Acknowledgement
This work was carried out with the support of Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ014947032024) Rural Development Administration, Republic of Korea.
References
- Adams, I. P., Glover, R. H., Monger, W. A., Mumford, R., Jackeviciene, E., Navalinskiene, M., Samuitiene, M. and Boonham, N. 2009. Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol. Plant Pathol. 10:537-545. https://doi.org/10.1111/j.1364-3703.2009.00545.x
- Ahmad, M., Padder, B. and Shah, M. D. 2023. Major viruses infecting temperate fruit crops and their impact on the fruit industry. In: Industrial applications of soil microbes, eds. by A. Gupta, S. Jain and N. Verma, Vol. 4. Bentham Science Publishers.
- Al Rwahnih, M., Daubert, S., Golino, D. and 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. https://doi.org/10.1016/j.virol.2009.02.028
- Aparicio, F., Pallas, V. and Sanchez-Navarro, J. 2010. Implication of the C terminus of the prunus necrotic ringspot virus movement protein in cell-to-cell transport and in its interaction with the coat protein. J. Gen. Virol. 91:1865-1870. https://doi.org/10.1099/vir.0.019950-0
- Bernard, H., Faber, M., Wilking, H., Haller, S., Hohle, M., Schielke, A., Ducomble, T., Siffczyk, C., Merbecks, S. S., Fricke, G., Hamouda, O., Stark, K., Werber, D. and Outbreak Investigation Team 2014. Large multistate outbreak of norovirus gastroenteritis associated with frozen strawberries, Germany, 2012. Eurosurveillance 19:pii=20719.
- Brazelton, C. 2013. World blueberry acreage and production. Folsom: USHBC 353:880-886.
- Bristow, P. R. and Martin, R. R. 1999. Transmission and the role of honeybees in field spread of blueberry shock ilarvirus, a pollen-borne virus of highbush blueberry. Phytopathology 89:124-130. https://doi.org/10.1094/PHYTO.1999.89.2.124
- Bujarski, J., Gallitelli, D., Garcia-Arenal, F., Pallas, V., Palukaitis, P., Reddy, M. K., Wang, A. and ICTV Report Consortium. 2019. ICTV virus taxonomy profile: Bromoviridae. J. Gen. Virol. 100:1206-1207. https://doi.org/10.1099/jgv.0.001282
- Caglayan, K., Ulubas-Serce, C., Gazel, M. and Varveri, C. 2011. Prune dwarf virus. In: Virus and virus-like diseases of pome and stone fruits, eds. by A. Hadidi, M. Barba, T. Candresse and W. Jelkmann, pp. 199-205. American Phytopathological Society, St. Paul, MN, USA.
- Collier, M. G., Khudyakov, Y. E., Selvage, D., Adams-Cameron, M., Epson, E., Cronquist, A., Jervis, R. H., Lamba, K., Kimura, A. C., Sowadsky, R., Hassan, R., Park, S. Y., Garza, E., Elliott, A. J., Rotstein, D. S., Beal, J., Kuntz, T., Lance, S. E., Dreisch, R., Wise, M. E., Nelson, N. P., Suryaprasad, A., Drobeniuc, J., Holmberg, S. D., Xu, F. and Hepatitis A Outbreak Investigation Team. 2014. Outbreak of hepatitis a in the USA associated with frozen pomegranate arils imported from turkey: an epidemiological case study. Lancet Infect. Dis. 14:976-981. https://doi.org/10.1016/S1473-3099(14)70883-7
- Czotter, N., Molnar, J., Szabo, E., Demian, E., Kontra, L., Baksa, I., Szittya, G., Kocsis, L., Deak, T., Bisztray, G., Tusnady, G. E., Burgyan, J. and Varallyay, E. 2018. NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of hungarian vineyards. Front. Microbiol. 9:122.
- de Souza Grilo, M. M., de Souza Pedrosa, G. T., da Silva, R. T., Campagnollo, F. B., Schaffner, D. W. and Magnani, M. 2022. Transfer of MS2 bacteriophage from surfaces to raspberry and pitanga fruits and virus survival in response to sanitization, frozen storage and preservation technologies. Food Microbiol. 104:103995.
