Skip to main content
SpringerLink
Log in

Cutting-Edge Technologies for Detection of Plant Viruses in Vegetatively Propagated Crop Plants

  • Chapter
  • First Online:
Plant Viruses: Evolution and Management

  • 1146 Accesses

Abstract

Plant virus diseases cause enormous loss which is estimated to be US$60 billion in crop yields worldwide each year. Seed is a propagating material in most of the crop plants, whereas most of the horticultural crops are vegetatively propagated. Horticultural crops like banana, bamboo, citrus, and grapes; commercial crops like sugarcane, black pepper, cardamom, orchids, and bulbous ornamentals; and tuber crops like potato, cassava, yam, etc., have been known to be infected by a range of viruses that belong to different genera and families. In these crops, the primary mode of transmission of viruses is through the use of infected plant propagule like corms, tubers, cutting, grafts, etc. An effective virus management strategy requires an accurate, rapid, and sensitive diagnosis for which understanding the disease cycle of etiological agents and its molecular nature, genome sequence and structure, coat protein information and sequences, etc. should be known in advance to design a detection strategy. Enzyme-linked immunosorbent assay (ELISA) or polymerase chain reaction (PCR) has been widely used for detection of plant viruses. These methods are time-consuming and laborious and require special skills such as in prior information on taxonomy to detect the pathogen responsible for the disease. On-site or point-of-care methods of detection are not new but limited to clinical use for human diseases. But recently this lateral flow devices (LFDs) are being made available for a number of viruses infecting plants. However, the widespread usage of this technology is delayed probably due to its limitation on robustness and lack of high-throughput nature. In this chapter, we have reviewed the recent developments on the early diagnosis using cutting-edge technologies like on-the-spot diagnostic tool lateral flow immunoassay (LFIA), loop-mediated isothermal amplification (LAMP), and multiplex technologies like microarray, microsphere immunoassay, etc. LAMP method is highly specific and requires less time to complete the indexing; however, this technique is yet to replace ELISA and PCR completely in agriculture possibly due to its specificity and viral variants that might escape from detection, and other possible reasons may be that the researchers and policy makers have not yet been convinced. Recent technologies such as rolling circle amplification which is dependent on a circular DNA genome and random hexamers do not require sequence data of the target, and similarly the next-generation sequencing also does not require a priori knowledge on the sequence of the causal agents. Principles and application of these cutting-edge technologies are reviewed in this chapter. The objective of the present chapter is not to cover all the details of diagnostics but to highlight the current status of various cutting-edge diagnostic techniques that can be applied for the biosecurity, by the quarantine departments, international exchange of germplasm, and on-site field detection by farmers, and use in the certification programs.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Abdullahi I, Rott M (2009) Microarray immunoassay for the detection of grapevine and tree fruit viruses. J Virol Methods 160:90–100

    Article  CAS  PubMed  Google Scholar 

  • Abdullahi I, Koerbler M, Stachewicz H, Winter S (2005) The 18S rDNA sequence of Synchytrium endobioticum and its utility in micro arrays for the simultaneous detection of fungal and viral pathogens of potato. Appl Microbiol Biotechnol 68:368–375

    Article  CAS  PubMed  Google Scholar 

  • Adams IP, Glover RH, Monger WA, Mumford R, Jackeviciene E, Navalin-skiene M, Samuitiene M, Boonham N (2009) Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol Plant Pathol 10(4):537–545

    Article  CAS  PubMed  Google Scholar 

  • Agindotan B, Perry KL (2007) Macroarray detection of plant RNA viruses using randomly primed and amplified complementary DNAs fromiInfected plants. Phytopathology 97:119–127

    Article  CAS  PubMed  Google Scholar 

  • Agindotan B, Perry KL (2008) Macroarray detection of eleven potato-infecting viruses and potato spindle tuber viroid. Plant Dis 92:730–740

    Article  CAS  Google Scholar 

  • Ahlawat YS, Pant RP, Lockhart BEL, Srivastava M, Chakraborty NK, Varma A (1996) Association of badnavirus with citrus mosaic disease in India. Plant Dis 80:590–592

    Article  Google Scholar 

  • Ahmadi S, Almasi MA, Fatehi F, Struik PC, Moradi A (2013) Visual Detection of Potato leafroll virus by One-step Reverse Transcription Loop-Mediated Isothermal Amplification of DNA with Hydroxynaphthol Blue Dye. J Phytopathol 161:120–124

    Article  CAS  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, Sudarshana MR, Uyemoto JK, Rowhani A (2012a) Complete genome sequence of a novel Vitivirus isolated from grapevine. In: Proceedings of the 17th Congress of ICVG, Davis, CA, USA, 7–14 October 2012

    Google Scholar 

  • Al Rwahnih M, Dave A, Anderson M, Uyemoto JK, Sudarshana MR (2012b) Association of a circular DNA virus in grapevine affected by red blotch disease in California. In: Proceedings of the 17th Congress of ICVG, Davis, CA, USA, 7–14 October 2012

