1
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Wang F, Zhang Q, An R, Lyu C, Xu J, Wang D. Reactive species of plasma-activated water for murine norovirus 1 inactivation. Food Res Int 2024; 194:114877. [PMID: 39232515 DOI: 10.1016/j.foodres.2024.114877] [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: 06/07/2024] [Revised: 07/25/2024] [Accepted: 08/05/2024] [Indexed: 09/06/2024]
Abstract
Human norovirus (HuNoV), the leading cause of foodborne acute gastroenteritis, poses a serious threat to public health. Traditional disinfection methods lead to destructions of food properties and functions, and/or environmental contaminations. Green and efficient approaches are urgently needed to disinfect HuNoV. Plasma-activated water (PAW) containing amounts of reactive species is an emerging nonthermal and eco-friendly disinfectant towards the pathogenic microorganisms. However, the disinfection efficacy and mechanism of PAW on HuNoV has not yet been studied. Murine norovirus 1 (MNV-1) is one of the most commonly used HuNoV surrogates to evaluate the efficacy of disinfectants. In the current study, the inactivation efficacy of MNV-1 by PAW was investigated. The results demonstrated that PAW significantly inactivated MNV-1, reducing the viral titer from approximately 6 log10 TCID50/mL to non-detectable level. The decreased pH, increased oxidation-reduction potential (ORP) and conductivity of PAW were observed compared with that of deionized water. Compositional analysis revealed that hydrogen peroxide (H2O2), nitrate (NO3-) and hydroxyl radical (OH) were the functional reactive species in MNV-1 inactivation. L-histidine could scavenge most of the inactivation effect in a concentration-dependent manner. Moreover, PAW could induce damage to viral proteins. Part of MNV-1 particles was destroyed, while others were structurally intact without infectiousness. After 45 days of storage at 4 °C, PAW generated with 80 % O2 and 100 % O2 could still reduce over 4 log10 TCID50/mL of the viral titer. In addition, PAW prepared using hard water induced approximately 6 log10 TCID50/mL reduction of MNV-1. PAW treatment of MNV-1-inoculated blueberries reduced the viral titer from 3.79 log10 TCID50/mL to non-detectable level. Together, findings of the current study uncovered the crucial reactive species in PAW inactivate MNV-1 and provided a potential disinfection strategy to combat HuNoV in foods, water, and environment.
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Affiliation(s)
- Fengqing Wang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Zhang
- State Key Laboratory of Advanced Optical Communication Systems and Networks, Key Laboratory for Laser Plasmas (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - Ran An
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Chenang Lyu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jialun Xu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Dapeng Wang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
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2
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Yamazaki Y, Alonso UA, Galay RL, Yamazaki W. Development of a simple and highly sensitive virion concentration method to detect SARS-CoV-2 in saliva. Heliyon 2024; 10:e33168. [PMID: 38994082 PMCID: PMC11238118 DOI: 10.1016/j.heliyon.2024.e33168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 07/13/2024] Open
Abstract
Background Controlling novel coronavirus pandemic infection (COVID-19) is a global challenge, and highly sensitive testing is essential for effective control. The saliva is a promising sample for high-sensitivity testing because it is easier to collect than nasopharyngeal swab samples and allows large-volume testing. Results We developed a simple SARS-CoV-2 concentration method from saliva samples that can be completed in less than 60 min. We performed a spike test using 12 ml of saliva samples obtained from healthy volunteer people, and the developed method performance was evaluated by comparison using a combination of automatic nucleic acid extraction followed by RT-qPCR detection. In saliva spike tests using a 10-fold dilution series of SARS-CoV-2, the developed method was consistently 100-fold more sensitive than the conventional method. Conclusions The developed method can improve the analytical sensitivity of the SARS-CoV-2 test using saliva and speed up and save labor in screening tests by pooling many samples. Furthermore, the developed method has the potential to contribute to the highly sensitive detection of various human and animal viral pathogens from the saliva and various clinical samples.
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Affiliation(s)
- Yasuko Yamazaki
- Center for Southeast Asian Studies, Kyoto University, 46 Shimoadachi-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Uxía Alonso Alonso
- Center for Southeast Asian Studies, Kyoto University, 46 Shimoadachi-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
- Animal Medicine and Health at Institut de Recerca i Tecnologia Agroalimentàries (IRTA) - Centre de Recerca en Sanitat Animal (CReSA), Spain
| | - Remil L Galay
- Center for Southeast Asian Studies, Kyoto University, 46 Shimoadachi-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
- Department of Veterinary Paraclinical Sciences, College of Veterinary Medicine, University of the Philippines Los Baños, Los Baños, Laguna, 4031, Philippines
| | - Wataru Yamazaki
- Center for Southeast Asian Studies, Kyoto University, 46 Shimoadachi-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
- Kyoto University School of Public Health, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8303, Japan
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3
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Boxman ILA, Molin R, Persson S, Juréus A, Jansen CCC, Sosef NP, Le Guyader SF, Ollivier J, Summa M, Hautaniemi M, Suffredini E, Di Pasquale S, Myrmel M, Khatri M, Jamnikar-Ciglenecki U, Kusar D, Moor D, Butticaz L, Lowther JA, Walker DI, Stapleton T, Simonsson M, Dirks RAM. An international inter-laboratory study to compare digital PCR with ISO standardized qPCR assays for the detection of norovirus GI and GII in oyster tissue. Food Microbiol 2024; 120:104478. [PMID: 38431324 DOI: 10.1016/j.fm.2024.104478] [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: 10/10/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 03/05/2024]
Abstract
An optimized digital RT-PCR (RT-dPCR) assay for the detection of human norovirus GI and GII RNA was compared with ISO 15216-conform quantitative real-time RT-PCR (RT-qPCR) assays in an interlaboratory study (ILS) among eight laboratories. A duplex GI/GII RT-dPCR assay, based on the ISO 15216-oligonucleotides, was used on a Bio-Rad QX200 platform by six laboratories. Adapted assays for Qiagen Qiacuity or ThermoFisher QuantStudio 3D were used by one laboratory each. The ILS comprised quantification of norovirus RNA in the absence of matrix and in oyster tissue samples. On average, results of the RT-dPCR assays were very similar to those obtained by RT-qPCR assays. The coefficient of variation (CV%) of norovirus GI results was, however, much lower for RT-dPCR than for RT-qPCR in intra-laboratory replicates (eight runs) and between the eight laboratories. The CV% of norovirus GII results was in the same range for both detection formats. Had in-house prepared dsDNA standards been used, the CV% of norovirus GII could have been in favor of the RT-dPCR assay. The ratio between RT-dPCR and RT-qPCR results varied per laboratory, despite using the distributed RT-qPCR dsDNA standards. The study indicates that the RT-dPCR assay is likely to increase uniformity of quantitative results between laboratories.
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Affiliation(s)
- Ingeborg L A Boxman
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
| | - Ramia Molin
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - Sofia Persson
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - Anna Juréus
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - Claudia C C Jansen
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
| | - Nils P Sosef
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
| | - Soizick F Le Guyader
- French Research Institute for Exploitation of the Sea (Ifremer) - Laboratoire de Santé, Environnement et Microbiologie, Nantes, France.
| | - Joanna Ollivier
- French Research Institute for Exploitation of the Sea (Ifremer) - Laboratoire de Santé, Environnement et Microbiologie, Nantes, France.
| | | | | | - Elisabetta Suffredini
- Istituto Superiore di Sanità, Department of Food Safety, Nutrition and Veterinary Public Health, Rome, Italy.
| | - Simona Di Pasquale
- Istituto Superiore di Sanità, Department of Food Safety, Nutrition and Veterinary Public Health, Rome, Italy.
| | - Mette Myrmel
- Norwegian University of Life Sciences (NMBU), Faculty of Veterinary Medicine, Virology Unit, Ås, Norway.
| | - Mamata Khatri
- Norwegian University of Life Sciences (NMBU), Faculty of Veterinary Medicine, Virology Unit, Ås, Norway.
| | - Urska Jamnikar-Ciglenecki
- University of Ljubljana Veterinary Faculty, Institute of Food Safety, Feed and Environment, Ljubljana, Slovenia.
| | - Darja Kusar
- University of Ljubljana Veterinary Faculty, Institute of Microbiology and Parasitology, Ljubljana, Slovenia.
| | - Dominik Moor
- Federal Institute of Metrology METAS, Biological Analysis and References Laboratory, Bern, Switzerland.
| | - Lisa Butticaz
- Federal Institute of Metrology METAS, Biological Analysis and References Laboratory, Bern, Switzerland.
| | - James A Lowther
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom.
| | - David I Walker
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom.
| | - Tina Stapleton
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom.
| | - Magnus Simonsson
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - René A M Dirks
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
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4
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Mabasa VV, van Zyl WB, Taylor MB, Mans J. Quantification and Potential Viability of Human Noroviruses in Final Effluent from Wastewater Treatment Works in Pretoria, South Africa. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:200-215. [PMID: 38555559 PMCID: PMC11390798 DOI: 10.1007/s12560-024-09589-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/12/2024] [Indexed: 04/02/2024]
Abstract
Growing global concerns over water scarcity, worsened by climate change, drive wastewater reclamation efforts. Inadequately treated wastewater presents significant public health risks. Previous studies in South Africa (SA) have reported high norovirus levels in final effluent and sewage-polluted surface water, indicating pathogen removal inefficiency. However, the viability of these virions was not explored. This study assessed human norovirus viability in final effluent from wastewater treatment works (WWTWs) in Pretoria, SA. Between June 2018 and August 2020, 200 samples were collected from two WWTWs, including raw sewage and final effluent. Norovirus concentrations were determined using in-house RNA standards. Viability of noroviruses in final effluent was assessed using viability RT-qPCR (vPCR) with PMAxx™-Triton X-100. There was no significant difference in GI concentrations between raw sewage (p = 0.5663) and final effluent (p = 0.4035) samples at WWTW1 and WWTW2. WWTW1 had significantly higher GII concentrations in raw sewage (p < 0.001) compared to WWTW2. No clear seasonal pattern was observed in norovirus concentrations. At WWTW1, 50% (7/14) of GI- and 64.9% (24/37) of GII-positive final effluent samples had no quantifiable RNA after vPCR. At WWTW2, the majority (92.6%, 25/27) of GII-positive final effluent samples showed a 100% RNA reduction post vPCR. PMAxx™-Triton X-100 vPCR provides a more accurate reflection of discharge of potentially viable noroviruses in the environment than standard RT-qPCR. Despite significant reductions in potentially viable noroviruses after wastewater treatment, the levels of potentially viable viruses in final effluent are still of concern due to the high initial load and low infectious dose of noroviruses.
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Affiliation(s)
- V V Mabasa
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria, 0031, South Africa
| | - W B van Zyl
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria, 0031, South Africa
- National Health Laboratory Service-Tshwane Academic Division, Pretoria, South Africa
| | - M B Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria, 0031, South Africa
| | - J Mans
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria, 0031, South Africa.
