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Reverse Transcription–Recombinase Polymerase Amplification Assay for the Detection of Sugarcane Streak Mosaic Virus in Sugarcane

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Abstract

Sugarcane streak mosaic virus (SCSMV, genus Poacevirus) causes sugarcane mosaic disease and leads to considerable economic losses. However, current methods for SCSMV diagnosis are limited. In this study, a novel isothermal assay was established on the basis of reverse transcription–recombinase polymerase amplification (RT-RPA) and evaluated in terms of its ability to detect SCSMV. The established RT-RPA assay with high specificity and reliability was 100-fold more sensitive than the RT-polymerase chain reaction. The evaluation of the temperature limit revealed that the assay had a flexible reaction temperature (26–46 °C), thereby indicating that the reaction mixture can be incubated with simple heating equipment, ambient temperature, or even human body heat. Time limit assessment results revealed that SCSMV can be detected in 5 min at 38 °C and in 20 min at 26 °C, thereby suggesting that the assay was rapid for SCSMV detection. Overall, the RT-RPA assay was specific, sensitive, reliable, and rapid for SCSMV detection, with a flexible and easily reachable reaction temperature. Thus, it can be an ideal method for SCSMV detection in sugarcane.

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Abbreviations

CP:

Coat protein

ELISA:

Enzyme-linked immunosorbent assay

IC:

Immunocapture

PCR:

Polymerase chain reaction

RPA:

Recombinase polymerase amplification

RT:

Reverse transcription

SCSMV:

Sugarcane streak mosaic virus

SMD:

Sugarcane mosaic disease

TriMV:

Triticum mosaic virus

References

  • Abd, E.W.A., P. Patel, O. Faye, S. Thaloengsok, D. Heidenreich, P. Matangkasombut, K. Manopwisedjaroen, A. Sakuntabhai, A.A. Sall, and F.T. Hufert. 2015. Recombinase polymerase amplification assay for rapid diagnostics of dengue infection. PLoS ONE 10(6): e0129682.

    Article  Google Scholar 

  • Amer, H.M., E.W.A. Abd, M.A. Shalaby, F.N. Almajhdi, F.T. Hufert, and M. Weidmann. 2013. A new approach for diagnosis of bovine coronavirus using a reverse transcription recombinase polymerase amplification assay. Journal of Virological Methods 193(2): 337–340.

    Article  CAS  Google Scholar 

  • Babu, B., B.K. Washburn, S.H. Miller, K. Poduch, T. Sarigul, G.W. Knox, F.M. Ochoa-Corona, and M.L. Paret. 2016. A rapid assay for detection of Rose rosette virus using reverse transcription–recombinase polymerase amplification using multiple gene targets. Journal of Virological Methods 240: 78–98.

    Article  Google Scholar 

  • Bagyalakshmi, K., B. Parameswari, C. Chinnaraja, R. Karuppaiah, V.G. Kumar, and R. Viswanathan. 2012. Genetic variability and potential recombination events in the HC-Pro gene of Sugarcane streak mosaic virus. Archives of Virology 157(7): 1371–1375.

    Article  CAS  Google Scholar 

  • Boyle, D.S., D.A. Lehman, L. Lillis, D. Peterson, M. Singhal, N. Armes, M. Parker, O. Piepenburg, and J. Overbaugh. 2013. Rapid detection of HIV-1 proviral DNA for early infant diagnosis using recombinase polymerase amplification. Mbio 4(2): 49–52.

    Article  Google Scholar 

  • Chandran, V., and P. Gajjeraman. 2013. A simple precipitation approach for isolation and enrichment of Sugarcane streak mosaic virus. Sugar Tech 15(4): 417–419.

    Article  CAS  Google Scholar 

  • Chatenet, M., C. Mazarin, J.C. Girard, E. Fernandez, D. Gargani, G.P. Rao, M. Royer, B. Lockhart, and P. Rott. 2005. Detection of Sugarcane streak mosaic virus in sugarcane from several Asian countries. Proceedings-International Society of Sugar Cane Technology 25: 656–663.

    Google Scholar 

  • Compton, J. 1991. Nucleic acid sequence-based amplification. Nature 350(6313): 91–92.

