Skip to main content
SpringerLink
Log in

Genomic organization and recombination analysis of human norovirus identified from China

  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Noroviruses (NoVs) are one of the major causal agents of acute gastroenteritis in both industrial and developing countries including China. Recent studies have revealed that NoV genome is highly prone to mutation and recombination which may lead to emergence of new strains. In the present study, three full-length genomes of human NoV from China were determined and the genomic organization and recombination were analyzed. They had similar genome organization and contained three predicted ORFs, though the 5′UTR of those three strains were 2, 4 and 8 nucleotides, respectively. Phylogenetic analysis showed that the HU/GII/SHANGHAI/SH312/2008/CHN strain may be a recombinant of GII-3 capsid and GII-4 polymerase. To confirm the finding and detect the breakpoints where the recombination event occurred, we performed recombination analysis based on the genomic sequences of HU/GII/SHANGHAI/SH312/2008/CHN as the query sequence, and AB220921/NOV/JP/GII-4 and AB365435/NOV/US/GII-3 as the background sequences, using RPD software. Results indicated that the two parental strains were AB220921/NOV/JP/GII-4 and AB365435/NOV/US/GII-3. The breakpoint for this recombination event located at position 5,107 nt of the genome (in the ORF1 and ORF2 overlap).

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Green KY, Belliot G, Taylor JL, Valdesuso J, Lew JF, Kapikian AZ, Lin FY (2002) A predominant role for Norwalk-like viruses as agents of epidemic gastroenteritis in Maryland nursing homes for the elderly. J Infect Dis 185:133–146

    Article  PubMed  CAS  Google Scholar 

  2. Lopman BA, Adak GK, Reacher MH, Brown DW (2003) Two epidemiologic patterns of norovirus outbreaks: surveillance in England and wales, 1992–2000. Emerg Infect Dis 9:71–77

    PubMed  Google Scholar 

  3. Marshall JA, Dimitriadis A, Wright PJ (2005) Molecular and epidemiological features of norovirus-associated gastroenteritis outbreaks in Victoria, Australia in 2001. J Med Virol 75:321–331

    Article  PubMed  Google Scholar 

  4. Widdowson MA, Cramer EH, Hadley L, Bresee JS, Beard RS, Bulens SN, Charles M, Chege W, Isakbaeva E, Wright JG, Mintz E, Forney D, Massey J, Glass RI, Monroe SS (2004) Outbreaks of acute gastroenteritis on cruise ships and on land: identification of a predominant circulating strain of norovirus–United States, 2002. J Infect Dis 190:27–36

    Article  PubMed  Google Scholar 

  5. van Der Poel WH, Vinje J, van Der Heide R, Herrera MI, Vivo A, Koopmans MP (2000) Norwalk-like calicivirus genes in farm animals. Emerg Infect Dis 6:36–41

    Google Scholar 

  6. Green KY CR, Kapikian AZ (2001) Fields virology, 4th edn. Lippincott Williams & Wilkins, Philadelphia

    Google Scholar 

  7. Hardy ME (2005) Norovirus protein structure and function. FEMS Microbiol Lett 253:1–8

    Article  PubMed  CAS  Google Scholar 

  8. Seah EL, Gunesekere IC, Marshall JA, Wright PJ (1999) Variation in ORF3 of genogroup 2 Norwalk-like viruses. Arch Virol 144:1007–1014

    Article  PubMed  CAS  Google Scholar 

  9. Glass PJ, White LJ, Ball JM, Leparc-Goffart I, Hardy ME, Estes MK (2000) Norwalk virus open reading frame 3 encodes a minor structural protein. J Virol 74:6581–6591

    Article  PubMed  CAS  Google Scholar 

  10. Okada M, Tanaka T, Oseto M, Takeda N, Shinozaki K (2006) Genetic analysis of noroviruses associated with fatalities in healthcare facilities. Arch Virol 151:1635–1641

    Article  PubMed  CAS  Google Scholar 

  11. Scipioni A, Mauroy A, Vinje J, Thiry E (2008) Animal noroviruses. Vet J 178:32–45

    Article  PubMed  CAS  Google Scholar 

  12. Zheng DP, Ando T, Fankhauser RL, Beard RS, Glass RI, Monroe SS (2006) Norovirus classification and proposed strain nomenclature. Virology 346:312–323

    Article  PubMed  CAS  Google Scholar 

  13. Noel JS, Fankhauser RL, Ando T, Monroe SS, Glass RI (1999) Identification of a distinct common strain of “Norwalk-like viruses” having a global distribution. J Infect Dis 179:1334–1344

    Article  PubMed  CAS  Google Scholar 

  14. Koopmans M, Vinje J, Duizer E, de Wit M, van Duijnhoven Y (2001) Molecular epidemiology of human enteric caliciviruses in The Netherlands. Novartis Found Symp 238:197–214 discussion 214-8

