EFSA Supporting PublicationsVolume 19, Issue 6 7348E External scientific reportOpen Access Application of Next Generation Sequencing on Norovirus-contaminated oyster samples Joanna Ollivier, Corresponding Author Joanna Ollivier biohaw@efsa.europa.eu Ifremer, Microbiology laboratory, Nantes, FranceCorrespondence:biohaw@efsa.europa.euSearch for more papers by this authorJames Lowther, James Lowther Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UKSearch for more papers by this authorMarion Desdouits, Marion Desdouits Ifremer, Microbiology laboratory, Nantes, FranceSearch for more papers by this authorJulien Schaeffer, Julien Schaeffer Ifremer, Microbiology laboratory, Nantes, FranceSearch for more papers by this authorCandice Wacrenier, Candice Wacrenier Ifremer, Microbiology laboratory, Nantes, FranceSearch for more papers by this authorBas B. Oude Munnink, Bas B. Oude Munnink Erasmus University Medical Center, Rotterdam, the NetherlandsSearch for more papers by this authorAlban Besnard, Alban Besnard Ifremer, Microbiology laboratory, Nantes, FranceSearch for more papers by this authorFrederico Mota Batista, Frederico Mota Batista Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UKSearch for more papers by this authorTina Stapleton, Tina Stapleton Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UKSearch for more papers by this authorAnna Charlotte Schultz, Anna Charlotte Schultz National Food Institute, Technical University of Denmark, Lyngby, Denmark Anna Charlotte Schultz left the DTU and the consortium in February 2020.Search for more papers by this authorFrank Aarestrup, Frank Aarestrup National Food Institute, Technical University of Denmark, Lyngby, DenmarkSearch for more papers by this authorMarion Koopmans, Marion Koopmans Erasmus University Medical Center, Rotterdam, the NetherlandsSearch for more papers by this authorMiranda de Graaf, Miranda de Graaf Erasmus University Medical Center, Rotterdam, the NetherlandsSearch for more papers by this authorSoizick Le Guyader, Soizick Le Guyader Ifremer, Microbiology laboratory, Nantes, FranceSearch for more papers by this author Joanna Ollivier, Corresponding Author Joanna Ollivier biohaw@efsa.europa.eu Ifremer, Microbiology laboratory, Nantes, FranceCorrespondence:biohaw@efsa.europa.euSearch for more papers by this authorJames Lowther, James Lowther Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UKSearch for more papers by this authorMarion Desdouits, Marion Desdouits Ifremer, Microbiology laboratory, Nantes, FranceSearch for more papers by this authorJulien Schaeffer, Julien Schaeffer Ifremer, Microbiology laboratory, Nantes, FranceSearch for more papers by this authorCandice Wacrenier, Candice Wacrenier Ifremer, Microbiology laboratory, Nantes, FranceSearch for more papers by this authorBas B. Oude Munnink, Bas B. Oude Munnink Erasmus University Medical Center, Rotterdam, the NetherlandsSearch for more papers by this authorAlban Besnard, Alban Besnard Ifremer, Microbiology laboratory, Nantes, FranceSearch for more papers by this authorFrederico Mota Batista, Frederico Mota Batista Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UKSearch for more papers by this authorTina Stapleton, Tina Stapleton Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UKSearch for more papers by this authorAnna Charlotte Schultz, Anna Charlotte Schultz National Food Institute, Technical University of Denmark, Lyngby, Denmark Anna Charlotte Schultz left the DTU and the consortium in February 2020.Search for more papers by this authorFrank Aarestrup, Frank Aarestrup National Food Institute, Technical University of Denmark, Lyngby, DenmarkSearch for more papers by this authorMarion Koopmans, Marion Koopmans Erasmus University Medical Center, Rotterdam, the NetherlandsSearch for more papers by this authorMiranda de Graaf, Miranda de Graaf Erasmus University Medical Center, Rotterdam, the NetherlandsSearch for more papers by this authorSoizick Le Guyader, Soizick Le Guyader Ifremer, Microbiology laboratory, Nantes, FranceSearch for more papers by this author First published: 15 June 2022 https://doi.org/10.2903/sp.efsa.2022.EN-7348 Question number:: EFSA-Q-2019-00153 Disclaimer:: The present document has been produced and adopted by the bodies identified above as author(s). This task has been carried out exclusively by the author(s) in the context of a contract between the European Food Safety Authority and the author(s), awarded following a tender procedure. The present document is published complying with the transparency principle to which the Authority is subject. It may not be considered as an output adopted by the Authority. The European Food Safety Authority reserves its rights, view and position as regards the issues addressed and the conclusions reached in the present document, without prejudice to the rights of the authors. AboutPDF ToolsExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Abstract Bivalve molluscan shellfish (BMS) contamination with gastroenteritis viruses such as norovirus (NoV) is recognized as a significant public health risk worldwide. These foodborne epidemics are characterized by very low viral concentrations in the implicated foods, and by diverse viruses or multiple NoV strains originating from human sewage, resulting in different strains (co-)infecting the consumers. Next-generation sequencing (NGS) offers promising means to describe the diversity of strains present in BMS or to retrace transmission chains in outbreak settings, but their sensitivity and reproducibility remained to be assessed for this application. In this work, we evaluated the ability of three promising NGS methods to sequence diverse NoV in environmental or food BMS and human stool samples. Using laboratory-prepared samples of known NoV composition, we evaluated the sensitivity, reproducibility, repeatability and selectivity of metabarcoding, capture-based metagenomics and long amplicon sequencing, considering representative NoV strains from genogroup I and II, and the impact of the BMS matrix. The metabarcoding, with separate amplification of polymerase and capsid gene segments followed by Illumina sequencing, was the most sensitive method. It was applied to a selection of 212 BMS samples collected through the European Commission's NoV baseline survey (BLS), demonstrating a high diversity of NoV sequences found in the BMS which reflect the diversity of NoV strains circulating in the European human population. Besides, a capture-based metagenomics with enrichment of vertebrate viruses was applied on 20 of these BLS samples as well as 20 BMS linked to outbreaks and 10 related human stool samples. In BMS, it yielded NoV sequences compatible with the genomes identified in stool samples, but they were too short to allow definitive confirmation of the infection source. The present report describes NGS methods, including the bioinformatic pipelines, applicable to molecular epidemiology of NoV in BMS, their current limitations and expected outcomes. Supporting Information Filename Description efs37348e-sup-0001-Annex_A.xlsxExcel 2007 spreadsheet , 255.9 KB efs37348e-sup-0002-Annex_B.xlsxExcel 2007 spreadsheet , 4.6 MB efs37348e-sup-0003-Annex_C.xlsxExcel 2007 spreadsheet , 79.3 KB efs37348e-sup-0004-Annex_D.pdfPDF document, 116 KB Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. Volume19, Issue6June 20227348E ReferencesRelatedInformation