    Article  CAS  Google Scholar 

  • Crannell, Z.A., B. Rohrman, and R. Richards-Kortum. 2014. Equipment-free incubation of recombinase polymerase amplification reactions using body heat. PLoS ONE 9(11): e112146.

    Article  Google Scholar 

  • Euler, M., Y.J. Wang, D. Heidenreich, P. Patel, O. Strohmeier, S. Hakenberg, M. Niedrig, F.T. Hufert, and M. Weidmann. 2013. Development of a panel of recombinase polymerase amplification assays for detection of biothreat agents. Journal of Clinical Microbiology 51(4): 1110–1117.

    Article  CAS  Google Scholar 

  • Feng, X.Y., L.B. Shen, W.Z. Wang, J.G. Wang, Z.Y. Cao, C.L. Feng, T.T. Zhao, and S.Z. Zhang. 2018. Development of a reverse transcription–recombinase polymerase amplification assay for detection of Sugarcane yellow leaf virus. Sugar Tech. https://doi.org/10.1007/s12355-018-0602-6.

    Article  Google Scholar 

  • Fu, W.L., S.R. Sun, H.Y. Fu, R.K. Chen, J.W. Su, and S.J. Gao. 2015. A one-step real-time RT-PCR assay for the detection and quantitation of Sugarcane streak mosaic virus. BioMed Research International 2015(2): 1–9.

    Google Scholar 

  • Gonzales, F.R., M. Castillo, T. Avina, M. Watson, M. Miyano, and M. Longiaru. 1995. Specific detection of HBV DNA in serum by transcription mediated amplification. Hepatology 22(4): 267A.

    Article  Google Scholar 

  • Gusev, Y., J. Sparkowski, A. Raghunathan, H. Ferguson, J. Montano, N. Bogdan, B. Schweitzer, S. Wiltshire, S.F. Kingsmore, W. Maltzman, and V. Wheeler. 2001. Rolling circle amplification: a new approach to increase sensitivity for immunohistochemistry and flow cytometry. American Journal of Pathology 159(1): 63–69.

    Article  CAS  Google Scholar 

  • He, Z., W.F. Li, R. Yasaka, Y.K. Huang, and Z.X. Zhang. 2014. Molecular variability of Sugarcane streak mosaic virus in China based on an analysis of the P1 and CP protein coding regions. Archives of Virology 159(5): 1149–1154.

    Article  CAS  Google Scholar 

  • Hema, M., N. Kirthi, P. Sreenivasulu, and H.S. Savithri. 2003. Development of recombinant coat protein antibody based IC-RT-PCR for detection and discrimination of Sugarcane streak mosaic virus isolates from Southern India. Archives of Virology 148(6): 1185–1193.

    Article  CAS  Google Scholar 

  • Hema, M., H.S. Savithri, and P. Sreenivasulu. 2001. Antibody and nucleic acid probe-based techniques for detection of Sugarcane streak mosaic virus causing mosaic disease of sugarcane in India. Current Science 81(8): 1105–1108.

    CAS  Google Scholar 

  • Hema, M., P. Sreenivasulu, and H.S. Savithri. 2002. Taxonomic position of Sugarcane streak mosaic virus in the family Potyviridae. Archives of Virology 147(10): 1997–2007.

    Article  CAS  Google Scholar 

  • Kasemsin, P., P. Chiemsombat, and R. Hongprayoon. 2016. Characterization and genetic variation of Sugarcane streak mosaic virus, a Poacevirus infecting sugarcane in Thailand. Modern Applied Science 10(4): 137–149.

    Article  CAS  Google Scholar 

  • Li, W.F., X.Y. Wang, Y.K. Huang, H.L. Shan, R.Y. Zhang, J. Yin, and Z.M. Luo. 2016. Molecular detection techniques of sugarcane important diseases. Plant Protection 42(5): 125–130. (In Chinese).

    CAS  Google Scholar 

  • Liang, S.S., O.J. Alabi, M.B. Damaj, W.L. Fu, S.R. Sun, H.Y. Fu, R.K. Chen, T.E. Mirkov, and S.J. Gao. 2016. Genomic variability and molecular evolution of Asian isolates of Sugarcane streak mosaic virus. Archives of Virology 161(6): 1493–1503.

