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

Petronella, Nicholas; Ronholm, Jennifer; Suresh, Menka; Harlow, Jennifer; Mykytczuk, Oksana; Corneau, Nathalie; Bidawid, Sabah; Nasheri, Neda

doi:10.1186/s12879-018-3419-8

Cited by 26 publications

(17 citation statements)

References 52 publications

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“…FCV, MNV or HAV RNA recovered by the ISO 15216-1 method and the bead assays were quantified using the One-Step dd-RT-PCR Advanced Kit for Probes (Bio-Rad Laboratories, Ltd.) according to manufacturer’s instructions and as described previously (Mykytczuk et al 2017 ; Petronella et al 2018 ). Primers and probes used to quantify FCV, MNV and HAV are listed in Table 1 .…”

Section: Methodsmentioning

confidence: 99%

Survival and Inactivation by Advanced Oxidative Process of Foodborne Viruses in Model Low-Moisture Foods

Nasheri

Harlow²,

Chen³

et al. 2021

Food Environ Virol

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Enteric viruses, such as human norovirus (NoV) and hepatitis A virus (HAV), are the major causes of foodborne illnesses worldwide. These viruses have low infectious dose, and may remain infectious for weeks in the environment and food. Limited information is available regarding viral survival and transmission in low-moisture foods (LMF). LMFs are generally considered as ready-to-eat products, which undergo no or minimal pathogen reduction steps. However, numerous foodborne viral outbreaks associated with LMFs have been reported in recent years. The objective of this study was to examine the survival of foodborne viruses in LMFs during 4-week storage at ambient temperature and to evaluate the efficacy of advanced oxidative process (AOP) treatment in the inactivation of these viruses. For this purpose, select LMFs such as pistachios, chocolate, and cereal were inoculated with HAV and the norovirus surrogates, murine norovirus (MNV) and feline calicivirus (FCV), then viral survival on these food matrices was measured over a four-week incubation at ambient temperature, by both plaque assay and droplet-digital RT-PCR (ddRT-PCR) using the modified ISO-15216 method as well as the magnetic bead assay for viral recovery. We observed an approximately 0.5 log reduction in viral genome copies, and 1 log reduction in viral infectivity for all three tested viruses following storage of select inoculated LMFs for 4 weeks. Therefore, the present study shows that the examined foodborne viruses can persist for a long time in LMFs. Next, we examined the inactivation efficacy of AOP treatment, which combines UV-C, ozone, and hydrogen peroxide vapor, and observed that while approximately 100% (4 log) inactivation can be achieved for FCV, and MNV in chocolate, the inactivation efficiency diminishes to approximately 90% (1 log) in pistachios and 70% (< 1 log) in cereal. AOP treatment could therefore be a good candidate for risk reduction of foodborne viruses from certain LMFs depending on the food matrix and surface of treatment.

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Section: Methodsmentioning

confidence: 99%

Survival and Inactivation by Advanced Oxidative Process of Foodborne Viruses in Model Low-Moisture Foods

Nasheri

Harlow²,

Chen³

et al. 2021

Food Environ Virol

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“…The P domain of VP1 is further subdivided into the P1 and P2 domain. The P2 region is the most variable and exposed region of the VP1 protein containing antigenic epitopes [ 4 , 5 , 6 , 7 , 8 ].…”

Section: Introductionmentioning

confidence: 99%

Diversity of Noroviruses throughout Outbreaks in Germany 2018

Niendorf

Faber

Tröger³

et al. 2020

Viruses

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Human norovirus accounts for the majority of viral gastroenteritis cases worldwide. It is a fast evolving virus generating diversity via mutation and recombination. Therefore, new variants and new recombinant strains emerge in the norovirus population. We characterized norovirus positive stool samples from one intensively studied district Märkisch-Oderland state Brandenburg with the samples from other states of Germany in order to understand the molecular epidemiological dynamics of norovirus outbreaks in Germany 2018. PCR systems, Sanger sequencing, and phylogenetic analyses were used for genotyping. Noroviruses of 250 outbreaks in Germany were genotyped, including 39 outbreaks for the district Märkisch-Oderland. Viral diversity in Märkisch-Oderland as compared to Germany was similar, but not identical. The predominant genogroup in Germany was GII with predominate genotype GII.P16-GII.4 Sydney, whereas GII.P31-GII.4 Sydney was the most frequent in Märkisch-Oderland. Genogroup I viruses were less frequently detected, regional and national. Within the sequences of GII.4 recombinants, two distinct clusters were identified with outbreaks from Märkisch-Oderland. Further analysis of sequence data and detailed epidemiological data are needed in order to understand the link between outbreaks in such clusters. Molecular surveillance should be based on samples collected nationally in order to trace comprehensive virus distribution and recombination events in virus population.