Consumption of dates has not been considered a common risk of hepatitis A virus (HAV) infection. In January 2018, an outbreak of hepatitis was identified with cases resident in all regions of Denmark. All the detected strains belonged to HAV genotype 3A. Epidemiological investigations through patients’ interviews, case-control and trace-back studies pointed toward different batches of dates from a single producer as the vehicle of infection. Boxes of dates from suspected batches were collected from homes of patients and healthy families and analyzed using a recently reported optimized direct lysis method, consisting of simultaneous viral RNA elution and extraction from dates followed by purification of the nucleic acids. Extracts were analyzed for HAV and norovirus (NoV) RNA using RT-qPCR, while detected HAV were genotyped by Sanger sequencing. Among 20 nucleic acid extracts representing eight batches of dates, RNA of HAV (9.3 × 102 genome copies/g) and NoV genogroup (G)II (trace amounts) were detected in one batch, while NoV GII RNA (trace amounts) was detected in another. Average extraction efficiency of spiked process control murine norovirus was 20 ± 13% and the inhibitions of RT-qPCR detection of NoV GI, NoV GII, and HAV were 31 ± 34, 9 ± 9, and 3 ± 7%, respectively. The HAV genome detected in the dates matched by sequence 100% to the HAV genotype 3A detected in stool samples from cases implicated in the outbreak. This confirmed, to our knowledge, for the first time a sequence link between HAV infection and consumption of contaminated dates, suggesting dates to be an important vehicle of HAV transmission.

