Quarantine Regulations and the Impact of Modern Detection Methods

Annual Review of Phytopathology

Volumn 54, Issue , 2016, Pages 189-205

  Martin, Robert R ^a   Constable, Fiona ^b   Tzanetakis, Ioannis E ^c  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b LA TROBE UNIVERSITY   (Australia)

^c UNIVERSITY OF ARKANSAS   (United States)

Author keywords

Bioassays; Biosecurity; International trade; Next generation sequencing; Pathogen detection

Indexed keywords

BIOLOGY; HIGH THROUGHPUT SEQUENCING; LEGISLATION AND JURISPRUDENCE; METAGENOMICS; MICROBIOLOGY; PARASITOLOGY; PLANT; PLANT DISEASE; QUARANTINE;

COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOMICS; PLANT DISEASES; PLANTS; QUARANTINE;

EID: 84981294932     PISSN: 00664286     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev-phyto-080615-100105     Document Type: Article

References (134)

1. Adams IP, Glover RH, Monger WA, Kemfor R, Jackerviceince E, et al. 2009. Next generation sequencing and metagenomics: a universal diagnostic tool in plant virology. Mol. Plant Pathol. 10:537-45
2. Adams MJ, Hendrickson RC, Dempsey DM, Lefkowitz EJ. 2015. Tracking the changes in virus taxonomy. Arch. Virol. 160:1375-83
3. Al Rwahnih M, Daubert S, Urbez-Torres JR, Cordero F, Rowhani A. 2011. Deep sequencing evidence from single grapevine plants reveals a virome dominated by mycoviruses. Arch. Virol. 156:397-403
4. 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 105:758-63
5. Altschul SF. 1991. Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol. 219:555-65
6. Anderson PK, Cunningham AA, Patel NG, Morales FJ, Epstein PR, Daszak P. 2004. Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers. Trends Ecol. Evol. 19:535-44
7. Bacon SJ, Aebi A, Calanca P, Bacher S. 2014. Quarantine arthropod invasions in Europe: the role of climate, hosts and propagule pressure. Divers. Distrib. 20:84-94
8. Bag S, Al Rwahnih M, Li A, Gonzalez A, Rowhani A, et al. 2015. Detection of a new luteovirus in imported nectarine trees: a case study to propose adoption of metagenomics in post-entry quarantine. Phytopathology 105:840-46
9. Barba M, Czosnek H, Hadidi A. 2014. Historical perspective, development and applications of nextgeneration sequencing in plant virology. Viruses 6:106-36
10. Barbisch D, Koenig KL, Shih FY. 2015. Is there a case for quarantine? Perspectives from SARS to Ebola. Disaster Med. Public Health Prep. 9:547-53
11. Beale R, Fairbrother J, Inglis A, Trebeck D. 2008. One biosecurity: a working partnership. Independent review of Australia's quarantine and biosecurity arrangements. Rep. Aust. Gov., Dep. Agric. Fish. For., Sydney
12. Bebber DP. 2015. Range-expanding pests and pathogens in a warming world. Annu. Rev. Phytopathol. 53:335-56
13. Bertazzon N, Angelini E. 2004. Advances in the detection of grapevine leafroll associated virus 2 variants. J. Plant Pathol. 86:283-90
14. Bertolini E, Teresani GR, Loiseau M, Tanaka FAO, Barbé S, et al. 2015. Transmission of "Candidatus Liberibacter solanacearum" in carrot seeds. Plant Pathol. 64:276-85
15. Blankenberg D, Kuster GV, Coraor N, Ananda G, Lazarus R, et al. 2010. Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol. 89:19.10:1-21
16. Boonham N, Kreuze J, Winter S, van der Vlugt R, Bergervoet J, et al. 2014. Methods in virus diagnostics: from ELISA to next generation sequencing. Virus Res. 186:20-31
17. Brasier CM. 2008. The biosecurity threat to the UK and global environment from international trade in plants. Plant Pathol. 57:792-808
18. Bull CT, Coutinho TA, Denny TP, Firrao G, Fischer-Le Saux M, et al. 2014. List of new names of plant pathogenic bacteria (2011-2012). J. Plant Pathol. 96:223-26
