DOI QR코드

DOI QR Code

Highly Sensitive Detection of Low-Abundance White Spot Syndrome Virus by a Pre-Amplification PCR Method

  • Pan, Xiaoming (College of Food Science and Engineering, Ocean University of China) ;
  • Zhang, Yanfang (College of Food Science and Engineering, Ocean University of China) ;
  • Sha, Xuejiao (College of Food Science and Nutritional Engineering, China Agriculture University) ;
  • Wang, Jing (College of Food Science and Engineering, Ocean University of China) ;
  • Li, Jing (College of Food Science and Engineering, Ocean University of China) ;
  • Dong, Ping (College of Food Science and Engineering, Ocean University of China) ;
  • Liang, Xingguo (College of Food Science and Engineering, Ocean University of China)
  • Received : 2016.06.24
  • Accepted : 2016.12.09
  • Published : 2017.03.28

Abstract

White spot syndrome virus (WSSV) is a major threat to the shrimp farming industry and so far there is no effective therapy for it, and thus early diagnostic of WSSV is of great importance. However, at the early stage of infection, the extremely low-abundance of WSSV DNA challenges the detection sensitivity and accuracy of PCR. To effectively detect low-abundance WSSV, here we developed a pre-amplification PCR (pre-amp PCR) method to amplify trace amounts of WSSV DNA from massive background genomic DNA. Combining with normal specific PCR, 10 copies of target WSSV genes were detected from ${\sim}10^{10}$ magnitude of backgrounds. In particular, multiple target genes were able to be balanced amplified with similar efficiency due to the usage of the universal primer. The efficiency of the pre-amp PCR was validated by nested-PCR and quantitative PCR, and pre-amp PCR showed higher efficiency than nested-PCR when multiple targets were detected. The developed method is particularly suitable for the super early diagnosis of WSSV, and has potential to be applied in other low-abundance sample detection cases.