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5
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Stoppel SM, Lunestad BT, Myrmel M. The effect of enzymatic and viability dye treatment in combination with long-range PCR on assessing Tulane virus infectivity. J Virol Methods 2024; 327:114919. [PMID: 38531509 DOI: 10.1016/j.jviromet.2024.114919] [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: 08/25/2023] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 03/28/2024]
Abstract
Human norovirus (HuNoV) is regularly involved in food-borne infections. To detect infectious HuNoV in food, RT-qPCR remains state of the art but also amplifies non-infectious virus. The present study combines pre-treatments, RNase and propidium monoazide, with three molecular analyses, including long-range PCR, to predominantly detect infectious Tulane virus (TuV), a culturable HuNoV surrogate. TuV was exposed to inactivating conditions to assess which molecular method most closely approximates the reduction in infectious virus determined by cell culture (TCID50). After thermal treatments (56 °C/5 min, 70 °C/5 min, 72 °C/20 min), TCID50 reductions of 0.3, 4.4 and 5.9 log10 were observed. UV exposure (40/100/1000 mJ/cm2) resulted in 1.1, 2.5 and 5.9 log10 reductions. Chlorine (45/100 mg/L for 1 h) reduced infectious TuV by 2.0 and 3.0 log10. After thermal inactivation standard RT-qPCR, especially with pre-treatments, showed the smallest deviation from TCID50. On average, RT-qPCR with pre-treatments deviated by 1.1-1.3 log10 from TCID50. For UV light, long-range PCR was closest to TCID50 results. Long-range reductions deviated from TCID50 by ≤0.1 log10 for mild and medium UV-conditions. However, long-range analyses often resulted in qPCR non-detects. At higher UV doses, RT-qPCR with pre-treatments differed by ≤1.0 log10 from TCID50. After chlorination the molecular methods repeatedly deviated from TCID50 by >1.0 log10, Overall, each method needs to be further optimized for the individual types of inactivation treatment.
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Affiliation(s)
- Sarah M Stoppel
- Institute of Marine Research, Section for Seafood Hazards, Nordnesgaten 50, Bergen 5005, Norway.
| | - Bjørn Tore Lunestad
- Institute of Marine Research, Section for Seafood Hazards, Nordnesgaten 50, Bergen 5005, Norway
| | - Mette Myrmel
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Elizabeth Stephansens vei 15, Ås 1430, Norway
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6
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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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7
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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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8
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Ahuja S, Tallur S, Kondabagil K. Simultaneous microbial capture and nucleic acid extraction from wastewater with minimal pre-processing and high recovery efficiency. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170347. [PMID: 38336063 DOI: 10.1016/j.scitotenv.2024.170347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/22/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
The COVID-19 pandemic accelerated research towards developing low-cost assays for automated urban wastewater monitoring assay that can be integrated into an environmental surveillance system for early warning of frequent disease outbreaks and future pandemics. Microbial concentration is one of the most challenging steps in wastewater surveillance, due to the sample heterogeneity and low pathogen load. Keeping in mind the requirements of large-scale testing in densely populated low- or middle-income countries (LMICs), such assays would need to be low-cost and have rapid turnaround time with high recovery efficiency. In this study, two such methods are presented and evaluated against commercially available kits for pathogen detection in wastewater. The first method utilizes paper dipsticks while the second method comprises of a PTFE membrane filter (PMF) integrated with a peristaltic pump. Both methods were used to concentrate and isolate nucleic acids from different microbes such as SARS-CoV-2, pepper mild mottle virus (PMMoV), bacteriophage Phi6, and E. coli from wastewater samples with minimal or no sample pre-processing. While the paper dipstick method is suitable for sub-milliliter sample volume, the PMF method can be used with larger volumes of wastewater sample (40 mL) and can detect multiple microbes with recovery efficiency comparable to commercially available kits.
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Affiliation(s)
- Shruti Ahuja
- Centre for Research in Nanotechnology & Science (CRNTS), IIT Bombay, Powai, Mumbai 400076, Maharashtra, India.
| | - Siddharth Tallur
- Department of Electrical Engineering, IIT Bombay, Powai, Mumbai 400076, Maharashtra, India.
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, Maharashtra, India.
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9
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Ossio A, Flores-Rodríguez F, Heredia N, García S, Merino-Mascorro JA. Foodborne Viruses and Somatic Coliphages Occurrence in Fresh Produce at Retail from Northern Mexico. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:109-119. [PMID: 38198031 DOI: 10.1007/s12560-023-09578-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/28/2023] [Indexed: 01/11/2024]
Abstract
Foodborne disease outbreaks linked to consumption of vegetables have been often attributed to human enteric viruses, such as Norovirus (NoV), Hepatitis A virus (HAV), and Rotavirus (RoV). Information about the occurrence of these viruses is scarce in many fresh-producing countries. Viral contamination detection of indicators, such as somatic coliphages, could indirectly reflect the presence of viral pathogens, being a valuable tool for better viral risk assessment in food industry. This study aimed to establish the occurrence and correlation of foodborne viruses and somatic coliphages in leafy greens in northern Mexico. A total of 320 vegetable samples were collected, resulting in 80 composite rinses, 40 of lettuce and 40 of parsley. Somatic coliphages were determined using the EPA 1602 method, while foodborne viruses (HAV, RoV, NoV GI, and GII) were determined by qPCR. The occurrence of RoV was 22.5% (9/40, mean 2.11 log gc/g) in lettuce and 20% (8/40, mean 1.91 log gc/g) in parsley. NoV and HAV were not detected in any samples. Somatic coliphages were present in all lettuce and parsley samples, with mean levels of 1.85 log PFU/100 ml and 2.28 log PFU/100 ml, respectively. Spearman analysis established the correlation of somatic coliphages and genomic copies of RoV, resulting in an r2 value of - 0.026 in lettuce and 0.349 in parsley. Although NoV or HAV were undetected in the samples, the presence of RoV is a matter of concern as leafy greens are usually eaten raw, which poses a potential risk of infection.
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Affiliation(s)
- Axel Ossio
- Laboratorio de Bioquímica y Genética de Microorganismos, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Fernanda Flores-Rodríguez
- Laboratorio de Bioquímica y Genética de Microorganismos, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Norma Heredia
- Laboratorio de Bioquímica y Genética de Microorganismos, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Santos García
- Laboratorio de Bioquímica y Genética de Microorganismos, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, 66455, San Nicolas de los Garza, N.L., Mexico
| | - Jose Angel Merino-Mascorro
- Laboratorio de Bioquímica y Genética de Microorganismos, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, 66455, San Nicolas de los Garza, N.L., Mexico.
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10
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Kim TY, Zhu X, Kim SM, Lim JA, Woo MA, Lim MC, Luo K. A review of nucleic acid-based detection methods for foodborne viruses: Sample pretreatment and detection techniques. Food Res Int 2023; 174:113502. [PMID: 37986417 DOI: 10.1016/j.foodres.2023.113502] [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: 07/25/2023] [Revised: 09/15/2023] [Accepted: 09/22/2023] [Indexed: 11/22/2023]
Abstract
Viruses are major pathogens that cause food poisoning when ingested via contaminated food and water. Therefore, the development of foodborne virus detection technologies that can be applied throughout the food distribution chain is essential for food safety. A common nucleic acid-based detection method is polymerase chain reaction (PCR), which has become the gold standard for monitoring food contamination by viruses due to its high sensitivity, and availability of commercial kits. However, PCR-based methods are labor intensive and time consuming, and are vulnerable to inhibitors that may be present in food samples. In addition, the methods are restricted with regard to site of analysis due to the requirement of expensive and large equipment for sophisticated temperature regulation and signal analysis procedures. To overcome these limitations, optical and electrical readout biosensors based on nucleic acid isothermal amplification technology and nanomaterials have emerged as alternatives for nucleic acid-based detection of foodborne viruses. Biosensors are promising portable detection tools owing to their easy integration into compact platforms and ability to be operated on-site. However, the complexity of food components necessitates the inclusion of tedious preprocessing steps, and the lack of stability studies on residual food components further restricts the practical application of biosensors as a universal detection method. Here, we summarize the latest advances in nucleic acid-based strategies for the detection of foodborne viruses, including PCR-based and isothermal amplification-based methods, gene amplification-free methods, as well as food pretreatment methods. The principles, strengths/disadvantages, and performance of each method, problems to be solved, and future prospects for the development of a universal detection method are discussed.
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Affiliation(s)
- Tai-Yong Kim
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Xiaoning Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong Province 266003, China
| | - Se-Min Kim
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju-gun, Jeollabuk-do 55365, Republic of Korea; Department of Food Science and Technology, Jeonbuk National University, Jeonju-si, Jeollabuk-do 54896, Republic of Korea
| | - Jeong-A Lim
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Min-Ah Woo
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Min-Cheol Lim
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju-gun, Jeollabuk-do 55365, Republic of Korea; Department of Food Biotechnology, Korea University of Science and Technology, Daejeon-si 34113, Republic of Korea.
| | - Ke Luo
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong Province 266003, China.
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11
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Santos-Silva S, da Silva Dias Moraes DF, López-López P, Rivero-Juarez A, Mesquita JR, Nascimento MSJ. Hepatitis E Virus in the Iberian Peninsula: A Systematic Review. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:193-211. [PMID: 37434079 PMCID: PMC10499749 DOI: 10.1007/s12560-023-09560-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/26/2023] [Indexed: 07/13/2023]
Abstract
One of the most frequent causes of acute viral hepatitis is hepatitis E virus (HEV) causing 20 million infections worldwide each year and 44,000 deaths. Studies on HEV in the Iberian Peninsula have been increasing through time with HEV infection being identified in humans and animals. The aim of the present systematic review was to compile and evaluate all the published data on HEV from studies performed in humans, animals and environmental samples in the Iberian Peninsula. The electronic databases Mendeley, PubMed, Scopus, and Web of Science were thoroughly searched, and research published up until February 01, 2023 were included. Resulting in a total of 151 eligible papers by full reading and application of PRISMA exclusion/inclusion criteria. Overall, the present review shows that several HEV genotypes, namely HEV-1, 3, 4, and 6 as well as Rocahepevirus, are circulating in humans, animals, and in the environment in the Iberian Peninsula. HEV-3 was the most common genotype circulating in humans in Portugal and Spain, as expected for developed countries, with HEV-1 only being detected in travelers and emigrants from HEV endemic regions. Spain is the biggest pork producer in Europe and given the high circulation of HEV in pigs, with HEV-3 being primarily associated to zoonotic transmission through consumption of swine meat and meat products, in our opinion, the introduction of an HEV surveillance system in swine and inclusion of HEV in diagnostic routines for acute and chronic human hepatitis would be important. Additionally, we propose that establishing a monitoring mechanism for HEV is crucial in order to gain a comprehensive understanding of the prevalence of this illness and the various strains present in the Iberian Peninsula, as well as their potential impact on public health.
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Affiliation(s)
- Sérgio Santos-Silva
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | | | - Pedro López-López
- Grupo de Virología Clínica y Zoonosis, Unidad de Enfermedades Infecciosas, Instituto Maimónides de Investigación Biomédica de Córdoba, Hospital Reina Sofía, Universidad de Córdoba, Córdoba, Spain
- CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - António Rivero-Juarez
- Grupo de Virología Clínica y Zoonosis, Unidad de Enfermedades Infecciosas, Instituto Maimónides de Investigación Biomédica de Córdoba, Hospital Reina Sofía, Universidad de Córdoba, Córdoba, Spain
- CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - João R Mesquita
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.
- Epidemiology Research Unit (EPIUnit), Instituto de Saúde Pública da Universidade do Porto, Porto, Portugal.
- Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), Porto, Portugal.
