Home LiteratureArticle Details
PMID: 16207981 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Characterization of new recombinant noroviruses.

Journal of clinical microbiology ·Vol. 43 ·No. 10 ·2005-10-00 ·Pages 5179-86

Ambert-Balay K, Bon F, Le Guyader F, Pothier P, Kohli E

Abstract

Noroviruses are important etiologic agents of acute gastroenteritis and show great genetic diversity. To characterize more fully previously detected strains that could not be assigned unequivocally to one particular genotype based on the RNA polymerase, we have sequenced a region in the capsid gene and, in some cases, in the junction between open reading frame 1 (ORF 1) and ORF 2. The results allowed us to identify several recombinant noroviruses: GGIIb viruses were detected for the first time in France in August 2000 and then spread through France and to Europe during the following winter. Here we present the characterization of three other probable GII recombinants which showed different phylogenetic positions depending on their ORF 1 and ORF 2 sequences. Analysis of the region located between ORF 1 and ORF 2 by a nucleotide identity window search showed a sudden shift in similarities. Moreover, recombination breakpoints were identified upstream and downstream of the beginning of ORF 2 by using a statistical test, thus confirming the involvement of this region in recombination. Unlike GGIIb, the three recombinants described here do not seem to have diffused widely in the community: one was found in a waterborne outbreak, and the other two were found in sporadic cases. Recombination is important for the evolution of RNA viruses and has already been described for noroviruses. Our results suggest that recombination is not a rare phenomenon among noroviruses, but not all these presumed recombinants that formed during RNA replication are able to spread widely.

