-informed design of loop-mediated isothermal amplification for detection of phytopathogenic Xanthomonas arboricola pv. Pruni at the intraspecific level. Plant Pathology, 62, 475–484.

    Article  CAS  Google Scholar 

  • Bühlmann, A., Pothier, J. F., Rezzonico, F., Smits, T. H. M., Andreou, M., Boonham, N., Duffy, B., & Frey, J. E. (2013b). Erwinia amylovora loop-mediated isothermal amplification (LAMP) assay for rapid pathogen detection and on-site diagnosis of fire blight. Journal of Microbiological Methods, 92, 332–339.

    Article  CAS  PubMed  Google Scholar 

  • Burns, K. N., Kluepfel, D. A., Strauss, S. L., Bokulich, N. A., Cantu, D., & Steenwerth, K. L. (2015). Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features. Soil Biology and Biochemistry, 91, 232–247.

    Article  CAS  Google Scholar 

  • Chen, P., Jeannotte, R., & Weimer, B. C. (2014). Exploring bacterial epigenomics in the next-generation sequencing era: A new approach for an emerging frontier. Trends in Microbiology, 22, 292–300.

    Article  CAS  PubMed  Google Scholar 

  • Cox-Foster, D. L., Conlan, S., Holmes, E. C., Palacios, G., Evans, J. D., Moran, N. A., Quan, P. L., Briese, T., Hornig, M., Geiser, D. M., Martinson, V., vanEngelsdorp, D., Kalkstein, A. L., Drysdale, A., Hui, J., Zhai, J., Cui, L., Hutchison, S. K., Simons, J. F., Egholm, M., Pettis, J. S., & Lipkin, W. I. (2007). A metagenomic survey of microbes in honey bee colony collapse disorder 99. Science, 318, 283–287.

    Article  CAS  PubMed  Google Scholar 

  • Cunniffe, N. J., Cobb, R. C., Meentemeyer, R. K., Rizzo, D. M., & Gilligan, C. A. (2016). Modeling when, where, and how to manage a forest epidemic, motivated by sudden oak death in California. Proceedings of the National Academy of Sciences, 113, 5640–5645.

    Article  CAS  Google Scholar 

  • Dahal, G., Hughes, J. D. A., Thottappilly, G., & Lockhart, B. (1998). Effect of temperature on symptom expression and reliability of banana streak badnavirus detection in naturally infected plantain and banana (Musa spp.). Plant Disease, 82, 16–21.

    Article  CAS  PubMed  Google Scholar 

  • De Clerck, C., Crew, K., Mcmichael, L., et al. (2017). Lessons learned from the virus indexing of Musa germplasm: Insights from a multiyear collaboration. Annals of Applied Biology, 171, 15–27.

    Article  Google Scholar 

  • Duan, Y., Zhou, L., Hall, D. G., Li, W., Doddapaneni, H., Lin, H., Liu, L., Vahling, C. M., Gabriel, D. W., Williams, K. P., Dickerman, A., Sun, Y., & Gottwald, T. (2009). Complete genome sequence of Citrus Huanglongbing bacterium, ‘Candidatus Liberibacter asiaticus’ obtained through metagenomics. Molecular Plant-Microbe Interactions, 22, 1011–1020.

    Article  CAS  PubMed  Google Scholar 

  • Evans, A. S. (1976). Causation and disease: The Henle-Koch postulates revisited. The Yale Journal of Biology and Medicine, 49, 175–195.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Eyre, D. W., Cule, M. L., Wilson, D. J., Griffiths, D., Vaughan, A., O'Connor, L., Ip, C. L. C., Golubchik, T., Batty, E. M., Finney, J. M., Wyllie, D. H., Didelot, X., Piazza, P., Bowden, R., Dingle, K. E., Harding, R. M., Crook, D. W., Wilcox, M. H., Peto, T. E. A., & Walker, A. S. (2013). Diverse sources of C. Difficile infection identified on whole-genome sequencing. New England Journal of Medicine, 369, 1195–1205.

    Article  CAS  PubMed  Google Scholar 

  • Fox, A., & Mumford, R. (2017). Plant viruses and viroids in the United Kingdom: An analysis of first detections and novel discoveries from 1980 to 2014. Virus Research, 241, 10–18.