    Google Scholar 

  • Alabi OJ, Zheng Y, Jagadeeswaran G, Sunkar R, Naidu RA (2012) High-throughput sequence analysis of small RNAs in grapevine (Vitis viniferaL.) affected by grapevine leafroll disease. Mol Plant Pathol 13(9):1060–1076

    Article  CAS  PubMed  Google Scholar 

  • Algar WR, Krull UJ (2007) Quantum dots as donors in fluorescence resonance energy transfer for the bioanalysis of nucleic acids, proteins, and other biological molecules. Anal Bioanal Chem 39:1609–1618

    Google Scholar 

  • Alivisatos AP, Gu W, Larabell C (2005) Quantum dots as cellular probes. Biomed Eng 7:55–76

    CAS  Google Scholar 

  • Almasi MA, Dehabadi SH (2013) Colorimetric Immunocapture Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Rapid Detection of the Potato virus Y. J Plant Pathol Microbiol 4:188. doi:10.4172/2157-7471.1000188

    Google Scholar 

  • Almasi MA, Moradi A, Nasiri J, Karami S, Nasiri M (2012) Assessment of performance ability of three diagnostic methods for detection of Potato Leafroll virus (PLRV) using different visualizing systems. Applied Biochem Biotechnol 168:770–784

    Article  CAS  Google Scholar 

  • Almasi MA, Manesh ME, Jafary H, Dehabadi SMH (2013) Visual detection of Potato Leafroll Virus by loop-mediated isothermal amplification of DNA with the Gene Finder TM dye. J Virological Methods 192:51–54

    Article  CAS  Google Scholar 

  • Anthony Johnson AM, Dasgupta I, Sai Gopal DVR (2014) Development of loop-mediated isothermal amplification and SYBR green real-time PCR methods for the detection of Citrus yellow mosaic badnavirus in citrus species. J Virol Methods 203:9–14

    Article  CAS  PubMed  Google Scholar 

  • Baptista PV, Koziol-Montewka M, Paluch-Oles J, Doria G, Franco R (2006) Gold-nanoparticle-probe-based assay for rapid and direct detection of Mycobacterium tuberculosis DNA in clinical samples. Clin Chem 52:1433–1434

    Article  CAS  PubMed  Google Scholar 

  • Barba M, Czosnek H, Hadidi A (2014) Historical perspective, development and applications of next-generation sequencing in plant virology. Viruses 6(1):106–136

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bar-Joseph M, Gera A (2012) On a revolutionary method for diagnosis of latent infections of viruses and the importance of its adoption to prevent the spread of citrus and other fruit tree diseases (in Hebrew). Alon Hanotea 66:46–48

    Google Scholar 

  • Bergervoet JH, Peters J, van Beckhoven JR, van den Bovenkamp GW, Jacobson JW et al (2008) Multiplex microsphere immuno-detection of potato virus Y, X and PLRV. J Virol Methods 149:63–68

    Article  CAS  PubMed  Google Scholar 

  • Bhat AI, Siljo A, Deeshma KP (2013) Rapid detection of Piper yellow mottle virus and Cucumber mosaic virus infecting black pepper(Piper nigrum) by loop- mediated isothermal amplification(LAMP). J Virol Methods 193:190–196

    Article  CAS  PubMed  Google Scholar 

  • Boonham N, Walsh K, Smith P, Madagan K, Graham I, Barker I (2003) Detection of potato viruses using microarray technology: towards a generic method for plant viral disease diagnosis. J Virol Methods 108:181–187

    Article  CAS  PubMed  Google Scholar 

  • Boonham N, Kreuze J, Winter S, van der Vlugt R, Bergervoet J, Tomlinson J, Mumford R (2014) Methods in virus diagnostics: from ELISA to next generation sequencing. Virus Res 186:20–31

    Article  CAS  PubMed  Google Scholar 

  • Bruchez M Jr, Moronne M, Gin P, Weiss S, Alivisatos AP (1998) Semiconductor nanocrystals as fluorescent biological labels. Science 281:2013–6

    Article  CAS  PubMed  Google Scholar 

  • Bystricka D, Lenz O, Mraz I, Dedic P, Sip M (2003) DNA microarrays: parallel detection of potato viruses. Acta Virol 47:41–44

    CAS  PubMed  Google Scholar 

  • Bystricka D, Lenz O, Mraz I, Piherova L, Kmoch S, Sip M (2005) Oligonucleotide-based microarray: A new improvement in microarray detection of plant viruses. J Virol Methods 128:176–182

    Article  CAS  PubMed  Google Scholar 

  • Byzova NA, Safenkova IV, Chirkov SN, Zherdev AV, Blintsov AN, Dzantiev BB, Atabekov IG (2009) Development of Immunochromatographic test systems for express detection of plant viruses. Appl Biochem Microbiol 45:204–209

