Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 11, Number 7—July 2005
Research

Norovirus Recombination in ORF1/ORF2 Overlap

Rowena Bull*, Grant S. Hansman†, Leighton E. Clancy*‡, Mark M. Tanaka*, William D. Rawlinson*‡, and Peter A. White*Comments to Author 
Author affiliations: *University of New South Wales, Sydney, New South Wales, Australia; †University of Tokyo, Tokyo, Japan; ‡Prince of Wales Hospital, Randwick, New South Wales, Australia

Main Article

Figure 1

Phylogenetic analysis of the nucleotide sequences of capsid and polymerase regions of 9 identified recombinant norovirus genogroup II strains in relation to 26 known strains and prototype strains. The left tree analyzes the relationship of a 420-bp region of the 3´ end of the polymerase region. The right tree shows the relationship of 550 bp of the 5´ end of the capsid sequence. Suspected recombinants are underlined to emphasize their different phylogenetic groupings, and strains described in th

Figure 1. . Phylogenetic analysis of the nucleotide sequences of capsid and polymerase regions of 9 identified recombinant norovirus genogroup II strains in relation to 26 known strains and prototype strains. The left tree analyzes the relationship of a 420-bp region of the 3´ end of the polymerase region. The right tree shows the relationship of 550 bp of the 5´ end of the capsid sequence. Suspected recombinants are underlined to emphasize their different phylogenetic groupings, and strains described in this study are represented in boldface. The percentage bootstrap values in which the major groupings were observed among 100 replicates are indicated. The branch lengths are proportional to the evolutionary distance between sequences and the distance scale, in nucleotide substitutions per position, is shown. The capsid clustering is shown in bold and is based on the classification of Vinjé et al. (23) (Table).