    Article  PubMed  CAS  Google Scholar 

  15. Jin M, Xie HP, Duan ZJ, Liu N, Zhang Q, Wu BS, Li HY, Cheng WX, Yang SH, Yu JM, Xu ZQ, Cui SX, Zhu L, Tan M, Jiang X, Fang ZY (2008) Emergence of the GII4/2006b variant and recombinant noroviruses in China. J Med Virol 80:1997–2004

    Article  PubMed  CAS  Google Scholar 

  16. Worobey M, Holmes EC (1999) Evolutionary aspects of recombination in RNA viruses. J Gen Virol 80(Pt 10):2535–2543

    PubMed  CAS  Google Scholar 

  17. Bull RA, Tanaka MM, White PA (2007) Norovirus recombination. J Gen Virol 88:3347–3359

    Article  PubMed  CAS  Google Scholar 

  18. Hardy ME, Kramer SF, Treanor JJ, Estes MK (1997) Human calicivirus genogroup II capsid sequence diversity revealed by analyses of the prototype Snow Mountain agent. Arch Virol 142:1469–1479

    Article  PubMed  CAS  Google Scholar 

  19. Phan TG, Yan H, Li Y, Okitsu S, Muller WE, Ushijima H (2006) Novel recombinant norovirus in China. Emerg Infect Dis 12:857–858

    PubMed  Google Scholar 

  20. Shen Q, Zhang W, Cao X, Mou J, Cui L, Hua X (2007) Cloning of full genome sequence of hepatitis E virus of Shanghai swine isolate using RACE method. Virol J 4:98

    Article  PubMed  Google Scholar 

  21. Wang QH, Han MG, Cheetham S, Souza M, Funk JA, Saif LJ (2005) Porcine noroviruses related to human noroviruses. Emerg Infect Dis 11:1874–1881

    PubMed  CAS  Google Scholar 

  22. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163

    Article  PubMed  CAS  Google Scholar 

  23. Martin DP, Posada D, Crandall KA, Williamson C (2005) A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retrovir 21:98–102

    Article  PubMed  CAS  Google Scholar 

  24. Lopman B, Vennema H, Kohli E, Pothier P, Sanchez A, Negredo A, Buesa J, Schreier E, Reacher M, Brown D, Gray J, Iturriza M, Gallimore C, Bottiger B, Hedlund KO, Torven M, von Bonsdorff CH, Maunula L, Poljsak-Prijatelj M, Zimsek J, Reuter G, Szucs G, Melegh B, Svennson L, van Duijnhoven Y, Koopmans M (2004) Increase in viral gastroenteritis outbreaks in Europe and epidemic spread of new norovirus variant. Lancet 363:682–688

    Article  PubMed  Google Scholar 

  25. Yun SI, Kim JK, Song BH, Jeong AY, Jee YM, Lee CH, Paik SY, Koo Y, Jeon I, Byun SJ, Lee YM (2010) Complete genome sequence and phylogenetic analysis of a recombinant Korean norovirus, CBNU1, recovered from a 2006 outbreak. Virus Res 152:137–152

    Article  PubMed  CAS  Google Scholar 

  26. Reuter G, Krisztalovics K, Vennema H, Koopmans M, Szucs G (2005) Evidence of the etiological predominance of norovirus in gastroenteritis outbreaks–emerging new-variant and recombinant noroviruses in Hungary. J Med Virol 76:598–607

    Article  PubMed  CAS  Google Scholar 

  27. Dey SK, Phan TG, Mizuguchia M, Okitsua S, Ushijima H (2010) Novel recombinant norovirus in Japan. Virus Genes 40:362–364

    Article  PubMed  CAS  Google Scholar 

  28. Lochridge VP, Hardy ME (2003) Snow Mountain virus genome sequence and virus-like particle assembly. Virus Genes 26:71–82

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We thank Kelly Scheuer for assistance in linguistic revision of the manuscript. This work was supported by Key Project of Shanghai Science and Technology Committee of China under Grant No.10JC1406500.

Author information

Authors and Affiliations

  1. Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai JiaoTong University, 800 Dongchuan Road, Shanghai, People’s Republic of China

    Quan Shen, Shixing Yang, Yan Chen, Tongling Shan, Li Cui & Xiuguo Hua

  2. School of Medical Technology, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People’s Republic of China

    Quan Shen & Wen Zhang

Authors
  1. Quan Shen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wen Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Shixing Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yan Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Tongling Shan
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Li Cui
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Xiuguo Hua
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xiuguo Hua.

Additional information

Quan Shen and Wen Zhang contributed equally to this study.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Shen, Q., Zhang, W., Yang, S. et al. Genomic organization and recombination analysis of human norovirus identified from China. Mol Biol Rep 39, 1275–1281 (2012). https://doi.org/10.1007/s11033-011-0845-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-011-0845-8

Keywords

Search

Navigation