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12
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Desdouits M, Reynaud Y, Philippe C, Guyader FSL. A Comprehensive Review for the Surveillance of Human Pathogenic Microorganisms in Shellfish. Microorganisms 2023; 11:2218. [PMID: 37764063 PMCID: PMC10537662 DOI: 10.3390/microorganisms11092218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Bivalve molluscan shellfish have been consumed for centuries. Being filter feeders, they may bioaccumulate some microorganisms present in coastal water, either naturally or through the discharge of human or animal sewage. Despite regulations set up to avoid microbiological contamination in shellfish, human outbreaks still occur. After providing an overview showing their implication in disease, this review aims to highlight the diversity of the bacteria or enteric viruses detected in shellfish species, including emerging pathogens. After a critical discussion of the available methods and their limitations, we address the interest of technological developments using genomics to anticipate the emergence of pathogens. In the coming years, further research needs to be performed and methods need to be developed in order to design the future of surveillance and to help risk assessment studies, with the ultimate objective of protecting consumers and enhancing the microbial safety of bivalve molluscan shellfish as a healthy food.
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Affiliation(s)
| | | | | | - Françoise S. Le Guyader
- Ifremer, Unité Microbiologie Aliment Santé et Environnement, RBE/LSEM, 44311 Nantes, France; (M.D.); (Y.R.); (C.P.)
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13
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Nemes K, Persson S, Simonsson M. Hepatitis A Virus and Hepatitis E Virus as Food- and Waterborne Pathogens-Transmission Routes and Methods for Detection in Food. Viruses 2023; 15:1725. [PMID: 37632066 PMCID: PMC10457876 DOI: 10.3390/v15081725] [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: 06/27/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Foodborne viruses are an important threat to food safety and public health. Globally, there are approximately 5 million cases of acute viral hepatitis due to hepatitis A virus (HAV) and hepatitis E virus (HEV) every year. HAV is responsible for numerous food-related viral outbreaks worldwide, while HEV is an emerging pathogen with a global health burden. The reported HEV cases in Europe have increased tenfold in the last 20 years due to its zoonotic transmission through the consumption of infected meat or meat products. HEV is considered the most common cause of acute viral hepatitis worldwide currently. This review focuses on the latest findings on the foodborne transmission routes of HAV and HEV and the methods for their detection in different food matrices.
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Affiliation(s)
- Katalin Nemes
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Dag Hammarskjölds väg 56 A, 75237 Uppsala, Sweden; (S.P.); (M.S.)
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14
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Wu R, Meng B, Corredig M, Griffiths MW. Rapid Detection of Hepatitis A Virus in Foods Using a Bioluminescent Assay in Real-Time (BART) and Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Technology. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:144-157. [PMID: 36640204 PMCID: PMC9839959 DOI: 10.1007/s12560-022-09548-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 12/30/2022] [Indexed: 06/13/2023]
Abstract
Foodborne hepatitis A infections have been considered as a major threat for public health worldwide. Increased incidences of hepatitis A virus (HAV) infection has been associated with growing global trade of food products. Rapid and sensitive detection of HAV in foods is very essential for investigating the outbreaks. Real-time RT-PCR has been most widely used for the detection of HAV by far. However, the technology relies on fluorescence determination of the amplicon and requires sophisticated, high-cost instruments and trained personnel, limiting its use in low resource settings. In this study, a robust, affordable, and simple assay, reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in combination with a bioluminescence-based determination of amplification in real-time (BART), was developed for the detection of HAV in different food matrices, including green onion, strawberry, mussel, and milk. The efficiencies of a one-step RT-LAMP-BART and a two-step RT-LAMP-BART were investigated for the detection of HAV in different food matrices and was compared with that of real-time RT-PCR. The sensitivity of the RT-LAMP-BART assay was significantly affected by Mg2+ concentration (P < 0.05), in addition to primer quality. The optimal Mg2+ concentration was 2 mM for one-step RT-LAMP-BART and 4 mM for two-step RT-LAMP-BART. Compared with cartridge-purified primers, HPLC-purified primers could greatly improve the sensitivity of the RT-LAMP-BART assay (P < 0.05). For detecting HAV in different food matrices, the performance of two-step RT-LAMP-BART was comparable with that of real-time RT-PCR and was better than that of one-step RT-LAMP-BART. The detection limit of the two-step RT-LAMP-BART for HAV in green onion, strawberry, mussel, and milk was 8.3 × 100 PFU/15 g, 8.3 × 101 PFU/50 g, 8.3 × 100 PFU/5 g, and 8.3 × 100 PFU/40 mL, respectively. The developed RT-LAMP-BART was an effective, simple, sensitive, and robust method for foodborne HAV detection.
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Affiliation(s)
- Ruiqin Wu
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
- Canadian Research Institute for Food Safety, 43 McGilvray Street, Guelph, ON, N1G 2W1, Canada.
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Milena Corredig
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Mansel W Griffiths
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
- Canadian Research Institute for Food Safety, 43 McGilvray Street, Guelph, ON, N1G 2W1, Canada
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15
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Batista FM, Hatfield R, Powell A, Baker-Austin C, Lowther J, Turner AD. Methodological advances in the detection of biotoxins and pathogens affecting production and consumption of bivalve molluscs in a changing environment. Curr Opin Biotechnol 2023; 80:102896. [PMID: 36773575 DOI: 10.1016/j.copbio.2023.102896] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/18/2022] [Accepted: 01/02/2023] [Indexed: 02/11/2023]
Abstract
The production, harvesting and safe consumption of bivalve molluscs can be disrupted by biological hazards that can be divided into three categories: (1) biotoxins produced by naturally occurring phytoplankton that are bioaccumulated by bivalves during filter-feeding, (2) human pathogens also bioaccumulated by bivalves and (3) bivalve pathogens responsible for disease outbreaks. Environmental changes caused by human activities, such as climate change, can further aggravate these challenges. Early detection and accurate quantification of these hazards are key to implementing measures to mitigate their impact on production and safeguard consumers. This review summarises the methods currently used and the technological advances in the detection of biological hazards affecting bivalves, for the screening of known hazards and discovery of new ones.
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Affiliation(s)
- Frederico M Batista
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, Dorset DT4 8UB, United Kingdom.
| | - Robert Hatfield
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, Dorset DT4 8UB, United Kingdom
| | - Andrew Powell
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, Dorset DT4 8UB, United Kingdom
| | - Craig Baker-Austin
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, Dorset DT4 8UB, United Kingdom
| | - James Lowther
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, Dorset DT4 8UB, United Kingdom
| | - Andrew D Turner
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, Dorset DT4 8UB, United Kingdom
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16
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Salazar EJ, Guerrero MJ, Villaquiran JA, Suárez K, Cevallos J. Development of enhanced primer sets for detection of Norovirus and Hepatitis A in food samples from Guayaquil (Ecuador) by reverse transcriptase-heminested PCR. BIONATURA 2023. [DOI: 10.21931/rb/2023.08.01.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
Norovirus (NV) is an infectious biological agent that causes gastrointestinal problems of the original nonbacterial appearance of foodborne illnesses. The genotype of NV responsible for the most frequent NV disease outbreaks is GII, accounting for 60–80% of the cases. Moreover, original and new NV variants are continuously emerging, concurrent with the recent global increase in NV infections. Hepatitis A virus (HAV) is another foodborne pathogen frequently implicated in acute gastroenteritis cases around the world. The virus is transmitted among humans via the fecal-oral route, and infection by HAV causes the most severe form of viral illness acquired from foods. In this study, we implemented primer sets to detect NV genotypes I and II. We also developed primer sets for the detection of HAV. The primers were used in a heminested reverse transcriptase PCR (hnRT-PCR) protocol that was rapid and sensitive for detecting NVG1, NVGII and HAV virus in food. The hnRT-PCR was applied successfully to strawberries and spinach obtained from a local fresh-food market, where we could see NVGI, NVGII and HAV.
Keywords: Norovirus1; Hepatitis A2; gastroenteritis3; genotypes4; NVG15; NVGII6; hnRT-PCR7.
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Affiliation(s)
- E. J. Salazar
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador; 2 Facultad de Ciencias Agropecuarias, Universidad Técnica de Babahoyo, Km 7.5 Vía Babahoyo - Montalvo
| | - M. J. Guerrero
- Facultad Ciencias de la Vida, Laboratorio para Investigaciones Biomédicas, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - J. A. Villaquiran
- Facultad Ciencias de la Vida, Laboratorio para Investigaciones Biomédicas, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - K.S. Suárez
- Facultad de Ingeniería Mecánica y Ciencias de la Producción, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - J.M. Cevallos
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador ; Facultad Ciencias de la Vidas, Escuela Superior Politécnica del Litoral, Km 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
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17
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Hennechart-Collette C, Dehan O, Fraisse A, Martin-Latil S, Perelle S. Development of an Extraction Method to Detect Hepatitis A Virus, Hepatitis E Virus, and Noroviruses in Fish Products. Microorganisms 2023; 11:microorganisms11030624. [PMID: 36985198 PMCID: PMC10051274 DOI: 10.3390/microorganisms11030624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Viruses are a leading cause of foodborne disease worldwide. Hepatitis viruses (hepatitis A (HAV) and hepatitis E (HEV)) and human norovirus are recognized as the main viruses of public health concern in food hygiene. ISO 15216 approved procedures are not validated for detection of HAV and human norovirus in foodstuffs, such as fishes, leading to an inability to ensure the safety of these products. This study aimed to provide a rapid and sensitive method for detecting these targets in fish products. An existing method that includes proteinase K treatment was selected for further validation using artificially contaminated fish products, according to the recent international standard ISO 16140-4. Recovery efficiencies in pure RNA extracts of viruses ranged from 0.2% to 66.2% for HAV, 4.0% to 100.0% for HEV, 2.2% to 100.0% for norovirus GI, and 0.2% to 12.5% for norovirus GII. LOD50 values were between 144 and 8.4 × 104 genome copies/g for HAV and HEV, and 104 and 2.0 × 103 copies/g for norovirus GI and norovirus GII, respectively. LOD95 values were between 3.2 × 103 and 3.6 × 105 genome copies/g for HAV and HEV, and between 8.8 × 103 and 4.4 × 104 genome copies/g for norovirus GI and norovirus GII, respectively. The method developed here was successfully validated in various fish products and can be applied for routine diagnostic needs.
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18
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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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19
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Benchmarking Bioinformatic Tools for Amplicon-Based Sequencing of Norovirus. Appl Environ Microbiol 2023; 89:e0152222. [PMID: 36541780 PMCID: PMC9888279 DOI: 10.1128/aem.01522-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In order to survey noroviruses in our environment, it is essential that both wet-lab and computational methods are fit for purpose. Using a simulated sequencing data set, denoising-based (DADA2, Deblur and USEARCH-UNOISE3) and clustering-based pipelines (VSEARCH and FROGS) were compared with respect to their ability to represent composition and sequence information. Open source classifiers (Ribosomal Database Project [RDP], BLASTn, IDTAXA, QIIME2 naive Bayes, and SINTAX) were trained using three different databases: a custom database, the NoroNet database, and the Human calicivirus database. Each classifier and database combination was compared from the perspective of their classification accuracy. VSEARCH provides a robust option for analyzing viral amplicons based on composition analysis; however, all pipelines could return OTUs with high similarity to the expected sequences. Importantly, pipeline choice could lead to more false positives (DADA2) or underclassification (FROGS), a key aspect when considering pipeline application for source attribution. Classification was more strongly impacted by the classifier than the database, although disagreement increased with norovirus GII.4 capsid variant designation. We recommend the use of the RDP classifier in conjunction with VSEARCH; however, maintenance of the underlying database is essential for optimal use. IMPORTANCE In benchmarking bioinformatic pipelines for analyzing high-throughput sequencing (HTS) data sets, we provide method standardization for bioinformatics broadly and specifically for norovirus in situations for which no officially endorsed methods exist at present. This study provides recommendations for the appropriate analysis and classification of norovirus amplicon HTS data and will be widely applicable during outbreak investigations.