    Article  CAS  Google Scholar 

  • Byzova NA, Safenkova IV, Chirkov SN, Avdienko VG, Guseva AN, Mitrofanova IV, Zherdev AV, Dzantiev BB, Atabekov JG (2010) Interaction of Plum Pox Virus with Specific Colloidal Gold Labeled Antibodies and Development of Immunochromatographic Assay of the Virus. Biokhimiya 75(11):1583–1595

    Google Scholar 

  • Candresse T, Marais A, Faure C, Carriere S, Gentit P (2012) Use of 454 pyrosequencing for the fast and efficient characterization of known or novel viral agents in Prunus materials. In: Proceedings of the 22nd international conference on virus and other transmissible diseases of fruit crops, Rome, Italy, 3–8 June 2012; Abstract No. 47

    Google Scholar 

  • Candresse T, Marais A, Faure C, Gentit P (2013) Association of Little cherry virus 1 (LChV1) with the Shirofugen stunt disease and characterization of the genome of a divergent LChV1 isolate. Phytopathology 103:293–308

    Article  CAS  PubMed  Google Scholar 

  • Charlermroj R, Himananto O, Seepiban C, Kumpoosiri M, Warin N et al (2013) Multiplex Detection of Plant Pathogens Using a Microsphere Immunoassay Technology. PLoS One 8(4), e62344. doi:10.1371/journal.pone.0062344

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chiumenti M, Roberto R, Bottalico G, Campanale A, de Stradis A, Minafra A, Boscia D, Savino V, Martelli GP (2012) Virus sanitation and deep sequence analysis of fig. In: Proceedings of the 22nd international conference on virus and other transmissible diseases of fruit crops, Rome, Italy, 3–8 June 2012; Abstract No. 163

    Google Scholar 

  • Coetzee B, Freeborough MJ, Maree HJ, Celton JM, Rees DJ, Burger JT (2010) Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard. Virology 400:157–163

    Article  CAS  PubMed  Google Scholar 

  • Dale JL (1987) Banana bunchy top: an economically important tropical plant virus disease. Adv Virus Res 33:301–325

    Article  CAS  PubMed  Google Scholar 

  • Danks C, Barker I (2000) On-site detection of plant pathogens using lateral-flow devices. OEPP/EPPO Bull 30:421–426

    Article  Google Scholar 

  • Dean FB, Nelson JR, Giesler TL, Lasken RS (2001) Rapid amplification of plasmid and phage DNA using Phi29 polymerase and multiply-primed rolling circle amplification. Genome Res 11:1095–1099

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deyong Z, Willingmann P, Heinze C, Adam G, Pfunder M, Frey B, Frey JE (2005) Differentiation of Cucumber mosaic virus isolates by hybridization to oligonucleotides in a microarray format. J Virol Methods 123:101–108

    Article  CAS  PubMed  Google Scholar 

  • Dombrovsky A, Glanz E, Sapkota R, Lachman O, Bronstein M, Schnitzer T, Antignus Y (2011) Next-generation sequencing a rapid and reliable method to obtain sequence data of the genomes of un described plant viruses. In: Proceedings of the BARD-Sponsored workshop—microarrays and next-generation sequencing for detection and identification of plant viruses, Beltsville, MD, USA, 17–19 November 2011; Abstract No. 24

    Google Scholar 

  • Drygin YF, Blintsov AN, Osipov AP, Grigorenko VG, Andreeva IP, Uskov AI, Varitsev YA, Anisimov BV, Novikov VK, Atabekov JG (2009) High-sensitivity express immunochromatographic method for detection of plant infection by tobacco mosaic virus. Biochem Moscow 74:986–993

    Article  CAS  Google Scholar 

  • Drygin YF, Blintsov AN, Osipov AP, Grigorenko VG, Andreeva IP, Osipov AP, Varitsev YA, Uskov AI, Kravchenko DV, Atabekov JG (2012) Highly sensitive field test lateral flow immunodiagnostics of PVX infection. Appl Microbiol Biotechnol 93:179–189

    Article  PubMed  CAS  Google Scholar 

  • Dunbar SA, Vander Zee CA, Oliver KG, Karem KL, Jacobson JW (2003) Quantitative, multiplexed detection of bacterial pathogens: DNA and protein applications of the Luminex LabMAPTM system. J Microbiol Methods 53:245–252

    Article  CAS  PubMed  Google Scholar 

  • Edgar R, McKinstry M, Hwang J, Oppenheim AB, Fekete RA, Giulian G, Merril C, Nagashima K, Adhya S (2006) High sensitivity bacterial detection using biotin tagged phage and quantum-dot nanocomplexes. Proceeding of National Academy of. Science U. Space Sci Rev 103:4841–4845

    CAS  Google Scholar 

  • Engel EA, Escobar PF, Rojas LA, Rivera PA, Fiore N, Valenzuela PD (2010) A diagnostic oligonucleotide microarray for simultaneous detection of grapevine viruses. J Virol Methods 163(2):445–451