    Article  CAS  PubMed  Google Scholar 

  • Fox, A., Adams, I., Hany, U., et al. (2015). The application of next-generation sequencing for screening seeds for viruses and viroids. Seed Science and Technology, 43, 531–535.

    Article  Google Scholar 

  • Fox A, Fowkes A, Buxton-Kirk A, et al., (2016). First report of Potato aucuba mosaic virus in Solanum jasminoides in the United Kingdom. New Disease Reports 34, 32.

  • Frampton, G. M., Fichtenholtz, A., Otto, G. A., Wang, K., Downing, S. R., He, J., Schnall-Levin, M., White, J., Sanford, E. M., An, P., Sun, J., Juhn, F., Brennan, K., Iwanik, K., Maillet, A., Buell, J., White, E., Zhao, M., Balasubramanian, S., Terzic, S., Richards, T., Banning, V., Garcia, L., Mahoney, K., Zwirko, Z., Donahue, A., Beltran, H., Mosquera, J. M., Rubin, M. A., Dogan, S., Hedvat, C. V., Berger, M. F., Pusztai, L., Lechner, M., Boshoff, C., Jarosz, M., Vietz, C., Parker, A., Miller, V. A., Ross, J. S., Curran, J., Cronin, M. T., Stephens, P. J., Lipson, D., & Yelensky, R. (2013). Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nature Biotechnology, 31, 1023–1031.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fredericks, D. N., & Relman, D. A. (1996). Sequence-based identification of microbial pathogens: A reconsideration of Koch's postulates. Clinical Microbiology Reviews, 9, 18–33.

    Article  PubMed Central  Google Scholar 

  • Hayden, E. (2014). Technology: The $1,000 genome. Nature, 507, 294–295.

    Article  CAS  PubMed  Google Scholar 

  • Hill, A. (1965). The Envrionment and disease: Association or causation? Proceedings of the Royal Society of Medicine, 58, 295–300.

    Article  CAS  Google Scholar 

  • Hubbard, A., Lewis, C. M., Yoshida, K., Ramirez-Gonzalez, R. H., de Vallavieille-Pope, C., Thomas, J., Kamoun, S., Bayles, R., Uauy, C., & Saunders, D. (2015). Field pathogenomics reveals the emergence of a diverse wheat yellow rust population. Genome Biology, 16, 23.

    Article  PubMed  PubMed Central  Google Scholar 

  • Jagger, I. C., & Chandler, N. (1934). Big vein, a disease of lettuce. Phytopathology, 24, 1253–1256.

    Google Scholar 

  • Jones, D. R., & Baker, R. H. A. (2007). Introductions of non-native plant pathogens into Great Britain, 1970–2004. Plant Pathology, 56, 891–910.

    Article  Google Scholar 

  • Kreuze, J. F., Perez, A., Untiveros, M., Quispe, D., Fuentes, S., Barker, I., & Simon, R. (2009). Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses. Virology, 388, 1–7.

    Article  CAS  PubMed  Google Scholar 

  • Kuwata, S., Kubo, S., Yamashita, S., & Doi, Y. (1983). Rod-shaped particles, a probable entity of lettuce big vein virus. Annals of the Phytopathological Society of Japan, 49, 246–251.

    Article  Google Scholar 

  • Land, M., Hauser, L., Jun, S.-R., Nookaew, I., Leuze, M. R., Ahn, T. H., Karpinets, T., Lund, O., Kora, G., Wassenaar, T., Poudel, S., & Ussery, D. W. (2015). Insights from 20 years of bacterial genome sequencing. Functional & Integrative Genomics, 15, 141–161.

    Article  CAS  Google Scholar 

  • Leboldus, J. M., Kinzer, K., Richards, J., Ya, Z., Yan, C., Friesen, T. L., & Brueggeman, R. (2015). Genotype-by-sequencing of the plant-pathogenic fungi Pyrenophora teres and Sphaerulina musiva utilizing ion torrent sequence technology. Molecular Plant Pathology, 16, 623–632.

    Article  CAS  PubMed  Google Scholar 

  • Lot, H., Campbell, R. N., Souche, S., Milne, R. G., & Roggero, P. (2002). Transmission by Olpidium brassicae of Mirafiori lettuce virus and lettuce big-vein virus, and their roles in lettuce big-vein etiology. Phytopathology, 92, 288–293.

