title: Characterization of the Genomic Diversity of Norovirus in Linked Patients Using a Metagenomic Deep Sequencing Approach.
abstract: Norovirus (NoV) is the leading cause of gastroenteritis worldwide. A robust cell culture system does not exist for NoV and therefore detailed characterization of outbreak and sporadic strains relies on molecular techniques. In this study, we employed a metagenomic approach that uses non-specific amplification followed by next-generation sequencing to whole genome sequence NoV genomes directly from clinical samples obtained from 8 linked patients. Enough sequencing depth was obtained for each sample to use ade novoassembly of near-complete genome sequences. The resultant consensus sequences were then used to identify inter-host nucleotide variations that occur after direct transmission, analyze amino acid variations in the major capsid protein, and provide evidence of recombination events. The analysis of intra-host quasispecies diversity was possible due to high coverage-depth. We also observed a linear relationship between NoV viral load in the clinical sample and the number of sequence reads that could be attributed to NoV. The method demonstrated here has the potential for future use in whole genome sequence analyses of other RNA viruses isolated from clinical, environmental, and food specimens.
authors.affiliation: National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada Ottawa, ON, Canada.
authors.forename: Neda
authors.initials: N
authors.lastname: Nasheri
authors.affiliation: Biostatistics and Modeling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada Ottawa, ON, Canada.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Petronella
authors.affiliation: Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill UniversityMontreal, QC, Canada; Department of Animal Science, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill UniversityMontreal, QC, Canada.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Ronholm
authors.affiliation: National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada Ottawa, ON, Canada.
authors.forename: Sabah
authors.initials: S
authors.lastname: Bidawid
authors.affiliation: National Food Virology Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada Ottawa, ON, Canada.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Corneau
keywords: antigenic variation; genetic variation; linked patients; next-generation sequencing (NGS); norovirus; recombination