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Chandran S, Gibson KE. Improving the Detection and Understanding of Infectious Human Norovirus in Food and Water Matrices: A Review of Methods and Emerging Models. Viruses 2024; 16:776. [PMID: 38793656 PMCID: PMC11125872 DOI: 10.3390/v16050776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Human norovirus (HuNoV) is a leading global cause of viral gastroenteritis, contributing to numerous outbreaks and illnesses annually. However, conventional cell culture systems cannot support the cultivation of infectious HuNoV, making its detection and study in food and water matrices particularly challenging. Recent advancements in HuNoV research, including the emergence of models such as human intestinal enteroids (HIEs) and zebrafish larvae/embryo, have significantly enhanced our understanding of HuNoV pathogenesis. This review provides an overview of current methods employed for HuNoV detection in food and water, along with their associated limitations. Furthermore, it explores the potential applications of the HIE and zebrafish larvae/embryo models in detecting infectious HuNoV within food and water matrices. Finally, this review also highlights the need for further optimization and exploration of these models and detection methods to improve our understanding of HuNoV and its presence in different matrices, ultimately contributing to improved intervention strategies and public health outcomes.
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Affiliation(s)
| | - Kristen E. Gibson
- Department of Food Science, Center for Food Safety, University of Arkansas System Division of Agriculture, Fayetteville, AR 72704, USA;
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2
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Trudel-Ferland M, Collard MÈ, Goulet-Beaulieu V, Jubinville E, Hamon F, Jean J. Evaluation of a new automated viral RNA extraction platform for hepatitis A virus and human norovirus in testing of berries, lettuce, and oysters. Int J Food Microbiol 2024; 416:110664. [PMID: 38492524 DOI: 10.1016/j.ijfoodmicro.2024.110664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/18/2024]
Abstract
Fruits, vegetables, and shellfish are often associated with outbreaks of illness caused particularly by human norovirus (HuNoV) and hepatitis A virus (HAV), the leading causative agents of foodborne illness worldwide. The aim of this study was to evaluate a new automated nucleic acid extraction platform (EGENE-UP EASYPREP) for enteric viruses in several at-risk food matrices and to test its limit of detection in comparison to a semi-automated method (EGENE-UP) using Boom methodology for nucleic acid extraction as suggested in the reference method ISO 15216-2:2019. Fresh and frozen raspberries, frozen blackberries, romaine lettuce and oyster digestive glands were artificially contaminated with HAV, HuNoV GII.4 or HuNoV GI.7 at 102, 103 or 104 genome copies/sample. Virus was then recovered from the food matrix using the ISO method. Viral RNA extracted from frozen berry samples by the automated system was purified on a column for additional removal of RT-qPCR inhibitors. For fresh raspberry, oysters, and romaine lettuce, the two extraction platforms were deemed equivalent. For frozen raspberry, the automated platform appeared to be more efficient for viral recovery, particularly for HAV and HuNoV GI at lower concentrations. With frozen blackberries, the two platforms may be considered equivalent for all targeted viruses. However, the automated method led to less sample-associated inhibition of the PCR, 56.5 % of samples versus 95.0 % for the semi-automated. We thus found that the automated extraction can be performed easily by users while obtaining equivalent or even superior results to the ISO 15216-2:2019 method, and therefore appears to be suitable for routine sanitary monitoring in food processing and for tracing outbreaks of illness.
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Affiliation(s)
- Mathilde Trudel-Ferland
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Marie-Ève Collard
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Valérie Goulet-Beaulieu
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Eric Jubinville
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | | | - Julie Jean
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada.
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3
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Trudel-Ferland M, Levasseur M, Goulet-Beaulieu V, Jubinville E, Hamon F, Jean J. Concentration of foodborne viruses eluted from fresh and frozen produce: Applicability of ultrafiltration. Int J Food Microbiol 2024; 416:110687. [PMID: 38554558 DOI: 10.1016/j.ijfoodmicro.2024.110687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/01/2024]
Abstract
Foodborne illnesses involving raw and minimally processed foods are often caused by human noroviruses (HuNoV) and hepatitis A virus (HAV). Since food is contaminated usually with small numbers of virions, these must be eluted from the food surface and then concentrated for detection. The objective of this study was to optimize an ultrafiltration (UF) concentration method for HAV and HuNoVs present on various fresh and frozen produce. The detection range of the optimized method and its applicability to different food matrices was compared to the reference method ISO 15216-1:2017. Strawberry, raspberry, blackberry, lettuce, and green onion (25 g) were contaminated with HAV, HuNoV GI.7 and HuNoV GII.4 and then recovered therefrom by elution. A commercial benchtop UF device was used for the concentration step. Viral RNA was extracted and detected by RT-qPCR. From fresh strawberries, recovery of HAV loaded at 104 genome copies per sample was 30 ± 13 %, elution time had no significant impact, and UF membrane with an 80-100 kDa cut-off in combination with Tris-glycine elution buffer at pH 9.5 was found optimal. At lower copy numbers on fresh strawberry, at least 1 log lower numbers of HuNoV were detectable by the UF method (103 vs 104 GII.4 copies/sample and 101 vs 103 GI.7 copies/sample), while HAV was detected at 101 genome copies/sample by both methods. Except on raspberry, the UF method was usually equivalent to the ISO method regardless of the virus tested. The UF method makes rapid viral concentration possible, while supporting the filtration of large volume of sample. With fewer steps and shorter analysis time than the ISO method, this method could be suitable for routine analysis of viruses throughout the food production and surveillance chain.