    Article  CAS  PubMed  Google Scholar 

  • Foord AJ, White JR, Colling A, Heine HG (2013) Microsphere suspension array assays for detection and differentiation of Hendra and Nipah viruses. Bio Med Res Int 2 [Article ID 89295]

    Google Scholar 

  • Frasco MF, Chaniotakis N (2009) Semiconductor quantum dots in chemical sensors and biosensors. Sensors 9:7266–7286

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fukuta S, Nimi Y, Oishi K, Yoshimura Y, Anai N, Hotta M, Fukaya M, Kato T, Oya T, Kambe M (2005) Development of reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for detection of two viruses and chrysanthemum stunt viroid. Ann Rep Kansai Plant Protection 47:31–36

    Article  Google Scholar 

  • Giampetruzzi A, Roumi V, Roberto R, Malossini U, Yoshikawa N, la Notte P, Terlizzi F, Credi R, Saldarelli P (2012) A new grapevine virus discovered by deep sequencing of virus- and viroid-derived small RNAs in Cv Pinot gris. Virus Res 163:262–268

    Article  CAS  PubMed  Google Scholar 

  • Goldman ER, Mattoussi H, Anderson GP, Medintz IL, Mauro JM (2005) Fluoroimmunoassays using antibodyconjugated quantum dots. Methods Mol Biol 303:19–34

    Google Scholar 

  • Goto M, Honda E, Ogura A, Nomoto A, Hanaki KI (2009) Colorimetric detection of loop-mediated isothermal amplification reaction by using hydroxy naphthol blue. Bio Techniques 46:167–172

    CAS  Google Scholar 

  • Grover V, Pierce ML, Hoyt P, Zhang F, Melcher U (2010) Oligonucleotide-based microarray for detection of plant viruses employing sequence-independent amplification of targets. J Virol Methods 163(1):57–67

    Article  CAS  PubMed  Google Scholar 

  • Hadidi A, Barba M (2012) Next-generation sequencing: Historical perspective and current applications in plant virology. Petria 22:262–277

    Google Scholar 

  • Haible D, Kober S, Jeske H (2006) Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. J Virol Methods 135:9–16

    Article  CAS  PubMed  Google Scholar 

  • Hany U, Adams IP, Glover R, Bhat AI, Boonham N (2014) The complete nucleotide sequence of Piper yellow mottle virus (PYMoV). Arch Virol 159:385–388. doi:10.1007/s00705-013-1824-2

    Article  CAS  PubMed  Google Scholar 

  • Jain KK (2005) Nanotechnology in clinical laboratory diagnostics. Clin Chim Acta 358:37–54

    Article  CAS  PubMed  Google Scholar 

  • Johne R, Müller H, Rector A, van Ranst M, Stevens H (2009) Rolling-circle amplification of viral DNA genomes using phi29 polymerase. Trends Microbiol 17:205–211

    Article  CAS  PubMed  Google Scholar 

  • Kaneko H, Kawana T, Fukushima E, Suzutani T (2007) Tolerance of loop-mediated isothermal amplification to a culture medium and biological substances. J Biochem Biophys Methods 70:499–501

    Article  CAS  PubMed  Google Scholar 

  • Kaweesi T, Kawuki R, Kyaligonza V, Baguma Y, Tusiime G, Ferguson EM (2014) Field evaluation of selected cassava genotypes for cassava brown streak disease based on symptom expression and virus load. Virol J 11:216

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kellar KL, Douglass JP (2003) Multiplexed microsphere-based flow cytometric immunoassays for human cytokines. J Immunol Methods 279:277–285

    Article  CAS  PubMed  Google Scholar 

  • Kreuze JF, 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 

  • Kuan CP, Wu MT, Lu YL, Huang HC (2010) Rapid detection of squash leaf curl virus by loop-mediated isothermal amplification. J Virol Methods 169:61–65

    Article  CAS  PubMed  Google Scholar 

  • Kusano N, Hirashima K, Narahara MKK, Imamura T, Nakahira TMK, Torii K (2007) Immunochromatographic assay for simple and rapid detection of Satsuma dwarf virus and related viruses using monoclonal antibodies. J Gen Plant Pathol 73:66–71

    Article  CAS  Google Scholar 

  • Lee GP, Min BE, Kim CS, Choi SH, Harn CH, Kim SU, Ryu KH (2003) Plant virus cDNA chip hybridization for detection and differentiation of four cucurbit-infecting Tobamoviruses. J Virol Methods 110(1):19–24

    Article  CAS  PubMed  Google Scholar 

  • Lee MS, Yang MJ, Hseu YC, Lai GH, Chang WT, Hsu YH, Lin MK (2011) One-step reverse transcription loop-mediated isothermal amplification assay for rapid detection of Cymbidium mosaic virus. J Virol Methods 173:43–48

    Article  CAS  PubMed  Google Scholar 

  • Li R, Ling K (2014) Development of reverse transcription loop-mediated isothermal amplification assay for rapid detection of an emerging potyvirus: Tomato necrotic stunt virus. J Virol Methods 200:35–40

