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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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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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Rachmadi AT, Gyawali P, Summers G, Jabed A, Fletcher GC, Hewitt J. PMAxx-RT-qPCR to Determine Human Norovirus Inactivation Following High-Pressure Processing of Oysters. FOOD AND ENVIRONMENTAL VIROLOGY 2024:10.1007/s12560-024-09585-4. [PMID: 38457095 DOI: 10.1007/s12560-024-09585-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/24/2024] [Indexed: 03/09/2024]
Abstract
Norovirus is the leading cause of viral gastroenteritis globally. While person-to-person transmission is most commonly reported route of infection, human norovirus is frequently associated with foodborne transmission, including through consumption of contaminated bivalve molluscan shellfish. Reverse transcription (RT)-qPCR is most commonly used method for detecting human norovirus detection in foods, but does not inform on its infectivity, posing challenges for assessing intervention strategies aimed at risk elimination. In this study, RT-qPCR was used in conjunction with a derivative of the photoreactive DNA binding dye propidium monoazide (PMAxx™) (PMAxx-RT-qPCR) to evaluate the viral capsid integrity of norovirus genogroup I and II (GI and GII) in shellfish following high pressure processing (HPP). Norovirus GI.3 and GII.4 bioaccumulated oysters were subjected to HPP at pressures of 300 and 450 MPa at 15 °C, and 300, 450 and 600 MPa at 20 °C. Samples were analysed using both RT-qPCR and PMAxx-RT-qPCR. For each sample, norovirus concentration (genome copies/g digestive tissue) determined by RT-qPCR was divided by the PMAxx-RT-qPCR concentration, giving the relative non-intact (RNI) ratio. The RNI ratio values relate to the amount of non-intact (non-infectious) viruses compared to fully intact (possible infectious) viruses. Our findings revealed an increasing RNI ratio value, indicating decreasing virus integrity, with increasing pressure and decreasing pressure. At 300 MPa, for norovirus GI, the median [95% confidence interval, CI] RNI ratio values were 2.6 [1.9, 3.0] at 15 °C compared to 1.1 [0.9, 1.8] at 20 °C. At 450 MPa, the RNI ratio values were 5.5 [2.9, 7.0] at 15 °C compared to 1.3 [1.0, 1.6] at 20 °C. At 600 MPa, the RNI ratio value was 5.1 [2.9, 13.4] at 20 °C. For norovirus GII, RT-qPCR and PMAxx-RT-qPCR detections were significantly reduced at 450 and 600 MPa at both 15 °C and 20 °C, with the median [95% CI] RNI ratio value at 300 MPa being 1.1 [0.8, 1.6]. Following HPP treatment, the use of PMAxx-RT-qPCR enables the selective detection of intact and potential infectious norovirus, enhancing our understanding of the inactivation profiles and supporting the development of more effective risk assessment strategies.
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Affiliation(s)
- Andri Taruna Rachmadi
- Institute of Environmental Science and Research Ltd (ESR), Kenepuru Science Centre, PO Box 50348, Porirua, 5240, New Zealand
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd (ESR), Kenepuru Science Centre, PO Box 50348, Porirua, 5240, New Zealand
| | - Graeme Summers
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Anower Jabed
- Institute of Environmental Science and Research Ltd (ESR), Kenepuru Science Centre, PO Box 50348, Porirua, 5240, New Zealand
| | - Graham C Fletcher
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Joanne Hewitt
- Institute of Environmental Science and Research Ltd (ESR), Kenepuru Science Centre, PO Box 50348, Porirua, 5240, New Zealand.
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Renault T, Faury N, Morga B. Propidium monoazide PCR, a method to determine OsHV-1 undamaged capsids and to estimate virus Lethal Dose 50. Virus Res 2024; 340:199307. [PMID: 38160910 PMCID: PMC10800765 DOI: 10.1016/j.virusres.2023.199307] [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: 08/07/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
Ostreid herpes virus 1 (OsHV-1) has been classified within the Malacoherpesviridae family from the Herpesvirales order. OsHV-1 is the etiological agent of a contagious viral disease of Pacific oysters, C. gigas, affecting also other bivalve species. Mortality rates reported associated with the viral infection vary considerably between sites and countries and depend on the age of affected stocks. A variant called μVar has been reported since 2008 in Europe and other variants in Australia and in New Zealand last decade. These variants are considered as the main causative agents of mass mortality events affecting C. gigas. Presently there is no established cell line that allows for the detection of infectious OsHV-1. In this context, a technique of propidium monoazide (PMA) PCR was developed in order to quantify "undamaged" capsids. This methodology is of interest to explore the virus infectivity. Being able to quantify viral particles getting an undamaged capsid (not only an amount of viral DNA) in tissue homogenates prepared from infected oysters or in seawater samples can assist in the definition of a Lethal Dose (LD) 50 and gain information in the experiments conducted to reproduce the viral infection. The main objectives of the present study were (i) the development/optimization of a PMA PCR technique for OsHV-1 detection using the best quantity of PMA and verifying its effectiveness through heat treatment, (ii) the definition of the percentage of undamaged capsids in four different tissue homogenates prepared from infected Pacific oysters and (iii) the approach of a LD50 during experimental viral infection assays on the basis of a number of undamaged capsids. Although the developped PMA PCR technique was unable to determine OsHV-1 infectivity in viral supensions, it could greatly improve interpretation of virus positive results obtained by qPCR. This technique is not intended to replace the quantification of viral DNA by qPCR, but it does make it possible to give a form of biological meaning to the detection of this DNA.