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Affiliation(s)
- Mathilde Trudel-Ferland
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Marianne Levasseur
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Valérie Goulet-Beaulieu
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Eric Jubinville
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | | | - Julie Jean
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada.
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Wales SQ, Kulka M, Keinard B, Ngo D, Papafragkou E. Use of Human Intestinal Enteroids for Recovery of Infectious Human Norovirus from Berries and Lettuce. Foods 2023; 12:4286. [PMID: 38231763 DOI: 10.3390/foods12234286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 01/19/2024] Open
Abstract
Norovirus (NoV) is the leading cause of viral foodborne gastroenteritis globally. Currently, the gold standard for detecting NoV in clinical, food, and environmental samples is via molecular-based methods, primarily RT-PCR. Nevertheless, there is a great need for confirmatory assays that can determine the infectivity of viral particles recovered from contaminated matrices. The use of the human intestinal enteroids system (HIEs) has allowed for the expansion of norovirus replication, although it still suffers from limitations of strain preferences and the requirement of high titer stocks for infection. In this study, we wanted to explore the feasibility of using the HIEs to support the replication of NoV that had been recovered from representative food matrices that have been associated with foodborne illness. We first confirmed that HIEs can support the replication of several strains of NoV as measured by RT-qPCR. We subsequently chose two of those strains that reproducibly replicated, GII.4 and GII.6, to evaluate in a TCID50 assay and for future experiments. Infectious NoV could be recovered and quantified in the HIEs from lettuce, frozen raspberries, or frozen strawberries seeded with high titers of either of these strains. While many experimental challenges still remain to be overcome, the results of this study represent an important step toward the detection of infectious norovirus from representative produce items.
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Affiliation(s)
- Samantha Q Wales
- Office of Applied Research and Safety Assessment, CFSAN FDA, Laurel, MD 20708, USA
| | - Michael Kulka
- Office of Applied Research and Safety Assessment, CFSAN FDA, Laurel, MD 20708, USA
| | - Brianna Keinard
- Office of Applied Research and Safety Assessment, CFSAN FDA, Laurel, MD 20708, USA
| | - Diana Ngo
- Office of Applied Research and Safety Assessment, CFSAN FDA, Laurel, MD 20708, USA
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Chatonnat E, Manseau-Ferland K, Jubinville E, Goulet-Beaulieu V, Jean J. Prevalence of Foodborne Viruses in Berries Harvested in Canada. Foods 2023; 12:723. [PMID: 36832797 PMCID: PMC9955551 DOI: 10.3390/foods12040723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
It is known that the transmission of different foodborne viruses can occur either via discharge of contaminated water close to the production environment or via close contact with animal feces. Cranberries are intimately associated with water throughout their production cycle, and blueberries grow close to the ground which could lead to contact with wildlife. The aim of this study was to evaluate the prevalence of human norovirus (HuNoV GI and GII), hepatitis A virus (HAV) and hepatitis E virus (HEV) in two berries produced commercially in Canada. The detection of HuNoV and HAV on RTE cranberries and of HEV on wild blueberries was evaluated using the ISO method 15216-1:2017. Only 3 of 234 cranberry samples tested positive for HuNoV GI (3.6, 7.4, 5.3 genome copies/g, respectively) and all were negative for HuNoV GII and HAV. PMA pre-treatment and sequencing confirmed the absence of potential intact HuNoV GI particles on cranberries. None of the 150 blueberry samples tested positive for HEV. Overall, the prevalence of foodborne viruses in RTE cranberries and wild blueberries harvested in Canada is low, making these products relatively safe for consumers.
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Affiliation(s)
| | | | | | | | - Julie Jean
- Food Science Department, Institute of Nutrition and Functional Foods, Université Laval, Quebec City, QC G1V 0A6, Canada
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Larocque É, Lévesque V, Lambert D. Crystal digital RT-PCR for the detection and quantification of norovirus and hepatitis A virus RNA in frozen raspberries. Int J Food Microbiol 2022; 380:109884. [PMID: 36055105 DOI: 10.1016/j.ijfoodmicro.2022.109884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 10/31/2022]
Abstract
Berries are important vehicles for norovirus (NoV) and hepatitis A virus (HAV) foodborne outbreaks. Sensitive and quantitative detection of these viruses in food samples currently relies on RT-qPCR, but remains challenging due to their low concentration and the presence of RT-qPCR inhibitors. Moreover, quantification requires a standard curve. In this study, crystal digital RT-PCR (RT-cdPCR) assays were adapted from RT-qPCR sets of primers and probe currently used in our diagnostic laboratory for the detection and precise quantification of norovirus genogroups I and II (NoV GI, GII) and hepatitis A virus (HAV) RNA in frozen raspberry samples. We selected assay conditions based on optimal separation of positive and negative droplets, and peak resolution. Using virus-specific in vitro RNA transcripts diluted in raspberry RNA extracts, we showed that all three RT-cdPCR assays were sensitive, and we estimated the 95 % detection limit at 9 copies per RT-cdPCR reaction for NoV GI, 3 for NoV GII, and 14 for HAV. Serial dilutions of the RNA transcripts showed excellent linearity over a range of four orders of magnitude. We achieved precise quantification (CV ≤ 35 %) of the RNA transcripts between runs down to 15-145 copies per reaction for NoV GI, <20 for NoV GII, and < 15 for HAV. The three RT-cdPCR assays also proved to be tolerant to inhibitors from frozen raspberries, although not as tolerant as the RT-qPCR assays in the case of NoV GI and HAV. We further evaluated the assays with inoculated frozen raspberry samples and compared their performance to that of the RT-qPCR assays. As compared to the corresponding RT-qPCR assays, the NoV GI and HAV RT-cdPCR assays showed a decreased qualitative sensitivity, while the NoV GII RT-cdPCR assay had an increased sensitivity. As for quantification, the NoV GI and NoV GII RT-cdPCR assays produced similar estimates of RNA copy number than their respective RT-qPCR assays, whereas for HAV, the RT-cdPCR assay produced lower estimates than the RT-qPCR assay. However, all the RT-cdPCR assays provided more precise quantitative measurements at low levels of contamination than the RT-qPCR assays. In conclusion, the potential of the RT-cdPCR assays in this study to detect viral RNA from frozen raspberries varied according to assay, but these RT-cdPCR assays should be considered for precise absolute quantification in difficult matrices such as frozen raspberries.