- Food and Agriculture Organization. 2022. The state of agricultural commodity markets. The geography of food and agricultural trade: policy approaches for sustainable development. Food and Agriculture Organization, Rome, Italy. 108 pp.
- FAOSTAT. 2022. Production: crop. Blueberry. Food and Agriculture Organization of the United Nations. URL https://www. fao.org/faostat [9 June 2024].
- Fiore, N., Zamorano, A., Pino, A., Gonzalez, F., Rosales, I., Sanchez-Navarro, J. A. and Pallas Benet, V. 2016. Survey of stone fruit viruses and viroids in chile. J. Plant Pathol. 98:631-635.
- Fitzpatrick, A. H., Rupnik, A., O'Shea, H., Crospie, F., Keaveney, S. and Cotter, P. 2021. High throughput sequencing for the detection and characterization of RNA viruses. Front. Microbiol. 12:621719.
- Forney, C. F. and Kalt, W. 2011. Blueberry and cranberry. In: Health-promoting properties of fruit and vegetables, ed. by L. A. Terry, pp. 51-73. CABI, Wallingford, UK.
- Fulton, R. W. 1966. Mechanical transmission of viruses of woody plants. Annu. Rev. Phytopathol. 4:79-98. https://doi.org/10.1146/annurev.py.04.090166.000455
- Gallardo, R. K., Zhang, Q., Dossett, M., Polashock, J. J., Rodriguez-Saona, C., Vorsa, N., Edger, P. P., Ashrafi, H., Babiker, E., Finn, C. E. and Iorizzo, M. 2018. Breeding trait priorities of the blueberry industry in the United States and Canada. HortScience 53:1021-1028. https://doi.org/10.21273/HORTSCI12964-18
- Gottula, J., Cox, K., Carroll, J. and Fuchs, M. F. 2012. Blueberry shock disease. URL https://ecommons.cornell.edu/server/api/core/bitstreams/50d73ab5-f9b7-48f7-ac8c-99503b85b973/content [9 June 2024].
- Hadidi, A., Barba, M., Candresse, T. and Jelkmann, W. 2011. Virus and virus-like diseases of pome and stone fruits. American Phytopathological Society, St. Paul, MN, USA. 429 pp.
- Hamza, I. A., Jurzik, L., uberla, K. and Wilhelm, M. 2011. Evaluation of pepper mild mottle virus, human picobirnavirus and torque teno virus as indicators of fecal contamination in river water. Water Res. 45:1358-1368. https://doi.org/10.1016/j.watres.2010.10.021
- International Plant Protection Convention. 2009. International stnadards for phytosanitary measures. Categorization of commodities according to their pest risk, ISPM No. 32. Food and Agriculture Organization, Rome, Italy. 15 pp.
- Jelkmann, W. 1995. Cherry virus A: cDNA cloning of dsRNA, nucleotide sequence analysis and serology reveal a new plant capillovirus in sweet cherry. J. Gen. Virol. 76:2015-2024. https://doi.org/10.1099/0022-1317-76-8-2015
- Jo, Y., Lian, S., Chu, H., Cho, J. K., Yoo, S.-H., Choi, H., Yoon, J.-Y., Choi, S.-K., Lee, B. C. and Cho, W. K. 2018. Peach RNA viromes in six different peach cultivars. Sci. Rep. 8:1844.
- Jones, R. A. C. 2021. Global plant virus disease pandemics and epidemics. Plants 10:233.
- Jones, R. A. C. and Naidu, R. A. 2019. Global dimensions of plant virus diseases: current status and future perspectives. Annu. Rev. Virol. 6:387-409. https://doi.org/10.1146/annurev-virology-092818-015606
- Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Meintjes, P. and Drummond, A. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647-1649. https://doi.org/10.1093/bioinformatics/bts199
- King, A. M. Q., Adams, M. J., Carstens, E. B. and Lefkowitz, E. J. 2012. Virus taxonomy: ninth report of the International Committee on Taxonomy of Viruses. Academic Press, London, UK. 1327 pp.