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Affiliation(s)
- Tristan Renault
- Département Ressources Biologiques et Environnement, Ifremer, Nantes, France.
| | - Nicole Faury
- ASIM, Adaptation Santé des Invertébrés, Ifremer, La Tremblade, France
| | - Benjamin Morga
- ASIM, Adaptation Santé des Invertébrés, Ifremer, La Tremblade, France
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Li Y, Wang Z, Qing J, Hu D, Vo HT, Thi KT, Wang X, Li X. Application of propidium monoazide quantitative PCR to discriminate of infectious African swine fever viruses. Front Microbiol 2024; 14:1290302. [PMID: 38268706 PMCID: PMC10805820 DOI: 10.3389/fmicb.2023.1290302] [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: 09/07/2023] [Accepted: 12/18/2023] [Indexed: 01/26/2024] Open
Abstract
Introduction The detection of African swine fever virus (ASFV) is commonly performed using quantitative real-time PCR (qPCR), a widely used virological method known for its high sensitivity and specificity. However, qPCR has a limitation in distinguishing between infectious and inactivated virus, which can lead to an overestimation of viral targets. Methods To provide insights into ASFV infectivity, we evaluated the suitability of PMAxx, an improved version of propidium monoazide (PMA), as a means to differentiate between infectious and non-infectious ASFV. Pre-treatment with 50 μM PMAxx for 15 min significantly reduced the qPCR signal of ASFV in the live vaccine. Additionally, thermal treatment at 85°C for 5 min effectively inactivated the live ASFV in the vaccine. Based on a standard curve, the sensitivity of the PMAxx-qPCR assay was estimated to be approximately 10 copies/μL. Furthermore, we observed a strong agreement between the results obtained from PMAxx-qPCR and pig challenge experiments. Moreover, we utilized the PMAxx-qPCR assay to investigate the persistence of ASFV, revealing a close relationship between viral persistence and factors such as temperature and type of piggery materials. Conclusion The findings of this study suggest that pre-treating viruses with PMAxx prior to qPCR is a reliable method for distinguishing between infectious and non-infectious ASFV. Thus, integrating of PMAxx-qPCR into routine diagnostic protocols holds potential for improving the interpretation of positive ASFV results obtained through qPCR.
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Affiliation(s)
- Yang Li
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd., (Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology), Dezhou, China
| | - Zewei Wang
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd., (Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology), Dezhou, China
| | - Jie Qing
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd., (Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology), Dezhou, China
| | - Dajun Hu
- New Hope Binh Phuoc livestock Co., Ltd., Huyen Hon Quan, Vietnam
| | - Hong Trang Vo
- New Hope Binh Phuoc livestock Co., Ltd., Huyen Hon Quan, Vietnam
| | - Kim Thanh Thi
- New Hope Binh Phuoc livestock Co., Ltd., Huyen Hon Quan, Vietnam
| | - Xinglong Wang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, Yangling, China
| | - Xiaowen Li
- Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd., (Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology), Dezhou, China
- New Hope Binh Phuoc livestock Co., Ltd., Huyen Hon Quan, Vietnam
- College of Veterinary Medicine, Northwest A&F University, Xianyang, Yangling, China
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Kevill JL, Farkas K, Ridding N, Woodhall N, Malham SK, Jones DL. Use of Capsid Integrity-qPCR for Detecting Viral Capsid Integrity in Wastewater. Viruses 2023; 16:40. [PMID: 38257740 PMCID: PMC10819219 DOI: 10.3390/v16010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Quantifying viruses in wastewater via RT-qPCR provides total genomic data but does not indicate the virus capsid integrity or the potential risk for human infection. Assessing virus capsid integrity in sewage is important for wastewater-based surveillance, since discharged effluent may pose a public health hazard. While integrity assays using cell cultures can provide this information, they require specialised laboratories and expertise. One solution to overcome this limitation is the use of photo-reactive monoazide dyes (e.g., propidium monoazide [PMAxx]) in a capsid integrity-RT-qPCR assay (ci-RT-qPCR). In