Skip to main content

Advertisement

SpringerLink
Log in

Whole genomic analysis reveals the co-evolutionary phylodynamics of Korean G9P[8] human rotavirus strains

  • Brief Report
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

Three human rotavirus G9P[8] strains, RVA/Human-tc/KOR/CAU05-202/2005/G9P[8], RVA/Human-tc/KOR/CAU09-371/2009/G9P[8], and RVA/Human-tc/KOR/CAU09-376/2009/G9P[8], were isolated from female pediatric patients with diarrhea from 2005 to 2009 using a cell culture system, and their complete genomic sequences were analyzed. The 11 gene segments of the three Korean strains possessed the G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 genotype, which is closely related to the Wa-like genotype 1 constellation. Interestingly, the NSP2 and the NSP3 genes of strain RVA/Human-tc/KOR/CAU09-376/2009/G9P[8] were related to the G9 porcine or human-porcine reassortant strains, providing evidence for porcine-to-human interspecies transmission.

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

References

  1. Abdel-Haq N, Amjad M, McGrath E, Chearskul P, Amer A, Salimnia H, Asmar BI (2011) Emergence of human rotavirus genotype G9 in metropolitan Detroit between 2007 and 2009. J Med Microbiol 60:761–767

    Article  PubMed  Google Scholar 

  2. Araujo EC, Clemens SA, Oliveira CS, Justino MC, Rubio P, Gabbay YB, da Silva VB, Mascarenhas JD, Noronha VL, Clemens R, Gusmao RH, Sanchez N, Monteiro TA, Linhares AC (2007) Safety, immunogenicity, and protective efficacy of two doses of RIX4414 live attenuated human rotavirus vaccine in healthy infants. J Pediatr (Rio J) 83:217–224

    Google Scholar 

  3. Arista S, Giammanco GM, De Grazia S, Colomba C, Martella V (2005) Genetic variability among serotype G4 Italian human rotaviruses. J Clin Microbiol 43:1420–1425

    Article  CAS  PubMed  Google Scholar 

  4. Armah GE, Steele AD, Binka FN, Esona MD, Asmah RH, Anto F, Brown D, Green J, Cutts F, Hall A (2003) Changing patterns of rotavirus genotypes in ghana: emergence of human rotavirus G9 as a major cause of diarrhea in children. J Clin Microbiol 41:2317–2322

    Article  PubMed  Google Scholar 

  5. Banyai K, Esona MD, Kerin TK, Hull JJ, Mijatovic S, Vasconez N, Torres C, de Filippis AM, Foytich KR, Gentsch JR (2009) Molecular characterization of a rare, human-porcine reassortant rotavirus strain, G11P[6], from Ecuador. Arch Virol 154:1823–1829

    Article  CAS  PubMed  Google Scholar 

  6. Bozdayi G, Dogan B, Dalgic B, Bostanci I, Sari S, Battaloglu NO, Rota S, Dallar Y, Nishizono A, Nakagomi O, Ahmed K (2008) Diversity of human rotavirus G9 among children in Turkey. J Med Virol 80:733–740

    Article  CAS  PubMed  Google Scholar 

  7. Breiman RF, Zaman K, Armah G, Sow SO, Anh DD, Victor JC, Hille D, Ciarlet M, Neuzil KM (2012) Analyses of health outcomes from the 5 sites participating in the Africa and Asia clinical efficacy trials of the oral pentavalent rotavirus vaccine. Vaccine 30(Suppl 1):A24–A29

    Article  PubMed  Google Scholar 

  8. Chitambar SD, Arora R, Chhabra P (2009) Molecular characterization of a rare G1P[19] rotavirus strain from India: evidence of reassortment between human and porcine rotavirus strains. J Med Microbiol 58:1611–1615

    Article  CAS  PubMed  Google Scholar 

  9. Cunliffe NA, Gondwe JS, Graham SM, Thindwa BD, Dove W, Broadhead RL, Molyneux ME, Hart CA (2001) Rotavirus strain diversity in Blantyre, Malawi, from 1997 to 1999. J Clin Microbiol 39:836–843

