Volume 96, Issue 2
  • ISSN: 0002-9637
  • E-ISSN: 1476-1645



Hantaan virus (HTNV), identified in the striped field mouse (), belongs to the genus of the family and contains tripartite RNA genomes, small (S), medium (M), and large (L) segments. HTNV is a major causative for hemorrhagic fever with renal syndrome (HFRS) with fatality rates ranging from 1% to 15% in the Republic of Korea (ROK) and China. Defining of HTNV whole-genome sequences and isolation of the infectious particle play a critical role in the characterization and preventive and therapeutic strategies of hantavirus outbreaks. Next-generation sequencing (NGS) provides an advanced tool for massive genomic sequencing of viruses. However, the isolation of viral infectious particles is a huge obstacle to investigate and develop anti-virals for hantaviruses. Here, we report 12 HTNV isolates from lung tissues of the striped field mouse in the highly HFRS-endemic areas. Sequence-independent, single-primer amplification (SISPA) NGS was attempted to recover the genomic sequences of HTNV isolates. The nucleotide sequence of HTNV S, M, and L segments were covered up to 99.4–100%, 97.5–100%, and 95.6–99.8%, respectively, based on the full length of the prototype HTNV 76-118. The whole-genome sequencing of HTNV isolates was accomplished by additional reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification cDNA ends (RACE) PCR. In conclusion, this study will lead to the attempt and usage of SISPA NGS technologies to delineate the whole-genome sequence of hantaviruses, providing a new era of viral genomics for the surveillance, trace, and disease risk management of HFRS incidents.