this study, we tested the efficiency of PMAxx dye at 50 μM and 100 μM concentrations on live and heat-inactivated model viruses commonly detected in wastewater, including adenovirus (AdV), hepatitis A (HAV), influenza A virus (IAV), and norovirus GI (NoV GI). The 100 μM PMAxx dye concentration effectively differentiated live from heat-inactivated viruses for all targets in buffer solution. This method was then applied to wastewater samples (n = 19) for the detection of encapsulated AdV, enterovirus (EV), HAV, IAV, influenza B virus (IBV), NoV GI, NoV GII, and SARS-CoV-2. Samples were negative for AdV, HAV, IAV, and IBV but positive for EV, NoV GI, NoV GII, and SARS-CoV-2. In the PMAxx-treated samples, EV, NoV GI, and NoV GII showed -0.52-1.15, 0.9-1.51, and 0.31-1.69 log reductions in capsid integrity, indicating a high degree of potentially infectious virus in wastewater. In contrast, SARS-CoV-2 was only detected using RT-qPCR but not after PMAxx treatment, indicating the absence of encapsulated and potentially infectious virus. In conclusion, this study demonstrates the utility of PMAxx dyes to evaluate capsid integrity across a diverse range of viruses commonly monitored in wastewater.
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Affiliation(s)
- Jessica L. Kevill
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; (K.F.); (N.R.); (N.W.); or (D.L.J.)
| | - Kata Farkas
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; (K.F.); (N.R.); (N.W.); or (D.L.J.)
| | - Nicola Ridding
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; (K.F.); (N.R.); (N.W.); or (D.L.J.)
| | - Nicholas Woodhall
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; (K.F.); (N.R.); (N.W.); or (D.L.J.)
| | - Shelagh K. Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK;
| | - Davey L. Jones
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; (K.F.); (N.R.); (N.W.); or (D.L.J.)
- Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
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Hata A, Meuchi Y, Liu M, Torii S, Katayama H. Activity- and gene-based quantification of enteric viruses, F- specific RNA phage genogroups, pepper mild mottle virus, and Escherichia coli in surface water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166338. [PMID: 37591377 DOI: 10.1016/j.scitotenv.2023.166338] [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: 06/01/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
Polymerase chain reaction (PCR) is widely applied for the monitoring of pathogenic viruses in water environments. To date, several pretreatments to selectively detect genes from infectious viruses via PCR have been developed. This study was aimed to characterize and validate methods for quantifying active viruses and indicators and to evaluate the proportion of their active fractions in surface water (n = 42). Active E. coli and F-specific RNA phage (FRNAPH) genogroups were quantified using culture assays. In addition to these microbes, norovirus genogroups I (GI) and II, Aichi virus 1, and pepper mild mottle virus (PMMoV) were quantified by (reverse transcription)-quantitative PCR (RT-qPCR) with and without cis-dichlorodiammineplatinum (CDDP) treatment to exclude genes in inactive viruses. CDDP-RT-qPCR showed concentrations and detection frequencies comparable to or higher than culture assays. Consequently, although CDDP-RT-qPCR can suggest the presence of an inactive virus, it can also overestimate the activity of the virus in the environment. Differences between culture and CDDP-RT-qPCR and between CDDP-RT-qPCR and RT-qPCR varied among the viruses. CDDP-RT-qPCR showed a concentration comparable to the culture assay (within 1 log10 difference) in 93 % of positive samples for GI-FRNAPH but in <63 % of positive samples for GII- and GIII-FRNAPHs. GII-NoV was detected from 5 and 30 out of 42 samples via CDDP-RT-qPCR and RT-qPCR, respectively, and was suggested as inactivated by 2.0 log10 or higher in most of the samples. By contrast, concentrations of PMMoV determined by these two assays were not notably different. It is suggested that the operational conditions of wastewater treatment plants around the sites, rather than environmental stresses, affected the microbial inactivation. To better understand the infectivity of viruses in the environment, it is important to investigate them using sensitive detection methods at various sites, including the source of contamination.