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Affiliation(s)
- Émilie Larocque
- Food Virology National Reference Centre, St. Hyacinthe Laboratory, Canadian Food Inspection Agency (CFIA), 3400 Casavant Boulevard West, St. Hyacinthe, QC J2S 8E3, Canada.
| | - Valérie Lévesque
- Food Virology National Reference Centre, St. Hyacinthe Laboratory, Canadian Food Inspection Agency (CFIA), 3400 Casavant Boulevard West, St. Hyacinthe, QC J2S 8E3, Canada
| | - Dominic Lambert
- Food Virology National Reference Centre, St. Hyacinthe Laboratory, Canadian Food Inspection Agency (CFIA), 3400 Casavant Boulevard West, St. Hyacinthe, QC J2S 8E3, Canada
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Hennechart-Collette C, Dehan O, Laurentie M, Fraisse A, Martin-Latil S, Perelle S. Method for detecting norovirus, hepatitis A and hepatitis E viruses in tap and bottled drinking water. Int J Food Microbiol 2022; 377:109757. [DOI: 10.1016/j.ijfoodmicro.2022.109757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022]
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Schilling-Loeffler K, Falkenhagen A, Johne R. Coronaviruses are stable on glass, but are eliminated by manual dishwashing procedures. Food Microbiol 2022; 106:104036. [PMID: 35690440 PMCID: PMC8986060 DOI: 10.1016/j.fm.2022.104036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/01/2022] [Accepted: 04/01/2022] [Indexed: 11/29/2022]
Abstract
Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is primarily transmitted from human to human via droplets and aerosols. While transmission via contaminated surfaces is also considered possible, the overall risk of this transmission route is assumed to be low. Nevertheless, transmission through contaminated drinking glasses may pose an increased risk as the glass is in direct contact with the mouth and oral cavity. Using human coronavirus 229E (HCoV-229E) as surrogate for SARS-CoV-2, this study examined coronavirus stability on glass, inactivation by dishwashing detergents, and virus elimination by a manual glass scrubbing device. Infectious HCoV-229E was recovered from glass for 7 and 21 days of storage under daylight and dark conditions, respectively. Near complete inactivation of HCoV-229E (>4 log10 reduction) was observed after incubation with two common dishwashing detergents at room temperature for 15 s, whereas incubation at 43 °C for 60 s was necessary for a third detergent to achieve a similar titer reduction. The virus was efficiently removed from contaminated drinking glasses using a manual glass scrubbing device in accordance with German standard DIN 6653-3. The results confirm that coronaviruses are relatively stable on glass, but indicate that common manual dishwashing procedures can efficiently eliminate coronaviruses from drinking glasses.
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Hrdy J, Vasickova P. Virus detection methods for different kinds of food and water samples – The importance of molecular techniques. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108764] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Detection of Enteric Viruses on Strawberries and Raspberries Using Capture by Apolipoprotein H. Foods 2021; 10:foods10123139. [PMID: 34945690 PMCID: PMC8701109 DOI: 10.3390/foods10123139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/06/2021] [Accepted: 12/14/2021] [Indexed: 02/02/2023] Open
Abstract
Human noroviruses (HuNoVs) and the hepatitis A virus (HAV) are the main viral causes of foodborne illness worldwide. These viruses are frequently transmitted via fresh and frozen berries, such as strawberries and raspberries. ISO 15216:1 (2017), currently the preferred method for their detection, involves several steps and is time-consuming. Apolipoprotein H (ApoH) has been shown to have a strong affinity for several microorganisms, including HuNoVs. In this article, we report an ApoH-based method of capturing the HAV and HuNoVs adherent to berries and concentrating them for assay. The limit of detection of both viruses suspended in a buffer was low. On strawberries, the HAV was detected down to 104 genome copies/25 g in 100% of cases and down to 103 genome copies/25 g on raspberries in 50% of cases. This sensitivity was not significantly different from that of the ISO method 15216:1 (2017). HuNoV GII.4 was more difficult to detect using the ApoH method. The ApoH CaptoVIR kit does, nevertheless, appear to be usable in the near future as a single-test, multiple-detection method for viruses on fresh and frozen berries.