    Article  CAS  PubMed  Google Scholar 

  10. de Rougemont A, Kaplon J, Pillet S, Mory O, Gagneur A, Minoui-Tran A, Meritet JF, Mollat C, Lorrot M, Foulongne V, Gillet Y, Nguyen-Bourgain C, Alain S, Agius G, Lazrek M, Colimon R, Fontana C, Gendrel D, Pothier P (2011) Molecular and clinical characterization of rotavirus from diarrheal infants admitted to pediatric emergency units in France. Pediatr Infect Dis J 30:118–124

    Article  PubMed  Google Scholar 

  11. Dennehy PH (2008) Rotavirus vaccines: an overview. Clin Microbiol Rev 21:198–208

    Article  CAS  PubMed  Google Scholar 

  12. Esona MD, Geyer A, Banyai K, Page N, Aminu M, Armah GE, Hull J, Steele DA, Glass RI, Gentsch JR (2009) Novel human rotavirus genotype G5P[7] from child with diarrhea, Cameroon. Emerg Infect Dis 15:83–86

    Article  PubMed  Google Scholar 

  13. Espinola EE, Amarilla A, Arbiza J, Parra GI (2008) Sequence and phylogenetic analysis of the VP4 gene of human rotaviruses isolated in Paraguay. Arch Virol 153:1067–1073

    Article  CAS  PubMed  Google Scholar 

  14. Estes MK, Cohen J (1989) Rotavirus gene structure and function. Microbiol Rev 53:410–449

    CAS  PubMed  Google Scholar 

  15. Estes MK, Kapikian AZ (2007) Rotaviruses. In: Knipe DM, Howley PM (eds) Fields virology, 5th edn. Wolters Kluwer Health/Lippincott Williams & Wilkins, Phildelphia, pp 1917–1974

  16. Felsenstein J (1993) PHYLIP (Phylogeny inference package) version 3.5c Department of Genetics, University of Washington

  17. Ghosh S, Kobayashi N, Nagashima S, Chawla-Sarkar M, Krishnan T, Ganesh B, Naik TN (2010) Full genomic analysis and possible origin of a porcine G12 rotavirus strain RU172. Virus Genes 40:382–388

    Article  CAS  PubMed  Google Scholar 

  18. Ghosh S, Paul SK, Yamamoto D, Nagashima S, Kobayashi N (2011) Full genomic analyses of human rotavirus strains possessing the rare P[8]b VP4 subtype. Infect Genet Evol 11:1481–1486

    Article  CAS  PubMed  Google Scholar 

  19. Gouvea V, Lima RC, Linhares RE, Clark HF, Nosawa CM, Santos N (1999) Identification of two lineages (WA-like and F45-like) within the major rotavirus genotype P[8]. Virus Res 59:141–147

    Article  CAS  PubMed  Google Scholar 

  20. Jeong HS, Lee KB, Jeong AY, Jo MY, Jung SY, Ahn JH, Jee Y, Kim J, Cheon DS (2011) Genotypes of the circulating rotavirus strains in the seven prevaccine seasons from September 2000 to August 2007 in South Korea. Clin Microbiol Infect 17:232–235

    Article  CAS  PubMed  Google Scholar 

  21. Jukes TH, Cantor C (1969) Evolution of protein molecules. Mammalian protein metabolism. Academic Press, New York, pp 21–132

    Google Scholar 

  22. Kim HH, Matthijnssens J, Kim HJ, Kwon HJ, Park JG, Son KY, Ryu EH, Kim DS, Lee WS, Kang MI, Yang DK, Hyun BH, Park SI, Park SJ, Cho KO (2012) Full-length genomic analysis of porcine G9P[23] and G9P[7] rotavirus strains isolated from pigs with diarrhea in South Korea. Infect Genet Evol 12:1427–1435

    Article  CAS  PubMed  Google Scholar 

  23. Kim JS, Kang JO, Cho SC, Jang YT, Min SA, Park TH, Nyambat B, Jo DS, Gentsch J, Bresee JS, Mast TC, Kilgore PE (2005) Epidemiological profile of rotavirus infection in the Republic of Korea: results from prospective surveillance in the Jeongeub District, 1 July 2002 through 30 June 2004. J Infect Dis 192(Suppl 1):S49–S56