- Kumar, S., Stecher, G., Li, M., Knyaz, C. and Tamura, K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35:1547-1549. https://doi.org/10.1093/molbev/msy096
- Lee, H.-J. and Jeong, R.-D. 2022. Metatranscriptomic analysis of plant viruses in imported pear and kiwifruit pollen. Plant Pathol. J. 38:220-228. https://doi.org/10.5423/PPJ.OA.03.2022.0047
- Marais, A., Candresse, T., Svanella-Dumas, L. and Jelkmann, W. 2011. Cherry virus A. In: Virus and virus-like diseases of pome and stone fruits, eds. by A. Hadidi, M. Barba, T. Candresse and W. Jelkmann, pp. 147-150. American Phytopathological Society, St. Paul, MN, USA.
- Maree, H. J., Fox, A., Al Rwahnih, M., Boonham, N. and Candresse, T. 2018. Application of HTS for routine plant virus diagnostics: state of the art and challenges. Front. Plant Sci. 9:1082.
- Martin, R. R., Constable, F. and Tzanetakis, I. E. 2016. Quarantine regulations and the impact of modern detection methods. Annu. Rev. Phytopathol. 54:189-205. https://doi.org/10.1146/annurev-phyto-080615-100105
- Martin, R. R., Polashock, J. J. and Tzanetakis, I. E. 2012. New and emerging viruses of blueberry and cranberry. Viruses 4:2831-2852. https://doi.org/10.3390/v4112831
- Matsumura, E. E., Coletta-Filho, H. D., Nouri, S., Falk, B. W., Nerva, L., Oliveira, T. S., Dorta, S. O. and Machado, M. A. 2017. Deep sequencing analysis of RNAs from citrus plants grown in a citrus sudden death-affected area reveals diverse known and putative novel viruses. Viruses 9:92.
- Mehle, N., Gutierrez-Aguirre, I., Kutnjak, D. and Ravnikar, M. 2018. Water-mediated transmission of plant, animal, and human viruses. Adv. Virus Res. 101:85-128. https://doi.org/10.1016/bs.aivir.2018.02.004
- Nasheri, N., Vester, A. and Petronella, N. 2019. Foodborne viral outbreaks associated with frozen produce. Epidemiol. Infect. 147:e291.
- Neto, C. C. 2007. Cranberry and blueberry: evidence for protective effects against cancer and vascular diseases. Mol. Nutr. Food Res. 51:652-664. https://doi.org/10.1002/mnfr.200600279
- Oshlack, A. and Wakefield, M. J. 2009. Transcript length bias in RNA-seq data confounds systems biology. Biol. Direct 4:14.
- Patel, S. 2014. Blueberry as functional food and dietary supplement: the natural way to ensure holistic health. Mediterr. J. Nutr. Metab. 7:133-143. https://doi.org/10.3233/MNM-140013
- Prado, T., Shubo, T., Freitas, L., Leomil, L., Maranhao, A. G. and Miagostovich, M. P. 2022. Virome in roof-harvested rainwater of a densely urbanized low-income region. Sci. Total Environ. 807:150778.
- Retamales, J. B., Palma, M. J., Morales, Y. A., Lobos, G. A., Moggia, C. E. and Mena, C. A. 2014. Blueberry production in Chile: current status and future developments. Rev. Bras. Frutic. 36:58-67. https://doi.org/10.1590/0100-2945-446/13
- Rispens, J. R., Freeland, A., Wittry, B., Kramer, A., Barclay, L., Vinje, J., Treffiletti, A. and Houston, K. 2020. Notes from the field: multiple cruise ship outbreaks of norovirus associated with frozen fruits and berries-United States, 2019. MMWR Morb. Mortal. Wkly. Rep. 69:501-502. https://doi.org/10.15585/mmwr.mm6916a3
- Saad, N., Olmstead, J. W., Jones, J. B., Varsani, A. and Harmon, P. F. 2021. Known and new emerging viruses infecting blueberry. Plants 10:2172.