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Affiliation(s)
- Akihiko Hata
- Department of Environmental and Civil Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
| | - Yuno Meuchi
- Department of Environmental and Civil Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Miaomiao Liu
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shotaro Torii
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroyuki Katayama
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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8
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Locus T, Lambrecht E, Lamoral S, Willems S, Van Gucht S, Vanwolleghem T, Peeters M. A Multifaceted Approach for Evaluating Hepatitis E Virus Infectivity In Vitro: Cell Culture and Innovative Molecular Methods for Integrity Assessment. Vet Sci 2023; 10:676. [PMID: 38133227 PMCID: PMC10748075 DOI: 10.3390/vetsci10120676] [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: 10/25/2023] [Revised: 11/18/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Hepatitis E virus is a prominent cause of viral hepatitis worldwide. In Western countries, most infections are asymptomatic. However, acute self-limiting hepatitis and chronic cases in immunocompromised individuals can occur. Studying HEV is challenging due to its difficulty to grow in cell culture. Consequently, the detection of the virus mainly relies on RT-qPCR, which cannot differentiate between infectious and non-infectious particles. To overcome this problem, methods assessing viral integrity offer a possible solution to differentiate between intact and damaged viruses. This study aims at optimizing existing HEV cell culture models and RT-qPCR-based assays for selectively detecting intact virions to establish a reliable model for assessing HEV infectivity. In conclusion, these newly developed methods hold promise for enhancing food safety by identifying approaches for inactivating HEV in food processing, thereby increasing food safety measures.
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Affiliation(s)
- Tatjana Locus
- Fisheries and Food, Technology and Food Unit, Flemish Research Institute for Agriculture (ILVO), Brusselsesteenweg 370, 9090 Melle, Belgium or (T.L.); (E.L.)
- Sciensano, Infectious Diseases in Humans, Viral Diseases, Engelandstraat 642, 1180 Ukkel, Belgium
- Laboratory of Experimental Medicine and Pediatrics, Viral Hepatitis Research Group, University of Antwerp, Drie Eikenstraat 655, 2650 Edegem, Belgium
| | - Ellen Lambrecht
- Fisheries and Food, Technology and Food Unit, Flemish Research Institute for Agriculture (ILVO), Brusselsesteenweg 370, 9090 Melle, Belgium or (T.L.); (E.L.)
| | - Sophie Lamoral
- Sciensano, Infectious Diseases in Humans, Viral Diseases, Engelandstraat 642, 1180 Ukkel, Belgium
| | - Sjarlotte Willems
- Fisheries and Food, Technology and Food Unit, Flemish Research Institute for Agriculture (ILVO), Brusselsesteenweg 370, 9090 Melle, Belgium or (T.L.); (E.L.)
| | - Steven Van Gucht
- Sciensano, Infectious Diseases in Humans, Viral Diseases, Engelandstraat 642, 1180 Ukkel, Belgium
| | - Thomas Vanwolleghem
- Laboratory of Experimental Medicine and Pediatrics, Viral Hepatitis Research Group, University of Antwerp, Drie Eikenstraat 655, 2650 Edegem, Belgium
| | - Michael Peeters
- Sciensano, Infectious Diseases in Humans, Viral Diseases, Engelandstraat 642, 1180 Ukkel, Belgium
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9
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Choix FJ, Palacios OA, Nevarez-Moorillón GV. Traditional and new proposals for environmental microbial indicators-a review. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1521. [PMID: 37995003 DOI: 10.1007/s10661-023-12150-4] [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: 09/20/2023] [Accepted: 11/18/2023] [Indexed: 11/24/2023]
Abstract
The continuous increment in world population coupled with the greatest natural resource consumption and waste generation has an enormous impact on the environment. To date, using biological indicators (bioindicators) to evaluate the biological quality of natural environments is very common. Nonetheless, selecting those suitable for each ecosystem or contaminant is one of the most important issues for environmental sciences. Bacteria and helminths are mainly related to fecal contamination, while antibiotic-resistant bacteria, fungi, viruses, and microalgae are organisms used to determine deteriorated ecosystems by diverse contaminants. Nowadays, each bioindicator is used as a specific agent of different contaminant types, but detecting and quantifying these bioindicator microorganisms can be performed from simple microscopy and culture methods up to a complex procedure based on omic sciences. Developing new techniques based on the metabolism and physiological responses of traditional bioindicators is shown in a fast environmental sensitivity analysis. Therefore, the present review focuses on analyzing different bioindicators to facilitate developing suitable monitoring environmental systems according to different pollutant agents. The traditional and new methods proposed to detect and quantify different bioindicators are also discussed. Their vital role is considered in implementing efficient ecosystem bioprospection, restoration, and conservation strategies directed to natural resource management.
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Affiliation(s)
- Francisco J Choix
- CONAHCYT - Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario S/N, C.P. 31125, Chihuahua, Chihuahua, México.
