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Archives of Virology

, Volume 158, Issue 4, pp 765–773 | Cite as

Novel marker for recombination in the 3′-untranslated region of members of the species Human enterovirus A

  • Chee Choy KokEmail author
  • Gough G. Au
Original Article

Abstract

Human enterovirus A (HEV-A) is a species in the genus Enterovirus. Viruses belonging to this species are often responsible for hand, foot and mouth disease and associated acute neurological disease. Studies of the 3′ untranslated region (UTR) of human enterovirus 71 (HEV71) revealed a possible role in virus replication. We compared the 3′-UTRs of all members of HEV-A and confirmed the presence of a secondary structure comprising three stem-loop domains (SLDs). SLD-Z is situated closest to the stop codon and has been shown previously to affect plaque morphology. The prototype strains of coxsackieviruses A4 (CVA4), CVA14, and CVA16 carried the longer group I SLD-Z, whilst other CVAs and HEV71 carried the shorter group II SLD-Z. We demonstrate the importance of SLD-Z as a marker for the emergence of newer strains of HEV71 and CVA16 through inter-typic recombination and propose that SLD-Z is a novel evolutionary marker for recombination in HEV-A.

Keywords

Prototype Strain Human Enterovirus Bootscan Analysis CVA16 Strain SimPlot Analysis 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgment

The authors would like to thank Professor Peter McMinn of the University of Sydney for past support.