19. Bull CT, De Boer SH, Denny TP, Firrao G, Fischer-Le Saux M, et al. 2010. Comprehensive list of names of plant pathogenic bacteria, 1980-2007. J. Plant Pathol. 92:551-92
20. Bull CT, De Boer SH, Denny TP, Firrao G, Fischer-Le Saux M, et al. 2012. List of new names of plant pathogenic bacteria (2008-2010). J. Plant Pathol. 94:21-27
21. Bull CT, Koike ST. 2015. Practical benefits of knowing the enemy:modern molecular tools for diagnosing the etiology of bacterial diseases and understanding the taxonomy and diversity of plant-pathogenic bacteria. Annu. Rev. Phytopathol. 53:157-80
22. Candresse T, Filloux D, Muhire B, Julian C, Galzi S, et al. 2014. Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context. PLOS ONE 9:e102945
23. Chakraborty S, Newton AC. 2011. Climate change, plant diseases and food security: an overview. Plant Pathol. 60:2-14
24. Chamberlain CJ, Kraus J, Kohnen PD, Finn CE, Martin RR. 2003. First report of Raspberry bushy dwarf virus in Rubus multibracteatus from China. Plant Dis. 87:603
25. Chevalier S, Greiff C, Clauzel JM, Walter B, Fritsch C. 1995. Use of immunocapture-polymerase chain reaction procedure for the detection of grapevine virus A in Kober stem grooving-infected grapevines. J. Phytopathol. 143:369-73
26. Christensen NM, Nicolaisen M, Hansen M, Schultz A. 2004. Distribution of phytoplasmas in infected plants as revealed by real time PCR and bioimaging. Mol. Plant-Microbe Interact. 17:1175-84
27. Clark CA, Davis JA, Abad JA, Cuellar WJ, Fuentes S, et al. 2012. Sweetpotato viruses: 15 years of progress on understanding and managing complex diseases. Plant Dis. 96:168-85
28. Clark MF. 1981. Immunosorbent assays in plant pathology. Annu. Rev. Phytopathol. 19:83-106
29. Clark MF, Adams AN. 1977. Characteristics of themicroplatemethod of enzyme-linked immunosorbent assay for the detection of plant viruses. J. Gen. Virol. 34:475-83
30. Coetzee B, Freeborough MJ, Maree HJ, Celton JM, Rees DJ. 2010. Deep sequencing analysis of viruses infecting grapevines: the virome of a vineyard. Virology 400:157-63
31. Constable FE, Gibb KS, Symons RH. 2003. The seasonal distribution of phytoplasmas in Australian grapevines. Plant Pathol. 52:267-76
32. Constable FE, Connellan J, Nicholas P, Rodoni BC. 2013. The reliability ofwoody indexing for detection of grapevine virus-associated diseases in three different climatic conditions in Australia. Aust. J. Grape Wine Res. 19:74-80
33. Constable FE, Nancarrow N, Kelly G, Milinkovic M, Ko L, et al. 2016. Improved diagnostic testing and on farm biosecurity plan to support Australian strawberry certification programs. Acta Hortic. 1117:171-76
34. Crespo-Pérez V, Régnière J, Chuine I, Rebaudo F, Dangles O. 2015. Changes in the distribution of multispecies pest assemblages affect levels of crop damage in warming tropical Andes. Glob. Change Biol. 21:82-96
35. Crous PW, Hawksworth DL, Wingfield MJ. 2015. Identifying and naming plant-pathogenic fungi: past, present, and future. Annu. Rev. Phytopathol. 53:247-67
36. Dayhoff MO, Schwartz RM, Orcutt BC. 1978. A model of evolutionary change in proteins. Atlas Protein Seq. Struct. 5(Suppl. 3):345-52
37. Domier LL. 2012. Family Luteoviridae. In Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses, ed. AMQ King, MJ Adams, EB Carstens, EJ Lefkowitz, pp. 1045-53. New York: Elsevier
38. Dossett M, Bassil NV, Lewers KS, Finn CE. 2012. Genetic diversity in wild and cultivated black raspberry (Rubus occidentalis L.) evaluated by simple sequence repeat markers. Genet. Resour. Crop Evol. 59:1849-65
39. EPPO. 2014. PM 7/76 (3) Use of EPPO diagnostic protocols. EPPO Bull. 44:335-37
40. Fajardo TVM, Barros DR, Nickel O, Kuhn GB, Zerbini FM. 2007. Variability of the coat protein gene of Grapevine leafroll-associated virus 3 in Brazil. Fitopatol. Brasil. 32:335-40
