Genetic analysis of the capsid gene of genotype GII.2 noroviruses

Journal of Virology

Volumn 82, Issue 15, 2008, Pages 7336-7345

  Iritani, Nobuhiro ^a,b   Vennema, Harry ^a   Siebenga, J Joukje ^a   Siezen, Roland J ^c   Renckens, Bernadet ^c   Seto, Yoshiyuki ^d   Kaida, Atsushi ^b   Koopmans, Marion ^a  

^a NATIONAL INSTITUTE FOR PUBLIC HEALTH AND THE ENVIRONMENT   (Netherlands)

^b OSAKA CITY INSTITUTE OF PUBLIC HEALTH AND ENVIRONMENTAL SCIENCES   (Japan)

^c RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^d Osaka Prefecture University   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSID PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; EPIDEMIC; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC DRIFT; GENOTYPE; JAPAN; NETHERLANDS; NONHUMAN; NOROVIRUS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; VIRUS CAPSID; VIRUS GENE; VIRUS GENOME; VIRUS INFECTION; VIRUS RECOMBINANT;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; CALICIVIRIDAE INFECTIONS; CAPSID PROTEINS; DISEASE OUTBREAKS; EVOLUTION, MOLECULAR; GASTROENTERITIS; GENOTYPE; HUMANS; JAPAN; MEMBRANE PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION, MISSENSE; NETHERLANDS; NOROVIRUS; PHYLOGENY; POLYMORPHISM, GENETIC; PROTEIN CONFORMATION; SELECTION (GENETICS); SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID;

MIRIDAE;

EID: 47749150727     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.02371-07     Document Type: Article

References (41)

