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BMC Infect Dis. 2018 Oct 17;18(1):521. doi: 10.1186/s12879-018-3419-8.

Genetic characterization of norovirus GII.4 variants circulating in Canada using a metagenomic technique.

Author information

1
Biostatistics and Modeling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada Ottawa, Ottawa, ON, Canada.
2
Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, QC, Canada.
3
Department of Animal Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, QC, Canada.
4
National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada.
5
National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada 251 Sir Frederick Banting Driveway, Ottawa, ON, K1A 0K9, Canada. neda.nasheri@canada.ca.

Abstract

BACKGROUND:

Human norovirus is the leading cause of viral gastroenteritis globally, and the GII.4 has been the most predominant genotype for decades. This genotype has numerous variants that have caused repeated epidemics worldwide. However, the molecular evolutionary signatures among the GII.4 variants have not been elucidated throughout the viral genome.

METHOD:

A metagenomic, next-generation sequencing method, based on Illumina RNA-Seq, was applied to determine norovirus sequences from clinical samples.

RESULTS:

Herein, the obtained deep-sequencing data was employed to analyze full-genomic sequences from GII.4 variants prevailing in Canada from 2012 to 2016. Phylogenetic analysis demonstrated that the majority of these sequences belong to New Orleans 2009 and Sydney 2012 strains, and a recombinant sequence was also identified. Genome-wide similarity analyses implied that while the capsid gene is highly diverse among the isolates, the viral protease and polymerase genes remain relatively conserved. Numerous amino acid substitutions were observed at each putative antigenic epitope of the VP1 protein, whereas few amino acid changes were identified in the polymerase protein. Co-infection with other enteric RNA viruses was investigated and the astrovirus genome was identified in one of the samples.

CONCLUSIONS:

Overall this study demonstrated the application of whole genome sequencing as an important tool in molecular characterization of noroviruses.

KEYWORDS:

Antigenic drift; Co-infection; Metagenomics; Next-generation sequencing; Norovirus; Recombination

PMID:
30333011
PMCID:
PMC6191920
DOI:
10.1186/s12879-018-3419-8
[Indexed for MEDLINE]
Free PMC Article

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