41. FAO. 2004. Pest risk analysis for quarantine pests, including analysis or environmental risks and living modified organisms. Int. Stand. Phytosanit. Meas. Number 11, Food Agric. Organ., Rome
42. FAO. 2007. Framework for pest risk analysis. Int. Stand. Phytosanit. Meas. Number 2, Food Agric. Organ., Rome
43. Fletcher J, Stack J. 2007. Agricultural biosecurity: threats and impacts for plant pathogens. In Forum on Microbial Threats, pp. 86-94. Washington, D.C.: Natl. Acad. Press
44. Frost KE, Groves RL, Charkowski AO. 2013. Integrated control of potato pathogens through seed potato certification and provision of clean seed potatoes. Plant Dis. 97:1268-80
45. Fry WE, Birch PRJ, Judelson HS, Grünwald NJ, Danies G, et al. 2015. Five reasons to consider Phytophthora infestans a reemerging pathogen. Phytopathology 105:966-81
46. Geering ADW, Olszewski NE, Dahal G, Thomas JE, Lockhart BEL. 2001. Analysis of the distribution and structure of integrated Banana streak virus DNA in a range of Musa cultivars. Mol. Plant Pathol. 2:207-13
47. Geering ADW, Olszewski NE, Harper G, Lockhart BEL, Hull R, Thomas JE. 2005. Banana contains a diverse array of endogenous badnaviruses. J. Gen. Virol. 86:511-20
48. Gergerich RC, Welliver RA, Gettys S, Osterbauer NK, Kamenidou S, et al. 2015. Safeguarding fruit crops in the age of agricultural globalization. Plant Dis. 99:176-87
49. Gibbs A, Mackenzie A. 1997. A primer pair for amplifying part of the genome of all potyvirids by RT-PCR. J. Virol. Methods 63:9-16
50. Godfray HC, Beddington JR, Crute IR, Haddad L, Lawrence D, et al. 2010. Food security: the challenge of feeding 9 billion people. Science 327:812-18
51. Gugerli P. 2009. 25 years of serological identification of grapevine leafroll-associated viruses: antiserum and monoclonal antibodies to GLRaV-1 to GLRaV-9. ICVG 16:24-28
52. Gundersen DE, Lee I-M. 1996. Ultrasensitive detection of phytoplasmas by nested-PCR assays using two universal primer pairs. Phytopathol. Mediterr. 35:144-51
53. Ho T, Tzanetakis IE. 2014. Developing a virus detection and discovery pipeline using next generation sequencing. Virology 471-73:54-60
54. Hopkins D, Purcell A. 2002. Xylella fastidiosa: cause of Pierce's disease of grapevine and other emergent diseases. Plant Dis. 86:1056-66
55. Hsu HT, Franssen JM, van der Hulst CTC, Derks AFLM, Lawson RH. 1988. Factors affecting selection of epitope specificity of monoclonal antibodies to tulip breaking potyvirus. Phytopathology 78:1337-40
56. Hull R. 2013. Plant Virology. New York: Academic. 5th ed.
57. Huttinga H. 1996. Sensitivity of indexing procedures for viruses and viroids. Adv. Bot. Res. 23:59-71
58. Isard SA, Gage SH, Comtois P, Russo JM. 2005. DATE principles of the atmospheric pathway for invasive species applied to soybean rust. BioScience 55:851-61
59. James AP, Geijskes RJ, Dale JL, Harding RM. 2011. Development of a novel rolling-circle amplification technique to detect Banana streak virus that also discriminates between integrated and episomal virus sequences. Plant Dis. 95:57-62
60. Jones AT, McGavin WJ, Gepp V, Zimmerman MT, Scott SW. 2006. Purification and properties of blackberry chlorotic ringspot, a new virus species in subgroup 1 of the genus Ilarvirus found naturally infecting blackberry in the UK. Ann. Appl. Biol. 149:125-35
61. Jones RAC. 2014. Trends in plant virus epidemiology: opportunities from new or improved technologies. Virus Res. 186:3-19
62. Jordan R, Hammond J. 1991. Comparison and differentiation of potyvirus isolates and identification of strain-, virus-, subgroup-specific and potyvirus group-common epitopes using monoclonal antibodies. J. Gen. Virol. 72:25-36
63. Kadohira M, Stevenson MA, Høgåsen HR, de Koeijer A. 2012. A quantitative risk assessment for bovine spongiform encephalopathy in Japan. Risk Anal. 32:2198-208