    Article  PubMed  Google Scholar 

  • Luvisi, A., Ampatzidis, Y. G., & De Bellis, L. (2016). Plant pathology and information technology: Opportunity for management of disease outbreak and applications in regulation frameworks. Sustainability, 8, 831.

    Article  Google Scholar 

  • Macdiarmid, R., Rodoni, B., Melcher, U., Ochoa-Corona, F., & Roossinck, M. (2013). Biosecurity implications of new technology and discovery in plant virus research. PLoS Pathogens, 9, e1003337.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mahuku, G., Lockhart, B. E., Wanjala, B., Jones, M. W., Kimunye, J. N., Stewart, L. R., Cassone, B. J., Sevgan, S., Nyasani, J. O., Kusia, E., Kumar, P. L., Niblett, C. L., Kiggundu, A., Asea, G., Pappu, H. R., Wangai, A., Prasanna, B. M., & Redinbaugh, M. G. (2015). Maize lethal necrosis (MLN), an emerging threat to maize-based food security in sub-Saharan Africa. Phytopathology, 105, 956–965.

    Article  PubMed  Google Scholar 

  • Malapi-Wight M, Salgado-Salazar C, Demers J, Clement DL, Rane K, Crouch JA, (2016). Sarcococca Blight: use of whole genome sequencing for fungal plant disease diagnosis. Plant Disease 100, 1093–1100.

  • Massart, S., Olmos, A., Jijakli, H., & Candresse, T. (2014). Current impact and future directions of high throughput sequencing in plant virus diagnostics. Virus Research, 188, 90–96.

    Article  CAS  PubMed  Google Scholar 

  • Massart S, Candresse T, Gil J, et al., 2017. A framework for the evaluation of biosecurity, commercial, regulatory, and scientific impacts of plant viruses and Viroids identified by NGS technologies. Frontiers in microbiology 8. 45.

  • Mastin, A. J., Van Den Bosch, F., Gottwald, T. R., Chavez, V. A., & Parnell, S. R. (2017). A method of determining where to target surveillance efforts in heterogeneous epidemiological systems. PLoS Computational Biology, 13, e1005712.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mattocks, C. J., Morris, M. A., Matthijs, G., et al. (2010). A standardized framework for the validation and verification of clinical molecular genetic tests. European Journal of Human Genetics, 18, 1276–1288.

    Article  PubMed  PubMed Central  Google Scholar 

  • Mccourt, C. M., Mcart, D. G., Mills, K., et al. (2013). Validation of next generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis. PLoS One, 8, e69604.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mumford, R., Macarthur, R., & Boonham, N. (2016). The role and challenges of new diagnostic technology in plant biosecurity. Food Security, 8, 103–109.

    Article  Google Scholar 

  • Nicolaisen, M., West, J. S., Sapkota, R., Canning, G. G., Schoen, C., & Justesen, A. F. (2017). Fungal communities including plant pathogens in near surface air are similar across northwestern Europe. Frontiers in Microbiology, 8, 1729.

    Article  PubMed  PubMed Central  Google Scholar 

  • Oepp/Eppo. (2007). PM 7/84 basic requirements for quality management in plant pest diagnosis laboratories. Bulletin OEPP/EPPO Bulletin, 37, 580–588.

    Article  Google Scholar 

  • Oepp/Eppo. (2014). PM7/98 specific requirements for laboratories preparing accreditation for a plant pest diagnostic activity. Bulletin OEPP/EPPO Bulletin, 44, 117–147.

    Article  Google Scholar 

  • Palacios G, Druce J, Du L, et al., (2008). A new arenavirus in a cluster of fatal transplant-associated diseases. A New England Journal of Medicine, 358, 991–998.

  • Pritchard, L., Humphris, S., Saddler, G. S., Parkinson, N. M., Bertrand, V., Elphinstone, J. G., & Toth, I. K. (2013). Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences. Plant Pathology, 62, 587–596.

    Article  CAS  Google Scholar 

  • Rodoni, B. (2009). The role of plant biosecurity in preventing and controlling emerging plant virus disease epidemics. Virus Research, 141, 150–157.

    Article  CAS  PubMed  Google Scholar 

  • Roggero, P., Ciuffo, M., Vaira, A. M., Accotto, G. P., Masenga, V., & Milne, R. G. (2000). An Ophiovirus isolated from lettuce with big-vein symptoms. Archives of Virology, 145, 2629–2642.