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario S/N, C.P. 31125, Chihuahua, Chihuahua, México.
| | - Oskar A Palacios
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario S/N, C.P. 31125, Chihuahua, Chihuahua, México
- The Bashan Institute of Science, 1730 Post Oak Court, Auburn, AL, 36830, USA
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10
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Lanzarini NM, Mannarino CF, Mata RM, Saggioro EM, Moreira JC, Miagostovich MP. Quantification and molecular characterization of intact rotavirus species A (RVA) in municipal solid waste leachate. J Appl Microbiol 2023; 134:lxad146. [PMID: 37429601 DOI: 10.1093/jambio/lxad146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/12/2023]
Abstract
AIMS Leachate comprises a solid waste decomposition product found fresh in collection trucks or as an effluent in landfills. This study aimed to assess the occurrence, concentrations, and genetic diversity of intact rotavirus species A (RVA) in solid waste leachate. METHODS AND RESULTS Leachate samples were concentrated by ultracentrifugation, treated with propidium monoazide (PMA), and exposed to LED photolysis. Treated and untread samples were extracted using the QIAamp Fast DNA Stool mini kit, and nucleic acids were screened for RVA employing a Taqman® Real-time PCR. The PMA RT-qPCR method detected RVA in eight out of nine truck samples and in 15.40% (2/13) of the landfill leachate samples. The RVA concentrations in the PMA-treated samples ranged from 4.57 × 103 to 2.15 × 107 genomic copies (GC) 100 mL-1 in truck leachate and from 7.83 × 103 to 1.42 × 104 GC 100 mL-1 in landfill samples. Six truck leachate samples were characterized as RVA VP6 genogroup I2 by partial nucleotide sequencing. CONCLUSIONS The high intact RVA detection rates and concentrations in truck leachate samples indicate potential infectivity and comprise a warning for solid waste collectors concerning hand-to-mouth contact and the splash route.
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Affiliation(s)
- Natália Maria Lanzarini
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Camille Ferreira Mannarino
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Rafaela Marinho Mata
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Enrico Mendes Saggioro
- Environmental Health Evaluation and Promotion Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Josino Costa Moreira
- Center for Studies on Workers' Health and Human Ecology, National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
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11
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Alegbeleye O, Sant'Ana AS. Microbiological quality of irrigation water for cultivation of fruits and vegetables: An overview of available guidelines, water testing strategies and some factors that influence compliance. ENVIRONMENTAL RESEARCH 2023; 220:114771. [PMID: 36586712 DOI: 10.1016/j.envres.2022.114771] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
Contaminated irrigation water is among many potential vehicles of human pathogens to food plants, constituting significant public health risks especially for the fresh produce category. This review discusses some available guidelines or regulations for microbiological safety of irrigation water, and provides a summary of some common methods used for characterizing microbial contamination. The goal of such exploration is to understand some of the considerations that influence formulation of water testing guidelines, describe priority microbial parameters particularly with respect to food safety risks, and attempt to determine what methods are most suitable for their screening. Furthermore, the review discusses factors that influence the potential for microbiologically polluted irrigation water to pose substantial risks of pathogenic contamination to produce items. Some of these factors include type of water source exploited, irrigation methods, other agro ecosystem features/practices, as well as pathogen traits such as die-off rates. Additionally, the review examines factors such as food safety knowledge, other farmer attitudes or inclinations, level of social exposure and financial circumstances that influence adherence to water testing guidelines and other safe water application practices. A thorough understanding of relevant risk metrics for the application and management of irrigation water is necessary for the development of water testing criteria. To determine sampling and analytical approach for water testing, factors such as agricultural practices (which differ among farms and regionally), as well as environmental factors that modulate how water quality may affect the microbiological safety of produce should be considered. Research and technological advancements that can improve testing approach and the determination of target levels for hazard characterization or description for the many different pollution contexts as well as farmer adherence to testing requirements, are desirable.
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Affiliation(s)
- Oluwadara Alegbeleye
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Anderson S Sant'Ana
- Department of Food Science and Nutrition, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil.
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12
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Wang Y, Fang W, Wang X, Zhou L, Zheng G. Spatial distribution of fecal pollution indicators in sewage sludge flocs and their removal and inactivation as revealed by qPCR/viability-qPCR during potassium ferrate treatment. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130262. [PMID: 36327846 DOI: 10.1016/j.jhazmat.2022.130262] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/11/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Sludge reuse and utilization is one of important routines of disseminating fecal pollution to surface water and groundwater. However, it remains unclear the spatial distribution of fecal pollution indicators in sludge flocs and their reductions during sludge treatment processes. In this study, the abundances of fecal pollution indicators including cross-assembly phage (crAssphage), JC and BK polyomavirus (JCPyV, BKPyV), human adenovirus (HAdV), the human-specific HF183 Bacteroides (HF183) and Escherichia coli (EC) in soluble extracellular polymeric substances (S-EPS), loosely-bound EPS (LB-EPS), tightly-bound EPS (TB-EPS), and pellets of sludge flocs were determined, and the effect of potassium ferrate (PF) treatment on their removal and inactivation was investigated by using both qPCR and viability-qPCR. Results showed that all investigated indicators were detected in each fraction of sludge flocs. The PF treatment led to a great migration of indicators from sludge pellets to sludge EPS and some extent of their inactivation in each fraction of sludge flocs. The overall reductions of human fecal indicators in sludge determined by qPCR were 0-1.30 logs, which were 0-2 orders of magnitude lower than those of 0.69-2.39 logs detected by viability-qPCR, implying their inactivation by PF treatment to potentially alleviate the associated human health risks.