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Hepatitis A: Viral Structure, Classification, Life Cycle, Clinical Symptoms, Diagnosis Error, and Vaccination. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:4263309. [PMID: 36644336 PMCID: PMC9833905 DOI: 10.1155/2023/4263309] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 12/14/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023]
Abstract
Hepatitis A virus (HAV) is one of the well-known viruses that cause hepatitis all around the globe. Although this illness has decreased in developed countries due to extensive immunization, numerous developing and under-developed countries are struggling with this virus. HAV infection can be spread by oral-fecal contact, and there are frequent epidemics through nutrition. Improvements in socioeconomic and sanitary circumstances have caused a shift in the disease's prevalence worldwide. Younger children are usually asymptomatic, but as they become older, the infection symptoms begin to appear. Symptoms range from slight inflammation and jaundice to acute liver failure in older individuals. While an acute infection may be self-limiting, unrecognized persistent infections, and the misapplication of therapeutic methods based on clinical guidelines are linked to a higher incidence of cirrhosis, hepatocellular carcinoma, and mortality. Fortunately, most patients recover within two months of infection, though 10-15% of patients will relapse within the first six months. A virus seldom leads to persistent infection or liver damage. The mainstay of therapy is based on supportive care. All children from 12-23 months, as well as some susceptible populations, should receive routine vaccinations, according to the Centers for Disease Control and Prevention and the American Academy of Pediatrics. Laboratory diagnosis of HAV is based on antigen detection, checking liver enzyme levels, and antibody screening. Furthermore, polymerase chain reaction (PCR) technology has identified HAV in suspected nutrition sources; therefore, this technique is used for preventative measures and food-related laws.
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21
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Yamazaki Y, Thongchankaew-Seo U, Yamazaki W. Very low likelihood that cultivated oysters are a vehicle for SARS-CoV-2: 2021-2022 seasonal survey at supermarkets in Kyoto, Japan. Heliyon 2022; 8:e10864. [PMID: 36217407 PMCID: PMC9535880 DOI: 10.1016/j.heliyon.2022.e10864] [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: 08/24/2022] [Revised: 09/03/2022] [Accepted: 09/28/2022] [Indexed: 11/25/2022] Open
Abstract
The pandemic caused by novel coronavirus disease of 2019 (COVID-19) is a global threat. Wastewater surveillance in Japan and abroad has led to the detection of SARS-CoV-2, causing concern that SARS-CoV-2 in the feces of infected persons may contaminate the aquatic environment. Bivalves such as oysters cultivated in coastal areas are known to filter and concentrate viruses such as norovirus present in seawater in their bodies; however, whether they do so with SARS-CoV-2 is unknown. Therefore, we examined cultivated oysters sold in Japan for the presence of SARS-CoV-2 between October 2021 and April 2022 to clarify the extent of viral contamination and evaluate the risk of food-borne transmission of SARS-CoV-2. Porcine epidemic diarrhea virus (PEDV), known as pig coronavirus, was used to spike midgut-gland samples as a whole process control. The presence of SARS-CoV-2 and PEDV was investigated using a modified polyethylene glycol precipitation method and RT-qPCR. While all samples spiked with the whole process control were positive, no SARS-CoV-2 was detected in any of the 145 raw oyster samples surveyed, despite a marked increase in infections caused by the Omicron variant from January to April 2022 in Japan. Therefore, our results suggest that with well-developed sewage treatment facilities, consumption of oysters cultivated in coastal areas may not be a risk factor for SARS-CoV-2 outbreaks.
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Affiliation(s)
- Yasuko Yamazaki
- Center for Southeast Asian Studies, Kyoto University, 46 Shimoadachicho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Uraiwan Thongchankaew-Seo
- Center for Southeast Asian Studies, Kyoto University, 46 Shimoadachicho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Wataru Yamazaki
- Center for Southeast Asian Studies, Kyoto University, 46 Shimoadachicho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan,Kyoto University School of Public Health, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8303, Japan,Corresponding author.
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22
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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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Norovirus GII.3[P12] Outbreak Associated with the Drinking Water Supply in a Rural Area in Galicia, Spain, 2021. Microbiol Spectr 2022; 10:e0104822. [PMID: 35867474 PMCID: PMC9431064 DOI: 10.1128/spectrum.01048-22] [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] [Indexed: 11/20/2022] Open
Abstract
Noroviruses are likely to be underrecognized in most suspected waterborne outbreaks. Therefore, effective norovirus detection and the early recognition of water as a possible source of infection are important to reduce morbidity as appropriate steps are taken to control the source.
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24
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Abstract
Standardised molecular methods are available for the detection of norovirus from water and specific food items. Detection of norovirus from stool samples also relies on molecular methods, but differences exist between nucleic acid extraction, reverse transcription, and amplification strategies recommended by the ISO 15216-1:2017, and those employed in clinical laboratories. Here, we conduct a direct comparison of two methods for the detection and quantitation of norovirus from a stool sample and from artificially contaminated swabs. We also compare use of linear dsDNA standards as recommended in ISO 15216:2017 against an in vitro-transcribed single-stranded RNA (ssRNA) for estimation of norovirus genome copy number. Our results show that the two methods have comparable sensitivity for the detection of norovirus RNA from a clinical sample or swab. The use of a ssRNA standard revealed that quantitation performed against a linear dsDNA standard consistently underestimated the genome copy numbers by 1.5 to 2 log due to the relative inefficiency of the reverse transcription step. This has important implications for the estimation of the sensitivity of norovirus detection methods, comparability of results across sites, and assessment of viral loads that may be clinically significant or estimated to constitute infectious doses.
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25
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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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26
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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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27
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Monitoring coliphages to reduce waterborne infectious disease transmission in the One Water framework. Int J Hyg Environ Health 2022; 240:113921. [DOI: 10.1016/j.ijheh.2022.113921] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 02/07/2023]
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28
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Wade MJ, Lo Jacomo A, Armenise E, Brown MR, Bunce JT, Cameron GJ, Fang Z, Farkas K, Gilpin DF, Graham DW, Grimsley JMS, Hart A, Hoffmann T, Jackson KJ, Jones DL, Lilley CJ, McGrath JW, McKinley JM, McSparron C, Nejad BF, Morvan M, Quintela-Baluja M, Roberts AMI, Singer AC, Souque C, Speight VL, Sweetapple C, Walker D, Watts G, Weightman A, Kasprzyk-Hordern B. Understanding and managing uncertainty and variability for wastewater monitoring beyond the pandemic: Lessons learned from the United Kingdom national COVID-19 surveillance programmes. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127456. [PMID: 34655869 PMCID: PMC8498793 DOI: 10.1016/j.jhazmat.2021.127456] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/23/2021] [Accepted: 10/05/2021] [Indexed: 05/18/2023]
Abstract
The COVID-19 pandemic has put unprecedented pressure on public health resources around the world. From adversity, opportunities have arisen to measure the state and dynamics of human disease at a scale not seen before. In the United Kingdom, the evidence that wastewater could be used to monitor the SARS-CoV-2 virus prompted the development of National wastewater surveillance programmes. The scale and pace of this work has proven to be unique in monitoring of virus dynamics at a national level, demonstrating the importance of wastewater-based epidemiology (WBE) for public health protection. Beyond COVID-19, it can provide additional value for monitoring and informing on a range of biological and chemical markers of human health. A discussion of measurement uncertainty associated with surveillance of wastewater, focusing on lessons-learned from the UK programmes monitoring COVID-19 is presented, showing that sources of uncertainty impacting measurement quality and interpretation of data for public health decision-making, are varied and complex. While some factors remain poorly understood, we present approaches taken by the UK programmes to manage and mitigate the more tractable sources of uncertainty. This work provides a platform to integrate uncertainty management into WBE activities as part of global One Health initiatives beyond the pandemic.
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Affiliation(s)
- Matthew J Wade
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK.
| | - Anna Lo Jacomo
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Bristol University, Department of Engineering Mathematics, Bristol BS8 1TW, UK
| | - Elena Armenise
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Mathew R Brown
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Joshua T Bunce
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK; Department for Environment, Food and Rural Affairs, Seacole Building, 2 Marsham Street, London SW1P 4DF, UK
| | - Graeme J Cameron
- Scottish Environment Protection Agency, Strathallan House, Stirling FK9 4TZ, UK
| | - Zhou Fang
- Biomathematics and Statistics Scotland, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Kata Farkas
- Bangor University, School of Natural Sciences, Deiniol Road, Bangor LL57 2UW, UK
| | - Deidre F Gilpin
- Queen's University Belfast, School of Pharmacy, Lisburn Road, Belfast BT9 7BL, UK
| | - David W Graham
- Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Jasmine M S Grimsley
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK
| | - Alwyn Hart
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Till Hoffmann
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Imperial College London, Department of Mathematics, London SW7 2AZ, UK
| | - Katherine J Jackson
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - David L Jones
- Bangor University, School of Natural Sciences, Deiniol Road, Bangor LL57 2UW, UK; The University of Western Australia, UWA School of Agriculture and Environment, Perth, WA 6009, Australia
| | - Chris J Lilley
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK
| | - John W McGrath
- Queen's University Belfast, School of Biological Sciences, Chlorine Gardens, Belfast BT9 5DL, UK
| | - Jennifer M McKinley
- Queen's University Belfast, School of Natural and Built Environment, Stranmills Road, Belfast BT9 5AG, UK
| | - Cormac McSparron
- Queen's University Belfast, School of Natural and Built Environment, Stranmills Road, Belfast BT9 5AG, UK
| | - Behnam F Nejad
- Queen's University Belfast, School of Natural and Built Environment, Stranmills Road, Belfast BT9 5AG, UK
| | - Mario Morvan
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; University College London, Department of Physics and Astronomy, Gower Street, London WC1E 6BT, UK
| | - Marcos Quintela-Baluja
- Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Adrian M I Roberts
- Biomathematics and Statistics Scotland, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Andrew C Singer
- UK Centre for Ecology and Hydrology, Benson Lane, Wallingford OX10 8BB, UK
| | - Célia Souque
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; University of Oxford, Department of Zoology, Mansfield Road, Oxford OX1 3SZ, UK
| | - Vanessa L Speight
- University of Sheffield, Department of Civil and Structural Engineering, Mappin Street, Sheffield S1 3JD, UK
| | - Chris Sweetapple
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; University of Exeter, Centre for Water Systems, College of Engineering, Mathematics and Physical Sciences, Exeter EX4 4QF, UK
| | - David Walker
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth DT4 8UB, UK
| | - Glenn Watts
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Andrew Weightman
- Cardiff University, Cardiff School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
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29
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Ezzatpanah H, Gómez-López VM, Koutchma T, Lavafpour F, Moerman F, Mohammadi M, Raheem D. Risks and new challenges in the food chain: Viral contamination and decontamination from a global perspective, guidelines, and cleaning. Compr Rev Food Sci Food Saf 2022; 21:868-903. [PMID: 35142438 DOI: 10.1111/1541-4337.12899] [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: 04/08/2021] [Revised: 11/10/2021] [Accepted: 12/08/2021] [Indexed: 11/27/2022]
Abstract
Even during the continuing world pandemic of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), consumers remain exposed to the risk of getting infected by existing, emerging, or re-emerging foodborne and waterborne viruses. SARS-CoV-2 is different in that it is transmitted directly via the airborne route (droplets and aerosols) or indirect contact (surfaces contaminated with SARS-CoV-2). International food and health organizations and national regulatory bodies have provided guidance to protect individuals active in food premises from potential occupational exposure to SARS-CoV-2, and have recommended chemicals effective in controlling the virus. Additionally, to exclude transmission of foodborne and waterborne viruses, hygiene practices to remove viral contaminants from surfaces are applied in different stages of the food chain (e.g., food plants, food distribution, storage, retail sector, etc.), while new and enhanced measures effective in the control of all types of viruses are under development. This comprehensive review aims to analyze and compare efficacies of existing cleaning practices currently used in the food industry to remove pathogenic viruses from air, nonfood, and food contact surfaces, as well as from food surfaces. In addition, the classification, modes of transmission, and survival of food and waterborne viruses, as well as SARS-CoV-2 will be presented. The international guidelines and national regulations are summarized in terms of virucidal chemical agents and their applications.