Keywords

References

  1. Escobedo-Bonilla CM, Alday-Sanz V, Wille M, Sorgeloos P, Pensaert M, Nauwynck H. 2008. A review on the morphology, molecular characterization, morphogenesis and pathogenesis of white spot syndrome virus. J. Fish Dis. 31: 1-18.
  2. Lightner D, Redman R, Pantoja C, Tang K, Noble B, Schofield P, et al. 2012. Historic emergence, impact and current status of shrimp pathogens in the Americas. J. Invertebr. Pathol. 110: 174-183. https://doi.org/10.1016/j.jip.2012.03.006
  3. van Hulten MC, Witteveldt J, Peters S, Kloosterboer N, Tarchini R, Fiers M, et al. 2001. The white spot syndrome virus DNA genome sequence. Virology 286: 7-22. https://doi.org/10.1006/viro.2001.1002
  4. Yang F, He J, Lin X, Li Q, Pan D, Zhang X, Xu X. 2001. Complete genome sequence of the shrimp white spot bacilliform virus. J. Virol. 75: 11811-11820. https://doi.org/10.1128/JVI.75.23.11811-11820.2001
  5. Chou H, Huang C, Wang C, Chiang H, Lo C. 1995. Pathogenicity of a baculovirus infection causing white spot syndrome in cultured penaeid shrimp in Taiwan. Dis. Aquat. Organ. 23: 165-173. https://doi.org/10.3354/dao023165
  6. Sanchez-Martinez JG, Aguirre-Guzman G, Mejia-Ruiz H. 2007. White spot syndrome virus in cultured shrimp: a review. Aquac. Res. 38: 1339-1354. https://doi.org/10.1111/j.1365-2109.2007.01827.x
  7. Sanchez-Paz A. 2010. White spot syndrome virus: an overview on an emergent concern. Vet. Res. 41: 43. https://doi.org/10.1051/vetres/2010015
  8. Hameed AS, Balasubramanian G, Musthaq SS, Yoganandhan K. 2003. Experimental infection of twenty species of Indian marine crabs with white spot syndrome virus (WSSV). Dis. Aquat. Organ. 57: 157-161. https://doi.org/10.3354/dao057157
  9. Li Q, Zhang J, Chen Y, Yang F. 2003. White spot syndrome virus (WSSV) infectivity for Artemia at different developmental stages. Dis. Aquat. Organ. 57: 261-264. https://doi.org/10.3354/dao057261
  10. Liu BH, Lin YC, Ho CS, Yang CC, Chang YT, Chang JF, et al. 2015. A novel detection platform for shrimp white spot syndrome virus using an ICP11-dependent immunomagnetic reduction (IMR) assay. PLoS One 10: e0138207. https://doi.org/10.1371/journal.pone.0138207
  11. Xia X, Yu Y, Weidmann M, Pan Y, Yan S, Wang Y. 2014. Rapid detection of shrimp white spot syndrome virus by real time, isothermal recombinase polymerase amplification assay. PLoS One 9: e104667. https://doi.org/10.1371/journal.pone.0104667
  12. Kono T, Savan R, Sakai M, Itami T. 2004. Detection of white spot syndrome virus in shrimp by loop-mediated isothermal amplification. J. Virol. Methods 115: 59-65. https://doi.org/10.1016/j.jviromet.2003.09.015
  13. Leal CA, Carvalho AF, Leite RC, Figueiredo HC. 2014. Development of duplex real-time PCR for the detection of WSSV and PstDV1 in cultivated shrimp. BMC Vet. Res. 10: 150. https://doi.org/10.1186/1746-6148-10-150
  14. Tsai Y, Wang H, Lo C, Tang-Nelson K, Lightner D, Ou B, et al. 2014. Validation of a commercial insulated isothermal PCRbased POCKIT test for rapid and easy detection of white spot syndrome virus infection in Litopenaeus vannamei. PLoS One 9: e90545. https://doi.org/10.1371/journal.pone.0090545
  15. Zhao Y, Yin W, Yue Z, Li B. 2014. A sensitive and specific hyperbranched rolling circle amplification assay and test strip for white spot syndrome virus. J. AOAC Int. 97: 1410-1415. https://doi.org/10.5740/jaoacint.13-387
  16. Musthaq SS, Sudhakaran R, Ahmed VI, Balasubramanian G, Hameed AS. 2006. Variability in the tandem repetitive DNA sequences of white spot syndrome virus (WSSV) genome and suitability of VP28 gene to detect different isolates of WSSV from India. Aquaculture 256: 34-41. https://doi.org/10.1016/j.aquaculture.2006.01.036
  17. Andersson D, Akrap N, Svec D, Godfrey TE, Kubista M, Landberg G, Stahlberg A. 2015. Properties of targeted preamplification in DNA and cDNA quantification. Expert Rev. Mol. Diagn. 15: 1085-1100. https://doi.org/10.1586/14737159.2015.1057124
  18. Korenkova V, Scott J, Novosadova V, Jindrichova M, Langerova L, Svec D, et al. 2015. Pre-amplification in the context of high-throughput qPCR gene expression experiment. BMC Mol. Biol. 16: 1. https://doi.org/10.1186/s12867-015-0029-5
  19. Pingoud A, Fuxreiter M, Pingoud V, Wende W. 2005. Type II restriction endonucleases: structure and mechanism. Cell. Mol. Life Sci. 62: 685-707. https://doi.org/10.1007/s00018-004-4513-1
  20. Piggott MP, Bellemain E, Taberlet P, Taylor AC. 2004. A multiplex pre-amplification method that significantly improves microsatellite amplification and error rates for faecal DNA in limiting conditions. Conserv. Genet. 5: 417-420. https://doi.org/10.1023/B:COGE.0000031138.67958.44
  21. Arandjelovic M, Guschanski K, Schubert G, Harris TR, Thalmann O, Siedel H, Vigilant L. 2009. Two-step multiplex polymerase chain reaction improves the speed and accuracy of genotyping using DNA from noninvasive and museum samples. Mol. Ecol. Resour. 9: 28-36. https://doi.org/10.1111/j.1755-0998.2008.02387.x
  22. Seetang-Nun Y, Jaroenram W, Sriurairatana S, Suebsing R, Kiatpathomchai W. 2013. Visual detection of white spot syndrome virus using DNA-functionalized gold nanoparticles as probes combined with loop-mediated isothermal amplification. Mol. Cell. Probes 27: 71-79. https://doi.org/10.1016/j.mcp.2012.11.005
  23. Tsai Y, Lin Y, Chou P, Teng P, Lee P. 2012. Detection of white spot syndrome virus by polymerase chain reaction performed under insulated isothermal conditions. J. Virol. Methods 181: 134-137. https://doi.org/10.1016/j.jviromet.2012.01.017
  24. Mendoza-Cano F, Sanchez-Paz A. 2013. Development and validation of a quantitative real-time polymerase chain assay for universal detection of the white spot syndrome virus in marine crustaceans. Virol. J. 10: 1. https://doi.org/10.1186/1743-422X-10-1
  25. Pan X, Wan B, Li C, Liu Y, Wang J, Mou H, Liang X. 2014. A novel whole genome amplification method using type IIS restriction enzymes to create overhangs with random sequences. J. Biotechnol. 184: 1-6. https://doi.org/10.1016/j.jbiotec.2014.04.020
  26. O’Geen H, Nicolet CM, Blahnik K, Green R, Farnham PJ. 2006. Comparison of sample preparation methods for ChIPchip assays. Biotechniques 41: 577. https://doi.org/10.2144/000112268
  27. Zhou L, Pollard AJ. 2012. A novel method of selective removal of human DNA improves PCR sensitivity for detection of Salmonella Typhi in blood samples. BMC Infect. Dis. 12: 164. https://doi.org/10.1186/1471-2334-12-164
  28. Bacconi A, Richmond GS, Baroldi MA, Laffler TG, Blyn LB, Carolan HE, et al. 2014. Improved sensitivity for molecular detection of bacterial and Candida infections in blood. J. Clin. Microbiol. 52: 3164-3174. https://doi.org/10.1128/JCM.00801-14
  29. Natividad KDT, Nomura N, Matsumura M. 2008. Detection of white spot syndrome virus DNA in pond soil using a 2-step nested PCR. J. Virol. Methods 149: 28-34. https://doi.org/10.1016/j.jviromet.2008.01.013
  30. Peinado-Guevara LI, Lopez-Meyer M. 2006. Detailed monitoring of white spot syndrome virus (WSSV) in shrimp commercial ponds in Sinaloa, Mexico by nested PCR. Aquaculture 251: 33-45. https://doi.org/10.1016/j.aquaculture.2005.05.022
  31. Marks H, Goldbach R, Vlak J, van Hulten M. 2004. Genetic variation among isolates of white spot syndrome virus. Arch. Virol. 149: 673-697. https://doi.org/10.1007/s00705-003-0248-9
  32. Chun J, Kim K, Hwang I, Kim Y, Lee D, Lee I, Kim J. 2007. Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene. Nucleic Acids Res. 35: e40. https://doi.org/10.1093/nar/gkm051

Cited by

  1. Causative agent, diagnosis and management of white spot disease in shrimp: A review vol.12, pp.2, 2017, https://doi.org/10.1111/raq.12352
  2. Simultaneous detection of multiple bacterial and viral aquatic pathogens using a fluorogenic loop‐mediated isothermal amplification‐based dual‐sample microfluidic chip vol.44, pp.4, 2021, https://doi.org/10.1111/jfd.13325