    Article  CAS  PubMed  Google Scholar 

  • Li JY, Wei QW, Liu Y, Zhang WN, Wu JY, Charimbu MK, Hu BS, Cheng ZB, Yu C, Tao XR (2013) One-step reverse transcription loop-isothermal amplification for the rapid detection of cucumber green mottle mosaic virus. J Virol Methods 193:583–588

    Article  CAS  PubMed  Google Scholar 

  • Lin A, Nguyen L, Lee T, Clotilde LM, Kase JA, Son I et al (2011) Rapid Osero group identification of the ten most clinically relevant STECs by Luminex microbead-based suspension array. J Microbiol Methods 87:105–110

    Article  CAS  PubMed  Google Scholar 

  • Ling KS, Li R, Bledsoe M (2013) Pepino mosaic virus genotype shift in North America and development of a loop-mediated isothermal amplification for rapid genotype identification. Virol J 10:117

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu K, Chen H, Zhou Y, Li Z (2015) Establishment of RT-LAMP Assay for Detection of Citrus yellow vein clearing virus. Acta Horticult Sinica 42(5):997–1002

    CAS  Google Scholar 

  • Loconsole G, Onelge N, Potere O, Giampetruzzi A, Bozan O, Satar S, de Stradis A, Savino V, Yokomi RK, Saponari M (2012a) Identification and characterization of Citrus Yellow vein clearing virus, a putative new member of the genus Mandarivirus. Phytopathology 102:1168–1175

    Article  CAS  PubMed  Google Scholar 

  • Loconsole G, Saldarelli P, Doddapaneni H, Savino V, Martelli GP, Saponari M (2012b) Identification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member of the family Geminiviridae. Virology 432:162–172

    Article  CAS  PubMed  Google Scholar 

  • Maree HJ, Nel Y, Visser M, Coetzec B, Manicom B, Burger JT, Rees DJG (2012) The study of plant virus disease etiology using next-generation sequencing technologies. In: Proceedings of the 22nd international conference on virus and other transmissible diseases of fruit crops, Rome, Italy, 3–8 June 2012; Abstract No. 48

    Google Scholar 

  • Martelli GP (2012) Grapevine virology highlights. In: Proceedings of the 17th Congress of ICVG, Davis, CA, USA, 7–14 October 2012

    Google Scholar 

  • Martelli GP, Boudon-Padieu E (2006) Directory of infectious diseases of grapevines. International Centre for Advanced Mediterranean Agronomic Studies. Options Méditerranéennes Ser B Studies Res 55:59–75

    Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Mirkin CA, Letsinger RL, Mucic RC, Storhoff JJ (1996) A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 382:607–609

    Article  CAS  PubMed  Google Scholar 

  • Monger WA, Alicai T, Ndunguru J, Kinyua ZM, Potts M, Reeder RH, Miano DW, Adams IP, Boonham N, Glover RH et al (2010) The complete genome sequence of the Tanzanian strain of Cassava brown streak virus and comparison with the Ugandan strain sequence. Arch Virol 2010(155):429–433

    Article  CAS  Google Scholar 

  • Muerhoff AS, Leary TP, Desai SM, Mushahwar IK (1997) Amplification and subtraction methods and their application to the discovery of novel human viruses. J Medical Virol 53:96–103

    Google Scholar 

  • Mukasa SB, Rubaihayo SB, Valkonen JPT (2006) Interactions between a crinivirus, an ipomovirus and a potyvirus in coinfected sweet potato plants. Plant Pathol 55:458–467

    Article  CAS  Google Scholar 

  • Muthukumar V, Melcher U, Pierce M, Wiley GB, Roe BA, Palmer MW, Thapa V, Ali A, Ding T (2009) Non-cultivated plants of the Tallgrass Prairie Preserve of northeastern Oklahoma frequently contain virus-like sequences in particulate fractions. Virus Res 141(2):169–173

    Article  CAS  PubMed  Google Scholar 

  • Nagamine K, Kuzuhara Y, Notomi T (2002) Isolation of single-stranded DNA from loop-mediated isothermal amplification products. Biochem Biophys Res Commun 290:1195–1198

    Article  CAS  PubMed  Google Scholar 

  • Nath S, Kaittanis C, Tinkham A, Perez JM (2008) Dextran coated gold nanoparticles for the assessment of antimicrobial susceptibility. Annal Chem 80:1033–1038

    Article  CAS  Google Scholar 

  • Ng JCK (2013) A quantum dot-immunofluorescent labeling method to investigate the interactions between a crinivirus and its whitefly vector. Front Microbiol 4(77):1–9

    Google Scholar 

  • Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N et al (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28, e63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Olmos A, Dasí MA, Candresse T, Cambra M (1996) Print-capture PCR: a simple and highly sensitive method for the detection of Plum pox virus (PPV) in plant tissues. Nucleic Acids Res 24(11):2192–2193