64. Kehoe MA, Coutts BA, Buirchell BJ, Jones RA. 2014. Plant virology and next generation sequencing: experiences with a potyvirus. PLOS ONE 9(8):e104580
65. Knobler S, Mahmoud A, Lemon S, Pray L. 2006. The Impact of Globalization on Infectious Disease Emergence and Control. Washington, D.C.: Natl. Acad. Press
66. Kreuze JF, Perez A, Untiveros M, Quispe D, Fuentes S. 2009. Complete viral genome sequence and discovery by deep sequencing of small RNAs: a generic method for diagnosis, discovery, and sequencing of virus. Virology 388:1-7
67. Krupa S, Bowersox V, Claybrooke R, Barnes CW, Szabo L, et al. 2006. Introduction of Asian soybean rust urediniospores into the midwestern United States: a case study. Plant Dis. 90:1254-59
68. Kyndt T, Quispe D, Zhai H, Jarret R, Ghislain M, et al. 2015. The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: an example of a naturally transgenic food crop. PNAS 112:5844-49
69. Laney AG, Hassan M, Tzanetakis IE. 2012. An integrated badnavirus is prevalent in fig germplasm. Phytopathology 102:1182-89
70. Lefebvre A, Scalla R, Pfeiffer P. 1990. The double-stranded RNA associated with the "447" cytoplasmic male sterility in Vicia faba is packaged together with its replicase in cytoplasmic membranous vesicles. Plant Mol. Biol. 14:477-90
71. Liebhold AM, Brockerhoff EG, Garrett LJ, Parke JL, Britton KO. 2012. Live plant imports: the major pathway for forest insect and pathogen invasions of the US. Front. Ecol. Environ. 10:135-43
72. López MM, Llop P, Olmos A, Marco-Noales E, Cambra M, Bertolini E. 2009. Are molecular tools solving the challenges posed by detection of plant pathogenic bacteria and viruses? Curr. Issues Mol. Biol. 11:13-46
73. MacDiarmid R, Rodoni B, Melcher U, Ochoa-Corona F, Roossinck M. 2013. Biosecurity implications of new technology and discovery in plant virus research. PLOS Pathog. 9:e1003337
74. Maliogka VI, Dovas CI, Katis NI. 2007. Demarcation of ilarviruses based on the phylogeny of RNA2-encoded RdRp and a generic ramped annealing RT-PCR. Arch. Virol. 152:1687-98
75. Mardis ER. 2013. Next-generation sequencing platforms. Annu. Rev. Anal. Chem. 6:287-303
76. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-80
77. Martin RR, James D, Levesque CA. 2000. Impacts ofmolecular diagnostics on plant disease management. Annu. Rev. Phytopathol. 38:207-39
78. Martin RR, MacFarlane S, Sabanadzovic S, Quito D, Poudel B, Tzanetakis IE. 2013. Viruses and virus diseases of Rubus. Plant Dis. 97:168-82
79. Martin RR, Tzanetakis IE. 2013. High risk strawberry viruses by region in the United States and Canada: implications for certification, nurseries, and fruit production. Plant Dis. 97:1358-62
80. Martin RR, Zhou J, Tzanetakis IE. 2011. Blueberry latent virus: an amalgam of Partitiviridae and Totiviridae. Virus Res. 155:175-80
81. Massart S, Olmos A, Jijakli H, Candresse T. 2014. Current impact and future directions of high throughput sequencing in plant virus diagnostics. Virus Res. 188:90-96
82. McCartney HA, Foster SJ, Fraaije BA, Ward E. 2003. Molecular diagnostics for fungal plant pathogens. Pest Manag. Sci. 59:129-42
83. Murad L, Bielawski JP, Matyasek R, Kovarík A, Nichols RA, et al. 2004. The origin and evolution of geminivirus-related DNA sequences in Nicotiana. Heredity 92:352-58
84. Murant AF. 1990. Dependence of groundnut rosette virus on its satellite RNA as well as on groundnut rosette assistor luteovirus for transmission by Aphis craccivora. J. Gen. Virol. 71:2163-66
85. Nairn ME, Allen PG, Inglis AR, Tanner C. 1996. Australian Quarantine:AShared Responsibility. Canberra, Aust.: Dep. Prim. Ind. Energy
86. Ndowora T, Dahal G, LaFleur D, Harper G, Hull R, et al. 1999. Evidence that badnavirus infection in Musa can originate from integrated pararetroviral sequences. Virology 255:214-20