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Polkowska A, Räsänen S, Nuorti P, Maunula L, Jalava K. Assessment of Food and Waterborne Viral Outbreaks by Using Field Epidemiologic, Modern Laboratory and Statistical Methods-Lessons Learnt from Seven Major Norovirus Outbreaks in Finland. Pathogens 2021; 10:pathogens10121624. [PMID: 34959579 PMCID: PMC8707936 DOI: 10.3390/pathogens10121624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 11/17/2022] Open
Abstract
Seven major food- and waterborne norovirus outbreaks in Western Finland during 2014–2018 were re-analysed. The aim was to assess the effectiveness of outbreak investigation tools and evaluate the Kaplan criteria. We summarised epidemiological and microbiological findings from seven outbreaks. To evaluate the Kaplan criteria, a one-stage meta-analysis of data from seven cohort studies was performed. The case was defined as a person attending an implicated function with diarrhoea, vomiting or two other symptoms. Altogether, 22% (386/1794) of persons met the case definition. Overall adjusted, 73% of norovirus patients were vomiting, the mean incubation period was 44 h (4 h to 4 days) and the median duration of illness was 46 h. As vomiting was a more common symptom in children (96%, 143/149) and diarrhoea among the elderly (92%, 24/26), symptom and age presentation should drive hypothesis formulation. The Kaplan criteria were useful in initial outbreak assessments prior to faecal results. Rapid food control inspections enabled evidence-based, public-health-driven risk assessments. This led to probability-based vehicle identification and aided in resolving the outbreak event mechanism rather than implementing potentially ineffective, large-scale public health actions such as the withdrawal of extensive food lots. Asymptomatic food handlers should be ideally withdrawn from high-risk work for five days instead of the current two days. Food and environmental samples often remain negative with norovirus, highlighting the importance of research collaborations. Electronic questionnaire and open-source novel statistical programmes provided time and resource savings. The public health approach proved useful within the environmental health area with shoe leather field epidemiology, combined with statistical analysis and mathematical reasoning.
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Affiliation(s)
- Aleksandra Polkowska
- Health Sciences Unit, Faculty of Social Sciences, Tampere University, 33100 Tampere, Finland; (A.P.); (P.N.)
| | - Sirpa Räsänen
- Pirkanmaa Hospital District, 33520 Tampere, Finland;
| | - Pekka Nuorti
- Health Sciences Unit, Faculty of Social Sciences, Tampere University, 33100 Tampere, Finland; (A.P.); (P.N.)
| | - Leena Maunula
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, 00100 Helsinki, Finland;
| | - Katri Jalava
- Department of Mathematics and Statistics, Faculty of Social Sciences, University of Helsinki, 00100 Helsinki, Finland
- Correspondence: ; Tel.: +44-73-4224-7186
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Raymond P, Paul S, Perron A, Deschênes L. Norovirus Extraction from Frozen Raspberries Using Magnetic Silica Beads. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:248-258. [PMID: 33651330 PMCID: PMC8116234 DOI: 10.1007/s12560-021-09466-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
Human noroviruses (HuNoV) are among the main causes of acute gastroenteritis worldwide. Frozen raspberries have been linked to several HuNoV food-related outbreaks. However, the extraction of HuNoV RNA from frozen raspberries remains challenging. Recovery yields are low, and real-time quantitative reverse transcriptase PCR (RT-qPCR) inhibitors limit the sensitivity of the detection methodologies. A new approach using fine magnetic silica beads was developed for the extraction of HuNoV spiked on frozen raspberries. Relatively low recovery yields were observed with both the magnetic silica bead and the reference ISO 15216-1:2017 methods. High RT-qPCR inhibition was observed with the ISO 15216-1:2017 recommended amplification kit but could be reduced by using an alternative kit. Reducing RT-qPCR inhibition is important to limit the number of inconclusive HuNoV assays thus increasing the capacity to assess the HuNoV prevalence in frozen raspberries.
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Affiliation(s)
- Philippe Raymond
- Canadian Food Inspection Laboratory (CFIA), St. Hyacinthe Laboratory, Food Virology, Saint Hyacinthe, QC, Canada.
| | - Sylvianne Paul
- Canadian Food Inspection Laboratory (CFIA), St. Hyacinthe Laboratory, Food Virology, Saint Hyacinthe, QC, Canada
| | - André Perron
- Canadian Food Inspection Laboratory (CFIA), St. Hyacinthe Laboratory, Food Virology, Saint Hyacinthe, QC, Canada
| | - Louise Deschênes
- Agriculture and Agri-Food Canada (AAFC), St. Hyacinthe Research and Development Centre, Saint Hyacinthe, QC, Canada
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Sun C, Chen J, Li H, Fang L, Wu S, Jayavanth P, Tang S, Sanchez G, Wu X. One-step duplex RT-droplet digital PCR assay for the detection of norovirus GI and GII in lettuce and strawberry. Food Microbiol 2021; 94:103653. [PMID: 33279078 DOI: 10.1016/j.fm.2020.103653] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 10/01/2020] [Accepted: 10/01/2020] [Indexed: 11/17/2022]
Abstract
The study was designed to develop a sensitive one-step duplex reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) to detect norovirus genogroup I and II (NoV GI and GII) in lettuce and strawberry. The specificity, sensitivity, repeatability and robustness of the assay was compared with RT-qPCR. The lowest concentration detected by RT-ddPCR for NoV GI and NoV GII were 4.68 and 8.47 copies/μL respectively, much lower than that of RT-qPCR with a number of 46.8 and 84.7 copies/μL, respectively. Lettuce and strawberry samples were artificially contaminated with NoV GI and GII suspensions, with inoculum size of 3.00 × 106 to 1.70 × 108 copies and 4.80 × 105 to 2.50 × 107 copies, respectively. Strawberry spiked with low inoculum size revealed positive results by RT-ddPCR, while recorded negative by RT-qPCR. Meanwhile, RT-ddPCR also showed a higher average recovery rate for NoV in lettuce and strawberry than RT-qPCR.The limit of detection (LoDs) of RT-ddPCR for NoVs in lettuce was 2.32 × 104 copies/25g (NoV GI) and 2.36 × 104 ciopies/25g (NoV GII), and that in strawberry was 2.56 × 104 copies/25g (NoV GI) and 2.64 × 104 ciopies/25g (NoV GII), which were 10 folds lower than that of RT-qPCR. The developed duplex RT-ddPCR assay exhibited stability and increased capacity to resist inhibitors in food samples with low concentration of NoV, making it a reliable method to avoid false negative result as opposed to RT-qPCR. In conclusion, one-step RT-ddPCR method developed in this study is pertinent in detecting foodborne virus such as NoV.