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Osman F, Leutenegger C, Golino D, Rowhani A (2008) Comparison of low-density arrays, RT-PCR and real-time TaqMan RT-PCR in detection of grapevine viruses. J Virol Methods 149:292–299

    Article  CAS  PubMed  Google Scholar 

  • Pantaleo V, Saldarelli P, Miozzi L, Giampetruzzi A, Gisel A, Moxon S, Dalmay T, Bisztray G, Burgyan J (2010) Deep sequencing analysis of viral short RNAs from an infected Pinot noir grapevine. Virology 408:49–56

    Article  CAS  PubMed  Google Scholar 

  • Pasquini G, Barba M, Hadidi A, Faggioli F, Negri R, Sobol I, Tiberini A, Caglayan K, Mazyad H, Anfoka G, Ghanim M, Zeidan M, Czosnek H (2008) Oligonucleotide microarray-based detection and genotyping of Plum pox virus. J Virol Methods 147(1):118–126

    Article  CAS  PubMed  Google Scholar 

  • Peng J, Zhang J, Xia Z, Li Y, Huang J, Fan Z (2012a) Rapid and sensitive detection of Banana bunchy top virus by loop-mediated isothermal amplification. J Virol Methods 185:254–258

    Article  CAS  PubMed  Google Scholar 

  • Peng J, Fan Z, Huang J (2012b) Rapid detection of banana streak virus by loop-mediated isothermal amplification assay in South China. J Phytopathol 160:248–250

    Article  CAS  Google Scholar 

  • Peng J, Shi M, Xia Z, Huang J, Fan Z (2012c) Detection of cucumber mosaic virus isolates from banana by one step reverse transcription loop-mediated isothermal amplification. Arch Virol 157:2213–2217

    Article  CAS  PubMed  Google Scholar 

  • Poojari S, Alabi OJ, Fofanov VY, Naidu RA (2013) A leafhopper-transmissible DNA virus with novel evolutionary lineage in the family Geminiviridae implicated in grapevine red leaf disease by next-Generation sequencing. PLoS One 8, e64194

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Prabha K, Baranwal VK, Jain RK (2013) Applications of next generation high throughput sequencing technologies in characterization, discovery and molecular interaction of plant viruses. Indian J Virol 24(2):157–165

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Price CP, Kricka LJ (2007) Improving healthcare accessibility through point –of – care technologies. Clin Chem 53:1665–1675

    Article  CAS  PubMed  Google Scholar 

  • Przewodowska A, Zacharzewska B, Chołuj J, Treder K (2015) A One-step, real-time reverse transcription loop-mediated isothermal amplification assay to detect potato virus Y. Am J Potato Res 92:303–311

    Article  CAS  Google Scholar 

  • Quito-Avila DF, Jelkmann W, Tzanetakis I, Keller K, Martin RR (2011) Complete sequence and genetic characterization of Raspberry latent virus, a novel member of the family Reoviridae. Virus Res 155:397–405

    Article  CAS  PubMed  Google Scholar 

  • Reagin MJ, Giesler TL, Merla AL, Resetar-Gerke JM, Kapolka KM, Mamone JA (2003) TempliPhi: A sequencing template preparation procedure that eliminates overnight cultures and DNA purification. J Biomol Tech 14:143–148

    PubMed  PubMed Central  Google Scholar 

  • Rodrigues JCV (2000) The relationships among the pathogen, vector and plant in the citrus leprosis system. Spo Paulo University, Piracicaba, SP, Brazil, PhD Dissertation

    Google Scholar 

  • Rosi NL, Mirkin CA (2005) Nanostructures in biodiagnostics. Chem Rev 105:1547–1562

    Article  CAS  PubMed  Google Scholar 

  • Roy A, Choudhary N, Guillermo LM, Shao J, Govindarajulu A, Achor D, Wei G, Picton DD, Levy L, Nakhla MK et al (2013) A novel virus of the Genus Cilevirus causing symptoms similar to citrus leprosis. Phytopathology 103:488–500

    Article  CAS  PubMed  Google Scholar 

  • Ruiz-Ruiz S, Navarro B, Gisel A, Pena L, Navarro L, Moreno P, di Serio F, Flores R (2011) Citrus tristeza virus infection induces the accumulation of viral small RNAs (21–24 nt) mapping preferentially at the terminal region 3′- of the genomic RNA and affects the host small RNA profile. Plant Mol Biol 75:607–619

    Article  CAS  PubMed  Google Scholar 

  • Safarpour H, Safarnejad MR, Tabatabaei M, Mohsenifar A, Rad F, Basirat M, Shahryari F, Hasanzadeh F (2012) Development of a quantum dots FRET-based biosensor for efficient detection of Polymyxa betae. Can J Plant Pathol 34(4):507–515

    Article  Google Scholar 

  • Safenkova I, Zherdev A, Dzantiev B (2012) Factors influencing the detection limit of the lateral-flow sandwich immunoassay: a case study with potato virus X. Anal Bio anal Chem 403:1595–1605

