Genetic Diversity and Molecular Epidemiology of Norwalk‐Like Viruses

Gonin, Patrick; Couillard, Michel; d'Halewyn, M A

doi:10.1086/315780

Cited by 33 publications

(26 citation statements)

References 26 publications

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“…Our findings that NLV genogroup II strains were the dominant type (identified in 94% of positive specimens) is in agreement with those of previous studies of NLV infections in pediatric populations in France, Finland, and Canada (1,4,9). Most genogroup II strains identified in our study (84%) belonged to the Lordsdale cluster, which has a worldwide distribution and is prominent in many countries, including Australia, the United States, and Canada (2, 4, 13).…”

supporting

confidence: 93%

“…Our study shows good agreement with previous surveys of the incidence of calicivirus infection in children hospitalized with acute gastroenteritis in France, China, and South Africa (1,11,12). In comparison, surveillance studies of young children with mild diarrhea from community or outbreak settings detected calicivirus in 19 to 88% of such cases in various countries, including Finland, Canada, and Mexico (3,4,9,10). …”

supporting

confidence: 91%

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Molecular Detection of Human Calicivirus in Young Children Hospitalized with Acute Gastroenteritis in Melbourne, Australia, during 1999

Kirkwood

Bishop

2001

J Clin Microbiol

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Reverse transcription-PCR and sequence analysis identified calciviruses in 32 of 60 stool specimens (negative for other enteric pathogens) obtained from children admitted to our hospital with acute gastroenteritis. The overall annual incidence rate for calcivirus was 9% (32 of 354 children). Molecular analysis identified 30 "Norwalk-like virus" genogroup II (predominantly Lordsdale cluster) and 2 "Sapporo-like virus" strains.Human calciviruses are the most common cause of nonbacterial gastroenteritis outbreaks in adults and older children worldwide (2, 13) and have been estimated to cause 95% of outbreaks of food-related viral gastroenteritis in the United States, representing millions of gastroenteritis episodes each year (8). Little is known about the importance of these viruses as causes of sporadic acute gastroenteritis in young children requiring admission to a hospital (5).Human calciviruses can be divided into two genera: "Norwalk-like viruses" (NLVs) and "Sapporo-like viruses" (SLVs) (2). NLVs are a genetically diverse group of viruses that can be classified phylogenetically into two distinct genogroups: genogroup I, which includes Norwalk virus, and genogroup II, which includes Lordsdale and Snow Mountain viruses. NLVs are the major cause of outbreaks and sporadic gastroenteritis in adults (2, 13). SLVs have been associated mainly with gastroenteritis in nonhospitalized children (9). The importance of calcivirus infection in child health in general is still largely unknown.The objectives of this study were to determine the minimum prevalence of human caliciviruses in stools from young children admitted to the Royal Children's Hospital, Melbourne, Australia, with acute gastroenteritis between January and December 1999 and to characterize the types and distribution of calicivirus strains identified.A total of 354 stool specimens were collected from all children under the age of 5 years. Routine diagnostic tests identified rotavirus (71.5%), astrovirus (5.7%), adenovirus (3.7%), and other pathogens (including bacterial and parasitic pathogens [2.8%]). The remaining specimens (n ϭ 60), where no etiologic agent was identified, were tested for the presence of calicivirus using two reverse transcription-PCR protocols that amplify either a 319-or 321-base fragment (P289 and P290 primers) or a 213-base fragment (degenerate primer set) of the RNA polymerase gene (2, 6).A total of 32 of 60 samples were positive by one or both of the reverse transcription-PCR methods. The nucleotide sequences of these products were determined by direct cycle sequencing and analyzed using E-CLUSTAL W (available through the Australian National Genomic Information Service, University of Sydney).Strains segregated genetically into three distinct NLV genogroup II clusters (n ϭ 30) and two clusters of the SLV genera (n ϭ 2). The majority of the genogroup II strains (26 of 30) belonged to the Lordsdale cluster, while three of the remaining strains were assigned to the Snow Mountain cluster and one was assigned to the rare Hillingdon clus...

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supporting

confidence: 93%

supporting

confidence: 91%

Molecular Detection of Human Calicivirus in Young Children Hospitalized with Acute Gastroenteritis in Melbourne, Australia, during 1999

Kirkwood

Bishop

2001

J Clin Microbiol

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“…Based on the amino acid sequence of the complete VP1 gene, NoVs can be classified into five genogroups and at least 32 genotypes (8 in GI. [1][2][3][4][5][6][7][8]19 in GII, 2 in GIII, 2 in GIV, and 1 in GV) (19,31,33). However, since several genotypes (e.g., GI.6) form distinct clusters at the nucleotide level, further standardization based on partial nucleotide sequences awaits international agreement.…”

Section: Discussionmentioning

confidence: 99%

“…Currently, classification of NoV genotypes is based on genetic diversity within the entire capsid gene (2,16,33). However, most laboratories sequence a small region (200 to 344 bp) of either the polymerase (regions A and B) or major capsid (VP1; regions C, D, and E) gene (1,2,8,14,21,27,28) to genotype strains (Fig. 1).…”

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confidence: 99%

Multicenter Comparison of Two Norovirus ORF2-Based Genotyping Protocols

et al. 2009

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Point source norovirus outbreaks can be difficult to track due to high background levels of the virus in the environment and the limited strain variation in some genotyping regions. However, rapid and accurate source identification can limit the spread of a foodborne outbreak and reduce the number of cases. Harmonization of genotyping assays is critical for enabling the rapid exchange of sequence data nationally and internationally. Several regions of the genome have been proposed for this purpose, but no consensus has been reached. In the present study, two standardized genotyping protocols (region C and region D) were evaluated by nine laboratories in Canada and the United States, using a coded panel of 96 fecal specimens representing 22 different norovirus genotypes. Overall, region C typing had a success rate of 78% compared to 52% for region D; however, region D provides greater nucleotide sequence diversity for identifying new GII.4 variant strains. Significant differences in the genotyping success rate were observed among the nine participating laboratories (10% to 100%) and among the different genotypes (6% to 100%). For several genogroup II strains, reduced region D amplification correlated directly with mismatches between primer sequences and the template. Based on overall performance, we recommend the region C protocol for routine genotyping of noroviruses, while the region D protocol may be useful for identifying new GII.4 variants. Standardized genotyping protocols will enable rapid exchange of outbreak and sequence data through electronic norovirus surveillance networks.

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“…In addition, primers directed to other regions of the Norovirus genome have been developed including relatively conserved regions at the 3'-end of ORF1 (region B 24,25,26 ), at the 5'-end of ORF2 (region C and E; 18,27,28 ) and at the 3' end of ORF2 (region D 29 ) (Figure 4). Real-time PCR systems are excellent diagnostic tools; they are more specific and sensitive than traditional PCRs.…”

Section: I63 Molecular Biological Techniquesmentioning

confidence: 99%

Comparative molecular genetic studies of nucleic acid detection of human noroviruses

Kele¹

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Genetic Diversity and Molecular Epidemiology of Norwalk‐Like Viruses

Cited by 33 publications

References 26 publications

Molecular Detection of Human Calicivirus in Young Children Hospitalized with Acute Gastroenteritis in Melbourne, Australia, during 1999

Molecular Detection of Human Calicivirus in Young Children Hospitalized with Acute Gastroenteritis in Melbourne, Australia, during 1999

Multicenter Comparison of Two Norovirus ORF2-Based Genotyping Protocols

Comparative molecular genetic studies of nucleic acid detection of human noroviruses

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