The leading causes of foodborne viral disease outbreaks are human norovirus and hepatitis A virus (HAV). Their environmental persistence enables contamination of kitchen surfaces and crops often consumed raw, such as berries. Many decontamination procedures are inefficient and unsuitable for surfaces of industrial kitchen environments and soft fruits. In this study, we investigated the efficiency of a novel surface decontamination technology, combining steam and ultrasound (steam-ultrasound). Plastic, steel or raspberry surfaces were spiked with the norovirus surrogate, murine norovirus (MNV), and HAV, and steam-ultrasound treated at 85, 90 and 95 °C for 0–5 s. Post treatment viruses were titrated for survival by plaque assay and for genome stability by real-time quantitative PCR (RT-qPCR) of nucleic acid extracts. Survival of viruses were estimated in a log-linear model and the treatment time requirements for each decimal reduction (D value) in viral survival were calculated. The estimated D values of MNV or HAV were 0.4–0.2 or 1.1–0.8 s on plastic, 0.9–0.7 or 1.4–0.8 s on steel and 1.6–1.7 or 3.2–4.7 s on raspberries. No clear trend of genome reduction was observed with tested treatment parameters. Raspberries treated up to 4 s retained its natural texture and visual appeal similar to untreated controls whilst monitored for 7 days. In conclusion, steam-ultrasound treatment can within seconds reduce the titre of foodborne viruses on surfaces of plastic, steel and raspberries. This may particularly benefit industrial scale production of soft fruits for raw consumption and for swift non-hazardous decontamination of industrial kitchen surfaces.

Reliable safe water supply is a pillar of society and a key to public health. The Nordic countries have an abundance of clean fresh water as a source for drinking water supplies. They have followed developments in safeguarding water, both the recommendations of the World Health Organization framework for safe drinking water and European legislation. Worldwide, including the Nordic countries, small water supplies are less compliant with water safety regulation. The forthcoming EU directive on drinking water require risk-based approaches and improved transparency on water quality. This research looks at the Nordic frameworks for safe water supply, with emphasis on risk-based approaches and smaller systems. We analyzed the legal frameworks for safe water, the structure of the water sector across the Nordic countries and explored how prepared these countries are to meet these requirements. Our findings show that, while legal requirements are mostly in place, delivery of information to the public needs to be improved. Most Nordic countries are in the process of implementing risk-based management in large and medium size water supplies, whereas small supplies are lagging. We conclude that a key to success is increased training and support for small supplies. We suggest wider adoption of the Nordic model of cooperation with benchmarking of safe water for all to transfer knowledge between the countries. This work provides insights into challenges and opportunities for the Nordic countries and provides insights relevant to countries worldwide in their effort towards realization of SDG Target 6.1.