    Article  CAS  Google Scholar 

  • Salomone A, Roggero P (2002) Host range, seed transmission and detection by ELISA and lateral flow of an Italian isolate of Pepino mosaic virus. J Plant Pathol 84:65–68

    Google Scholar 

  • Salomone A, Bruzzone C, Minuto G, Minuto A, Roggero P (2002) A comparison of lateral flow and ELISA for the detection of Tomato mosaic virus in tomato. J Plant Pathol 84:193

    Google Scholar 

  • Salomone A, Mongelli M, Roggero P, Boscia D (2004) Reliability of detection of Citrus tristeza virus an immunochromatographic flow assay in comparison with ELISA. J Plant Pathol 86:43–48

    CAS  Google Scholar 

  • Sastry KS (2013) Plant virus and viroid diseases in the tropics. Volume-1: Introduction of plant viruses and sub-viral agents, classification, assessment of loss, transmission and diagnosis. Springer, New York p 361

    Google Scholar 

  • Seif AA (1982) Effect of cassava mosaic virus on yield of cassava. Plant Dis 66:661–662

    Article  Google Scholar 

  • Shen W, Tuo D, Yana P, Li X, Zhoua P (2014) Detection of Papaya leaf distortion mosaic virus by reverse-transcription loop-mediated isothermal amplification. J Virol Methods 195:174–179

    Article  CAS  PubMed  Google Scholar 

  • Siljo A, Bhat AI (2014) Reverse transcription loop-mediated isothermal amplification assay for rapid and sensitive detection of Banana bract mosaic virus in cardamom (Elettaria cardamomum). Eur J Plant Pathol 138:209–214

    Article  CAS  Google Scholar 

  • Sip M, Bystricka D, Kmoch S, Noskova L, Hartmannova H, Dedic P (2010) Detection of viral infections by an oligonucleotide microarray. J Virol Methods 165(1):64–70

    Article  CAS  PubMed  Google Scholar 

  • Sugiyama S, Masuta C, Sekiguchi H, Uehara T, Shimura H, Maruta Y (2008) A simple, sensitive, specific detection of mixed infection of multiple plant viruses using macroarray and microtube hybridization. J Virol Methods 153:241–244

    Article  CAS  PubMed  Google Scholar 

  • Thapa V, Melcher U, Wiley GB, Doust A, Palmer MW, Roewe K, Roe BA, Shen G, Roossinck MJ, Wang YM, Kamath N (2012) Detection of members of the Secoviridae in the Tall grass Prairie Preserve, Osage County, Oklahoma, USA. Virus Res 167(1):34–42

    Article  CAS  PubMed  Google Scholar 

  • Thekke-Veetil T, Sabanadzovic S, Keller KE, Martin RR, Tzanetakis IE (2012) Genome organization and sequence diversity of a novel blackberry Ampelovirus. In: Proceedings of the 22nd international conference on virus and other transmissible diseases of fruit crops, Rome, Italy, 3–8 June 2012; Abstract No. 191

    Google Scholar 

  • Thompson JR, Fuchs M, McLane H, Celebi-Toprak F, Fischer KF, Potter JL et al (2014) Profiling viral infections in grapevine using a randomly primed reverse transcription-polymerase chain reaction/macroarray multiplex platform. Phytopathology 104:211–219

    Article  CAS  PubMed  Google Scholar 

  • Tiberini A, Tomassoli L, Barba M, Hadidi A (2010) Oligonucleotide microarray-based and identification of ten major tomato viruses. J Virol Methods 168:133–140

    Article  CAS  PubMed  Google Scholar 

  • Tomlinson JA, Boonham N, Dickinson M (2010) Development and evaluation of a one-hour DNA extraction and loop-mediated isothermal amplification assay for rapid detection of phytoplasmas. Plant Pathol 59:465–471

    Article  CAS  Google Scholar 

  • Tomlinson JA, Ostoja-Starzewska S, Adams IP, Miano DW, Abidrabo P, Kinyua Z, Alicai T, Dickinson MJ, Peters D, Boonham N, Smith J (2013) Loop-mediated isothermal amplification for rapid detection of the causal agents of cassava brown streak disease. J Virol Methods 191:148–154

    Article  CAS  PubMed  Google Scholar 

  • Van Brunschot SL, Bergervoet JHW, Pagendam DE, de Weerdt M, Geering ADW, Drenth A et al (2014) Development of a multiplexed bead-based suspension array for the detection and discrimination of pospiviroid plant pathogens. PLoS One 9(1), e84743

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Vives MC, Velazquez K, Pina JA, Moreno P, Guerri J, Navarro L (2013) Identification of a new enamovirus associated with citrus vein enation disease by deep sequencing of small RNAs. Phytopathology 103:1077–1086

    Article  CAS  PubMed  Google Scholar 

  • Von Lode P (2005) Point-of-care immune-testing: approaching the analytical performance of central laboratory methods. Clin Biochem 38:591–606