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Affiliation(s)
- Hamid Ezzatpanah
- Department of Food Science and Technology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Tatiana Koutchma
- Guelph Research and Development Center, Agriculture and Agri-Food Canada, Guelph, Ontario, Canada
| | | | - Frank Moerman
- Department of Chemistry, Catholic University of Leuven - KU Leuven, Leuven, Belgium
| | | | - Dele Raheem
- Arctic Centre (NIEM), University of Lapland, Rovaniemi, Finland
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30
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Efficient capturing and sensitive detection of hepatitis A virus from solid foods (green onion, strawberry, and mussel) using protamine-coated iron oxide (Fe 3O 4) magnetic nanoparticles and real-time RT-PCR. Food Microbiol 2021; 102:103921. [PMID: 34809947 DOI: 10.1016/j.fm.2021.103921] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 09/11/2021] [Accepted: 09/29/2021] [Indexed: 11/21/2022]
Abstract
Hepatitis A virus (HAV) continues to be a public health concern and has caused large foodborne outbreaks and economic losses worldwide. Rapid detection of HAV in foods can help to confirm the source of outbreaks in a timely manner and prevent more people getting infected. In order to efficiently detect HAV at low levels of contamination in foods, rapid and easy-to-use techniques are required to separate and concentrate viral particles to a small volume. In the current study, HAV particles were eluted from green onion, strawberry, and mussel using glycine buffer (0.05 M glycine, 0.14 M NaCl, 0.2% (v/v) Tween 20, pH 9.0) and suspended viral particles were captured using protamine-coated magnetic nanoparticles (PMNPs). This process caused a selective concentration of the viral particles, which could be followed by quantitative real-time RT-PCR analysis. Results showed that pH, NaCl concentration, and PMNP amount used for the capturing had significant effects on the recovery efficiency of HAV (P < 0.05). The highest recovery rate was obtained at pH 9.0, 0.14 M NaCl, and 50 μL of PMNPs. The optimized PMNP capturing method enabled the rapid capture and concentration of HAV. A sensitive real-time RT-PCR test was developed with detection limits of 8.3 × 100 PFU/15 g, 8.3 × 101 PFU/50 g, and 8.3 × 100 PFU/5 g of HAV in green onion, strawberry, and mussel, respectively. In conclusion, the PMNP method is rapid and convenient in capturing HAV from complex solid food samples and can generate concentrated HAV sample solutions suitable for high-sensitivity real time RT-PCR detection of the virus.
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31
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Yang L, Yi W, Sun F, Xu M, Zeng Z, Bi X, Dong J, Xie Y, Li M. Application of Lab-on-Chip for Detection of Microbial Nucleic Acid in Food and Environment. Front Microbiol 2021; 12:765375. [PMID: 34803990 PMCID: PMC8600318 DOI: 10.3389/fmicb.2021.765375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/08/2021] [Indexed: 12/26/2022] Open
Abstract
Various diseases caused by food-borne or environmental pathogenic microorganisms have been a persistent threat to public health and global economies. It is necessary to regularly detect microorganisms in food and environment to prevent infection of pathogenic microorganisms. However, most traditional detection methods are expensive, time-consuming, and unfeasible in practice in the absence of sophisticated instruments and trained operators. Point-of-care testing (POCT) can be used to detect microorganisms rapidly on site and greatly improve the efficiency of microbial detection. Lab-on-chip (LOC) is an emerging POCT technology with great potential by integrating most of the experimental steps carried out in the laboratory into a single monolithic device. This review will primarily focus on principles and techniques of LOC for detection of microbial nucleic acid in food and environment, including sample preparation, nucleic acid amplification and sample detection.
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Affiliation(s)
- Liu Yang
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Wei Yi
- Department of Gynecology and Obstetrics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Fangfang Sun
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Mengjiao Xu
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Zhan Zeng
- Department of Hepatology Division 2, Peking University Ditan Teaching Hospital, Beijing, China
| | - Xiaoyue Bi
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jianping Dong
- Department of Infectious Diseases, Haidian Hospital, Beijing Haidian Section of Peking University Third Hospital, Beijing, China
| | - Yao Xie
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Hepatology Division 2, Peking University Ditan Teaching Hospital, Beijing, China
| | - Minghui Li
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Hepatology Division 2, Peking University Ditan Teaching Hospital, Beijing, China
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32
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Migueres M, Lhomme S, Izopet J. Hepatitis A: Epidemiology, High-Risk Groups, Prevention and Research on Antiviral Treatment. Viruses 2021; 13:1900. [PMID: 34696330 PMCID: PMC8540458 DOI: 10.3390/v13101900] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 12/17/2022] Open
Abstract
The hepatitis A virus (HAV) is a leading cause of acute viral hepatitis worldwide. It is transmitted mainly by direct contact with patients who have been infected or by ingesting contaminated water or food. The virus is endemic in low-income countries where sanitary and sociodemographic conditions are poor. Paradoxically, improving sanitary conditions in these countries, which reduces the incidence of HAV infections, can lead to more severe disease in susceptible adults. The populations of developed countries are highly susceptible to HAV, and large outbreaks can occur when the virus is spread by globalization and by increased travel and movement of foodstuffs. Most of these outbreaks occur among high-risk groups: travellers, men who have sex with men, people who use substances, and people facing homelessness. Hepatitis A infections can be prevented by vaccination; safe and effective vaccines have been available for decades. Several countries have successfully introduced universal mass vaccination for children, but high-risk groups in high-income countries remain insufficiently protected. The development of HAV antivirals may be important to control HAV outbreaks in developed countries where a universal vaccination programme is not recommended.
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Affiliation(s)
- Marion Migueres
- Virology Laboratory, Hôpital Purpan, CHU Toulouse, 31300 Toulouse, France; (S.L.); (J.I.)
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, 31300 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Sébastien Lhomme
- Virology Laboratory, Hôpital Purpan, CHU Toulouse, 31300 Toulouse, France; (S.L.); (J.I.)
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, 31300 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Jacques Izopet
- Virology Laboratory, Hôpital Purpan, CHU Toulouse, 31300 Toulouse, France; (S.L.); (J.I.)
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, 31300 Toulouse, France
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
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33
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Sommer J, Bobal M, Bromberger B, Mester PJ, Rossmanith P. A new long-term sampling approach to viruses on surfaces. Sci Rep 2021; 11:17545. [PMID: 34475462 PMCID: PMC8413268 DOI: 10.1038/s41598-021-96873-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 08/04/2021] [Indexed: 11/10/2022] Open
Abstract
The importance of virus disease outbreaks and its prevention is of growing public concern but our understanding of virus transmission routes is limited by adequate sampling strategies. While conventional swabbing methods provide merely a microbial snapshot, an ideal sampling strategy would allow reliable collection of viral genomic data over longer time periods. This study has evaluated a new, paper-based sticker approach for collection of reliable viral genomic data over longer time periods up to 14 days and after implementation of different hygiene measures. In contrast to swabbing methods, which sample viral load present on a surface at a given time, the paper-based stickers are attached to the surface area of interest and collect viruses that would have otherwise been transferred onto that surface. The major advantage of one-side adhesive stickers is that they are permanently attachable to a variety of surfaces. Initial results demonstrate that stickers permit stable recovery characteristics, even at low virus titers. Stickers also allow reliable virus detection after implementation of routine hygiene measures and over longer periods up to 14 days. Overall, results for this new sticker approach for virus genomic data collection are encouraging, but further studies are required to confirm anticipated benefits over a range of virus types.
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Affiliation(s)
- Julia Sommer
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health Department for Farm Animals and Public Health in Veterinary Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria.
| | - Martin Bobal
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health Department for Farm Animals and Public Health in Veterinary Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
- Vetfarm and Clinical Unit of Herd Health Management for Ruminants, Department for Farm Animals and Public Health in Veterinary Medicine, University of Veterinary Medicine, Kremesberg 14, 2563, Pottenstein, Austria
| | - Birgit Bromberger
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health Department for Farm Animals and Public Health in Veterinary Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Patrick-Julian Mester
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health Department for Farm Animals and Public Health in Veterinary Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Peter Rossmanith
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health Department for Farm Animals and Public Health in Veterinary Medicine, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, USA
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34
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Amoroso MG, Di Concilio D, Langellotti AL, Martello A, Cioffi B, Suffredini E, Cozzi L, Russo V, Mauriello G, Di Pasquale S, Galiero G, Fusco G. Quantitative Real-Time PCR and Digital PCR to Evaluate Residual Quantity of HAV in Experimentally Depurated Mussels. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:329-336. [PMID: 33730340 DOI: 10.1007/s12560-021-09470-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/27/2021] [Indexed: 06/12/2023]
Abstract
Kinetics of hepatitis A virus (HAV) accumulation and depuration from mussels (Mytilus galloprovincialis) was studied in an experimental depuration system. Different parameters likely to influence the rate of virus accumulation and elimination were evaluated. Analyses were carried out by both real-time RT-qPCR and digital PCR. Results demonstrated that the animals start to concentrate the virus already after one hour and reach the maximum level of contamination in 6 h of experiment. With respect to depuration, HAV showed a rapid reduction of the concentration (89%) during the first 24-48 h of experiment and a very slow virus decrement in the following days with a 1% residual RNA at the ninth day of depuration. When process parameters likely to increase the depuration rate (presence of ozone, microalgal feeding, presence of lactic bacteria, pre-treatment with digestive enzymes) were tested, no significant differences in the kinetics were observed. Only treatment with pancreatin seemed to positively affect depuration in the first two days of the experiment.