Detection of norovirus (NoV) and hepatitis A virus (HAV) on fruits and vegetables using current standard methodologies can be inefficient. Method optimisation focussing on ease, rapidity and increased viral RNA recovery is needed for efficient reverse transcription (RT)-qPCR detection of viruses. A simple and quick direct lysis method for RNA extraction was optimised (method A) to achieve increased viral RNA recovery and minimised RT-qPCR inhibition by increasing the volume of lysis buffer and inclusion of pectinase, Plant RNA Isolation Aid and OneStep PCR Inhibitor Removal Kit. Method A and an internal method structurally comparable to the ISO 15216 standard (method B) were compared for their efficiencies to recover viral RNA from the process controls, mengovirus (MC0) and murine norovirus (MNV), spiked in 13 types of fruits, vegetables, compound foods or seeds/nuts. All extracts (> 61) were also analysed for RT-qPCR inhibition and for natural contamination of NoV and HAV. The overall mean extraction efficiencies of MC0 and MNV were 36 ± 31 and 44 ± 38%, respectively, for method A and 9 ± 16 and 5 ± 11%, respectively, for method B. Inhibition of RT-qPCR amplification of RNA from NoV genogroup (G)I, NoV GII, and HAV ranged from 5 ± 10 to 13 ± 14% for method A and 34 ± 36 to 48 ± 40% for method B. NoV GII was detected in samples of strawberries and seaweed processed by both methods. In conclusion, the new direct lysis method showed an overall better performance compared to the modified ISO 15216 standard and should be validated for implementation in analysis of viruses in foods of plant origin.

Human viral pathogens are a major public health threat. Reliable information that accurately describes and characterizes the global occurrence and transmission of human viruses is essential to support national and global priority setting, public health actions, and treatment decisions. However, large areas of the globe are currently without surveillance due to limited health care infrastructure and lack of international cooperation. We propose a novel surveillance strategy, using metagenomic analysis of toilet material from international air flights as a method for worldwide viral disease surveillance. The aim of this study was to design, implement, and evaluate a method for viral analysis of airplane toilet waste enabling simultaneous detection and quantification of a wide range of human viral pathogens. Toilet waste from 19 international airplanes was analyzed for viral content, using viral capture probes followed by high-throughput sequencing. Numerous human pathogens were detected including enteric and respiratory viruses. Several geographic trends were observed with samples originating from South Asia having significantly higher viral species richness as well as higher abundances of salivirus A, aichivirus A and enterovirus B, compared to samples originating from North Asia and North America. In addition, certain city specific trends were observed, including high numbers of rotaviruses in airplanes departing from Islamabad. Based on this study we believe that central sampling and analysis at international airports could be a useful supplement for global viral surveillance, valuable for outbreak detection and for guiding public health resources.

In a recent report by risk assessment experts on the identification of food safety priorities using the Delphi technique, foodborne viruses were recognized among the top rated food safety priorities and have become a greater concern to the food industry over the past few years. Food safety experts agreed that control measures for viruses throughout the food chain are required. However, much still needs to be understood with regard to the effectiveness of these controls and how to properly validate their performance, whether it is personal hygiene of food handlers or the effects of processing of at risk foods or the interpretation and action required on positive virus test result. This manuscript provides a description of foodborne viruses and their characteristics, their responses to stress and technologies developed for viral detection and control. In addition, the gaps in knowledge and understanding, and future perspectives on the application of viral detection and control strategies for the food industry, along with suggestions on how the food industry could implement effective control strategies for viruses in foods. The current state of the science on epidemiology, public health burden, risk assessment and management options for viruses in food processing environments will be highlighted in this review.

INTRODUCTION:In early April 2016, an unusual high number of point-source outbreaks of gastrointestinal disease were reported to occur in Denmark.METHODS:Outbreaks were individually investigated. Two analytical studies were performed. Patient stool samples collected and analysed; positive stool samples were sequenced over the polymerase and/or capsid gene areas. Implicated lettuce heads were collected and analysed for the presence of norovirus. Foods were traced-back and traced-forward and international alert systems applied.RESULTS:A total of 23 linked point-source outbreaks occurred over the course of one week. Fresh green coral lettuce (Lollo Bionda lettuce) had been consumed in all settings. In a cohort study including 234 participants a dish containing green lettuce was associated with illness. Norovirus of Genogroup I (GI) was detected in samples from 28 patients comprising eight of the outbreaks. Sequencing showed GI.P2-GI.2. GI norovirus was detected in one of 20 examined lettuce heads. All lettuce consumed was supplied by the same packer who in turn had bought the lettuce from a wholesaler in France. The two lots of lettuce came from two different growers in different parts of France.DISCUSSION:Green coral lettuce produced in France was found to have caused a large series of linked norovirus outbreaks in Denmark as established by a number of lines of evidence. A similar incidence occurred in 2010. Fresh lettuce increasingly appear to be a risk food for norovirus infections.