Main Article

References
  1. Koopmans  MPG, von Bonsdorrf  CH, Vinje  J, DeMedici  D, Monroe  SS. Foodborne enteric viruses. FEMS Microbiol Rev. 2002;26:187–205.PubMedGoogle Scholar
  2. Fankhauser  RL, Monroe  SS, Noel  JS, Humphrey  CD, Bresee  JS, Parashar  UD, Epidemiological and molecular trends of "Norwalk-like viruses" associated with outbreaks of gastroenteritis in the United States. J Infect Dis. 2002;186:1–7. DOIPubMedGoogle Scholar
  3. Noel  JS, Fankhauser  RL, Ando  T, Monroe  SS, Glass  RI. Identification of a distinct common strain of "Norwalk-like viruses" having a global distribution. J Infect Dis. 1999;179:1334–44. DOIPubMedGoogle Scholar
  4. Atmar  RL, Estes  MK. Diagnosis of noncultivatable gastroenteritis viruses, the human caliciviruses. Clin Microbiol Rev. 2001;14:15–37. DOIPubMedGoogle Scholar
  5. Green  KY, Chanock  RM, Kapikan  AZ. Human calicivirus. In: Knipe DM, Howley PM, editors. Fields virology. Volume 1. 4th ed. Philadelphia: Lippincott Williams & Wilkins; 2001. p. 841–74.
  6. Bertolotti-Ciarlet  A, White  LJ, Chen  R, Prasad  BV, Estes  MK. Structural requirements for the assembly of Norwalk virus-like particles. J Virol. 2002;76:4044–55. DOIPubMedGoogle Scholar
  7. Worobey  M, Holmes  EC. Evolutionary aspects of recombination in RNA viruses. J Gen Virol. 1999;80:2535–43.PubMedGoogle Scholar
  8. Lai  MMC. RNA recombination in animal and plant viruses. Microbiol Rev. 1992;56:61–79.PubMedGoogle Scholar
  9. Hardy  ME, Kramer  SE, Treanor  JJ, Estes  MK. Human calicivirus genogroup II capsid sequence diversity revealed by analyses of the prototype Snow Mountain agent. Arch Virol. 1997;142:1469–79. DOIPubMedGoogle Scholar
  10. Katayama  K, Shirato-Horikoshi  H, Kojima  S, Kageyama  T, Oka  T, Hoshino  FB, Phylogenetic analysis of the complete genome of 18 Norwalk-like viruses. Virology. 2002;299:225–39. DOIPubMedGoogle Scholar
  11. Hansman  GS, Katayama  K, Peerakome  N, Khamrin  P, Tonusin  S, Okitsu  S, Genetic diversity of norovirus and sapovirus in hospitalized infants with sporadic cases of acute gastroenteritis in Thailand. J Clin Microbiol. 2004;42:1305–7. DOIPubMedGoogle Scholar
  12. Jiang  X, Espul  C, Zhong  WM, Cuello  H, Matson  DO. Characterization of a novel human calicivirus that may be a naturally occurring recombinant. Arch Virol. 1999;144:2377–87. DOIPubMedGoogle Scholar
  13. Hansman  GS, Doan  LTP, Kguyen  TA, Okitsu  S, Katayama  K, Ogawa  S, Detection of norovirus and sapovirus infection among children with gastroenteritis in Ho Chi Minh City, Vietnam. Arch Virol. 2004;149:1673–88. DOIPubMedGoogle Scholar
  14. Han  MG, Smiley  JR, Thomas  C, Saif  LJ. Genetic recombination between two genotypes of genogroup III bovine noroviruses (BoNVs) and capsid sequence diversity among BoNVs and Nebraska-like bovine enteric caliciviruses. J Clin Microbiol. 2004;42:5214–24. DOIPubMedGoogle Scholar
  15. Oliver  SL, Brown  DW, Green  J, Bridger  JC. A chimeric bovine enteric calicivirus: evidence for genomic recombination in genogroup III of the Norovirus genus of the Caliciviridae. Virology. 2004;326:231–9. DOIPubMedGoogle Scholar
  16. Katayama  K, Miyoshi  T, Uchino  K, Oka  T, Tanaka  T, Naokazu  T, Novel recombinant sapovirus. Emerg Infect Dis. 2004;10:1874–6.PubMedGoogle Scholar
  17. White  PA, Hansman  GS, Li  A, Dable  J, Isaacs  M, Ferson  M, Norwalk-like virus 95/96-US strain is a major cause of gastroenteritis outbreaks in Australia. J Med Virol. 2002;68:113–8. DOIPubMedGoogle Scholar
  18. Felsenstein  J. PHYLIP inference package, version 3.5c. Seattle: University of Washington; 1993.
  19. Page  RDM. TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci. 1996;12:357–8.PubMedGoogle Scholar
  20. Smith  JM. Analyzing the mosaic structure of genes. J Mol Evol. 1992;34:126–9. DOIPubMedGoogle Scholar
  21. Lole  K, Bollinger  R, Paranjape  R, Gadkari  D, Kulkarni  S, Novak  N, Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol. 1999;73:152–60.PubMedGoogle Scholar
  22. Posada  D. Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol Biol Evol. 2002;19:708–17. DOIPubMedGoogle Scholar
  23. Vinjé  J, Hamidjaja  RA, Sobsey  MD. Developmental and application of a capsid VP1 (region D) based reverse transcription PCR assay for genotyping of genogroup I and II noroviruses. J Virol Methods. 2004;116:109–17. DOIPubMedGoogle Scholar
  24. Vinjé  J, Green  J, Lewis  DC, Gallimore  CI, Brown  DW, Koopmans  MP. Genetic polymorphism across regions of the three open reading frames of "Norwalk-like viruses.". Arch Virol. 2000;145:223–41. DOIPubMedGoogle Scholar
  25. Gallimore  CI, Green  J, Richards  AF, Cotterill  H, Curry  A, Brown  DW, Methods for the detection and characterisation of noroviruses associated with outbreaks of gastroenteritis: outbreaks occurring in the north-west of England during two norovirus seasons. J Med Virol. 2004;73:280–8. DOIPubMedGoogle Scholar
  26. Meyers  G, Wirblich  C, Thiel  HJ. Rabbit hemorrhagic disease virus—molecular cloning and nucleotide sequencing of a calicivirus genome. Virology. 1991;184:664–76. DOIPubMedGoogle Scholar
  27. Herbert  TP, Brierley  I, Brown  TDK. Detection of the ORF3 polypeptide of feline calicivirus in infected cells and evidence for its expression from a single, functionally bicistronic, subgenomic RNA. J Gen Virol. 1996;77:123–7. DOIPubMedGoogle Scholar
  28. Pletneva  MA, Sosnovtsev  SV, Green  KY. The genome of Hawaii virus and its relationship with other members of the Caliciviridae. Virus Genes. 2001;23:5–16. DOIPubMedGoogle Scholar
  29. Miller  WA, Dreher  TW, Hall  TC. Synthesis of brome mosaic virus subgenomic RNA in vitro by internal initiation on (-) sense genomic RNA. Nature. 1985;313:68–70. DOIPubMedGoogle Scholar
  30. Morales  M, Barcena  J, Ramirez  MA, Boga  JA, Parra  F, Torres  JM. Synthesis in vitro of rabbit hemorrhagic disease virus subgenomic RNA by internal initiation on (-) sense genomic RNA. J Biol Chem. 2004;279:17013–8. DOIPubMedGoogle Scholar
  31. Kao  CC, Singh  P, Ecker  DJ. De novo initiation of viral RNA-dependent RNA synthesis. Virology. 2001;287:251–60. DOIPubMedGoogle Scholar
  32. Cooper  PD, Steiner-Pryor  A, Scotti  PD, Delong  D. On the nature of poliovirus genetic recombinants. J Gen Virol. 1974;23:41–9. DOIPubMedGoogle Scholar
  33. Miller  WA, Koev  G. Minireview: synthesis of subgenomic RNAs by positive-strand RNA viruses. Virology. 2000;273:1–8. DOIPubMedGoogle Scholar
  34. Ishikawa  M, Janda  M, Krol  MA, Ahlquist  P. In vivo DNA expression of functional brome mosaic virus RNA replicons in Saccharomyces cerevisiae. J Virol. 1997;71:7781–90.PubMedGoogle Scholar
  35. Haseltine  WA, Kleid  DG, Panet  A, Rothenberg  E, Baltimore  D. Ordered transcription of RNA tumor virus genomes. J Mol Biol. 1976;106:109–31. DOIPubMedGoogle Scholar
  36. van Marle  G, Dobbe  JC, Gultyaev  AP, Luytjes  W, Spaan  WJ, Snijder  EJ. Artevirus discontinuous mRNA transcription is guided by base pairing between sense and antisense transcription-regulation sequences. Proc Natl Acad Sci U S A. 1999;96:12056–61. DOIPubMedGoogle Scholar

Main Article

Page created: April 24, 2012
Page updated: April 24, 2012
Page reviewed: April 24, 2012
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external