    Article  PubMed  Google Scholar 

  24. Le VP, Kim JY, Cho SL, Nam SW, Lim I, Lee HJ, Kim K, Chung SI, Song W, Lee KM, Rhee MS, Lee JS, Kim W (2008) Detection of unusual rotavirus genotypes G8P[8] and G12P[6] in South Korea. J Med Virol 80:175–182

    Article  CAS  PubMed  Google Scholar 

  25. Martel-Paradis O, Laurin MA, Martella V, Sohal JS, L’Homme Y (2013) Full-length genome analysis of G2, G9 and G11 porcine group A rotaviruses. Vet Microbiol 162:94–102

    Article  CAS  PubMed  Google Scholar 

  26. Martinez-Laso J, Roman A, Head J, Cervera I, Rodriguez M, Rodriguez-Avial I, Picazo JJ (2009) Phylogeny of G9 rotavirus genotype: a possible explanation of its origin and evolution. J Clin Virol 44:52–57

    Article  CAS  PubMed  Google Scholar 

  27. Matthijnssens J, Ciarlet M, Heiman E, Arijs I, Delbeke T, McDonald SM, Palombo EA, Iturriza-Gomara M, Maes P, Patton JT, Rahman M, Van Ranst M (2008) Full genome-based classification of rotaviruses reveals a common origin between human Wa-Like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains. J Virol 82:3204–3219

    Article  CAS  PubMed  Google Scholar 

  28. Matthijnssens J, Ciarlet M, Rahman M, Attoui H, Banyai K, Estes MK, Gentsch JR, Iturriza-Gomara M, Kirkwood CD, Martella V, Mertens PP, Nakagomi O, Patton JT, Ruggeri FM, Saif LJ, Santos N, Steyer A, Taniguchi K, Desselberger U, Van Ranst M (2008) Recommendations for the classification of group A rotaviruses using all 11 genomic RNA segments. Arch Virol 153:1621–1629

    Article  CAS  PubMed  Google Scholar 

  29. Matthijnssens J, Bilcke J, Ciarlet M, Martella V, Banyai K, Rahman M, Zeller M, Beutels P, Van Damme P, Van Ranst M (2009) Rotavirus disease and vaccination: impact on genotype diversity. Future Microbiol 4:1303–1316

    Article  CAS  PubMed  Google Scholar 

  30. Matthijnssens J, Rahman M, Ciarlet M, Zeller M, Heylen E, Nakagomi T, Uchida R, Hassan Z, Azim T, Nakagomi O, Van Ranst M (2010) Reassortment of human rotavirus gene segments into G11 rotavirus strains. Emerg Infect Dis 16:625–630

    Article  PubMed  Google Scholar 

  31. Matthijnssens J, Ciarlet M, McDonald SM, Attoui H, Banyai K, Brister JR, Buesa J, Esona MD, Estes MK, Gentsch JR, Iturriza-Gomara M, Johne R, Kirkwood CD, Martella V, Mertens PP, Nakagomi O, Parreno V, Rahman M, Ruggeri FM, Saif LJ, Santos N, Steyer A, Taniguchi K, Patton JT, Desselberger U, Van Ranst M (2011) Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG). Arch Virol 156:1397–1413

    Article  CAS  PubMed  Google Scholar 

  32. Matthijnssens J, Otto PH, Ciarlet M, Desselberger U, Van Ranst M, Johne R (2012) VP6-sequence-based cutoff values as a criterion for rotavirus species demarcation. Arch Virol 157:1177–1182

    Article  CAS  PubMed  Google Scholar 

  33. Mattion NM, Cohen J, Aponte C, Estes MK (1992) Characterization of an oligomerization domain and RNA-binding properties on rotavirus nonstructural protein NS34. Virology 190:68–83