    Article  CAS  PubMed  Google Scholar 

  • Roossinck, M. J. (2010). Lifestyles of plant viruses. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 365, 1899–1905.

    Article  PubMed  PubMed Central  Google Scholar 

  • Roossinck, M. J. (2013). Plant virus ecology. PLoS Pathogens, 9, e1003304.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rott, M., Xiang, Y., Boyes, I., Belton, M., Saeed, H., Kesanakurti, P., Hayes, S., Lawrence, T., Birch, C., Bhagwat, B., & Rast, H. (2017). Application of next generation sequencing for diagnostic testing of tree fruit viruses and viroids. Plant Disease, 101, 1489–1499.

    Article  CAS  PubMed  Google Scholar 

  • Salto-Tellez, M., & Gonzalez De Castro, D. (2014). Next-generation sequencing: A change of paradigm in molecular diagnostic validation. The Journal of Pathology, 234, 5–10.

    Article  PubMed  Google Scholar 

  • Sapp, M., Harrison, M., Hany, U., Charlton, A., & Thwaites, R. (2015). Comparing the effect of digestate and chemical fertiliser on soil bacteria. Applied Soil Ecology, 86, 1–9.

    Article  Google Scholar 

  • Schumpp O, Dupuis B, Bréchon A, Al. E, (2016). Diagnostic moléculaire à haut debit pour détecter les viroses des plants de pommes de terre. Recherche Agronomique Suisse, 7, 456–465.

  • Skelton A, Uzayisenga B, Fowkes A, et al., (2018). First report of pepper veinal mottle virus, pepper yellows virus and a novel enamovirus in chilli pepper (Capsicum sp.) in Rwanda. New Disease Reports 37, 5.

  • Talbot, N., Mccafferty, H., Ma, M., Moore, K., & Hamer, J. (1997). Nitrogen starvation of the rice blast fungusMagnaporthe griseamay act as an environmental cue for disease symptom expression. Physiological and Molecular Plant Pathology, 50, 179–195.

    Article  CAS  Google Scholar 

  • Thompson, R. N., Gilligan, C. A., & Cunniffe, N. J. (2018). Control fast or control smart: When should invading pathogens be controlled? PLoS Computational Biology, 14, e1006014.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Verbeek, M., Dullemans, A. M., Van Bekkum, P. J., & Van Der Vlugt, R. A. (2013). Evidence for lettuce big-vein associated virus as the causal agent of a syndrome of necrotic rings and spots in lettuce. Plant Pathology, 62, 444–451.

    Article  Google Scholar 

  • Yu, D. W., Ji, Y., Emerson, B. C., Wang, X., Ye, C., Yang, C., & Ding, Z. (2012). Biodiversity soup: Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution, 3, 613–623.

    Article  Google Scholar 

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Acknowledgements

The data presented on viruses in Kenyan farms was produced in collaboration with Francesca Stomeo, funded by the Swedish International Development Cooperation Agency (SIDA) through an award to the BecA-ILRI Hub. This publication is partially based upon work and exchanges carried out in the frame of COST Action FA1407 (DIVAS), supported by COST (European Cooperation in Science and Technology).This work has received support from the UK government Department for Environment, Food and Rural Affairs funded "future proofing plant health" project (PH0469).

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  1. Fera Science Ltd, Sand Hutton, York, YO41 1LZ, UK

    Ian P. Adams & Adrian Fox

  2. IAFRI, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE1 7RU, UK

    Neil Boonham

  3. Laboratory of Integrated and Urban Phytopathology, TERRA, Gembloux AgroBio Tech, Université de Liège, 5030, Gembloux, Belgium

    Sébastien Massart

  4. Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Burgemeester Van Gansberghelaan 96, 9820, Merelbeke, Belgium

    Kris De Jonghe

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  1. Ian P. Adams
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Adams, I.P., Fox, A., Boonham, N. et al. The impact of high throughput sequencing on plant health diagnostics. Eur J Plant Pathol 152, 909–919 (2018). https://doi.org/10.1007/s10658-018-1570-0

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Keywords

  • High throughput sequencing
  • NGS
  • Diagnostics
  • Validation
  • Accreditation