References

  1. 1.
    ICTV (2011) International Committee on Taxonomy of Viruses. http://ictvonline.org/virusTaxonomy.asp?version=2011. Accessed 22 Aug 2012
  2. 2.
    Chang LY, Lin TY, Huang YC, Tsao KC, Shih SR, Kuo ML, Ning HC, Chung PW, Kang CM (1999) Comparison of enterovirus 71 and coxsackievirus A16 clinical illness during the Taiwan enterovirus epidemic, 1998. Pediatr Infect Dis J 18:1092–1096PubMedCrossRefGoogle Scholar
  3. 3.
    Hosoya M, Kawasaki Y, Sato M, Honzumi K, Hayashi A, Hiroshima T, Ishiko H, Kato K, Suzuki H (2007) Genetic diversity of coxsackievirus A16 associated with hand, foot, and mouth disease epidemics in Japan from 1983 to 2003. J Clin Microbiol 45:112–120PubMedCrossRefGoogle Scholar
  4. 4.
    Melnick JL (1984) Enterovirus type 71 infections: a varied clinical pattern sometimes mimicking paralytic poliomyelitis. Rev Infect Dis 6(Suppl 2):S387–S390PubMedCrossRefGoogle Scholar
  5. 5.
    Gilbert GL, Dickson KE, Waters MJ, Kennett ML, Land SA, Sneddon M (1988) Outbreak of enterovirus 71 infection in Victoria, Australia, with a high incidence of neurologic involvement. Pediatr Infect Dis J 7:484–488PubMedCrossRefGoogle Scholar
  6. 6.
    Alexander JP Jr, Baden L, Pallansch MA, Anderson LJ (1994) Enterovirus 71 infections and neurologic disease – United States, 1977–1991. J Infect Dis 169:905–908PubMedCrossRefGoogle Scholar
  7. 7.
    McMinn PC (2002) An overview of the evolution of EV71 and its clinical and public health significance. FEMS Microbiol Rev 26:91–107PubMedCrossRefGoogle Scholar
  8. 8.
    Pilipenko EV, Maslova SV, Sinyakov AN, Agol VI (1992) Towards identification of cis-acting elements involved in the replication of enterovirus and rhinovirus RNAs: a proposal for the existence of tRNA-like terminal structures. Nucleic Acids Res 20:1739–1745PubMedCrossRefGoogle Scholar
  9. 9.
    Merkle I, van Ooij MJM, van Kuppeveld FJM, Glaudemans DHRF, Galama JMD, Henke A, Zell R, Melchers WJG (2002) Biological significance of a human enterovirus B-specific RNA element in the 3′ nontranslated region. J Virol 76:9900–9909PubMedCrossRefGoogle Scholar
  10. 10.
    Todd S, Semler BL (1996) Structure-infectivity analysis of the human rhinovirus genomic RNA 3′ non-coding region. Nucleic Acids Res 24:2133–2142PubMedCrossRefGoogle Scholar
  11. 11.
    Dobrikova EY, Florez P, Bradrick S, Gromeier M (2003) Activity of a type 1 picornavirus internal ribosomal entry site is determined by sequences within the 3′ nontranslated region. PNAS 100:15125–15130PubMedCrossRefGoogle Scholar
  12. 12.
    Zell R, Stelzner A (1997) Application of genome sequence information to the classification of bovine enteroviruses: the importance of 5′- and 3′-nontranslated regions. Virus Res 51:213–229PubMedCrossRefGoogle Scholar
  13. 13.
    Dobrikova EY, Grisham RN, Kaizer C, Lin J, Gromeier M (2006) Competitive translation efficiency and the picornavirus type I internal ribosome entry site facilitated by viral cis and trans factors. J Virol 80:3310–3321PubMedCrossRefGoogle Scholar
  14. 14.
    Melchers WJG, Hoendrop JGJ, Bruins Slot HJ, Pleij CWA, Pilipenko EV, Agol VI, Galama JMD (1997) Kissing of two predominant hairpin loops in the coxsackievirus B virus 3′ untranslated region is the essential structural feature of the origin of replication required for negative-strand RNA synthesis. J Virol 71:686–696PubMedGoogle Scholar
  15. 15.
    Wang J, Bakkers JMJE, Galama JMD, Bruins Slot HJ, Pilipenko EV, Agol VI, Melchers WJ (1999) Structural requirements of the higher order RNA kissing element in the enteroviral 3′UTR. Nucleic Acids Res 27:485–490PubMedCrossRefGoogle Scholar
  16. 16.
    Todd S, Towner JS, Brown DM, Semler BL (1997) Replication-competent picornaviruses with complete genomic RNA 3′ noncoding region deletions. J Virol 71:8868–8874PubMedGoogle Scholar
  17. 17.
    Kok CC, Phuektes P, Bek E, McMinn PC (2012) Modification of the untranslated regions of human enterovirus 71 impairs growth in a cell-specific manner. J Virol 86:542–552PubMedCrossRefGoogle Scholar
  18. 18.
    Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680PubMedCrossRefGoogle Scholar
  19. 19.
    Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415PubMedCrossRefGoogle Scholar
  20. 20.
    Lole KS, Bollinger RC, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC (1999) Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73:152–160PubMedGoogle Scholar
  21. 21.
    Lin TY, Twu SJ, Ho MS, Chang LY, Lee CY (2003) Enterovirus 71 outbreaks, Taiwan: occurrence and recognition. Emerg Infect Dis 9:291–293PubMedCrossRefGoogle Scholar
  22. 22.
    Li L, He Y, Yang H, Zhu J, Xu X, Dong J, Zhu Y, Jin Q (2005) Genetic characteristics of human enterovirus 71 and coxsackievirus A16 circulating from 1999 to 2004 in Shenzhen, People’s Republic of China. J Clin Microbiol 43:3835–3839PubMedCrossRefGoogle Scholar
  23. 23.
    Podin Y, Gias ELM, Ong F, Leong Y-W, Yee S-F, Yusof MA, Perera D, Teo B, Wee T-Y, Yao S-C, Yao S-K, Kiyu A, Arif MT, Cardosa MJ (2006) Sentinel surveillance for human enterovirus 71 in Sarawak, Malaysia: lessons from the first 7 years. BMC Public Health 6:180PubMedCrossRefGoogle Scholar
  24. 24.
    Rohll JB, Moon DH, Evans DJ, Almond JW (1995) The 3′ untranslated region of picornavirus RNA: features required for efficient genome replication. J Virol 69:7835–7844PubMedGoogle Scholar
  25. 25.
    Oberste MS, Penaranda S, Maher K, Pallansch MA (2004) Complete genome sequences of all members of the species human enterovirus A. J Gen Virol 85:1597–1607PubMedCrossRefGoogle Scholar
  26. 26.
    Phuektes P, Chua BH, Sanders S, Bek EJ, Kok CC, McMinn PC (2011) Mapping genetic determinants of cell-culture growth phenotype of enterovirus 71. J Gen Virol 92:1380–1390PubMedCrossRefGoogle Scholar
  27. 27.
    Chan YF, AbuBakar S (2006) Phylogenetic evidence for inter-typic recombination in the emergence of human enterovirus 71 subgenotypes. BMC Microbiol 6:1–11CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Wien 2012

Authors and Affiliations

  1. 1.Virology Division, Department of Microbiology, SEALSPrince of Wales HospitalRandwickAustralia
  2. 2.The Picornaviral Research Unit, The School of Biomedical Sciences and Pharmacy, Faculty of HealthThe University of NewcastleNewcastleAustralia
  3. 3.Blood Borne Virus Laboratory, SEALS MicrobiologyPrince of Wales HospitalRandwickAustralia

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