87. Nyrén P. 2007. The history of pyrosequencing. Methods Mol. Biol. 373:1-13
88. Ochoa-Corona FM. 2011. Biosecurity, microbial forensics and plant pathology: education challenges, overlapping disciplines and research needs. Australas. Plant Pathol. 40:335-38
89. Palm ME. 2001. Systematics and the impact of invasive fungi on agriculture in the United States. BioScience 51:141-47
90. Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, et al. 2013. Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science 341:281-86
91. Plant Health Australia. 2013. Industry biosecurity plan for the potato industry. Version 2.0. Canberra, Aust.: Plant Health Aust. http://www.planthealthaustralia.com.au
92. Pleško IM, Marn MV, Širca S, Urek G. 2009. Biological, serological and molecular characterisation of Raspberry bushy dwarf virus from grapevine and its detection in the nematode Longidorus juvenilis. Eur. J. Plant Pathol. 123:261-68
93. Poudel B, Tzanetakis IE. 2013. Population structure of Blackberry chlorotic ringspot virus in the United States. Arch. Virol. 158:667-72
94. Powney R, Beer S, Plummer K, Luck J, Rodoni B. 2011. The specificity of PCR-based protocols for detection of Erwinia amylovora. Australas. J. Plant Pathol. 40:87-97
95. Purcell AH, Saunders SR. 1999. Fate of Pierce's disease strains of Xylella fastidiosa in common riparian plants in California. Plant Dis. 83:825-30
96. Qiagen. 2015. CLC Genomics Workbench 8.0.3. https://www.qiagenbioinformatics.com/
97. Redinbaugh MG, Zambrano JL. 2014. Control of virus diseases in maize. Adv. Virus Res. 90:391-429
98. Reardon T, Barrett CB, Berdegué JA, Swinnen JF. 2009. Agrifood industry transformation and small farmers in developing countries. World Dev. 37:1717-27
99. Reinert K, Langmead B, Weese D, Evers DJ. 2015. Alignment of next-generation sequencing reads. Annu. Rev. Genom. Hum. Genet. 16:133-51
100. Riley MB, Williamson MR, Maloy O. 2002. Plant disease diagnosis. Plant Health Instr. doi:10.1094/PHII-2002-1021-01
101. Rojas MR, Gilbertson RL, Maxwell DP. 1993. Use of degenerate primers in the polymerase chain reaction to detect whitefly-transmitted geminiviruses. Plant Dis. 77:340-47
102. Roossinck MJ. 2005. Symbiosis versus competition in plant virus evolution. Nat. Rev. Microbiol. 3:917-24
103. Roossinck MJ. 2011. The good viruses: viral mutualistic symbioses. Nat. Rev. Microbiol. 9:99-108
104. Roossinck MJ. 2012. Plant virus metagenomics: biodiversity and ecology. Annu. Rev. Genet. 46:359-69
105. Roossinck MJ, Saha P, Wiley GB, Quan J, White JD, et al. 2010. Ecogenomics: using massively parallel pyrosequencing to understand virus ecology. Mol. Ecol. 19:81-88
106. Roux S, Tournayre J, Mahul A, Debroas D, Enault F. 2014. Metavir 2: new tools for viral metagenome comparison and assembled virome analysis. BMC Bioinform. 15:76
107. Rowhani A, Uyemoto JK, Golino D, Martelli GP. 2005. Pathogen testing and certification of Vitis and Prunus species. Annu. Rev. Phytopathol. 43:261-78
108. Schaad NW, Frederick RD, Shaw J, Schneider WL, Hickson R, Petrillo MD. 2003. Advances in molecular-based diagnostics in meeting crop biosecurity and phytosanitary issues. Annu. Rev. Phytopathol. 41:305-24
109. Sefc KM, Leonhardt W, Steinkellner H. 2000. Partial sequence identification of Grapevine-leafrollassociated virus-1 and development of a highly sensitive IC-RT-PCR detection method. J. Virol. Methods 86:101-6
110. Seyrig G, Stedtfeld RD, Tourlousse DM, Ahmad F, Towery K, et al. 2015. Selection of fluorescent DNA dyes for real-time LAMP with portable and simple optics. J. Microbiol. Methods 119:223-27