1. Ambert-Balay, K., F. Bon, F. L. Guyader, P. Pothier, and E. Kohli. 2005. Characterization of new recombinant noroviruses. J. Clin. Microbiol. 43:5179-5186.
2. Ando, T., J. S. Noel, and R. L. Fankhauser. 2000. Genetic classification of "Norwalk-like viruses. J. Infect. Dis. 181(Suppl. 2):S336-S348.
3. Bates, P. A., L. A. Kelley, R. M. MacCallum, and M. J. E. Sternberg. 2001. Enhancement of protein modelling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins 45(Suppl. 5):39-46.
4. Bull, R. A., G. S. Hansman, L. E. Clancy, M. M. Tanaka, W. D. Rawlinson, and P. A. White. 2005. Norovirus recombination in ORF1/ORF2 overlap. Emerg. Infect. Dis. 11:1079-1085.
5. Bull, R. A., T. V. Elise, C. J. McIver, W. D. Rawlinson, and P. A. White. 2006. Emergence of a new norovirus genotype II.4 variant associated with global outbreaks of gastroenteritis. J. Clin. Microbiol. 44:327-333.
6. Cao, S., Z. Lou, M. Tan, Y. Chen, Y. Liu, Z. Zhang, X. C. Zhang, X. Jiang, X. Li, and Z. Rao. 2007. Structural basis for the recognition of blood group trisaccharides by norovirus. J. Virol. 81:5949-5957.
7. Chen, R., J. D. Neil, J. S. Noel, A. M. Hutson, R. I. Glass, and B. V. Prasad. 2004. Inter- and intragenus structural variations in caliciviruses and their functional implications. J. Virol. 78:6469-6479.
8. de Bruin, E., E. Duizer, H. Vennema, and M. P. G. Koopmans. 2006. Diagnosis of norovirus outbreaks by commercial ELISA or RT-PCR. J. Virol. Methods 137:259-264.
9. Dingle, K. E., and Norovirus Infection Control in Oxfordshire Communities Hospitals. 2004. Mutation in a Lordsdale norovirus epidemic strain as a potential indicator of transmission routes. J. Clin. Microbiol. 42:3950-3957.
10. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
11. Fankhauser, R. L., J. S. Noel, S. S. Monroe, T. Ando, and R. I. Glass. 1998. Molecular epidemiology of "Norwalk-like viruses" in outbreaks of gastroenteritis in the United states. J. Infect. Dis. 178:1571-1578.
12. Filatov, D. A. 2002. ProSeq: a software for preparation and evolutionary analysis of DNA sequence data sets. Mol. Ecol. Notes 2:621-624.
13. Green, K. Y. 2007. Caliciviridae: The noroviruses, p. 949-979. In B. N. Fields, D. M. Knipe, P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Martin, B. Roizman, and S. E. Straus (ed.), Fields virology, 5th ed. Lippincott, Williams & Wilkins, Philadelphia, PA.
14. Green, S. M., K. E. Dingle, P. R. Lambden, E. O. Caul, C. R. Ashley, and I. N. Clarke. 1994. Human enteric Caliciviridae: a new prevalent small round-structured virus group defined by RNA-dependent RNA polymerase and capsid diversity. J. Gen. Virol. 75:1883-1888.
15. Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41:95-98.
16. Hardy, M. E., S. F. Kramer, J. J. Treanor, and M. K. Estes. 1997. Human calicivirus genogroup II capsid sequence diversity revealed by analyses of the prototype Snow Mountain agent. Arch. Virol. 142:1469-1479.
17. Iritani, N., A. Kaida, H. Kubo, N. Abe, T. Murakami, H. Venemma, M. Koopmans, N. Takeda, H. Ogura, and Y. Seto. 21 May 2008. An epidemic of GII.2 genotype noroviruses in the spring of 2004 in Osaka City, Japan. J. Clin. Microbiol. doi:10.1128/JCM.01993-07.
18. Jiang, X., M. Wang, K. Wang, and M. K. Estes. 1993. Sequence and genomic organization of Norwalk virus. Virology 195:51-61.
19. Kageyama, T., S. Kojima, M. Shinohara, K. Uchida, S. Fukushi, F. B. Hoshino, N. Takeda, and K. Katayama. 2003. Broadly reactive and highly sensitive assay for Norwalk-like viruses based on real-time quantitative reverse transcription-PCR. J. Clin. Microbiol. 41:1548-1557.
20. Kageyama, T., M. Shinohara, K. Uchida, S. Fukushi, F. B. Hoshino, S. Kojima, R. Takai, T. Oka, N. Takeda, and K. Katayama. 2004. Coexistence of multiple genotypes, including newly identified genotypes, in outbreaks of gastroenteritis due to norovirus in Japan. J. Clin. Microbiol. 42:2988-2995.
21. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
22. Kojima, S., T. Kageyama, S. Fukushi, F. B. Hoshino, M. Shinohara, K. Uehida, K. Natori, N. Takeda, and K. Katayama. 2002. Genogroup-specific PCR primers for detection of Norwalk-like viruses. J. Virol. Methods 100:107-114.
23. Koopmans, M., J. Vinje, M. de Wit, I. Leenen, W. van der Poel, and Y. van Duynhoven. 2000. Molecular epidemiology of human enteric caliciviruses in The Netherlands. J. Infect. Dis. 181(Suppl. 2):S262-S269.
24. Krieger, E., G. Koraimann, and G. Vriend. 2002. Increasing the precision of comparative models with YASARA NOVA - a self-parameterizing force field. Proteins 47:393-402.
25. Lambert, C., N. Leonard, X. De Bolle, and E. Depiereux. 2002. ESyPred3D: prediction of proteins 3D structures. Bioinformatics 18:1250-1256.
26. Lewis, D. C., A. Hale, X. Jiang, R. Eglin, and D. W. G. Brown. 1997. Epidemiology of Mexico virus, a small round-structured virus in Yorkshire, United Kingdom, between January 1992 and March 1995. J. Infect. Dis. 175:951-954.
27. Lopman, B., H. Vennema, E. Kohli, P. Pothier, A. Sanchez, A. Negredo, J. Buesa, E. Schreier, M. Reacher, D. Brown, J. Gray, M. Iturriza, C. Gallimore, B. Bottiger, K. Hedlund, M. Torven, C. Bonsdorff, L. Maunula, M. Poljsak-Prijatelj, J. Zimsek, G. Reuter, G. Szucs, B. Melegh, L. Svennson, Y. Duijnhoven, and M. Koopmans. 2004. Increase in viral gastroenteritis outbreaks in Europe and epidemic spread of new norovirus variant. Lancet 363:682-688.
28. Nilsson, M., K. O. Hedlund, M. Thorhagen, G. Larson, K. Johansen, A. Ekspong, and L. Svensson. 2003. Evolution of human calicivirus RNA in vivo: accumulation of mutations in the protruding P2 domain of the capsid leads to structural changes and possibly a phenotype. J. Virol. 77:13117-13124.
29. Noel, J. S., R. L. Fankhauser, T. Ando, S. S. Monroe, and R. I. Glass. 1999. Identification of a distinct common strain of "Norwalk-like viruses" having a global distribution. J. Infect. Dis. 179:1334-1344.
30. Okada, M., T. Ogawa, I. Kaiho, and K. Shinozaki. 2005. Genetic analysis of noroviruses in Chiba Prefecture, Japan, between 1999 and 2004. J. Clin. Microbiol. 43:4391-4401.
31. Prasad, B. V., M. E. Hardy, T. Dokland, J. Bella, M. G. Rossmann, and M. K. Estes. 1999. X-ray crystallographic structure of the Norwalk virus capsid. Science 286:287-290.
32. Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
33. Siebenga, J. J., H. Vennema, B. Renckens, E. de Bruin, B. van der Veer, R. J. Siezen, and M. Koopmans. 2007. Epochal evolution of GGII.4 norovirus capsid proteins from 1995 to 2006. J. Virol. 81:9932-9941.
34. Tan, M., P. Huang, J. Meller, W. Zhong, T. Farkas, and X. Jiang. 2003. Mutations within the P2 domain of norovirus capsid affect binding to human histo-blood group antigens: evidence for a binding pocket. J. Virol. 77:12562-12571.
35. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The Clustal X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
36. Vinjé, J., J. Green, D. C. Lewis, C. I. Gallimore, D. W. Brown, and M. P. Koopmans. 2000. Genetic polymorphism across regions of the three open reading frames of "Norwalk-like viruses." Arch. Virol. 145:223-241.
37. Vinjé, J., R. A. Hamidjaja, and M. D. Sobsey. 2004. Development and application of a capsid VP1 (region D) based reverse transcription PCR assay for genotyping of genogroup I and II noroviruses. J. Virol. Methods 116:109-117.
38. Vriend, G. 1990. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8:52-56.
39. Wang, J., X. Jiang, H. P. Madore, J. Gray, U. Desselberger, T. Ando, Y. Seto, I. Oishi, J. F. Lew, K. Y. Green, et al. 1994. Sequence diversity of small, round-structured viruses in the Norwalk virus group. J. Virol. 68:5982-5990.
40. Widdowson, M. A., E. H. Cramer, L. Hadley, J. S. Bresse, R. S. Beard, S. N. Bulens, M. Charles, W. Chege, E. Isakbaeva, J. G. Wright, E. Mintz, D. Forney, J. Massey, R. I. Glass, and S. S. Monroe. 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.
41. Xi, J. N., D. Y. Graham, K. N. Wang, and M. K. Estes. 1990. Norwalk virus genome cloning and characterization. Science 250:1580-1583.