    Article  CAS  PubMed  Google Scholar 

  34. Mijatovic-Rustempasic S, Banyai K, Esona MD, Foytich K, Bowen MD, Gentsch JR (2011) Genome sequence based molecular epidemiology of unusual US Rotavirus A G9 strains isolated from Omaha, USA between 1997 and 2000. Infect Genet Evol 11:522–527

    Article  CAS  PubMed  Google Scholar 

  35. Mukherjee A, Dutta D, Ghosh S, Bagchi P, Chattopadhyay S, Nagashima S, Kobayashi N, Dutta P, Krishnan T, Naik TN, Chawla-Sarkar M (2009) Full genomic analysis of a human group A rotavirus G9P[6] strain from Eastern India provides evidence for porcine-to-human interspecies transmission. Arch Virol 154:733–746

    Article  CAS  PubMed  Google Scholar 

  36. Mukherjee A, Ghosh S, Bagchi P, Dutta D, Chattopadhyay S, Kobayashi N, Chawla-Sarkar M (2011) Full genomic analyses of human rotavirus G4P[4], G4P[6], G9P[19] and G10P[6] strains from North-eastern India: evidence for interspecies transmission and complex reassortment events. Clin Microbiol Infect 17:1343–1346

    CAS  PubMed  Google Scholar 

  37. O’Ryan M, Linhares AC (2009) Update on Rotarix: an oral human rotavirus vaccine. Expert Rev Vaccines 8:1627–1641

    Article  PubMed  Google Scholar 

  38. Phan TG, Okitsu S, Maneekarn N, Ushijima H (2007) Genetic heterogeneity, evolution and recombination in emerging G9 rotaviruses. Infect Genet Evol 7:656–663

    Article  CAS  PubMed  Google Scholar 

  39. Piron M, Vende P, Cohen J, Poncet D (1998) Rotavirus RNA-binding protein NSP3 interacts with eIF4GI and evicts the poly(A) binding protein from eIF4F. EMBO J 17:5811–5821

    Article  CAS  PubMed  Google Scholar 

  40. Rao CD, Das M, Ilango P, Lalwani R, Rao BS, Gowda K (1995) Comparative nucleotide and amino acid sequence analysis of the sequence-specific RNA-binding rotavirus nonstructural protein NSP3. Virology 207:327–333

    Article  CAS  PubMed  Google Scholar 

  41. Ribas Mde L, Nagashima S, Calzado A, Acosta G, Tejero Y, Cordero Y, Piedra D, Kobayashi N (2011) Emergence of G9 as a predominant genotype of human rotaviruses in Cuba. J Med Virol 83:738–744

    Article  PubMed  Google Scholar 

  42. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  43. Santos N, Volotao EM, Soares CC, Albuquerque MC, da Silva FM, de Carvalho TR, Pereira CF, Chizhikov V, Hoshino Y (2001) Rotavirus strains bearing genotype G9 or P[9] recovered from Brazilian children with diarrhea from 1997 to 1999. J Clin Microbiol 39:1157–1160

    Article  CAS  PubMed  Google Scholar 

  44. Santos N, Hoshino Y (2005) Global distribution of rotavirus serotypes/genotypes and its implication for the development and implementation of an effective rotavirus vaccine. Rev Med Virol 15:29–56

    Article  PubMed  Google Scholar 

  45. Seo JK, Sim JG (2000) Overview of rotavirus infections in Korea. Pediatr Int 42:406–410

    Article  CAS  PubMed  Google Scholar 

  46. Shim JO, Baek IH, Le VP, Ko EM, Seok WS, Uh Y, Kim JK, Ahn SY, Lee HS, Ryoo E, Shim SY, Song W, Lim I, Kim W (2011) Molecular characterization of rotavirus diarrhea among children in South Korea: detection of an unusual G11 strain. Arch Virol 156:887–892

    Article  CAS  PubMed  Google Scholar 

  47. Shim SY, Jung YC, Le VP, Son DW, Ryoo E, Shim JO, Lim I, Kim W (2010) Genetic variation of G4P[6] rotaviruses: evidence for novel strains circulating between the hospital and community. J Med Virol 82:700–706

