Virus Genes

, Volume 54, Issue 4, pp 536–542 | Cite as

Next-generation sequencing library preparation method for identification of RNA viruses on the Ion Torrent Sequencing Platform

  • Guiqian Chen
  • Yuan Qiu
  • Qingye Zhuang
  • Suchun Wang
  • Tong Wang
  • Jiming Chen
  • Kaicheng WangEmail author


Next generation sequencing (NGS) is a powerful tool for the characterization, discovery, and molecular identification of RNA viruses. There were multiple NGS library preparation methods published for strand-specific RNA-seq, but some methods are not suitable for identifying and characterizing RNA viruses. In this study, we report a NGS library preparation method to identify RNA viruses using the Ion Torrent PGM platform. The NGS sequencing adapters were directly inserted into the sequencing library through reverse transcription and polymerase chain reaction, without fragmentation and ligation of nucleic acids. The results show that this method is simple to perform, able to identify multiple species of RNA viruses in clinical samples.


Next-generation sequencing Library preparation RNA virus 



This study was funded by the National Key Research and Development Program of China (2017YFC120050) and China Animal Health and Epidemiology Center Innovation Fund (2015IF-0004FF).

Author contributions

KW supervised the research, contributed to the design and development of the experimental work, and wrote the paper. GC contributed to the experimental work and the bioinformatics analysis. YQ and QZ contributed to the experimental work. SW performed the revise of the language. TW performed the bioinformatics analysis.

Compliance with ethical standards

Conflict of interest

Kaicheng Wang, Guiqian Chen, Yuan Qiu, Qingye Zhuang, Suchun Wang, and Tong Wang have received research grants from China Animal Health and Epidemiology Center. All the authors declare that they have no conflict of interest.

Informed consent

Informed consent was obtained from all individual participants included in the study.

Research involving human participants and/or animals

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.


  1. 1.
    F.A. Al-Ateeg, Saudi Med. J. 24, 794–798 (2003)PubMedGoogle Scholar
  2. 2.
    W. Li, Z. Shi, M. Yu, W. Ren, C. Smith, J.H. Epstein, H. Wang, G. Crameri, Z. Hu, H. Zhang, J. Zhang, J. McEachern, H. Field, P. Daszak, B.T. Eaton, S. Zhang, L.F. Wang, Science 310, 676–679 (2005)CrossRefPubMedGoogle Scholar
  3. 3.
    J. Parry, BMJ 346, f2568 (2013)CrossRefPubMedGoogle Scholar
  4. 4.
    J. Chen, B.X. Huang, Guidelines of Epidemilogical Surveys of Important Animal Infectious Diseases (Chinese Agricultural Science and Technology Press, Beijing, 2000)Google Scholar
  5. 5.
    K.C. Wang, G.Q. Chen, W.M. Jiang, S. Liu, G.Y. Hou, J.M. Yu, J.P. Li, Q.Y. Zhuang, J.M. Chen, Genome Announc. 1, e0004513 (2013)PubMedCrossRefGoogle Scholar
  6. 6.
    N. Fischer, D. Indenbirken, T. Meyer, M. Lutgehetmann, H. Lellek, M. Spohn, M. Aepfelbacher, M. Alawi, A. Grundhoff, J. Clin. Microbiol. 53, 2238–2250 (2015)CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    A. Routh, P. Ordoukhanian, J.E. Johnson, J. Mol. Biol. 424, 257–269 (2012)CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Y. Wang, B. Lupiani, S.M. Reddy, S.J. Lamont, H. Zhou, Poult. Sci. 93, 485–493 (2014)CrossRefPubMedGoogle Scholar
  9. 9.
    M.A. Quail, M. Smith, P. Coupland, T.D. Otto, S.R. Harris, T.R. Connor, A. Bertoni, H.P. Swerdlow, Y. Gu, BMC Genomics 13, 341 (2012)CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Y. Qiu, J.M. Chen, T. Wang, G.Y. Hou, Q.Y. Zhuang, R. Wu, K.C. Wang, Virus Res. 237, 22–26 (2017)CrossRefPubMedGoogle Scholar
  11. 11.
    R.C. Edgar, Nucleic Acids Res. 32, 1792–1797 (2004)CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    G.Q. Chen, Q.Y. Zhuang, K.C. Wang, S. Liu, J.Z. Shao, W.M. Jiang, G.Y. Hou, J.P. Li, J.M. Yu, Y.P. Li, J.M. Chen, PLoS ONE 8, e72918 (2013)CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    N. Buisine, R. Chalmers, Biotechniques 37, 987–989 (2004)CrossRefPubMedGoogle Scholar
  14. 14.
    D.H. Huson, A.F. Auch, J. Qi, S.C. Schuster, Genome Res. 17, 377–386 (2007)CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    A. Djikeng, R. Halpin, R. Kuzmickas, J. Depasse, J. Feldblyum, N. Sengamalay, C. Afonso, X. Zhang, N.G. Anderson, E. Ghedin, D.J. Spiro, BMC Genomics 9, 5 (2008)CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    G. Palacios, J. Druce, L. Du, T. Tran, C. Birch, T. Briese, S. Conlan, P.L. Quan, J. Hui, J. Marshall, J.F. Simons, M. Egholm, C.D. Paddock, W.J. Shieh, C.S. Goldsmith, S.R. Zaki, M. Catton, W.I. Lipkin, N. Engl. J. Med. 358, 991–998 (2008)CrossRefPubMedGoogle Scholar
  17. 17.
    M. Kuroda, H. Katano, N. Nakajima, M. Tobiume, A. Ainai, T. Sekizuka, H. Hasegawa, M. Tashiro, Y. Sasaki, Y. Arakawa, S. Hata, M. Watanabe, T. Sata, PLoS ONE 5, e10256 (2010)CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    L.K. McMullan, M. Frace, S.A. Sammons, T. Shoemaker, S. Balinandi, J.F. Wamala, J.J. Lutwama, R.G. Downing, U. Stroeher, A. MacNeil, S.T. Nichol, Virology 422, 1–5 (2012)CrossRefPubMedGoogle Scholar
  19. 19.
    C.L. Afonso, Biotechniques 43, 188, 190, 192 (2007)CrossRefPubMedGoogle Scholar
  20. 20.
    H.A. Westbury, B. Sinkovic, Aust. Vet. J. 54, 81–85 (1978)CrossRefPubMedGoogle Scholar
  21. 21.
    S.R. Head, H.K. Komori, S.A. LaMere, T. Whisenant, F. Van Nieuwerburgh, D.R. Salomon, P. Ordoukhanian, Biotechniques 56, 61–64, 66, 68, passim (2014)CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Guiqian Chen
    • 1
    • 2
  • Yuan Qiu
    • 1
  • Qingye Zhuang
    • 1
  • Suchun Wang
    • 1
  • Tong Wang
    • 1
  • Jiming Chen
    • 1
  • Kaicheng Wang
    • 1
    Email author
  1. 1.China Animal Health and Epidemiology CenterQingdaoChina
  2. 2.College of MedicineJiaxing UniversityJiaxingChina

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