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Affiliation(s)
- Chongzhen Sun
- Department of Food Science and Engineering, Jinan University, 601 Huangpu Avenue, Guangzhou, 510632, China
| | - Jiayin Chen
- Department of Food Science and Engineering, Jinan University, 601 Huangpu Avenue, Guangzhou, 510632, China
| | - Hui Li
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, 160 Qunxian Road, Guangzhou, 511430, China.
| | - Ling Fang
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, 160 Qunxian Road, Guangzhou, 511430, China
| | - Shiwei Wu
- Institute of Pathogenic Microbiology, Guangdong Provincial Center for Disease Control and Prevention, 160 Qunxian Road, Guangzhou, 511430, China
| | - Pallavi Jayavanth
- International School, Jinan University, 601 Huangpu Avenue, Guangzhou, 510632, China
| | - Shuze Tang
- Department of Food Science and Engineering, Jinan University, 601 Huangpu Avenue, Guangzhou, 510632, China
| | - Gloria Sanchez
- Department of Biotechnology, Institute of Agrochemistry and Food Technology (IATA-CSIC), Av. AgustÍn Escardino 7, 46980, Paterna, Valencia, Spain
| | - Xiyang Wu
- Department of Food Science and Engineering, Jinan University, 601 Huangpu Avenue, Guangzhou, 510632, China.
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14
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Trudel-Ferland M, Jubinville E, Jean J. Persistence of Hepatitis A Virus RNA in Water, on Non-porous Surfaces, and on Blueberries. Front Microbiol 2021; 12:618352. [PMID: 33613487 PMCID: PMC7890088 DOI: 10.3389/fmicb.2021.618352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/15/2021] [Indexed: 11/17/2022] Open
Abstract
Enteric viruses, such as human norovirus and hepatitis A virus (HAV), are the leading cause of transmissible foodborne illness. Fresh produce such as berries are often contaminated by infected food handlers, soiled water, or food contact surfaces. The gold-standard method for virus detection throughout the food chain is RT-qPCR, which detects portions of genomes including non-infectious viral particles and naked viral RNA. The aim of this study was to evaluate the persistence of heat-inactivated HAV in water, phosphate-buffered saline, on stainless steel and polyvinyl chloride, and on blueberries at −80°C, −20°C, 4°C, and room temperature. In water and phosphate-buffered saline, viral RNA could be detected for up to 90 days regardless of temperature when the initial load was 2.5 × 104 or 2.5 × 106 genome copies. It was detected on polyvinyl chloride and blueberries under most conditions. On stainless steel, the large initial load persisted for 90 days, while the medium-level load was detected only up to 16 days at room temperature or 60 days at 4°C. The detection of non-infectious viral RNA can confound investigations of gastroenteritis outbreaks. Pretreatments that discriminate between naked RNA, non-infectious virions and infectious virions need to be included in the RT-qPCR method in order to reduce the risk of positive results associated with non-infectious viral particles.
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Affiliation(s)
- Mathilde Trudel-Ferland
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Eric Jubinville
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Julie Jean
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
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15
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Li SY, Shu M, Zhong C, Chen H, Bi Y, Hou PF, Wu GP. Characterization and Kinetic Study of Bentonite-Coated Activated Carbon for Adsorption of DNA Polymerase Inhibitors to Improve the Detection Sensitivity of Salmonella Derived from Vegetables by Rti-LAMP. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01814-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Rajiuddin SM, Midgley SE, Jensen T, Müller L, Schultz AC. Application of an Optimized Direct Lysis Method for Viral RNA Extraction Linking Contaminated Dates to Infection With Hepatitis A Virus. Front Microbiol 2020; 11:516445. [PMID: 33042044 PMCID: PMC7522280 DOI: 10.3389/fmicb.2020.516445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 08/24/2020] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Sheikh Md Rajiuddin
- Division of Microbiology and Production, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sofie Elisabeth Midgley
- Department of Virus and Specialist Microbiological Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Tenna Jensen
- Division for Food and Feed Safety, Danish Veterinary and Food Administration, Glostrup, Denmark
| | - Luise Müller
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Anna Charlotte Schultz
- Division of Microbiology and Production, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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17
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Rajiuddin SM, Jensen T, Hansen TB, Schultz AC. An Optimised Direct Lysis Method for Viral RNA Extraction and Detection of Foodborne Viruses on Fruits and Vegetables. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:226-239. [PMID: 32651775 DOI: 10.1007/s12560-020-09437-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
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.
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Affiliation(s)
- Sheikh Md Rajiuddin
- Division for Microbiology and Production, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800, Kgs. Lyngby, Denmark
| | - Tenna Jensen
- Division for Food and Feed Safety, Danish Veterinary and Food Administration, Stationsparken 31-33, 2600, Glostrup, Denmark
| | - Tina Beck Hansen
- Division for Microbiology and Production, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800, Kgs. Lyngby, Denmark
| | - Anna Charlotte Schultz
- Division for Microbiology and Production, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, 2800, Kgs. Lyngby, Denmark.