111. Simpson M, Srinivasan V. 2014. Australia's Biosecurity Future: Preparing for Future Biological Challenges. Canberra, Aust.: CSIRO. https://publications.csiro.au/rpr/download?pid=csiro:EP146693& dsid=DS4
112. Simmonds P. 2015. Methods for virus classification and the challenge of incorporating metagenomic sequence data. J. Gen. Virol. 96:1193-206
113. Singh RP, Hodson DP, Huerta-Espino J, Jin Y, Bhavani S, et al. 2011. The emergence of Ug99 races of the stem rust fungus is a threat to world wheat production. Annu. Rev. Phytopathol. 49:465-81
114. Stack JP. 2006. Challenges to crop biosecurity. In Crop Biosecurity: Assuring Our Global Food Supply (NATO Science for Peace and Security Series-C: Environmental Security), ed. ML Guillino, J Fletcher, A Gamliel, JP Stack, pp. 15-23. Dordrecht: Springer
115. Stobbe AH, Daniels J, Espindola AS, Verma R, Melcher U, et al. 2013. E-probe diagnostic nucleic acid analysis (EDNA): a theoretical approach for handling of next generation sequencing data for diagnostics. J. Microbiol. Methods 94:356-66
116. Stobbe AH, Roossinck MJ. 2014. Plant virus metagenomics: what we know and why we need to know more. Front. Plant Sci. 5:e150
117. Susaimuthu J, Gergerich RC, Bray MM, Clay KA, Clark JR, et al. 2007. The incidence and ecology of Blackberry yellow vein associated virus. Plant Dis. 91:809-13
118. Susaimuthu J, Tzanetakis IE, Gergerich RC, Kim KS, Martin RR. 2008. Viral interactions lead to decline of blackberry plants. Plant Dis. 92:1288-92
119. Thompson JR, Fuchs M, McLane H, Celebi-Toprak F, Fischer KF, et al. 2014. Profiling viral infections in grapevine using a randomly primed reverse transcription-polymerase chain reaction/macroarray multiplex platform. Phytopathology 104:211-19
120. Tzanetakis IE, Gergerich RC, Martin RR. 2006. A new Ilarvirus found in rose. Plant Pathol. 55:568
121. Untiveros M, Perez-Egusquiza Z, Clover G. 2010. PCR assays for the detection ofmembers of the genus Ilarvirus and family Bromoviridae. J. Virol. Methods 165:97-104
122. van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. 2014. Ten years of next-generation sequencing technology. Trends Genet. 30:418-26
123. Vermeulen SJ, Campbell BM, Ingram JS. 2012. Climate change and food systems. Annu. Rev. Environ. Resour. 37:195-222
124. Vincelli P, Tisserat N. 2008. Nucleic acid-based pathogen detection in applied plant pathology. Plant Dis. 92:660-69
125. Wang Q, Jia P, Zhao Z. 2013. Virus Finder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. PLOS ONE 8:e64465
126. Weisberg W, Barns S, Pelletier D, Lane D. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173:697-703
127. Welliver R. 2012. Plum pox virus case study: the eradication road is paved in gold. Phytopathology 102:S4.154
128. Wilson IG. 1997. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 63:3741-51
129. World Trade Organization. 1994. Agreement on the application of sanitary and phytosanitary measures. In Results of the Uruguay Round of Multilateral Trade Negotiations: The Legal Texts, pp. 69-84. Geneva, Switz.:WTO
130. Wren JD, Roossinck MJ, Nelson RS, Scheets K, Palmer MW, Melcher U. 2006. Plant virus biodiversity and ecology. PLOS Biol. 4:e80
131. Wu Q, Ding SW, Zhang Y, Zhu SF. 2015. Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms. Annu. Rev. Phytopathol. 53:425-44
132. Wu Q, Wang Y, Cao MJ, Pantaleo V, Burgyan J, et al. 2012. Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. PNAS 109:3938-43
133. Xiang Y, Bernardy M, Bhagwat B, Wiersma PA, DeYoung R, Bouthillier M. 2015. The complete genome sequence of a new polerovirus in strawberry plants from eastern Canada showing strawberry decline symptoms. Arch. Virol. 160:553-56
134. Zheng L, Rodoni BC, Gibbs MJ, Gibbs AJ. 2010. A novel pair of universal primers for the detection of potyviruses. Plant Pathol. 59:211-20