A sensitive real-time RT-PCR reveals a high incidence of Southern tomato virus (STV) in Spanish tomato crops

Laura Elvira-González, Caterina Carpino, Ana Alfaro-Fernández, María I. Font-San Ambrosio, Rosa Peiró, Luis Rubio, Luis Galipienso

Abstract


Southern tomato virus (STV) is a double-stranded RNA (dsRNA) virus belonging to genus Amalgavirus (family Amalgamaviridae). STV has been detected in tomato plants showing different symptoms although it has not been demonstrated that STV is the causal agent. To study the STV incidence and its pathogenic role, a sensitive and quantitative real-time reverse transcription-polymerase chain reaction assay (RT-qPCR) was developed. The standard curve performed with viral RNA transcripts allowed a wide dynamic range for STV quantitation from 104 to 1011 copies/ng of total RNA. STV detection by RT-qPCR was 102-fold more sensitive than conventional RT-PCR or RT-LAMP and 104-fold more sensitive than molecular hybridization. STV was detected in different tomato plant tissues, as well as in the coat and the embryo of individual seeds. Also, viral concentration remained constant over time in leaf tissues of STV-infected tomato plants. Surveys on different tomato fields from Spain revealed that STV was widespread. In addition, the virus was detected in almost every tomato variety and nursery analyzed. STV-infected tomato plants did not show any disease-related symptom suggesting that the virus was not directly the causal agent of any tomato disease. However, there is no information about the STV effect in mixed infections or in abiotic stressed conditions and further studies must be performed to clarify it. The RT-qPCR assay developed in this work could be implemented on sanitation programs in order to limit the virus spread and could be used to study the effect of STV in mix infections or abiotic stressed conditions.


Keywords


Solanum lycopersicum; Amalgaviridae; Amalgavirus; persistent viruses; RT-qPCR

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References


Alcala-Briseno RI, Coskan S, Londono MA, Polston JE, 2017. Genome sequence of Southern tomato virus in asymptomatic tomato 'Sweet Hearts'. Genome Announc 5 (7): e01374-16. https://doi.org/10.1128/genomeA.01374-16

Alfaro-Fernández A, Sánchez-Navarro JA, del Carmen Cebrián M, del Carmen Córdoba-Sellés M, Pallás V, Jordá C, 2009. Simultaneous detection and identification of Pepino mosaic virus (PepMV) isolates by multiplex one-step RT-PCR. Eur J Plant Pathol 125: 143-158. https://doi.org/10.1007/s10658-009-9466-7

Ali A, Kobayashi M, 2010. Seed transmission of Cucumber mosaic virus in pepper. J Virol Methods 163: 234-237. https://doi.org/10.1016/j.jviromet.2009.09.026

Aramburu J, Galipienso L, 2005. First report in Spain of a variant of Tomato mosaic virus (ToMV) overcoming the Tm‐22 resistance gene in tomato (Lycopersicon esculentum). Plant Pathol 54: 566-566. https://doi.org/10.1111/j.1365-3059.2005.01197.x

Arancibia R, Valverde R, Can F, 1995. Properties of a cryptic virus from pepper (Capsicum annuum). Plant Pathol 44: 164-168.

Blanc S, 2007. Virus transmission-getting out and in. In: Viral transport in plants, pp: 1-28. Springer. https://doi.org/10.1007/7089_2006_099

Boccardo G, Lisa V, Luisoni E, Milne RG, 1987. Cryptic plant viruses. Adv Virus Res 32: 171-214. https://doi.org/10.1016/S0065-3527(08)60477-7

Bustin SA, Benes V, Nolan T, Pfaffl MW, 2005. Quantitative real-time RT-PCR a perspective. J Mol Endocrinol 34: 597-601. https://doi.org/10.1677/jme.1.01755

Candresse T, Marais A, Faure C, 2015. First report of Southern tomato virus on tomatoes in southwest France. Genome 3: e01226-15.