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Affiliation(s)
- Maria Grazia Amoroso
- Unit of Virology, Department of Animal Health, Zooprofilactic and Experimental Institute of Southern Italy, Via Salute n. 2, Portici (Naples), Italy.
| | - Denise Di Concilio
- Unit of Virology, Department of Animal Health, Zooprofilactic and Experimental Institute of Southern Italy, Via Salute n. 2, Portici (Naples), Italy
| | - Antonio Luca Langellotti
- CAISIAL-Aquaculture division, University of Naples Federico II, Via Università n.133, Portici (Naples), Italy.
| | - Anna Martello
- CAISIAL-Aquaculture division, University of Naples Federico II, Via Università n.133, Portici (Naples), Italy
| | - Barbara Cioffi
- Unit of Virology, Department of Animal Health, Zooprofilactic and Experimental Institute of Southern Italy, Via Salute n. 2, Portici (Naples), Italy
| | - Elisabetta Suffredini
- Dipartimento Di Sicurezza Alimentare, Istituto Superiore Di Sanità, Nutrizione E Sanità Pubblica Veterinaria, Rep. Sicurezza Alimentare E Malattie Trasmesse Dagli Alimenti, Viale Regina Elena n. 299, Rome, Italy
| | - Loredana Cozzi
- Dipartimento Di Sicurezza Alimentare, Istituto Superiore Di Sanità, Nutrizione E Sanità Pubblica Veterinaria, Rep. Sicurezza Alimentare E Malattie Trasmesse Dagli Alimenti, Viale Regina Elena n. 299, Rome, Italy
| | - Valeria Russo
- Department of Veterinary Medicine, University of Naples Federico II, Via Delpino n. 2, Naples, Italy
| | - Gianluigi Mauriello
- Department of Agriculture, University of Naples Federico II, Via Università n.133, Portici, Naples, Italy
| | - Simona Di Pasquale
- Dipartimento Di Sicurezza Alimentare, Istituto Superiore Di Sanità, Nutrizione E Sanità Pubblica Veterinaria, Rep. Sicurezza Alimentare E Malattie Trasmesse Dagli Alimenti, Viale Regina Elena n. 299, Rome, Italy
| | - Giorgio Galiero
- Unit of Virology, Department of Animal Health, Zooprofilactic and Experimental Institute of Southern Italy, Via Salute n. 2, Portici (Naples), Italy
| | - Giovanna Fusco
- Unit of Virology, Department of Animal Health, Zooprofilactic and Experimental Institute of Southern Italy, Via Salute n. 2, Portici (Naples), Italy
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Development of an RNA Extraction Protocol for Norovirus from Raw Oysters and Detection by qRT-PCR and Droplet-Digital RT-PCR. Foods 2021; 10:foods10081804. [PMID: 34441580 PMCID: PMC8393641 DOI: 10.3390/foods10081804] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 12/17/2022] Open
Abstract
Foodborne viruses such as norovirus and hepatitis A virus cause frequent outbreaks associated with the consumption of raw or undercooked oysters. Viral particles are bioaccumulated in the oyster's digestive glands, making RNA extraction and RT-PCR detection difficult due to the complex nature of the food matrix and the presence of RT-PCR inhibitors. Herein, we have developed a viral RNA extraction protocol from raw oysters using murine norovirus (MNV) as a surrogate for human noroviruses. The method combines lysis in Tri-Reagent reagent, followed by RNA extraction using Direct-Zol purification columns and lithium chloride precipitation. Viral load quantification was performed by both qRT-PCR and droplet-digital RT-PCR. We have demonstrated that this method can efficiently remove RT-PCR inhibitors, and is sensitive enough to reliably detect viral contamination at 25 PFU/0.2 g. We have also compared the efficiency of this method with the ISO 15216-1:2017 method and Method E developed by Quang and colleagues, and observed significantly higher efficiency compared with the ISO 15216-1 method and comparable efficiency with Method E, with less steps, and shorter hands-on time.
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36
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Leifels M, Cheng D, Sozzi E, Shoults DC, Wuertz S, Mongkolsuk S, Sirikanchana K. Capsid integrity quantitative PCR to determine virus infectivity in environmental and food applications - A systematic review. WATER RESEARCH X 2021; 11:100080. [PMID: 33490943 DOI: 10.1101/2020.05.08.20095364] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 11/08/2020] [Accepted: 12/06/2020] [Indexed: 05/19/2023]
Abstract
Capsid integrity quantitative PCR (qPCR), a molecular detection method for infectious viruses combining azo dye pretreatment with qPCR, has been widely used in recent years; however, variations in pretreatment conditions for various virus types can limit the efficacy of specific protocols. By identifying and critically synthesizing forty-one recent peer-reviewed studies employing capsid integrity qPCR for viruses in the last decade (2009-2019) in the fields of food safety and environmental virology, we aimed to establish recommendations for the detection of infectious viruses. Intercalating dyes are effective measures of viability in PCR assays provided the viral capsid is damaged; viruses that have been inactivated by other causes, such as loss of attachment or genomic damage, are less well detected using this approach. Although optimizing specific protocols for each virus is recommended, we identify a framework for general assay conditions. These include concentrations of ethidium monoazide, propidium monoazide or its derivates between 10 and 200 μM; incubation on ice or at room temperature (20 - 25 °C) for 5-120 min; and dye activation using LED or high light (500-800 Watts) exposure for periods ranging from 5 to 20 min. These simple steps can benefit the investigation of infectious virus transmission in routine (water) monitoring settings and during viral outbreaks such as the current COVID-19 pandemic or endemic diseases like dengue fever.
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Affiliation(s)
- Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Dan Cheng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Emanuele Sozzi
- Gilling's School of Global Public Health, Department of Environmental Science and Engineering, University of North Carolina at Chapel Hill, NC, USA
| | - David C Shoults
- Civil and Resource Engineering, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- School of Civil and Environmental Engineering, NTU, Singapore
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand
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37
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Leifels M, Cheng D, Sozzi E, Shoults DC, Wuertz S, Mongkolsuk S, Sirikanchana K. Capsid integrity quantitative PCR to determine virus infectivity in environmental and food applications - A systematic review. WATER RESEARCH X 2021; 11:100080. [PMID: 33490943 PMCID: PMC7811166 DOI: 10.1016/j.wroa.2020.100080] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 11/08/2020] [Accepted: 12/06/2020] [Indexed: 05/19/2023]
Abstract
Capsid integrity quantitative PCR (qPCR), a molecular detection method for infectious viruses combining azo dye pretreatment with qPCR, has been widely used in recent years; however, variations in pretreatment conditions for various virus types can limit the efficacy of specific protocols. By identifying and critically synthesizing forty-one recent peer-reviewed studies employing capsid integrity qPCR for viruses in the last decade (2009-2019) in the fields of food safety and environmental virology, we aimed to establish recommendations for the detection of infectious viruses. Intercalating dyes are effective measures of viability in PCR assays provided the viral capsid is damaged; viruses that have been inactivated by other causes, such as loss of attachment or genomic damage, are less well detected using this approach. Although optimizing specific protocols for each virus is recommended, we identify a framework for general assay conditions. These include concentrations of ethidium monoazide, propidium monoazide or its derivates between 10 and 200 μM; incubation on ice or at room temperature (20 - 25 °C) for 5-120 min; and dye activation using LED or high light (500-800 Watts) exposure for periods ranging from 5 to 20 min. These simple steps can benefit the investigation of infectious virus transmission in routine (water) monitoring settings and during viral outbreaks such as the current COVID-19 pandemic or endemic diseases like dengue fever.
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Affiliation(s)
- Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Dan Cheng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Emanuele Sozzi
- Gilling's School of Global Public Health, Department of Environmental Science and Engineering, University of North Carolina at Chapel Hill, NC, USA
| | - David C. Shoults
- Civil and Resource Engineering, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- School of Civil and Environmental Engineering, NTU, Singapore
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand
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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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Bertrand I, Challant J, Jeulin H, Hartard C, Mathieu L, Lopez S, Schvoerer E, Courtois S, Gantzer C. Epidemiological surveillance of SARS-CoV-2 by genome quantification in wastewater applied to a city in the northeast of France: Comparison of ultrafiltration- and protein precipitation-based methods. Int J Hyg Environ Health 2021; 233:113692. [PMID: 33592569 PMCID: PMC7847400 DOI: 10.1016/j.ijheh.2021.113692] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 02/08/2023]
Abstract
The aim of the present study was to develop a simple, sensitive, and specific approach to quantifying the SARS-CoV-2 genome in wastewater and to evaluate this approach as a means of epidemiological surveillance. Twelve wastewater samples were collected from a metropolitan area in north-eastern France during April and May 2020. In addition to the quantification of the SARS-CoV-2 genome, F-specific RNA phages of genogroup II (FRNAPH GGII), naturally present in wastewater, were used as an internal process control for the viral concentration and processing of RT-PCR inhibitors. A concentration method was required to allow the quantification of the SARS-CoV-2 genome over the longest possible period. A procedure combining ultrafiltration, phenol-chloroform-isoamyl alcohol purification, and the additional purification of the RNA extracts was chosen for the quantification of the SARS-CoV-2 genome in 100-mL wastewater samples. At the same time, the COVID-19 outbreak was evaluated through patients from the neighbouring University Hospital of Nancy, France. A regular decrease in the concentration of the SARS-CoV-2 genome from ~104 gc/L to ~102 gc/L of wastewater was observed over the eight weeks of the study, during which the population was placed under lockdown. The SARS-CoV-2 genome was even undetectable during one week in the second half of May and present but non-quantifiable in the last sample (28 May). A concordant circulation in the human community was highlighted by virological diagnosis using respiratory samples, which showed a decrease in the number of COVID-19 cases from 677 to 52 per week over the same period. The environmental surveillance of COVID-19 using a reliable viral quantification procedure to test wastewater is a key approach. The real-time detection of viral genomes can allow us to predict and monitor the circulation of SARS-CoV-2 in clinical settings and survey the entire urban human population.
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Affiliation(s)
| | - Julie Challant
- Université de Lorraine, CNRS, LCPME, F-54000, Nancy, France
| | - Hélène Jeulin
- Université de Lorraine, CNRS, LCPME, F-54000, Nancy, France; Laboratoire de Virologie, CHRU de Nancy Brabois, F-54500, Vandœuvre-lès-Nancy, France
| | - Cédric Hartard
- Université de Lorraine, CNRS, LCPME, F-54000, Nancy, France; Laboratoire de Virologie, CHRU de Nancy Brabois, F-54500, Vandœuvre-lès-Nancy, France
| | - Laurence Mathieu
- Université de Lorraine, CNRS, LCPME, F-54000, Nancy, France; EPHE, PSL, UMR CNRS 7564, LCPME, F-54000, Nancy, France
| | - Séverine Lopez
- Université de Lorraine, CNRS, LCPME, F-54000, Nancy, France
| | - Evelyne Schvoerer
- Université de Lorraine, CNRS, LCPME, F-54000, Nancy, France; Laboratoire de Virologie, CHRU de Nancy Brabois, F-54500, Vandœuvre-lès-Nancy, France
| | - Sophie Courtois
- SUEZ, CIRSEE, 38 rue du Président Wilson, F-78230, Le Pecq, France
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40
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Lekshmi M, Kumar SH, Rajendran KV, Nayak BB. Development of a reverse transcription (RT) polymerase chain reaction (PCR) method for the detection of human norovirus in bivalve molluscs. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2021; 83:1103-1107. [PMID: 33724939 DOI: 10.2166/wst.2021.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Noroviruses are significant seafood-borne pathogens, commonly associated with the consumption of filter feeding bivalve molluscs. Here, we report the development of a reverse transcription polymerase chain reaction (RT-PCR) method using primers based on the RNA-dependent RNA polymerase gene of norovirus genogroup II (NoV GII). Samples of bivalves were processed for the concentration of virus and extraction of RNA, followed by reverse transcription PCR. A total of 50 molluscan shellfish samples were analyzed, of which 16 samples yielded positive amplifications of norovirus nucleic acid. The PCR method described here, involving a single set of primers, is useful for rapid screening of shellfish for NoV GII.