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18
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Zhao MY, Li D. Discovery of Components Acting as the Obstacles in the Detection of Enteric Viruses from Berries. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:191-197. [PMID: 32323159 DOI: 10.1007/s12560-020-09428-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
This study investigated the obstacles in detecting enteric viruses from berry fruits, which are on the one hand often associated with outbreaks of viral enteric disease, and on the other hand recognized as a challenging food matrix for molecular detection of enteric viruses. According to the ISO 15216 protocol, for soft fruit samples, virus extraction is by elution with agitation followed by precipitation with polyethylene glycol/NaCl. As a result, first, the phenolic content in the berry eluate was found to be weakly correlated with the detection of coliphage MS2 spiked in the berry samples. Second and more importantly, it was observed that the gel-like pellets formed after precipitation could entrap considerable portions of viruses from being further purified and recovered for detection, suggesting that the low virus detection sensitivity from berries is largely due to the pectin content with complicated chemical structures in the berry fruits. Future research is needed to solve this problem in a targeted way.
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Affiliation(s)
- Mitchie Y Zhao
- Department of Food Science & Technology, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Dan Li
- Department of Food Science & Technology, Faculty of Science, National University of Singapore, Singapore, Singapore.
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19
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Chen J, Wu X, Sánchez G, Randazzo W. Viability RT-qPCR to detect potentially infectious enteric viruses on heat-processed berries. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106818] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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20
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Becker B, Dabisch-Ruthe M, Pfannebecker J. Inactivation of Murine Norovirus on Fruit and Vegetable Surfaces by Vapor Phase Hydrogen Peroxide. J Food Prot 2020; 83:45-51. [PMID: 31821018 DOI: 10.4315/0362-028x.jfp-19-238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Vapor phase hydrogen peroxide (H2O2) can be utilized to inactivate murine norovirus (MNV), a surrogate of human norovirus, on surface areas. However, vapor phase H2O2 inactivation of virus on fruits and vegetables has not been characterized. In this study, MNV was used to determine whether vaporized H2O2 inactivates virus on surfaces of various fruits and vegetables (apples, blueberries, cucumbers, and strawberries). The effect of vapor phase H2O2 decontamination was investigated with two application systems. Plaque assays were performed after virus recovery from untreated and treated fresh produce to compare the quantity of infective MNV. The Mann-Whitney U test was applied to the test results to evaluate the virus titer reductions of treated food samples, with significance set at P ≤ 0.05. The infective MNV populations were significantly reduced on smooth surfaces by 4.3 log PFU (apples, P < 0.00001) and 4 log PFU or below the detection limit (blueberries, P = 0.0074) by treatment with vapor phase H2O2 (60 min, maximum of 214 ppm of H2O2). Similar treatments of artificially contaminated cucumbers resulted in a virus titer reduction of 1.9 log PFU. Treatment of inoculated strawberries resulted in 0.1- and 2.8-log reductions of MNV. However, MNV reduction rates on cucumbers (P = 0.3809) and strawberries (P = 0,7414) were not significant. Triangle tests and color measurements of untreated and treated apples, cucumbers, blueberries, and strawberries revealed no differences in color and consistency after H2O2 treatment. No increase of the H2O2 concentration in treated fruits and vegetables compared with untreated produce was observed. This study reveals for the first time the conditions under which vapor phase H2O2 inactivates MNV on selected fresh fruit and vegetable surfaces.
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Affiliation(s)
- Barbara Becker
- Department of Life Science Technologies, Microbiology, OWL University of Applied Sciences and Arts, Campusallee 12, D-32657 Lemgo, Germany
| | - Mareike Dabisch-Ruthe
- Department of Life Science Technologies, Microbiology, OWL University of Applied Sciences and Arts, Campusallee 12, D-32657 Lemgo, Germany
| | - Jens Pfannebecker
- Department of Life Science Technologies, Microbiology, OWL University of Applied Sciences and Arts, Campusallee 12, D-32657 Lemgo, Germany
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21
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Tunyakittaveeward T, Rupprom K, Pombubpa K, Howteerakul N, Kittigul L. Norovirus Monitoring in Oysters Using Two Different Extraction Methods. FOOD AND ENVIRONMENTAL VIROLOGY 2019; 11:374-382. [PMID: 31342414 DOI: 10.1007/s12560-019-09396-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
Detection of noroviruses in bivalve shellfish is difficult because of the low concentration of norovirus and the presence of reverse transcription (RT)-PCR inhibitors. This study aimed to assess the presence of noroviruses in oysters extracted using a proteinase K extraction (ISO 15216 method) and an adsorption-elution method. Seventy oyster samples were extracted using the two extraction methods and evaluated using RT-nested PCR. The results showed norovirus detection rates at an equal frequency of 28.6%, of which a total of 48 (68.6%) samples had corresponding positive or negative results, while there were 22 (31.4%) samples with discrepant results. Norovirus genogroup (G)I, GII, and mixed GI and GII were detected in 20%, 4.3%, and 4.3% of samples, respectively, by the proteinase K extraction method, which comprised of GI.2, GI.5b, GI.6b, GII.4, and GII.17 genotypes. With the adsorption-elution method noroviruses were detected in 17.1%, 8.6%, and 2.9% of samples, respectively, which comprised of GI.2, GII.2, GII.4, and GII.17 genotypes. All norovirus-positive oyster samples were further estimated for genome copy number using RT-quantitative PCR. The oyster samples processed using the adsorption-elution method contained norovirus GI of 3.36 × 101-1.06 × 105 RNA copies/g of digestive tissues and GII of 1.29 × 103-1.62 × 104 RNA copies/g. Only GII (2.20 × 101 and 7.83 × 101 RNA copies/g) could be quantified in samples prepared using the proteinase K extraction method. The results demonstrate the different performance of the two sample-processing methods, and suggest the use of either extraction method in combination with RT-nested PCR for molecular surveillance of norovirus genotypes in oysters.