    Article  CAS  Google Scholar 

  • Londoño, M.A., C.L. Harmon, and J.E. Polston. 2016. Evaluation of recombinase polymerase amplification for detection of begomoviruses by plant diagnostic clinics. Virology Journal 13(1): 1–9.

    Article  Google Scholar 

  • Mekuria, T.A., S.L. Zhang, and K.C. Eastwell. 2014. Rapid and sensitive detection of Little cherry virus 2 using isothermal reverse transcription–recombinase polymerase amplification. Journal of Virological Methods 205: 24–30.

    Article  CAS  Google Scholar 

  • Notomi, T., H. Okayama, H. Masubuchi, T. Yonekawa, K. Watanabe, N. Amino, and T. Hase. 2000. Loop-mediated isothermal amplification of DNA. Nucleic Acids Research 28(12): e63.

    Article  CAS  Google Scholar 

  • Piepenburg, O., C.H. Williams, D.L. Stemple, and N.A. Armes. 2006. DNA detection using recombination proteins. PLoS Biology 4(7): 1115–1121.

    Article  CAS  Google Scholar 

  • Prabowo, D.B., T. Hadiastono, T. Himawan, and L.K. Putra. 2014. Detection disease of Sugarcane streak mosaic virus (SCSMV) via serological test on sugarcane (Saccharum officinarum L.), weed and insect vector. International Journal of Science and Research 3(1): 88–92.

    Google Scholar 

  • Putra, L.K., T.H. Astono, S.R.C. Syamsidi, and S. Djauhari. 2015a. Dispersal, yield losses and varietal resistance of Sugarcane streak mosaic virus (SCSMV) in Indonesia. International Journal of Virology 11(1): 32–40.

    Article  CAS  Google Scholar 

  • Putra, L.K., T.H. Astono, S.R.C. Syamsidi, and S. Djauhari. 2015b. Investigation on transmission modes and host range of Sugarcane streak mosaic virus in sugarcane (Saccharum officinarum L.) in Indonesia. Journal of Agricultural and Crop Research 3(4): 59–66.

    Google Scholar 

  • Putra, L.K., A. Kristini, and E.M.A. Achadian. 2014. Sugarcane streak mosaic virus in Indonesia: distribution, characterisation, yield losses and management approaches. Sugar Tech 16(4): 392–399.

    Article  CAS  Google Scholar 

  • Rao, G.P., M. Chatenet, J.G. Girard, and P. Rott. 2006. Distribution of sugarcane mosaic and sugarcane streak mosaic virus in India. Sugar Tech 8(1): 79–81.

    Article  Google Scholar 

  • Rosser, A., D. Rollinson, M. Forrest, and B.L. Webster. 2015. Isothermal recombinase polymerase amplification (RPA) of Schistosoma haematobium DNA and oligochromatographic lateral flow detection. Parasites and Vectors 8(1): 446–450.

    Article  CAS  Google Scholar 

  • Silva, G., M. Bömer, C. Nkere, P.L. Kumar, and S.E. Seal. 2015. Rapid and specific detection of Yam mosaic virus by reverse-transcription recombinase polymerase amplification. Journal of Virological Methods 222: 138–144.

    Article  CAS  Google Scholar 

  • Singh, D., and G.P. Rao. 2010. Sudan grass (Sorghum sudanense Stapf): a new Sugarcane streak mosaic virus mechanical host. Guangxi Agricultural Sciences 41(5): 436–438.

    Google Scholar 

  • Srinivas, K.P., C.V. Subba Reddy, B. Ramesh, P.L. Kumar, and P. Sreenivasulu. 2010. Identification of a virus naturally infecting sorghum in India as Sugarcane streak mosaic virus. European Journal of Plant Pathology 127: 13–19.

    Article  CAS  Google Scholar 

  • Subba Reddy, C.V., P. Sreenivasulu, and G. Sekhar. 2011. Duplex-immunocapture-RT-PCR for detection and discrimination of two distinct potyviruses naturally infecting sugarcane (Saccharum spp. hybrid). Indian Journal of Experimental Biology 49(1): 68–73.

    Google Scholar 

  • Tatineni, S., F. Qu, R. Li, T.J. Morris, and R. French. 2012. Triticum mosaic poacevirus enlists P1 rather than HC-Pro to suppress RNA silencing-mediated host defense. Virology 433(1): 104–115.