The amount of animal manure used in modern agriculture is increasing due to the increase in global animal production. Pig slurry is known to contain zoonotic bacteria such as E. coli , Salmonella spp. and Campylobacter spp., and viruses such as hepatitis E virus and group A rotavirus. Coliform bacteria, present in manure, have previously been shown to leach into tile drains. This poses a potential threat to aquatic environments and may also influence the quality of drinking water. As knowledge is especially scarce about the fate of viruses when applied to fields in natural settings, this project sets out to investigate the leaching potential of six different microorganisms: E. coli and Enterococcus spp. (detected by colony assay), somatic coliphages (using plaque assays), and hepatitis E virus, porcine circovirus type 2, and group A rotavirus (by real-time polymerase chain reaction). All six microorganisms leached through the soil entering the tile drains situated at 1-m depth the first day following pig slurry application. The leaching pattern of group A rotavirus differed substantially from the pattern for somatic coliphages, which are otherwise used as indicators for virus contamination. Furthermore, group A rotavirus was detected in monitoring wells at 3.5-m depth up to 2 months after pig slurry application. The detection of viral genomic material in drainage water and shallow groundwater signifies a potential hazard to human health that needs to be investigated further, as water reservoirs used for recreational use and drinking water are potentially contaminated with zoonotic pathogens.

Viral sewage metagenomics is a novel field of study used for surveillance, epidemiological studies, and evaluation of waste water treatment efficiency. In raw sewage human waste is mixed with household, industrial and drainage water, and virus particles are, therefore, only found in low concentrations. This necessitates a step of sample concentration to allow for sensitive virus detection. Additionally, viruses harbor a large diversity of both surface and genome structures, which makes universal viral genomic extraction difficult. Current studies have tackled these challenges in many different ways employing a wide range of viral concentration and extraction procedures. However, there is limited knowledge of the efficacy and inherent biases associated with these methods in respect to viral sewage metagenomics, hampering the development of this field. By the use of next generation sequencing this study aimed to evaluate the efficiency of four commonly applied viral concentrations techniques (precipitation with polyethylene glycol, organic flocculation with skim milk, monolithic adsorption filtration and glass wool filtration) and extraction methods (Nucleospin RNA XS, QIAamp Viral RNA Mini Kit, NucliSENS® miniMAG®, or PowerViral® Environmental RNA/DNA Isolation Kit) to determine the viriome in a sewage sample. We found a significant influence of concentration and extraction protocols on the detected viriome. The viral richness was largest in samples extracted with QIAamp Viral RNA Mini Kit or PowerViral® Environmental RNA/DNA Isolation Kit. Highest viral specificity were found in samples concentrated by precipitation with polyethylene glycol or extracted with Nucleospin RNA XS. Detection of viral pathogens depended on the method used. These results contribute to the understanding of method associated biases, within the field of viral sewage metagenomics, making evaluation of the current literature easier and helping with the design of future studies.