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Affiliation(s)
- Thamapan Tunyakittaveeward
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok, 10400, Thailand
| | - Kitwadee Rupprom
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok, 10400, Thailand
| | - Kannika Pombubpa
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok, 10400, Thailand
| | - Nopporn Howteerakul
- Department of Epidemiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Leera Kittigul
- Department of Microbiology, Faculty of Public Health, Mahidol University, 420/1 Ratchawithi Road, Bangkok, 10400, Thailand.
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22
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Enkirch T, Eriksson R, Persson S, Schmid D, Aberle SW, Löf E, Wittesjö B, Holmgren B, Johnzon C, Gustafsson EX, Svensson LM, Sandelin LL, Richter L, Lindblad M, Brytting M, Maritschnik S, Tallo T, Malm T, Sundqvist L, Ederth JL. Hepatitis A outbreak linked to imported frozen strawberries by sequencing, Sweden and Austria, June to September 2018. ACTA ACUST UNITED AC 2019; 23. [PMID: 30326994 PMCID: PMC6194910 DOI: 10.2807/1560-7917.es.2018.23.41.1800528] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Between June–September 2018, 20 hepatitis A cases were notified in six counties in Sweden. Combined epidemiological and microbiological investigations identified imported frozen strawberries produced in Poland as the source of the outbreak. Sequence analysis confirmed the outbreak strain IB in the strawberries with 100 % identity and the respective batch was withdrawn. Sharing the sequence information internationally led to the identification of 14 additional cases in Austria, linked to strawberries from the same producer.
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Affiliation(s)
- Theresa Enkirch
- European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden.,Public Health Agency of Sweden, Solna, Sweden
| | | | | | - Daniela Schmid
- Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Stephan W Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Emma Löf
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden.,Public Health Agency of Sweden, Solna, Sweden
| | - Bengt Wittesjö
- Department of Communicable Disease Control and Prevention, Blekinge County, Sweden
| | - Birgitta Holmgren
- Department of Communicable Disease Control and Prevention, Skåne County, Sweden
| | - Charlotte Johnzon
- The Environment and Health Administration of Stockholm Municipality, Stockholm, Sweden
| | - Eva X Gustafsson
- Department of Communicable Disease Control and Prevention, Skåne County, Sweden
| | - Lena M Svensson
- Department of Communicable Disease Control and Prevention, Östergötland County, Sweden
| | - Lisa Labbé Sandelin
- Department of Communicable Disease Control and Prevention, Kalmar County, Sweden
| | - Lukas Richter
- Austrian Agency for Health and Food Safety, Vienna, Austria
| | | | | | | | | | - Therese Malm
- Department of Communicable Disease Control and Prevention, Gävleborg County, Sweden
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23
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Extended direct lysis method for virus detection on berries including droplet digital RT-PCR or real time RT-PCR with reduced influence from inhibitors. J Virol Methods 2019; 271:113638. [DOI: 10.1016/j.jviromet.2019.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 03/11/2019] [Accepted: 04/02/2019] [Indexed: 11/24/2022]
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24
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Persson S, Karlsson M, Borsch-Reniers H, Ellström P, Eriksson R, Simonsson M. Missing the Match Might Not Cost You the Game: Primer-Template Mismatches Studied in Different Hepatitis A Virus Variants. FOOD AND ENVIRONMENTAL VIROLOGY 2019; 11:297-308. [PMID: 31004336 PMCID: PMC6689102 DOI: 10.1007/s12560-019-09387-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/10/2019] [Indexed: 05/11/2023]
Abstract
Mismatches between template sequences and reverse transcription (RT) or polymerase chain reaction (PCR) primers can lead to underestimation or false negative results during detection and quantification of sequence-diverse viruses. We performed an in silico inclusivity analysis of a widely used RT-PCR assay for detection of hepatitis A virus (HAV) in food, described in ISO 15216-1. One of the most common mismatches found was a single G (primer) to U (template) mismatch located at the terminal 3'-end of the reverse primer region. This mismatch was present in all genotype III sequences available in GenBank. Partial HAV genomes with common or potentially severe mismatches were produced by in vitro transcription and analysed using RT-ddPCR and RT-qPCR. When using standard conditions for RT-qPCR, the mismatch identified resulted in underestimation of the template concentration by a factor of 1.7-1.8 and an increase in 95% limit of detection from 8.6 to 19 copies/reaction. The effect of this mismatch was verified using full-length viral genomes. Here, the same mismatch resulted in underestimation of the template concentration by a factor of 2.8. For the partial genomes, the presence of additional mismatches resulted in underestimation of the template concentration by up to a factor of 232. Quantification by RT-ddPCR and RT-qPCR was equally affected during analysis of RNA templates with mismatches within the reverse primer region. However, on analysing DNA templates with the same mismatches, we found that ddPCR quantification was less affected by mismatches than qPCR due to the end-point detection technique.