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Affiliation(s)
- Yuhang Wang
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; College of Materials and Chemical Engineering, Pingxiang University, Pingxiang 337055, China
| | - Wenhao Fang
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinxin Wang
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lixiang Zhou
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
| | - Guanyu Zheng
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China.
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13
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Fernandes LS, Galvão A, Santos R, Monteiro S. Impact of water reuse on agricultural practices and human health. ENVIRONMENTAL RESEARCH 2023; 216:114762. [PMID: 36356670 DOI: 10.1016/j.envres.2022.114762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/27/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
Climate change is altering the habits of the population. Extensive drought periods and overuse of potable water led to significant water shortages in many different places. Therefore, new water sources are necessary for usage in applications where the microbiological and chemical water quality demands are less stringent, as for agriculture. In this study, we planted, germinated, and grew vegetables/fruits (cherry tomato, lettuce, and carrot) using three types of potential waters for irrigation: secondary-treated wastewater, chlorine-treated wastewater, and green wall-treated greywater, to observe potential health risks of foodstuff consumption. In this study the waters and crops were analyzed for three taxonomic groups: bacteria, enteric viruses, and protozoa. Enteric viruses, human Norovirus I (hNoVGI) and Enterovirus (EntV), were detected in tomato and carrots irrigated with secondary-treated and chlorine-treated wastewater, in concentrations as high as 2.63 log genome units (GU)/g. On the other hand, Aichi viruses were detected in lettuce. Bacteria and protozoa remained undetected in all fresh produce although being detected in both types of wastewaters. Fresh produce irrigated with green wall-treated greywater were free from the chosen pathogens. This suggests that green wall-treated greywater may be a valuable option for crop irrigation, directly impacting the cities of the future vision, and the circular and green economy concepts. On the other hand, this work demonstrates that further advancement is still necessary to improve reclaimed water to the point where it no longer constitutes risk of foodborne diseases and to human health.
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Affiliation(s)
| | - Ana Galvão
- Department of Civil Engineering - SHRHA, Técnico Lisboa, Universidade de Lisboa, Portugal
| | - Ricardo Santos
- Laboratorio Analises, Técnico Lisboa, Universidade de Lisboa, Portugal
| | - Sílvia Monteiro
- Laboratorio Analises, Técnico Lisboa, Universidade de Lisboa, Portugal.
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14
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Zeng D, Qian B, Li Y, Zong K, Peng W, Liao K, Yu X, Sun J, Lv X, Ding L, Wang M, Zhou T, Jiang Y, Li J, Xue F, Wu X, Dai J. Prospects for the application of infectious virus detection technology based on propidium monoazide in African swine fever management. Front Microbiol 2022; 13:1025758. [PMID: 36246220 PMCID: PMC9563241 DOI: 10.3389/fmicb.2022.1025758] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
African swine fever (ASF) is a hemorrhagic and often fatal disease occurring in domestic pigs and wild boars. ASF can potentially greatly impact the global trade of pigs and pork products and threaten global food security. Outbreaks of ASF must be notified to the World Organization for Animal Health. In this study, we analyzed the feasibility of applying propidium monoazide (PMA) pretreatment-based infectious virus detection technology to ASF prevention and control and investigated the prospects of applying this technology for epidemic monitoring, disinfection effect evaluation, and drug development. PMA as a nucleic acid dye can enter damaged cells and undergo irreversible covalent crosslinking with nucleic acid under halogen light to prevent its amplification. Although this technology has been widely used for the rapid detection of viable bacteria, its application in viruses is rare. Therefore, we analyzed the theoretical feasibility of applying this technology to the African swine fever virus (ASFV) in terms of gene and cell composition. Rapid infectious ASFV detection technology based on PMA pretreatment would greatly enhance all aspects of ASF prevention and control, such as epidemic monitoring, disinfection treatment, and drug development. The introduction of this technology will also greatly improve the ability to prevent and control ASF.