Chávez-Calvillo G, Contreras-Paredes CA, Mora-Macias J, Noa-Carrazana JC, Serrano-Rubio AA, Dinkova TD, Carrillo-Tripp M, Silva-Rosales L, 2016. Antagonism or synergism between Papaya ringspot virus and Papaya mosaic virus in Carica papaya is determined by their order of infection. Virology 489: 179-191. https://doi.org/10.1016/j.virol.2015.11.026

Córdoba-Sellés MC, García-Rández A, Alfaro-Fernández A, Jordá-Gutiérrez C, 2007. Seed transmission of Pepino mosaic virus and efficacy of tomato seed disinfection treatments. Plant Dis 91: 1250-1254. https://doi.org/10.1094/PDIS-91-10-1250

Debreczeni D, Ruiz-Ruiz S, Aramburu J, López C, Belliure B, Galipienso L, Soler S, Rubio L, 2011. Detection, discrimination and absolute quantitation of Tomato spotted wilt virus isolates using real time RT-PCR with TaqMan® MGB probes. J Virol Methods 176: 32-37. https://doi.org/10.1016/j.jviromet.2011.05.027

Elvira-González L, Puchades A, Carpino C, Alfaro-Fernandez A, Font-San-Ambrosio M, Rubio L, Galipienso L, 2017. Fast detection of Southern tomato virus by one-step transcription loop-mediated isothermal amplification (RT-LAMP). J Virol Methods 241: 11-14. https://doi.org/10.1016/j.jviromet.2016.12.004

Falk BW, Tsai JH, 1998. Biology and molecular biology of viruses in the genus Tenuivirus. Annu Rev Phytopathol 36: 139-163. https://doi.org/10.1146/annurev.phyto.36.1.139

Ferriol I, Ruiz-Ruiz S, Rubio L, 2011. Detection and absolute quantitation of Broad bean wilt virus 1 (BBWV-1) and BBWV-2 by real-time RT-PCR. J Virol Methods 177: 202-205. https://doi.org/10.1016/j.jviromet.2011.08.003

Gandía M, Bernad L, Rubio L, Duran-Vila N, 2007. Host effect on the molecular and biological properties of a Citrus exocortis viroid isolate from Vicia faba. Phytopathology 97: 1004-1010. https://doi.org/10.1094/PHYTO-97-8-1004

Gil-Salas F, Peters J, Boonham N, Cuadrado I, Janssen D, 2012. Co-infection with Cucumber vein yellowing virus and Cucurbit yellow stunting disorder virus leading to synergism in cucumber. Plant Pathol 61: 468-478. https://doi.org/10.1111/j.1365-3059.2011.02545.x

Gómez P, Sempere R, Amari K, Gómez-Aix C, Aranda M, 2010. Epidemics of Tomato torrado virus, Pepino mosaic virus and Tomato chlorosis virus in tomato crops: do mixed infections contribute to torrado disease epidemiology? Ann Appl Biol 156: 401-410. https://doi.org/10.1111/j.1744-7348.2010.00397.x

Hadas R, Pearlsman M, Gefen T, Lachman O, Hadar E, Sharabany G, Antignus Y, 2004. Indexing system for Tomato mosaic virus (ToMV) in commercial tomato seed lots. Phytoparasitica 32: 421-424. https://doi.org/10.1007/BF02979856

Hanssen IM, Mumford R, Blystad D, Cortez I, Hasiów-Jaroszewska B, Hristova D, Pagán I, Pereira A, Peters J, Pospieszny H, 2010. Seed transmission of Pepino mosaic virus in tomato. Eur J Plant Pathol 126: 145-152. https://doi.org/10.1007/s10658-009-9528-x

Hu W, Wong S, Loh C, Goh C, 1998. Synergism in replication of Cymbidium mosaic potexvirus (CymMV) and Odontoglossum ringspot tobamovirus (ORSV) RNA in orchid protoplasts. Arch Virol 143: 1265-1275. https://doi.org/10.1007/s007050050374

Iacono G, Hernandez-Llopis D, Alfaro-Fernandez A, Davino M, Font M, Panno S, Galipenso L, Rubio L, Davino S, 2015. First report of Southern tomato virus in tomato crops in Italy. New Disease Reports 32: 27.