    Article  CAS  Google Scholar 

  • Tomita, N., Y. Mori, H. Kanda, and T. Notomi. 2008. Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nature Protocols 3(5): 877–882.

    Article  CAS  Google Scholar 

  • Vincent, M., Y. Xu, and H. Kong. 2004. Helicase-dependent isothermal DNA amplification. EMBO Reports 5(8): 795–800.

    Article  CAS  Google Scholar 

  • Viswanathan, R., M. Balamuralikrishnan, and R. Karuppaiah. 2007. Sugarcane mosaic in India: a cause of combined infection of Sugarcane mosaic virus and Sugarcane streak mosaic virus. Sugar Cane International 25(2): 6–14.

    CAS  Google Scholar 

  • Viswanathan, R., M. Balamuralikrishnan, and R. Karuppaiah. 2008. Characterization and genetic diversity of Sugarcane streak mosaic virus causing mosaic in sugarcane. Virus Genes 36(3): 553–564.

    Article  CAS  Google Scholar 

  • Walker, G.T., M.S. Fraiser, J.L. Schram, M.C. Little, J.G. Nadeau, and D.P. Malinowski. 1992. Strand displacement amplification–an isothermal, in vitro DNA amplification technique. Nucleic Acids Research 20(7): 1691–1696.

    Article  CAS  Google Scholar 

  • Wang, Z.P., H.J. Sun, Q. Guo, S.Q. Xu, J.H. Wang, S.H. Lin, and M.Q. Zhang. 2017. Artificial inoculation method of pokkah boeng disease of sugarcane and screening of resistant germplasm resources in subtropical China. Sugar Tech 19(3): 1–10.

    Article  Google Scholar 

  • Xie, Y.J., M.Q. Wang, D.L. Xu, R.H. Li, and G.H. Zhou. 2009. Simultaneous detection and identification of four sugarcane viruses by one-step RT-PCR. Journal of Virological Methods 162(1–2): 64–68.

    Article  CAS  Google Scholar 

  • Xu, C., L. Li, W.J. Jin, and Y.S. Wan. 2014. Recombinase polymerase amplification (RPA) of CaMV-35S promoter and nos terminator for rapid detection of genetically modified crops. International Journal of Molecular Sciences 15: 18197–18205.

    Article  CAS  Google Scholar 

  • Zhang, S.L., M. Ravelonandro, P. Russell, N. Mcowen, P. Briard, S. Bohannon, and A. Vrient. 2014. Rapid diagnostic detection of plum pox virus in Prunus plants by isothermal AmplifyRP® using reverse transcription–recombinase polymerase amplification. Journal of Virological Methods 207(3): 114–120.

    Article  CAS  Google Scholar 

  • Zhou, D.G., J.L. Guo, L.Q. Xu, S.W. Gao, Q.L. Lin, Q.B. Wu, L.G. Wu, and Y.X. Que. 2014. Establishment and application of a loop-mediated isothermal amplification (LAMP) system for detection of cry1Ac transgenic sugarcane. Scientific Reports 4(6184): 4912.

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This study is supported by the National Natural Science Foundation of China (31771865) and the Sugar Crop Research System (CARS-170301).

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Authors and Affiliations

  1. Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No. 4, College Road, Longhua District, Haikou, 571101, Hainan, China

    Xiao-Yan Feng, Lin-Bo Shen, Wen-Zhi Wang, Jun-Gang Wang, Zheng-Ying Cao & Shu-Zhen Zhang

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  1. Xiao-Yan Feng
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  2. Lin-Bo Shen
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  3. Wen-Zhi Wang
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  4. Jun-Gang Wang
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  5. Zheng-Ying Cao
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Contributions

SZ-Z conceived and designed the experiments. XY-F performed the experiments, result analysis, and manuscript drafting. LB-S, WZ-W, JG-W, and ZY-C revised the manuscript. All authors have read and approved the final manuscript.

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Correspondence to Shu-Zhen Zhang.

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Feng, XY., Shen, LB., Wang, WZ. et al. Reverse Transcription–Recombinase Polymerase Amplification Assay for the Detection of Sugarcane Streak Mosaic Virus in Sugarcane. Sugar Tech 21, 645–652 (2019). https://doi.org/10.1007/s12355-018-0675-2

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