    Article  CAS  PubMed  Google Scholar 

  48. Shin JW, Le VP, Than VT, Lim I, Yoon Y, Kim K, Chung SI, Myung SC, Kim W (2012) Genomic characterization of a cell-culture-adapted Korean human G9P[8] rotavirus, CAU05-202. Arch Virol 157:753–759

    Article  CAS  PubMed  Google Scholar 

  49. Tate JE, Burton AH, Boschi-Pinto C, Steele AD, Duque J, Parashar UD (2012) 2008 estimate of worldwide rotavirus-associated mortality in children younger than 5 years before the introduction of universal rotavirus vaccination programmes: a systematic review and meta-analysis. Lancet Infect Dis 12:136–141

    Article  PubMed  Google Scholar 

  50. Than VT, Kang H, Lim I, Kim W (2013) Molecular characterization of serotype G9 rotaviruses circulating in South Korea between 2005 and 2010. J Med Virol 85:171–178

    Article  CAS  PubMed  Google Scholar 

  51. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  CAS  PubMed  Google Scholar 

  52. Tort LF, Volotao Ede M, de Mendonca MC, da Silva MF, Siqueira AA, Assis RM, Moratorio G, Cristina J, Leite JP (2010) Phylogenetic analysis of human P[8]G9 rotavirus strains circulating in Brazil reveals the presence of a novel genetic variant. J Clin Virol 47:345–355

    Article  CAS  PubMed  Google Scholar 

  53. Varghese V, Das S, Singh NB, Kojima K, Bhattacharya SK, Krishnan T, Kobayashi N, Naik TN (2004) Molecular characterization of a human rotavirus reveals porcine characteristics in most of the genes including VP6 and NSP4. Arch Virol 149:155–172

    Article  CAS  PubMed  Google Scholar 

  54. Vesikari T, Karvonen A, Prymula R, Schuster V, Tejedor JC, Cohen R, Meurice F, Han HH, Damaso S, Bouckenooghe A (2007) Efficacy of human rotavirus vaccine against rotavirus gastroenteritis during the first 2 years of life in European infants: randomised, double-blind controlled study. Lancet 370:1757–1763

    Article  CAS  PubMed  Google Scholar 

  55. WHO (2008) Rotavirus surveillance-worldwide. Morb Mortal Wkly Rep 57:1255–1257

    Google Scholar 

  56. WHO (2009) Rotavirus surveillance worldwide: 2009. Wkly Epidemiol Rec 86:174–176

    Google Scholar 

  57. Wu FT, Banyai K, Huang JC, Wu HS, Chang FY, Hsiung CA, Huang YC, Lin JS, Hwang KP, Jiang B, Gentsch JR (2011) Human infection with novel G3P[25] rotavirus strain in Taiwan. Clin Microbiol Infect 17:1570–1573

    Article  CAS  PubMed  Google Scholar 

  58. Yen C, Figueroa JR, Uribe ES, Carmen-Hernandez LD, Tate JE, Parashar UD, Patel MM, Richardson Lopez-Collado V (2011) Monovalent rotavirus vaccine provides protection against an emerging fully heterotypic G9P[4] rotavirus strain in Mexico. J Infect Dis 204:783–786

    Article  CAS  PubMed  Google Scholar 

  59. Zeller M, Heylen E, De Coster S, Van Ranst M, Matthijnssens J (2012) Full genome characterization of a porcine-like human G9P[6] rotavirus strain isolated from an infant in Belgium. Infect Genet Evol 12:1492–1500

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgement

This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science, and Technology (2010-0012857).

Author information

Authors and Affiliations

  1. Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea

    Van Thai Than, In Hyuk Baek & Wonyong Kim

Authors
  1. Van Thai Than
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. In Hyuk Baek
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wonyong Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Wonyong Kim.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Than, V.T., Baek, I.H. & Kim, W. Whole genomic analysis reveals the co-evolutionary phylodynamics of Korean G9P[8] human rotavirus strains. Arch Virol 158, 1795–1803 (2013). https://doi.org/10.1007/s00705-013-1662-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-013-1662-2

Keywords

Search

Navigation