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Affiliation(s)
- Manjusha Lekshmi
- QC Laboratory, Post Harvest Technology, ICAR- Central Institute of Fisheries Education (CIFE), Mumbai, 400061, India E-mail:
| | - Sanath H Kumar
- QC Laboratory, Post Harvest Technology, ICAR- Central Institute of Fisheries Education (CIFE), Mumbai, 400061, India E-mail:
| | - Kooloth Valappil Rajendran
- Aquatic Environment & Health Management Division, ICAR- Central Institute of Fisheries Education (CIFE), Mumbai, 400061, India
| | - Binaya Bhusan Nayak
- QC Laboratory, Post Harvest Technology, ICAR- Central Institute of Fisheries Education (CIFE), Mumbai, 400061, India E-mail:
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41
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Imamura S, Shibata S, Kishine M, Kushida A, Uema M, Noda M, Zou B, Kawasaki C, Miura T, Fukunaga Y. Interlaboratory Evaluation of a Method for Quantification of Norovirus RNA as an Alternative Use for ISO 15216-1:2017 to Conduct Japan Baseline Survey of Oysters. Foodborne Pathog Dis 2021; 18:331-336. [PMID: 33600236 DOI: 10.1089/fpd.2020.2874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this study, we aimed to investigate the standard method used for quantification of norovirus in oysters in Japan for the provisional adaptation of the method as an alternative to ISO 15216-1:2017, to conduct a Japan baseline survey of norovirus in oysters. For this purpose, the method provided by the Japan Committee for Standardization of Virus Detection in Food was subjected to an interlaboratory study to determine the performance characteristics of the standard method used in Japan. As a result, the theoretical limit of quantification for norovirus GI and GII in oysters by the standard method used in Japan was expected to be 1.92 and 1.85 log10 copies/g, respectively. The repeatability standard deviations (Sr) were 0.26 and 0.30 log10 copies/g for GI and GII, respectively, and the reproducibility standard deviations (SR) were 0.47 and 0.44 log10 copies/g for GI and GII, respectively. Through the interlaboratory study, we specified several critical points to obtain scientifically reliable results by using the standard method used in Japan. Especially, necessity for application of using process control virus was the most crucial point that needed to be improved. In addition, there are many participating laboratories that could not handle dilution of standard and quantify or detect the viruses in the test samples. To ensure scientifically reliable test result, capacity building of laboratories and implementation of proficiency testing should be considered for future tasks in combination with an application of process control materials in the method. On the assumption that the problems revealed in this study will be solved, the standard method used in Japan would be suitable for use in Japan baseline survey of norovirus in oysters, which will contribute to the international action against norovirus in oysters, led by the EU.
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Affiliation(s)
- Saiki Imamura
- Agriculture, Forestry and Fisheries Research Council Secretariat, Ministry of Agriculture Forestry and Fisheries, Chiyoda-ku, Japan.,Food Safety and Consumer Affairs Bureau, Ministry of Agriculture Forestry and Fisheries, Chiyoda-ku, Japan
| | - Shiori Shibata
- Food Safety and Consumer Affairs Bureau, Ministry of Agriculture Forestry and Fisheries, Chiyoda-ku, Japan
| | - Masahiro Kishine
- Food Safety and Consumer Affairs Bureau, Ministry of Agriculture Forestry and Fisheries, Chiyoda-ku, Japan
| | - Aya Kushida
- Food Safety and Consumer Affairs Bureau, Ministry of Agriculture Forestry and Fisheries, Chiyoda-ku, Japan
| | - Masashi Uema
- National Institute of Health Sciences, Kawasaki City, Japan
| | - Mamoru Noda
- National Institute of Health Sciences, Kawasaki City, Japan
| | - Bizhen Zou
- Incorporated Foundation Tokyo Kenbikyo-in, Chuo-ku, Japan
| | | | - Takayuki Miura
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Yoko Fukunaga
- Food Safety and Consumer Affairs Bureau, Ministry of Agriculture Forestry and Fisheries, Chiyoda-ku, Japan
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42
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Fuentes C, Pérez-Rodríguez FJ, Sabrià A, Beguiristain N, Pintó RM, Guix S, Bosch A. Inactivation of Hepatitis A Virus and Human Norovirus in Clams Subjected to Heat Treatment. Front Microbiol 2021; 11:578328. [PMID: 33510715 PMCID: PMC7835484 DOI: 10.3389/fmicb.2020.578328] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/17/2020] [Indexed: 02/01/2023] Open
Abstract
Bivalve mollusk contamination by enteric viruses, especially human noroviruses (HuNoV) and hepatitis A virus (HAV), is a problem with health and economic implications. The aim of the study was the evaluation of the effect of heat treatment in clams (Tawera gayi) experimentally contaminated with HuNoV using a PMA-viability RTqPCR assay to minimize measurement of non-infectious viruses, and used HAV as a model to estimate infectivity loss. Spiked clams were immersed in water at 90°C to ensure that internal meat temperature was maintained above 90°C for at least 5 min. The treatment resulted in >3.89 ± 0.24 log10 TCID50/g reduction of infectious HAV, confirming inactivation. For HuNoV, RTqPCR assays showed log10 reductions of 2.96 ± 0.79 and 2.56 ± 0.56, for GI and GII, respectively, and the use of PMA resulted in an additional log10 reduction for GII, providing a better correlation with risk reduction. In the absence of a cell culture system which could be used to determine HuNoV infectivity reduction, a performance criteria based on PMA-RTqPCR log reduction could be used to evaluate food product safety. According to data from this study, heat treatments of clams which cause reductions >3.5 log10 for GII as measured by PMA-RTqPCR assay may be regarded as an acceptable inactivation treatment, and could be set as a performance criterion to test the effectiveness of other time-temperature inactivation processes.
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Affiliation(s)
- Cristina Fuentes
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA⋅UB), University of Barcelona, Barcelona, Spain
| | - Francisco J. Pérez-Rodríguez
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA⋅UB), University of Barcelona, Barcelona, Spain
| | - Aurora Sabrià
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA⋅UB), University of Barcelona, Barcelona, Spain
| | - Nerea Beguiristain
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA⋅UB), University of Barcelona, Barcelona, Spain
| | - Rosa M. Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA⋅UB), University of Barcelona, Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA⋅UB), University of Barcelona, Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA⋅UB), University of Barcelona, Barcelona, Spain
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43
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D'Aoust PM, Mercier E, Montpetit D, Jia JJ, Alexandrov I, Neault N, Baig AT, Mayne J, Zhang X, Alain T, Langlois MA, Servos MR, MacKenzie M, Figeys D, MacKenzie AE, Graber TE, Delatolla R. Quantitative analysis of SARS-CoV-2 RNA from wastewater solids in communities with low COVID-19 incidence and prevalence. WATER RESEARCH 2021; 188:116560. [PMID: 33137526 PMCID: PMC7583624 DOI: 10.1016/j.watres.2020.116560] [Citation(s) in RCA: 239] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 05/02/2023]
Abstract
In the absence of an effective vaccine to prevent COVID-19 it is important to be able to track community infections to inform public health interventions aimed at reducing the spread and therefore reduce pressures on health-care, improve health outcomes and reduce economic uncertainty. Wastewater surveillance has rapidly emerged as a potential tool to effectively monitor community infections through measuring trends of RNA signal in wastewater systems. In this study SARS-CoV-2 viral RNA N1 and N2 gene regions are quantified in solids collected from influent post grit solids (PGS) and primary clarified sludge (PCS) in two water resource recovery facilities (WRRF) serving Canada's national capital region, i.e., the City of Ottawa, ON (pop. ≈ 1.1M) and the City of Gatineau, QC (pop. ≈ 280K). PCS samples show signal inhibition using RT-ddPCR compared to RT-qPCR, with PGS samples showing similar quantifiable concentrations of RNA using both assays. RT-qPCR shows higher frequency of detection of N1 and N2 gene regions in PCS (92.7, 90.6%, n = 6) as compared to PGS samples (79.2, 82.3%, n = 5). Sampling of PCS may therefore be an effective approach for SARS-CoV-2 viral quantification, especially during periods of declining and low COVID-19 incidence in the community. The pepper mild mottle virus (PMMoV) is determined to have a less variable RNA signal in PCS over a three month period for two WRRFs, regardless of environmental conditions, compared to Bacteroides 16S rRNA or human 18S rRNA, making PMMoV a potentially useful biomarker for normalization of SARS-CoV-2 signal. PMMoV-normalized PCS RNA signal from WRRFs of two cities correlated with the regional public health epidemiological metrics, identifying PCS normalized to a fecal indicator (PMMoV) as a potentially effective tool for monitoring trends during decreasing and low-incidence of infection of SARS-Cov-2 in communities.
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Affiliation(s)
- Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Elisabeth Mercier
- Department of Chemical Engineering, University of Ottawa, K1N 6N5, Canada
| | - Danika Montpetit
- Department of Chemical Engineering, University of Ottawa, K1N 6N5, Canada
| | - Jian-Jun Jia
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Ilya Alexandrov
- ActivSignal LLC., 27 Strathmore Rd Natick, MA 01760, United States
| | - Nafisa Neault
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Aiman Tariq Baig
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Janice Mayne
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Xu Zhang
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Marc-André Langlois
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo N2L 3G1, Canada
| | | | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada; Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada; Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
| | - Alex E MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada.
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44
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D'Aoust PM, Mercier E, Montpetit D, Jia JJ, Alexandrov I, Neault N, Baig AT, Mayne J, Zhang X, Alain T, Langlois MA, Servos MR, MacKenzie M, Figeys D, MacKenzie AE, Graber TE, Delatolla R. Quantitative analysis of SARS-CoV-2 RNA from wastewater solids in communities with low COVID-19 incidence and prevalence. WATER RESEARCH 2021. [PMID: 33137526 DOI: 10.1101/2020.08.11.20173062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In the absence of an effective vaccine to prevent COVID-19 it is important to be able to track community infections to inform public health interventions aimed at reducing the spread and therefore reduce pressures on health-care, improve health outcomes and reduce economic uncertainty. Wastewater surveillance has rapidly emerged as a potential tool to effectively monitor community infections through measuring trends of RNA signal in wastewater systems. In this study SARS-CoV-2 viral RNA N1 and N2 gene regions are quantified in solids collected from influent post grit solids (PGS) and primary clarified sludge (PCS) in two water resource recovery facilities (WRRF) serving Canada's national capital region, i.e., the City of Ottawa, ON (pop. ≈ 1.1M) and the City of Gatineau, QC (pop. ≈ 280K). PCS samples show signal inhibition using RT-ddPCR compared to RT-qPCR, with PGS samples showing similar quantifiable concentrations of RNA using both assays. RT-qPCR shows higher frequency of detection of N1 and N2 gene regions in PCS (92.7, 90.6%, n = 6) as compared to PGS samples (79.2, 82.3%, n = 5). Sampling of PCS may therefore be an effective approach for SARS-CoV-2 viral quantification, especially during periods of declining and low COVID-19 incidence in the community. The pepper mild mottle virus (PMMoV) is determined to have a less variable RNA signal in PCS over a three month period for two WRRFs, regardless of environmental conditions, compared to Bacteroides 16S rRNA or human 18S rRNA, making PMMoV a potentially useful biomarker for normalization of SARS-CoV-2 signal. PMMoV-normalized PCS RNA signal from WRRFs of two cities correlated with the regional public health epidemiological metrics, identifying PCS normalized to a fecal indicator (PMMoV) as a potentially effective tool for monitoring trends during decreasing and low-incidence of infection of SARS-Cov-2 in communities.
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Affiliation(s)
- Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Elisabeth Mercier
- Department of Chemical Engineering, University of Ottawa, K1N 6N5, Canada
| | - Danika Montpetit
- Department of Chemical Engineering, University of Ottawa, K1N 6N5, Canada
| | - Jian-Jun Jia
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Ilya Alexandrov
- ActivSignal LLC., 27 Strathmore Rd Natick, MA 01760, United States
| | - Nafisa Neault
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Aiman Tariq Baig
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Janice Mayne
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Xu Zhang
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Marc-André Langlois
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Mark R Servos
- Department of Biology, University of Waterloo, Waterloo N2L 3G1, Canada
| | | | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada; Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada; Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
| | - Alex E MacKenzie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa K1N 6N5, Canada.
