Evaluation of porcine gastric mucin assay for detection and quantification of human norovirus in fresh herbs and leafy vegetables.

Leafy vegetables and fresh herbs are important parts of a healthy diet, however, they can be common vehicles of norovirus (NoV) infection and lead to serious health and economic concerns globally. NoV is highly infectious and persistent in the food and the environment, while being resistant to conventional food decontamination practices. Herbs and leafy greens are often consumed raw, and if contaminated with NoV, they may cause illness. Consequently, for outbreak prevention and surveillance purposes, sensitive and rapid methods are required to detect the presence of infectious NoV in naturally contaminated produce during its shelf life. Herein, we compared the extraction efficiency of the ISO/TS 15216-1:2017 method with the porcine gastric mucin coated magnetic beads (PGM-MB) assay, combined with heat-denaturation for RNA extraction, for detection of human NoV in artificially contaminated fresh green seaweed, basil, mint, and baby spinach. Droplet-digital RT-PCR was used to quantify the extracted genome by both methods. Our data demonstrated that while the PGM-MB assay takes considerably less time, it yields significantly higher recovery rates compared with the ISO/TS 15216-1:2017. Furthermore, since this method has the ability to be adapted in high-throughput and automated systems, it can be further modified to be employed by the food industry to reduce the number of NoV illnesses and outbreaks at the source of distribution.

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

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.