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Affiliation(s)
- Dexin Zeng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
- Technical Center of Hefei Customs, Hefei, China
| | - Bingxu Qian
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
| | - Yunfei Li
- Technical Center of Hefei Customs, Hefei, China
- Technology Center of Hefei Customs, Anhui Province Key Laboratory of Analysis and Detection for Food Safety, Hefei, China
| | - Kai Zong
- Technical Center of Hefei Customs, Hefei, China
- Technology Center of Hefei Customs, Anhui Province Key Laboratory of Analysis and Detection for Food Safety, Hefei, China
| | - Wanqing Peng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
| | - Kai Liao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
| | - Xiaofeng Yu
- Technical Center of Hefei Customs, Hefei, China
- Technology Center of Hefei Customs, Anhui Province Key Laboratory of Analysis and Detection for Food Safety, Hefei, China
| | | | - Xiaying Lv
- Technical Center of Hefei Customs, Hefei, China
| | - Liu Ding
- Technical Center of Hefei Customs, Hefei, China
| | - Manman Wang
- Technical Center of Hefei Customs, Hefei, China
| | | | - Yuan Jiang
- Animal, Plant and Food Inspection Center of Nanjing Customs, Nanjing, China
| | - Jinming Li
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Feng Xue
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
- Sanya Institute of Nanjing Agricultural University, Sanya, China
- *Correspondence: Feng Xue,
| | - Xiaodong Wu
- China Animal Health and Epidemiology Center, Qingdao, China
- *Correspondence: Feng Xue,
| | - Jianjun Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
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15
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Dhakar V, Geetanjali AS. Role of pepper mild mottle virus as a tracking tool for fecal pollution in aquatic environments. Arch Microbiol 2022; 204:513. [PMID: 35864362 PMCID: PMC9303839 DOI: 10.1007/s00203-022-03121-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/23/2022] [Accepted: 07/01/2022] [Indexed: 11/28/2022]
Abstract
The plant pathogen pepper mild mottle virus (PMMoV) has recently been proposed as a water quality indicator, it is a RNA virus belonging to the genus Tobamovirus in the family Virgoviridae that causes harm to the pepper crops. After consuming processed food products containing infected peppers, such as hot sauces, PMMoV is excreted in high concentrations in feces; therefore, this is the most common RNA virus, constantly found in the feces of humans. The fecal-oral pathway is emerging as an environmental problem. The presence of high concentrations of pathogens associated with human excreta in environmental waters or water reuse supplies poses a threat to public health. Due to the difficulty in determining the presence of pathogens effectively in water, attempts to monitor microbial water quality often use surrogates or indicator organisms that can be easily detected; therefore, PMMoV is used as a viral surrogate in aquatic environment. This paper describes the incidence and persistence of PMMoV in aquatic environments and in waste treatment plants and its usefulness for quantifying virus reductions by advanced water treatment technologies. In recent research, SARS-CoV-2 was reported to be found in wastewater and utilized for the purpose of monitoring coronavirus illness outbreaks. Since PMMoV is readily identified in the human feces and can also serve as an indicator of human waste, the determined PMMoV concentrations may be utilized to give the normalized report of the SARS-CoV-2 concentration, so that, the amount of human waste found in the wastewater can be taken into consideration.
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Affiliation(s)
- Vaishali Dhakar
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
| | - A. Swapna Geetanjali
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu India
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16
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Canh VD, Liu M, Sangsanont J, Katayama H. Capsid integrity detection of pathogenic viruses in waters: Recent progress and potential future applications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154258. [PMID: 35248642 DOI: 10.1016/j.scitotenv.2022.154258] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/26/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Waterborne diseases caused by pathogenic human viruses are a major public health concern. To control the potential risk of viral infection through contaminated waters, a rapid, reliable tool to assess the infectivity of pathogenic viruses is required. Recently, an advanced approach (i.e., capsid integrity (RT-)qPCR) was developed to discriminate intact viruses (potentially infectious) from inactivated viruses. In this approach, samples were pretreated with capsid integrity reagents (e.g., monoazide dyes or metal compounds) before (RT -)qPCR. These reagents can only penetrate inactivated viruses with compromised capsids to bind to viral genomes and prevent their amplification, but they cannot enter viruses with intact capsids. Therefore, only viral genomes of intact viruses were amplified or detected by (RT-)qPCR after capsid integrity treatment. In this study, we reviewed recent progress in the development and application of capsid integrity (RT-)qPCR to assess the potential infectivity of viruses (including non-enveloped and enveloped viruses with different genome structures [RNA and DNA]) in water. The efficiency of capsid integrity (RT-)qPCR has been shown to depend on various factors, such as conditions of integrity reagent treatment, types of viruses, environmental matrices, and the capsid structure of viruses after disinfection treatments (e.g., UV, heat, and chlorine). For the application of capsid integrity (RT-)qPCR in real-world samples, the use of suitable virus concentration methods and process controls is important to control the efficiency of capsid integrity (RT-)qPCR. In addition, potential future applications of capsid integrity (RT-)qPCR for determining the mechanism of disinfection treatment on viral structure (e.g., capsid or genome) and a combination of capsid integrity treatment and next-generation sequencing (NGS) (capsid integrity NGS) for monitoring the community of intact pathogenic viruses in water are also discussed. This review provides essential information on the application of capsid integrity (RT-)qPCR as an efficient tool for monitoring the presence of pathogenic viruses with intact capsids in water.