Kormelink R, Garcia ML, Goodin M, Sasaya T, Haenni A, 2011. Negative-strand RNA viruses: the plant-infecting counterparts. Virus Res 162: 184-202. https://doi.org/10.1016/j.virusres.2011.09.028

Krupovic M, Dolja VV, Koonin EV, 2015. Plant viruses of the Amalgaviridae family evolved via recombination between viruses with double-stranded and negative-strand RNA genomes. Biol Direct 10: 12. https://doi.org/10.1186/s13062-015-0047-8

Kumar S, Nei M, Dudley J, Tamura K, 2008. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9: 299-306. https://doi.org/10.1093/bib/bbn017

Ling K, Wechter WP, Jordan R, 2007. Development of a one-step immunocapture real-time TaqMan RT-PCR assay for the broad spectrum detection of Pepino mosaic virus. J Virol Methods 144: 65-72. https://doi.org/10.1016/j.jviromet.2007.03.022

Logan J, Edwards KJ, Saunders NA (eds), 2009. Real-time PCR: Current technology and applications. A practical handbook. Caister Academic Press, 284 pp.

Mackay IM, Arden KE, Nitsche A, 2002. Real-time PCR in Virology. Nucleic Acids Res 30: 1292-1305. https://doi.org/10.1093/nar/30.6.1292

Martin RR, Zhou J, Tzanetakis IE, 2011. Blueberry latent virus: an amalgam of the Partitiviridae and Totiviridae. Virus Res 155: 175-180. https://doi.org/10.1016/j.virusres.2010.09.020

Murphy JF, Bowen KL, 2006. Synergistic disease in pepper caused by the mixed infection of Cucumber mosaic virus and Pepper mottle virus. Phytopathology 96: 240-247. https://doi.org/10.1094/PHYTO-96-0240

Padmanabhan C, Zheng Y, Li R, Fei Z, Ling KS, 2015a. Complete genome sequence of Southern tomato virus naturally infecting tomatoes in Bangladesh. Genome Announc 3 (6): e01522-15. https://doi.org/10.1128/genomeA.01522-15

Padmanabhan C, Zheng Y, Li R, Sun S.E, Zhang D, Liu Y, Fei Z, Ling KS, 2015b. Complete genome sequence of Southern tomato virus identified in China using next-generation sequencing. Genome Announc 3 (5): e01226-15. https://doi.org/10.1128/genomeA.01226-15

Puchades A, Carpino C, Alfaro-Fernandez A, Font-San-Ambrosio M, Davino S, Guerri J, Rubio L, Galipienso L, 2017. Detection of Southern tomato virus by molecular hybridization. Ann Appl Biol 171: 172-178. https://doi.org/10.1111/aab.12367

Roossinck MJ, 2010. Lifestyles of plant viruses. Philos T R Soc B 365: 1899-1905. https://doi.org/10.1098/rstb.2010.0057

Sabanadzovic S, Valverde RA, Brown JK, Martin RR, Tzanetakis IE, 2009. Southern tomato virus: the link between the families Totiviridae and Partitiviridae. Virus Res 140: 130-137. https://doi.org/10.1016/j.virusres.2008.11.018

Sabanadzovic S, Ghanem-Sabanadzovic NA, Valverde R, 2010. A novel monopartite dsRNA virus from rhododendron. Arch Virol 155: 1859-1863. https://doi.org/10.1007/s00705-010-0770-5

Sabanadzovic S, Valverde RA, 2011. Properties and detection of two cryptoviruses from pepper (Capsicum annuum). Virus Genes 43: 307-312. https://doi.org/10.1007/s11262-011-0634-4

SAS Institute, 2003. SAS/STAT User's Guide. Vers. 9.1. Vol 1-7. SAS Inst. Inc., Cary, NC, USA.

Sastry KS, 2013. Methods of combating seed-transmitted virus diseases. In: Seed-borne plant virus diseases, pp: 185-284. Springer. https://doi.org/10.1007/978-81-322-0813-6_8

Tromas N, Zwart MP, Lafforgue G, Elena SF, 2014. Within-host spatiotemporal dynamics of plant virus infection at the cellular level. PLoS Genet 10: e1004186. https://doi.org/10.1371/journal.pgen.1004186

Verbeek M, Dullemans AM, Espino A, Botella M, Alfaro-Fernández A, Font MI, 2015. First report of Southern tomato virus in tomato in the Canary Islands, Spain. J Plant Pathol 97 (2): 392.

Wintermantel WM, 2005. Co-infection of Beet mosaic virus with Beet yellowing viruses leads to increased symptom expression on sugar beet. Plant Dis 89: 325-331. https://doi.org/10.1094/PD-89-0325




DOI: 10.5424/sjar/2018163-12961