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“…To determine genomic changes that might have occurred during the incubation on LMF, or whether the incubation on LMF would select for certain quasispecies, we performed next-generation sequencing (NGS) on extracted viruses from T 0 and week 4 (W4) samples to compare their genomes. For this purpose, we employed a metagenomic WGS method that we had successfully used for WGS analysis of human norovirus from clinical samples (24, 25). The metagenomic approach also allowed for capturing all the possible variations within the extracted population, and the de novo assembly further reduced any sequencing bias.…”

Section: Resultsmentioning

confidence: 99%

“…FCV, MNV or HAV RNA recovered by the ISO 15216-1 and PGM-MB or HAV antibody methods was quantified using the One-Step dd-RT-PCR Advanced Kit for Probes (Bio-Rad Laboratories, Ltd.) according to manufacturer’s instructions and as described previously (23, 24). Primers and probes used to quantify FCV, MNV and HAV are listed in Table 1.…”

Section: Methodsmentioning

confidence: 99%

Survival and Inactivation by Advanced Oxidative Process of Foodborne Viruses in Model Low-Moisture Foods

Nasheri

Harlow

Chen

et al. 2020

Preprint

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16Enteric viruses, such as human norovirus (NoV) and hepatitis A virus (HAV), are the major 17 causes of foodborne illnesses worldwide. These viruses are shed in high numbers, have low 18 infectious dose, and may remain infectious for weeks in the environment and food. While 19 numerous viral survival studies have been conducted in fresh fruits and produce, limited 20 information is available regarding viral survival and transmission in low moisture foods (LMF). 21 LMFs are generally considered as ready-to-eat products, which undergo no or minimal pathogen 22 reduction steps. However, numerous foodborne outbreaks associated with LMFs have been 23 reported in recent years. The objective of this study was to examine the survival of foodborne 24 viruses in LMFs during long-term storage at ambient temperature and to evaluate the efficacy of 25 advanced oxidative process (AOP) treatment in the inactivation of these viruses. For this 26 purpose, select LMFs such as pistachios, chocolate, and cereal were inoculated with HAV and 27 the norovirus surrogates, murine norovirus (MNV) and feline calicivirus (FCV), then viral 28 survival on these food matrices was measured over a four-week incubation at ambient 29 temperature, by both plaque assay and droplet-digital RT-PCR (ddRT-PCR). We observed an 30 approximately 0.5 log reduction in viral genome copies, and 1 log reduction in viral infectivity 31 for all three tested viruses following storage of select inoculated LMFs for 4 weeks. Therefore, 32 the present study shows that foodborne viruses can persist for long-time in LMFs. Next, we 33 examined the inactivation efficacy of AOP treatment, which combines UV-C, ozone, and 34 hydrogen peroxide vapor, and observed that while approximately 100% inactivation can be 35 achieved for FCV, MNV, and HAV in chocolate, the inactivation efficiency diminishes to 36 approximately 90% in pistachios and 70% in cereal. AOP treatment could therefore be a good 37 candidate for the elimination of foodborne viruses from certain LMFs depending on the food 38 matrix and surface of treatment. 39 Importance 40 Low moisture foods have been increasingly recognized as important vehicles of foodborne 41 pathogens. In the present study, we demonstrated that foodborne viruses remain infectious during 42 long-term storage on select low moisture foods. In addition, we evaluated the efficacy of an 43 advanced oxidative process in the inactivation of foodborne viruses in low moisture foods. This 44 research will help increase the safety of low moisture foods and reduce the number of foodborne 45 illnesses due to contaminated products. 46 Keywords: Hepatitis A virus, norovirus surrogates, low moisture foods, bead-based assay, 47 whole genome sequencing, advanced oxidative process 48 49 50 51 Gastroenteritis outbreaks and illnesses due to the consumption of contaminated low moisture 52 foods (LMFs) are recently emerging as food safety burden in developed countries, with 53 norovirus and hepatitis A virus being important causes of LMF-associated outbreaks...

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

Cited by 26 publications

References 52 publications

Survival and Inactivation by Advanced Oxidative Process of Foodborne Viruses in Model Low-Moisture Foods

Survival and Inactivation by Advanced Oxidative Process of Foodborne Viruses in Model Low-Moisture Foods

Diversity of Noroviruses throughout Outbreaks in Germany 2018

Survival and Inactivation by Advanced Oxidative Process of Foodborne Viruses in Model Low-Moisture Foods

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