Exposure to bioaerosols can pose a health risk to workers at wastewater treatment plants (WWTPs) and to habitants of their surroundings. The main objective of this study was to examine the presence of harmful microorganisms in the air emission from a new type of hospital WWTP employing advanced wastewater treatment technologies. Air particle measurements and sampling of inhalable bacteria, endotoxin and noroviruses (NoVs) were performed indoor at the WWTP and outside at the WWTP ventilation air exhaust, downwind of the air exhaust, and upwind of the WWTP. No significant differences were seen in particle and endotoxin concentrations between locations. Bacterial concentrations were comparable or significantly lower in the exhaust air than inside the WWTP and in the upwind reference. Bacterial isolates were identified using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry. In total, 35 different bacterial genera and 64 bacterial species were identified in the air samples. Significantly higher genus and species richness was found with an Andersen Cascade Impactor compared with filter-based sampling. No pathogenic bacteria were found in the exhaust air. Streptomyces was the only bacterium found in the air both inside the WWTP and at the air emission, but not in the upwind reference. NoV genomes were detected in the air inside the WWTP and at the air exhaust, albeit in low concentrations. As only traces of NoV genomes could be detected in the exhaust air they are unlikely to pose a health risk to surroundings. Hence, we assess the risk of airborne exposure to pathogenic bacteria and NoVs from the WWTP air emission to surroundings to be negligible. However, as a slightly higher NoV concentration was detected inside the WWTP, we cannot exclude the possibility that exposure to airborne NoVs can pose a health risk to susceptible to workers inside the WWTP, although the risk may be low.

The aim of this study was to identify the most efficient sampling method for quantitative PCR‐based detection of airborne human norovirus (NoV).

Background: Viruses cause a major proportion of human infections, especially gastroenteritis and respiratory infections in children and adults. Indirect transmission between humans via environmental surfaces may play a role in infections, but methods to investigate this have been sparse.Aim: To validate and test efficient and reliable procedures to detect multiple human pathogenic viruses on surfaces.Methods: The study was divided into two parts. In Part A, six combinations of three different swabs (consisting of cotton, foamed cotton, or polyester head) and two different elution methods (direct lysis or immersion in alkaline glycine buffer before lysis) were tested for efficient recovery of human norovirus GII.7 and mengovirus from artificially contaminated surfaces. In Part B we determined the detection limit for norovirus GI.1 and GII.3 using the best procedure found in Part A linked with a commercial multiplex real-time quantitative polymerase chain reaction detection assay.Findings: Combining the polyester swab with direct lysis allowed recovery down to 100 and 10 genome copies/cm(2) of norovirus GI.1 and GII.3, respectively. This procedure resulted in the significant highest recovery of both norovirus and mengovirus, whereas no differences in amplification efficiencies were observed between the different procedures.Conclusion: The results indicate that it is possible to detect low concentrations of virus on environmental surfaces. We therefore suggest that a polyester swab, followed by direct lysis, combined with a multiplex qPCR detection assay is an efficient screening tool that merits study of different respiratory and gastrointestinal viruses on environment surfaces. (C) 2016 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Evaluation of methods for the concentration and extraction of viruses from sewage water in the context of metagenomic sequencing

To the Editor: Since chikungunya virus (CHIKV) was first isolated in 1952 (in Tanzania), outbreaks have occurred every 7-20 years in countries in Africa and Asia, and since 2013, it has been identified in the Americas (1,2).However, no cases have been reported from the Horn of Africa (3,4).We confirmed CHIKV infection acquired in 2016 by 2 travelers to Somalia who returned to Italy.

The number of children in daycare centers (DCCs) is rising. This increases exposure to microorganisms and infectious diseases. Little is known about which bacteria and viruses are present in the DCC environment and where they are located. In the study described in this article, the authors set out to determine the prevalence of pathogenic bacteria and viruses and to find the most contaminated fomites in DCCs. Fifteen locations in each DCC were sampled for bacteria, respiratory viruses, and gastrointestinal viruses. The locations were in the toilet, kitchen, and playroom areas and included nursery pillows, toys, and tables, among other things. Coliform bacteria were primarily found in the toilet and kitchen areas whereas nasopharyngeal bacteria were found mostly on toys and fabric surfaces in the playroom. Respiratory viruses were omnipresent in the DCC environment, especially on the toys.