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Affiliation(s)
- Sofia Persson
- European Union Reference Laboratory (EURL) for Foodborne Viruses, National Food Agency, Hamnesplanaden 5, 453 23, Uppsala, Sweden
- Department of Medical Sciences, Zoonosis Science Centre, Uppsala University, Uppsala, Sweden
| | - Måns Karlsson
- Department of Mathematics, Stockholm University, Stockholm, Sweden
| | | | - Patrik Ellström
- Department of Medical Sciences, Zoonosis Science Centre, Uppsala University, Uppsala, Sweden
| | - Ronnie Eriksson
- European Union Reference Laboratory (EURL) for Foodborne Viruses, National Food Agency, Hamnesplanaden 5, 453 23, Uppsala, Sweden
| | - Magnus Simonsson
- European Union Reference Laboratory (EURL) for Foodborne Viruses, National Food Agency, Hamnesplanaden 5, 453 23, Uppsala, Sweden.
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25
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26
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Predictive models for thermal inactivation of human norovirus and surrogates in strawberry puree. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.08.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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27
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da Silva Luz I, Miagostovich MP. Comparison of viral elution-concentration methods for recovering noroviruses from deli meats. J Virol Methods 2018; 260:49-55. [DOI: 10.1016/j.jviromet.2018.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 07/02/2018] [Accepted: 07/02/2018] [Indexed: 12/31/2022]
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28
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Bartsch C, Höper D, Mäde D, Johne R. Analysis of frozen strawberries involved in a large norovirus gastroenteritis outbreak using next generation sequencing and digital PCR. Food Microbiol 2018; 76:390-395. [PMID: 30166165 DOI: 10.1016/j.fm.2018.06.019] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/25/2018] [Accepted: 06/30/2018] [Indexed: 12/30/2022]
Abstract
Virus-contaminated frozen berries have been frequently identified as cause of foodborne disease outbreaks. To provide new tools for virus detection and characterization in berries, next generation sequencing (NGS) and reverse transcription-digital PCR (RT-dPCR) techniques were tested here with strawberries previously involved in a large-scale norovirus (NoV) gastroenteritis outbreak in Germany. By NGS, about 29 million sequence reads were generated, which mainly showed identities to sequences from the plant matrix and from the bacterial flora. Most abundant virus sequences originated from plant-specific viruses, whereas sequences with high identity to human viruses were rare. Only two sequence reads showed homologies to human NoV. They were identical to GII.P16/GII.13 NoV sequences from patients and a strawberry sample independently analyzed during the outbreak. Quantification of the GII NoV RNA of the berries using RT-dPCR confirmed a low mean virus amount of 185 copies/25 g, which is similar to independently assessed RT-qPCR results (257 copies/25 g). The study shows that identification of human-pathogenic viruses in naturally contaminated frozen berries is possible using NGS technologies. However, the method needs to be further optimized in order to enable convenient and reproducible detection of a low amount of human-pathogenic virus sequences in a background of highly abundant nucleic acids of other sources.
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Affiliation(s)
- Christina Bartsch
- German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Dirk Höper
- Friedrich Loeffler Institute, Südufer 10, 17493, Greifswald (Insel Riems), Germany
| | - Dietrich Mäde
- State Office for Consumer Protection, Freiimfelder Str. 68, 06112, Halle (Saale), Saxony-Anhalt, Germany
| | - Reimar Johne
- German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589, Berlin, Germany.
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29
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Hida K, Papafragkou E, Kulka M. Testing for Human Norovirus and Recovery of Process Control in Outbreak-Associated Produce Items. J Food Prot 2018; 81:105-114. [PMID: 29280676 DOI: 10.4315/0362-028x.jfp-17-134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The development of rapid and sensitive detection methods for human noroviruses (HuNoV) in produce items is critical, especially with the recent rise in outbreaks associated with this food commodity. In this study, 50-g portions of various produce items linked to a norovirus outbreak (celery, cucumber, lettuce, grapes, and radish) were artificially inoculated with murine norovirus (MNV-1) and concentrated either by ultracentrifugation or polyethylene glycol (PEG) precipitation after elution with an alkaline Tris-glycine-beef extract buffer supplemented with pectinase. As a viral concentration step following virus elution and clarification, ultracentrifugation yielded a faster method (<8 h, including reverse transcription quantitative PCR), with MNV-1 recoveries similar to or better, than those obtained with PEG precipitation. The addition of polyvinylpyrrolidone to the elution buffer, to remove polyphenolic inhibitors, improved MNV-1 recoveries by over two- and fivefold for cucumber and grapes, respectively. However, despite MNV-1 recoveries ranging from 10 to 38% as calculated with 10-fold diluted RNA, contaminating HuNoV was not detected in any of the outbreak-associated samples tested. For store-bought produce samples, the limit of detection for artificially seeded HuNoV GII.4 was determined to be 103 copies per 50 g, with reproducible detection achieved in grapes, radish, and celery. The results support the use of ultracentrifugation as an alternative approach to PEG precipitation to concentrate norovirus from a variety of produce items.
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Affiliation(s)
- Kaoru Hida
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, Maryland 20708, USA
| | - Efstathia Papafragkou
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, Maryland 20708, USA
| | - Michael Kulka
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, Maryland 20708, USA
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30
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Fraisse A, Coudray-Meunier C, Martin-Latil S, Hennechart-Collette C, Delannoy S, Fach P, Perelle S. Digital RT-PCR method for hepatitis A virus and norovirus quantification in soft berries. Int J Food Microbiol 2017; 243:36-45. [DOI: 10.1016/j.ijfoodmicro.2016.11.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 11/16/2022]
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