    Article  CAS  Google Scholar 

  • Walsha HA, Pietersen G (2013) Rapid detection of Grapevine leafroll-associated virus type 3 using a reverse transcription loop-mediated amplification method. J Virol Methods 194:308–316

    Article  CAS  Google Scholar 

  • Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, DeRisi JL (2002) Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci U S A 99(24):15687–15692

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang YJ, Zhou Y, Li ZA et al (2013) A RT-LAMP assay for detection of citrus tristeza virus. J China Agric Sci 46(3):517–524

    CAS  Google Scholar 

  • Wang ZY, Gu QS, Sun H, Li HL, Sun BJ, Liang XZ, Yuan Y, Liu RL, Shi Y (2014) One-step reverse transcription loop mediated isothermal amplification assay for sensitive and rapid detection of Cucurbit chlorotic yellows virus. J Virol Methods 195:63–66

    Article  CAS  PubMed  Google Scholar 

  • Warren M, Krüger K, Schoeman AS (2005) Potato virus Y ad potato leaf roll virus. University of Pretoria, A South African Perspective

    Google Scholar 

  • Wei T, Pearson MN, Blohm D, Nolte M, Armstrong K (2009) Development of a short oligonucleotide microarray for the detection and identification of multiple potyviruses. J Virol Methods 162:109–118

    Article  CAS  PubMed  Google Scholar 

  • Wetzel T, Candresse T, Macquaire G, Ravelonandro M, Dunez J (1992) A highly sensitive immunocapture polymerase chain reaction method for plum pox potyvirus detection. J Virolological Methods 39(1–2):27–37

    Article  CAS  Google Scholar 

  • Wyant PS, Strohmeier S, Schäfer B, Krenz B, Assunҫão IP, Lima GSDA, Jeske H (2012) Circular DNA genomics (circomics) exemplified for geminiviruses in bean crops and weeds of northeastern Brazil. Virology 427(2):151–157

    Article  CAS  PubMed  Google Scholar 

  • Yoon JY, Choi GS, Cho IS, Choi SK (2014) Development of rapid immune-gold strip kit for on-site diagnosis of tomato spotted wilt virus. Res Plant Disease 20(1):15–20

    Article  CAS  Google Scholar 

  • Yoshikawa N, Yamagishi N, Yaegashi H, Ito T (2012) Deep sequence analysis of viral small RNAs from a green crinkle-diseased apple tree. Petria 22:292–297

    Google Scholar 

  • Zhang Y, Yin J, Li G, Li M, Huang X, Chen H, Zhao W, Zhu S (2010) Oligonucleotide microarray with a minimal number of probes for the detection and identification of thirteen genera of plant viruses. J Virol Methods 167(1):53–60

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Singh K, Kaur R, Qiu W (2011) Association of a novel DNA virus with the grapevine vein-clearing and decline syndrome. Phytopathology 101:1081–1090

    Article  CAS  PubMed  Google Scholar 

  • Zhao L, Feng CH, Li BQ, Hao XA, Liu H, Wu YF, Wang QC (2014) Rapid detection of apple stem grooving virus by reverse transcription loop-mediated isothermal amplification. J Plant Pathol 96(2):407–409

    Article  CAS  Google Scholar 

  • Zhao LM, Li G, Gao Y, Zhu Y, Liu J, Zhu X (2015) Reverse transcription loop-mediated isothermal amplification assay for detecting tomato chlorosis virus. J Virol Methods 213:93–97

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Molecular Virology Lab, ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchiraplalli, 620102, TN, India

    R. Selvarajan & V. Balasubramanian

Authors
  1. R. Selvarajan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. V. Balasubramanian
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to R. Selvarajan .

Editor information

Editors and Affiliations

  1. Department of Biosciences, College of Arts, Science and Commerce, Mody University of Science and Technology, Sikar, Rajasthan, India

    Rajarshi Kumar Gaur

  2. Department of Plant Protection, Section of Phytopathology, Institute of Soil Science, Agrotechnologies and Plant Protection “Nikola Pushkarov”, Sofia, Bulgaria

    Nikolay Manchev Petrov

  3. ICAR-National Research Centre on Plant BiotechnologyLBS Centre, IARI Campus, Delhi, India

    Basavaprabhu L. Patil

  4. Department of Phytopathology, Institute of Soil Science, Agrotechnologies and Plant Protection “Nikola Pushkarov”, Sofia, Bulgaria

    Mariya Ivanova Stoyanova

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Science+Business Media Singapore

About this chapter

Cite this chapter

Selvarajan, R., Balasubramanian, V. (2016). Cutting-Edge Technologies for Detection of Plant Viruses in Vegetatively Propagated Crop Plants. In: Gaur, R., Petrov, N., Patil, B., Stoyanova, M. (eds) Plant Viruses: Evolution and Management. Springer, Singapore. https://doi.org/10.1007/978-981-10-1406-2_5

Download citation

Publish with us

Policies and ethics

Search

Navigation