MeSH Terms
Base Sequence Caliciviridae Infections/virology Capsid Capsid Proteins/genetics Cloning, Molecular DNA-Directed RNA Polymerases/genetics Humans Molecular Sequence Data Norovirus/classification,genetics Phylogeny RNA, Viral/analysis,isolation & purification Recombination, Genetic Reverse Transcriptase Polymerase Chain Reaction Sequence Analysis, DNA
Chemicals
Capsid Proteins RNA, Viral DNA-Directed RNA Polymerases
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Ambert-Balay K
Laboratoire de Virologie, Reference Laboratory for Enteric Viruses, Center Hospitalier Universitaire, 21079 Dijon, France. [email protected]
Bon F
Le Guyader F
Pothier P
Kohli E
References (41)
41 references, click to expand
  1. Epidemiologic and molecular trends of "Norwalk-like viruses" associated with outbreaks of gastroenteritis in the United States.
    J Infect Dis. 2002 Jul 1;186(1):1-7 PMID: 12089655
  2. Evidence of recombination in the norovirus capsid gene.
    J Virol. 2005 Apr;79(8):4977-90 PMID: 15795283
  3. Phylogenetic analysis of the complete genome of 18 Norwalk-like viruses.
    Virology. 2002 Aug 1;299(2):225-239 PMID: 12202225
  4. Virus diversity in a winter epidemic of acute diarrhea in France.
    J Clin Microbiol. 2002 Nov;40(11):4266-72 PMID: 12409408
  5. A waterborne outbreak of Norwalk-like virus among snowmobilers-Wyoming, 2001.
    J Infect Dis. 2003 Jan 15;187(2):303-6 PMID: 12552455
  6. STAT1-dependent innate immunity to a Norwalk-like virus.
    Science. 2003 Mar 7;299(5612):1575-8 PMID: 12624267
  7. Laboratory capability in Europe for foodborne viruses.
    Euro Surveill. 2002 Apr;7(4):61-5 PMID: 12631939
  8. Snow Mountain virus genome sequence and virus-like particle assembly.
    Virus Genes. 2003 Jan;26(1):71-82 PMID: 12680695
  9. RNA recombination plays a major role in genomic change during circulation of coxsackie B viruses.
    J Virol. 2004 Mar;78(6):2948-55 PMID: 14990713
  10. Genetic diversity of norovirus and sapovirus in hospitalized infants with sporadic cases of acute gastroenteritis in Chiang Mai, Thailand.
    J Clin Microbiol. 2004 Mar;42(3):1305-7 PMID: 15004104
  11. Evolutionary aspects of recombination in RNA viruses.
    J Gen Virol. 1999 Oct;80 ( Pt 10):2535-43 PMID: 10573145
  12. High rate of recombination throughout the human immunodeficiency virus type 1 genome.
    J Virol. 2000 Feb;74(3):1234-40 PMID: 10627533
  13. Characterization of a novel human calicivirus that may be a naturally occurring recombinant.
    Arch Virol. 1999;144(12):2377-87 PMID: 10664391
  14. Genetic polymorphism across regions of the three open reading frames of "Norwalk-like viruses".
    Arch Virol. 2000;145(2):223-41 PMID: 10752550
  15. Genetic classification of "Norwalk-like viruses..
    J Infect Dis. 2000 May;181 Suppl 2:S336-48 PMID: 10804147
  16. Capsid protein diversity among Norwalk-like viruses.
    Virus Genes. 2000;20(3):227-36 PMID: 10949950
  17. Gastroenteritis in sentinel general practices,The Netherlands.
    Emerg Infect Dis. 2001 Jan-Feb;7(1):82-91 PMID: 11266298
  18. Sensor, a population-based cohort study on gastroenteritis in the Netherlands: incidence and etiology.
    Am J Epidemiol. 2001 Oct 1;154(7):666-74 PMID: 11581101
  19. Molecular characterization of a novel recombinant strain of human astrovirus associated with gastroenteritis in children.
    Arch Virol. 2001 Dec;146(12):2357-67 PMID: 11811685
  20. Human caliciviruses in Europe.
    J Clin Virol. 2002 Apr;24(3):137-60 PMID: 11856616
  21. Food-borne outbreak of gastroenteritis associated with genogroup I calicivirus.
    J Clin Microbiol. 2002 Mar;40(3):794-8 PMID: 11880395
  22. International collaborative study to compare reverse transcriptase PCR assays for detection and genotyping of noroviruses.
    J Clin Microbiol. 2003 Apr;41(4):1423-33 PMID: 12682125
  23. Waterborne outbreak of gastroenteritis associated with a norovirus.
    Appl Environ Microbiol. 2003 Sep;69(9):5263-8 PMID: 12957912
  24. Early identification of common-source foodborne virus outbreaks in Europe.
    Emerg Infect Dis. 2003 Sep;9(9):1136-42 PMID: 14519252
  25. Detection and characterization of norovirus outbreaks in Germany: application of a one-tube RT-PCR using a fluorogenic real-time detection system.
    J Med Virol. 2004 Feb;72(2):312-9 PMID: 14695676
  26. Emerging genotype (GGIIb) of norovirus in drinking water, Sweden.
    Emerg Infect Dis. 2003 Dec;9(12):1548-52 PMID: 14720394
  27. 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. 2004 Mar 15;116(2):109-17 PMID: 14738976
  28. Development and evaluation of a new commercial test allowing the simultaneous detection of noroviruses and sapoviruses by reverse transcription-PCR and microplate hybridization.
    J Clin Microbiol. 2004 May;42(5):2218-20 PMID: 15131194
  29. Coexistence of multiple genotypes, including newly identified genotypes, in outbreaks of gastroenteritis due to Norovirus in Japan.
    J Clin Microbiol. 2004 Jul;42(7):2988-95 PMID: 15243049
  30. RNA recombination in animal and plant viruses.
    Microbiol Rev. 1992 Mar;56(1):61-79 PMID: 1579113
  31. Sequence and genome organization of a human small round-structured (Norwalk-like) virus.
    Science. 1993 Jan 22;259(5094):516-9 PMID: 8380940
  32. Sequence and genomic organization of Norwalk virus.
    Virology. 1993 Jul;195(1):51-61 PMID: 8391187
  33. Polioviruses with natural recombinant genomes isolated from vaccine-associated paralytic poliomyelitis.
    Virology. 1993 Sep;196(1):199-208 PMID: 8102826
  34. Broadly reactive reverse transcriptase polymerase chain reaction for the diagnosis of SRSV-associated gastroenteritis.
    J Med Virol. 1995 Dec;47(4):392-8 PMID: 8636708
  35. Seminested RT-PCR systems for small round structured viruses and detection of enteric viruses in seafood.
    Int J Food Microbiol. 1997 Jun 17;37(1):27-36 PMID: 9237119
  36. Mixed genogroup SRSV infections among a party of canoeists exposed to contaminated recreational water.
    J Med Virol. 1997 Aug;52(4):425-9 PMID: 9260692
  37. Human calicivirus genogroup II capsid sequence diversity revealed by analyses of the prototype Snow Mountain agent.
    Arch Virol. 1997;142(7):1469-79 PMID: 9267456
  38. Correlation of patient immune responses with genetically characterized small round-structured viruses involved in outbreaks of nonbacterial acute gastroenteritis in the United States, 1990 to 1995.
    J Med Virol. 1997 Dec;53(4):372-83 PMID: 9407386
  39. Intragenic recombinations in rotaviruses.
    FEBS Lett. 1998 May 8;427(2):183-7 PMID: 9607308
  40. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.
    J Virol. 1999 Jan;73(1):152-60 PMID: 9847317
  41. Molecular epidemiology of caliciviruses causing outbreaks and sporadic cases of acute gastroenteritis in Spain.
    J Clin Microbiol. 2002 Aug;40(8):2854-9 PMID: 12149342
Article Info
Journal
Journal of clinical microbiology
Abbr.
J Clin Microbiol
ISSN
0095-1137
DOI
10.1128/JCM.43.10.5179-5186.2005
Email
[email protected]
Published
2005-10-00
Pages
5179-86
Language
English
Region
United States
NLM ID
7505564
PMCID
PMC1248523
Subset
IM
Databases
GENBANK
AY682550, AY682551, AY682552
External Links
PubMed source DOI: 10.1128/JCM.43.10.5179-5186.2005 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2