- Santini, A., Liebhold, A., Migliorini, D. and Woodward, S. 2018. Tracing the role of human civilization in the globalization of plant pathogens. ISME J. 12:647-652. https://doi.org/10.1038/s41396-017-0013-9
- Sastry, K. S. and Zitter, T. A. 2014. Management of virus and viroid diseases of crops in the tropics. In: Plant virus and viroid diseases in the tropics. Vol. 2. Epidemiology and management, eds. by K. S. Sastry and T. A. Zitter, pp. 149-480. Springer, Dordrecht, Netherlands.
- Smith, I. M., Dunez, J., Phillips, D. H., Lelliott, R. A. and Archer, S. A. 2009. European handbook of plant diseases. John Wiley & Sons, Oxford, UK. 598 pp.
- Sutic, D. D., Ford, R. E. and Tosic, M. T. 1999. Handbook of plant virus diseases. CRC Press, Boca Raton, CA, USA. 584 pp.
- Tahzima, R., Foucart, Y., Peusens, G., Belien, T., Massart, S. and De Jonghe, K. 2019. High-throughput sequencing assists studies in genomic variability and epidemiology of little cherry virus 1 and 2 infecting Prunus spp. in Belgium. Viruses 11:592.
- Thresh, J. M. 2006. Crop viruses and virus diseases: a global perspective. In: Virus diseases and crop biosecurity, eds. by I. Cooper, T. Kuhne and V. P. Polishchuk. Springer Netherlands, Dordrecht, Netherlands. pp. 9-32.
- Tricase, C., Rana, R., Andriano, A. M. and Ingrao, C. 2017. An input flow analysis for improved environmental sustainability and management of cherry orchards: a case study in the Apulia region. J. Clean. Prod. 156:766-774. https://doi.org/10.1016/j.jclepro.2017.04.088
- United States Department of Agriculture. 2022. Fresh peach and cherries: world markets and trade. URL https://usda.library.cornell.edu/concern/publications/0g354f20t?locale=en [9 June 2024].
- Uyemoto, J. K. and Scott, S. W. 1992. Important diseases of Prunus caused by viruses and other graft-transmissible pathogens in California and South Carolina. Plant Dis. 76:5-11. https://doi.org/10.1094/PD-76-0005
- Verhoef, L., Hewitt, J., Barclay, L., Ahmed, S. M., Lake, R., Hall, A. J., Lopman, B., Kroneman, A., Vennema, H., Vinje, J. and Koopmans, M. 2015. Norovirus genotype profiles associated with foodborne transmission, 1999-2012. Emerg. Infect Dis. 21:592-599. https://doi.org/10.3201/eid2104.141073
- Villacres, J. F. and Cheein, F. A. 2020. Detection and characterization of cherries: a deep learning usability case study in Chile. Agronomy 10:835.
- Villamor, D. E. V., Pillai, S. S. and Eastwell, K. C. 2017. High throughput sequencing reveals a novel fabavirus infecting sweet cherry. Arch. Virol. 162:811-816. https://doi.org/10.1007/s00705-016-3141-z
- Von Braun, J. and Diaz-Bonilla, E. 2008. Globalization of food and agriculture and the poor. International Food Policy Research Institute, Washington, DC, USA. 6 pp.
- Wani, A. A., Singh, P., Gul, K., Wani, M. H. and Langowski, H. C. 2014. Sweet cherry (Prunus avium): critical factors affecting the composition and shelf life. Food Packag. Shelf Life 1:86-99. https://doi.org/10.1016/j.fpsl.2014.01.005
- Wright, A. A., Cross, A. R. and Harper, S. J. 2020. A bushel of viruses: identification of seventeen novel putative viruses by RNA-seq in six apple trees. PLoS ONE 15:e0227669.
- Zhao, Y., Li, M.-C., Konate, M. M., Chen, L., Das, B., Karlovich, C., Williams, P. M., Evrard, Y. A., Doroshow, J. H. and McShane, L. M. 2021. TPM, FPKM, or normalized counts? A comparative study of quantification measures for the analysis of RNA-seq data from the NCI patient-derived models repository. J. Transl. Med. 19:269.
- Zong, X., Wang, W., Wei, H., Wang, J., Yan, X., Hammond, R. W. and Liu, Q. 2015. Incidence of sweet cherry viruses in Shandong province, China and a case study on multiple infection with five viruses. J. Plant Pathol. 97:61-68.