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Hunt K, Doré B, Keaveney S, Rupnik A, Butler F. Estimating the distribution of norovirus in individual oysters. Int J Food Microbiol 2020; 333:108785. [DOI: 10.1016/j.ijfoodmicro.2020.108785] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/18/2022]
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Detection of norovirus, hepatitis A and hepatitis E viruses in multicomponent foodstuffs. Int J Food Microbiol 2020; 337:108931. [PMID: 33188986 DOI: 10.1016/j.ijfoodmicro.2020.108931] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/16/2020] [Accepted: 10/20/2020] [Indexed: 11/21/2022]
Abstract
Among the enteric viruses implicated in foodborne outbreaks, the human norovirus and hepatitis viruses A and E (HAV and HEV) represent a serious public health concern. International standard ISO 15216 proposes methods for detecting HAV and norovirus (genogroups I and II) RNA from soft fruit, leaf, stem and bulb vegetables, bottled water or food surfaces. These methods had not previously been validated for detecting the targeted viruses in other foodstuffs such as multicomponent foods, nor for detecting other viruses in foodstuffs. The aim of this study was to characterise a method derived from the vegetable method described in ISO 15216 to detect HAV, HEV and norovirus in artificially-contaminated multicomponent foodstuffs according to the recent international standard ISO 16140-4. Results showed that the mean recovery rates for all settings did not differ according to the operator. The mean extraction yields ranged from 0.35% to 40.44% for HAV, 5.19% to 100% for HEV, 0.10% to 40.61% for norovirus GI and 0.88% to 69.16% for norovirus GII. The LOD95 was 102 genome copies/g for HAV, HEV and norovirus GII and 103 genome copies/g for norovirus GI. The LOQ was 2.90 × 104, 1.40 × 103, 1.60 × 104 and 1.30 × 104 genome copies/g for HAV, HEV, norovirus GI and norovirus GII respectively. The MNV-1 process control was detected in 120 out of 128 RNA extracts analysed and was recovered with an efficiency of between 3.83% and 50.22%. The mean inhibition rates of quantitative real-time RT-PCR reaction ranged from 3.25% to 28.70% and varied significantly with the type of food matrix. The described method could be used to detect viruses in composite food products for routine diagnosis needs.
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Trojnar E, Contzen M, Moor D, Carl A, Burkhardt S, Kilwinski J, Berghof-Jäger K, Mormann S, Schotte U, Kontek A, Althof N, Mäde D, Johne R. Interlaboratory Validation of a Detection Method for Hepatitis E Virus RNA in Pig Liver. Microorganisms 2020; 8:microorganisms8101460. [PMID: 32977593 PMCID: PMC7598171 DOI: 10.3390/microorganisms8101460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/16/2020] [Accepted: 09/21/2020] [Indexed: 01/24/2023] Open
Abstract
Background: In the last years, the number of notified hepatitis E cases in humans has continuously increased in Europe. Foodborne infection with the zoonotic hepatitis E virus (HEV) genotype 3 is considered the major cause of this disease. Undercooked liver and raw sausages containing the liver of pigs and wild boar are at high risk of containing HEV. However, so far, no standardized method for the detection of HEV-RNA in pig liver is available. Methods: An international collaborative study on method reproducibility involving 11 laboratories was performed for an HEV-RNA detection method, which consists of steps of sample homogenization, RNA extraction and real-time RT-PCR detection, including a process control. Naturally contaminated pork liver samples containing two different amounts of HEV and a HEV-negative pork liver sample were tested by all laboratories using the method. Results: Valid results were retrieved from 10 laboratories. A specificity of 100% and a sensitivity of 79% were calculated for the method. False negative results were only retrieved from the sample containing very low HEV amounts near the detection limit. Conclusions: The results show that the method is highly specific, sufficiently sensitive and robust for use in different laboratories. The method can, therefore, be applied to routine food control as well as in monitoring studies.
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Affiliation(s)
- Eva Trojnar
- German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (E.T.); (N.A.)
| | - Matthias Contzen
- Chemisches und Veterinäruntersuchungsamt Stuttgart, 70736 Fellbach, Germany;
| | - Dominik Moor
- Bundesamt für Lebensmittelsicherheit und Veterinärwesen, 3003 Bern, Switzerland;
| | - Anja Carl
- Bayrisches Landesamt für Gesundheit und Lebensmittelsicherheit, 91058 Erlangen, Germany;
| | | | - Jochen Kilwinski
- Chemisches und Veterinäruntersuchungsamt Westfalen, 59821 Arnsberg, Germany; (J.K.); (S.M.)
| | | | - Sascha Mormann
- Chemisches und Veterinäruntersuchungsamt Westfalen, 59821 Arnsberg, Germany; (J.K.); (S.M.)
| | - Ulrich Schotte
- Zentrales Institut des Sanitätsdienstes der Bundeswehr Kiel, 24119 Kronshagen, Germany;
| | - Anne Kontek
- Niedersächsisches Landesamt für Verbraucherschutz und Lebensmittelsicherheit, 26133 Oldenburg, Germany;
| | - Nadine Althof
- German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (E.T.); (N.A.)
| | - Dietrich Mäde
- Landesamt für Verbraucherschutz Sachsen-Anhalt, 06112 Halle (Saale), Germany;
| | - Reimar Johne
- German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (E.T.); (N.A.)
- Correspondence:
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48
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Yu C, Hida K, Papafragkou E, Kulka M. Evaluation of U.S. Food and Drug Administration Enteric Viruses Microarray for Detection of Hepatitis A Virus and Norovirus in Inoculated Tomatoes, Green Onions, and Celery. J Food Prot 2020; 83:1576-1583. [PMID: 32379890 DOI: 10.4315/jfp-19-574] [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: 11/27/2019] [Accepted: 05/03/2020] [Indexed: 11/11/2022]
Abstract
ABSTRACT Foodborne viral contamination of fresh produce has been associated with numerous outbreaks. Detection of such contaminated foods is important in protecting public health. Here, we demonstrate for the first time the capability of the U.S. Food and Drug Administration Enteric Viruses tiling microarray (FDA-EVIR) to perform rapid molecular identification of hepatitis A virus (HAV) and human norovirus extracted from artificially inoculated fresh produce. Two published viral extraction strategies, total RNA extraction or virus particle isolation, were used to prepare the viral targets. The total RNA extraction method was used on material eluted from tomatoes, using an alkaline Tris-glycine-beef extract (TGBE) buffer. Optimization procedures including DNase treatment and poly(A)-RNA enrichment were adopted to improve microarray sensitivity. For green onions or celery, material was eluted using either glycine buffer or TGBE buffer supplemented with pectinase, respectively, and then virus particles were concentrated by ultracentrifugation. We also assessed the amount of viral RNA extracted from celery using three commercially available kits and how well that RNA performed on FDA-EVIR. Our results confirm that FDA-EVIR can identify common enteric viruses isolated from fresh produce when present as either a single or mixed species of viruses. Using total RNA extraction from tomatoes yielded a limit of detection of 1.0 × 105 genome equivalents (ge) of HAV per array input. The limit of detection for viral RNA obtained using ultracentrifugation was 1.2 × 105 ge of HAV from green onions and 1.0 × 103 ge of norovirus from celery per array input. Extending microarray methods to other food matrices should provide important support to surveillance and outbreak investigations. HIGHLIGHTS
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Affiliation(s)
- Christine Yu
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Molecular Biology, 8301 Muirkirk Road, Laurel, Maryland 20708, USA (ORCID: https://orcid.org/0000-0003-0731-7118 [C.Y.])
| | - Kaoru Hida
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Molecular Biology, 8301 Muirkirk Road, Laurel, Maryland 20708, USA (ORCID: https://orcid.org/0000-0003-0731-7118 [C.Y.])
| | - Efstathia Papafragkou
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Molecular Biology, 8301 Muirkirk Road, Laurel, Maryland 20708, USA (ORCID: https://orcid.org/0000-0003-0731-7118 [C.Y.])
| | - Michael Kulka
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Division of Molecular Biology, 8301 Muirkirk Road, Laurel, Maryland 20708, USA (ORCID: https://orcid.org/0000-0003-0731-7118 [C.Y.])
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49
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Sarmento SK, Guerra CR, Malta FC, Coutinho R, Miagostovich MP, Fumian TM. Human norovirus detection in bivalve shellfish in Brazil and evaluation of viral infectivity using PMA treatment. MARINE POLLUTION BULLETIN 2020; 157:111315. [PMID: 32658680 DOI: 10.1016/j.marpolbul.2020.111315] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
Noroviruses are the most common cause of gastroenteritis outbreaks in humans and bivalve shellfish consumption is a recognized route of infection. Our aim was to detect and characterize norovirus in bivalves from a coastal city of Brazil. Nucleic acid was extracted from the bivalve's digestive tissue concentrates using magnetic beads. From March 2018 to June 2019, 77 samples were screened using quantitative RT-PCR. Noroviruses were detected in 41.5%, with the GII being the most prevalent (37.7%). The highest viral load was 3.5 × 106 and 2.5 × 105 GC/g in oysters and mussels, respectively. PMA-treatment demonstrated that a large fraction of the detected norovirus corresponded to non-infectious particles. Genetic characterization showed the circulation of the GII.2[P16] and GII.4[P4] genotypes. Norovirus detection in bivalves reflects the anthropogenic impact on marine environment and serves as an early warning for the food-borne disease outbreaks resulting from the consumption of contaminated molluscs.
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Affiliation(s)
- Sylvia Kahwage Sarmento
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ CEP 21045-900, Brazil
| | - Caroline Rezende Guerra
- Laboratório de Genética Marinha, Departamento de Biotecnologia Marinha, Instituto de Estudos do Mar Almirante Paulo Moreira (IEAPM), Arraial do Cabo , RJ CEP 28930-000, Brazil
| | - Fábio Correia Malta
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ CEP 21045-900, Brazil
| | - Ricardo Coutinho
- Laboratório de Genética Marinha, Departamento de Biotecnologia Marinha, Instituto de Estudos do Mar Almirante Paulo Moreira (IEAPM), Arraial do Cabo , RJ CEP 28930-000, Brazil
| | - Marize Pereira Miagostovich
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ CEP 21045-900, Brazil
| | - Tulio Machado Fumian
- Laboratório de Virologia Comparada e Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ CEP 21045-900, Brazil.
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50
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Desdouits M, de Graaf M, Strubbia S, Oude Munnink BB, Kroneman A, Le Guyader FS, Koopmans MPG. Novel opportunities for NGS-based one health surveillance of foodborne viruses. ONE HEALTH OUTLOOK 2020; 2:14. [PMID: 33829135 PMCID: PMC7993515 DOI: 10.1186/s42522-020-00015-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/01/2020] [Indexed: 05/15/2023]
Abstract
Foodborne viral infections rank among the top 5 causes of disease, with noroviruses and hepatitis A causing the greatest burden globally. Contamination of foods by infected food handlers or through environmental pollution are the main sources of foodborne illness, with a lesser role for consumption of products from infected animals. Viral partial genomic sequencing has been used for more than two decades to track foodborne outbreaks and whole genome or metagenomics next-generation-sequencing (NGS) are new additions to the toolbox of food microbiology laboratories. We discuss developments in the field of targeted and metagenomic NGS, with an emphasis on application in food virology, the challenges and possible solutions towards future routine application.
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Affiliation(s)
- Marion Desdouits
- IFREMER, Laboratoire de Microbiologie, LSEM/SG2M, Nantes, France
| | - Miranda de Graaf
- Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Sofia Strubbia
- IFREMER, Laboratoire de Microbiologie, LSEM/SG2M, Nantes, France
| | - Bas B. Oude Munnink
- Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Annelies Kroneman
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Marion P. G. Koopmans
- Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
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