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  1. Elliott RM, , 1990. Molecular biology of the Bunyaviridae. J Gen Virol 71: 501522.[Crossref]
  2. Bi Z, Formenty PB, Roth CE, , 2008. Hantavirus infection: a review and global update. J Infect Dev Ctries 2: 323.[Crossref]
  3. Schmaljohn C, Hjelle B, , 1997. Hantaviruses: a global disease problem. Emerg Infect Dis 3: 95104.[Crossref]
  4. Lee HW, Lee PW, Johnson KM, , 2004. Isolation of the etiologic agent of Korean hemorrhagic fever. 1978. J Infect Dis 190: 17111721.[Crossref]
  5. Song JW, Baek LJ, Kim SH, Kho EY, Kim JH, Yanagihara R, Song KJ, , 2000. Genetic diversity of Apodemus agrarius-borne hantaan virus in Korea. Virus Genes 21: 227232.[Crossref]
  6. Zhang WY, Yin WW, Hu WB, Magalhaes RJS, Ding F, Sun HL, Zhou H, Li SL, Haque U, Tong SL, Glass GE, Bi P, Clements ACA, Liu QY, Li CY, , 2014. Spatiotemporal transmission dynamics of hemorrhagic fever with renal syndrome in China, 2005–2012. PLoS Negl Trop Dis 8: e3344.[Crossref]
  7. Ladner JT, Wiley MR, Mate S, Dudas G, Prieto K, Lovett S, Nagle ER, Beitzel B, Gilbert ML, Fakoli L, Diclaro JW, 2nd Schoepp RJ, Fair J, Kuhn JH, Hensley LE, Park DJ, Sabeti PC, Rambaut A, Sanchez-Lockhart M, Bolay FK, Kugelman JR, Palacios G, , 2015. Evolution and spread of Ebola virus in Liberia, 2014–2015. Cell Host Microbe 18: 659669.[Crossref]
  8. Neverov A, Chumakov K, , 2010. Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines. Proc Natl Acad Sci USA 107: 2006320068.[Crossref]
  9. Prachi P, Donati C, Masciopinto F, Rappuoli R, Bagnoli F, , 2013. Deep sequencing in pre- and clinical vaccine research. Public Health Genomics 16: 6268.[Crossref]
  10. Quinones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA, , 2014. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 61: 919.[Crossref]
  11. Barzon L, Lavezzo E, Costanzi G, Franchin E, Toppo S, Palù G, , 2013. Next-generation sequencing technologies in diagnostic virology. J Clin Virol 58: 346350.[Crossref]
  12. Kim WK, Kim JA, Song DH, Lee D, Kim YC, Lee SY, Lee SH, No JS, Kim JH, Kho JH, Gu SH, Jeong ST, Wiley M, Kim HC, Klein TA, Palacios G, Song JW, , 2016. Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing. Sci Rep 6: 26017.[Crossref]
  13. Rosseel T, Scheuch M, Höper D, De Regge N, Caij AB, Vandenbussche F, Van Borm S, , 2012. DNase SISPA-next generation sequencing confirms Schmallenberg virus in Belgian field samples and identifies genetic variation in Europe. PLoS One 7: e41967.[Crossref]
  14. Thorburn F, Scheuch M, Höper D, De Regge N, Caij AB, Vandenbussche F, Van Borm S, , 2015. The use of next generation sequencing in the diagnosis and typing of respiratory infections. J Clin Virol 69: 96100.[Crossref]
  15. Prachayangprecha S, Schapendonk CM, Koopmans MP, Osterhaus AD, Schürch AC, Pas SD, van der Eijk AA, Poovorawan Y, Haagmans BL, Smits SL, , 2014. Exploring the potential of next-generation sequencing in detection of respiratory viruses. J Clin Microbiol 52: 37223730.[Crossref]
  16. Marston DA, McElhinney LM, Ellis RJ, Horton DL, Wise EL, Leech SL, David D, de Lamballerie X, Fooks AR, , 2013. Next generation sequencing of viral RNA genomes. BMC Genomics 14: 444.[Crossref]
  17. Barzon L, Lavezzo E, Militello V, Toppo S, Palù G, , 2011. Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci 12: 78617884.[Crossref]
  18. Djikeng A, Halpin R, Kuzmickas R, Depasse J, Feldblyum J, Sengamalay N, Afonso C, Zhang X, Anderson NG, Ghedin E, Spiro DJ, , 2008. Viral genome sequencing by random priming methods. BMC Genomics 9: 5.[Crossref]
  19. Lambden PR, Cooke SJ, Caul EO, Clarke IN, , 1992. Cloning of noncultivatable human rotavirus by single primer amplification. J Virol 66: 18171822.
  20. Matsui SM, Kim JP, Greenberg HB, Young LM, Smith LS, Lewis TL, Herrmann JE, Blacklow NR, Dupuis K, Reyes GR, , 1993. Cloning and characterization of human astrovirus immunoreactive epitopes. J Virol 67: 17121715.
  21. Jones MS, Kapoor A, Lukashov VV, Simmonds P, Hecht F, Delwart E, , 2005. New DNA viruses identified in patients with acute viral infection syndrome. J Virol 79: 82308236.[Crossref]
  22. Song JW, Gu SH, Bennett SN, Arai S, Puorger M, Hilbe M, Yanagihara R, , 2007. Seewis virus, a genetically distinct hantavirus in the Eurasian common shrew (Sorex araneus). Virol J 4: 114.[Crossref]
  23. Yanagihara R, Goldgaber D, Lee PW, Amyx HL, Gajdusek DC, Gibbs CJ, Jr Svedmyr A, , 1984. Propagation of nephropathia epidemica virus in cell culture. Lancet 1: 1013.[Crossref]
  24. Ronquist F, Huelsenbeck JP, , 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 15721574.[Crossref]
  25. Posada D, Crandall KA, , 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817818.[Crossref]
  26. Posada D, , 2008. jModelTest: phylogenetic model averaging. Mol Biol Evol 25: 12531256.[Crossref]
  27. Radford AD, Chapman D, Dixon L, Chantrey J, Darby AC, Hall N, , 2012. Application of next-generation sequencing technologies in virology. J Gen Virol 93: 18531868.[Crossref]
  28. Plyusnin A, Vapalahti O, Vaheri A, , 1996. Hantaviruses: genome structure, expression and evolution. J Gen Virol 77: 26772687.[Crossref]
  29. Piiparinen H, Vapalahti O, Plyusnin A, Vaheri A, Lankinen H, , 1997. Sequence analysis of the Puumala hantavirus Sotkamo strain L segment. Virus Res 51: 17.[Crossref]
  30. Kim JA, Kim WK, No JS, Lee SH, Lee SY, Kim JH, Kho JH, Lee D, Song DH, Gu SH, Jeong ST, Park MS, Kim HC, Klein TA, Song JW, , 2016. Genetic diversity and reassortment of Hantaan virus tripartite RNA genomes in nature, the Republic of Korea. PLoS Negl Trop Dis 10: e0004650.[Crossref]

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  • Received : 22 Aug 2016
  • Accepted : 16 Oct 2016

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