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Affiliation(s)
- Vu Duc Canh
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Miaomiao Liu
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jatuwat Sangsanont
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Water Science and Technology for Sustainable Environmental Research Group, Chulalongkorn University, Bangkok 10330, Thailand
| | - Hiroyuki Katayama
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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17
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Quantification of infectious Human mastadenovirus in environmental matrices using PMAxx-qPCR. Braz J Microbiol 2022; 53:1465-1471. [PMID: 35666431 PMCID: PMC9168632 DOI: 10.1007/s42770-022-00775-5] [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: 03/30/2022] [Accepted: 05/27/2022] [Indexed: 11/02/2022] Open
Abstract
Molecular methodologies providing data on viral concentration and infectivity have been successfully used in environmental virology, supporting quantitative risk assessment studies. The present study aimed to assess human mastadenovirus (HAdV) intact particles using a derivative of propidium monoazide associated with qPCR (PMAxx-qPCR) in aquatic matrices. Initially, different concentrations of PMAxx were evaluated to establish an optimal protocol for treating different naturally contaminated matrices, using 10 min incubation in the dark at 200 rpm at room temperature and 15 min of photoactivation in the PMA-Lite™ LED photolysis device. There was no significant reduction in the quantification of infectious HAdV with increasing concentration of PMAxx used (20 μM, 50 μM, and 100 μM), except for sewage samples. In this matrix, a reduction of 5.01 log of genomic copies (GC)/L was observed from the concentration of 50 μM and revealed 100% HAdV particles with damaged capsids. On the other hand, the mean reduction of 0.51 log in stool samples using the same concentration mentioned above demonstrated 83% of damaged particles eliminated in the stool. Following, 50 μM PMAxx-qPCR protocol revealed a log reduction of 0.91, 0.67, and 1.05 in other samples of raw sewage, brackish, and seawater where HAdV concentration reached 1.47 × 104, 6.81 × 102, and 2.33 × 102 GC/L, respectively. Fifty micrometers of PMAxx protocol helped screen intact viruses from different matrices, including sea and brackish water.
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18
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Cuevas-Ferrando E, Pérez-Cataluña A, Falcó I, Randazzo W, Sánchez G. Monitoring Human Viral Pathogens Reveals Potential Hazard for Treated Wastewater Discharge or Reuse. Front Microbiol 2022; 13:836193. [PMID: 35464930 PMCID: PMC9026171 DOI: 10.3389/fmicb.2022.836193] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/21/2022] [Indexed: 01/22/2023] Open
Abstract
Wastewater discharge to the environment or its reuse after sanitization poses a concern for public health given the risk of transmission of human viral diseases. However, estimating the viral infectivity along the wastewater cycle presents technical challenges and still remains underexplored. Recently, human-associated crAssphage has been investigated to serve as viral pathogen indicator to monitor fecal impacted water bodies, even though its assessment as biomarker for infectious enteric viruses has not been explored yet. To this end, the occurrence of potentially infectious norovirus genogroup I (GI), norovirus GII, hepatitis A virus (HAV), rotavirus A (RV), and human astrovirus (HAstV) along with crAssphage was investigated in influent and effluent water sampled in four wastewater treatment plants (WWTPs) over 1 year by a PMAxx-based capsid integrity RT-qPCR assay. Moreover, influent and effluent samples of a selected WWTP were additionally assayed by an in situ capture RT-qPCR assay (ISC-RT-qPCR) as estimate for viral infectivity in alternative to PMAxx-RT-qPCR. Overall, our results showed lower viral occurrence and concentration assessed by ISC-RT-qPCR than PMAxx-RT-qPCR. Occurrence of potentially infectious enteric virus was estimated by PMAxx-RT-qPCR as 88–94% in influent and 46–67% in effluent wastewaters with mean titers ranging from 4.77 to 5.89, and from 3.86 to 4.97 log10 GC/L, with the exception of HAV that was sporadically detected. All samples tested positive for crAssphage at concentration ranging from 7.41 to 9.99 log10 GC/L in influent and from 4.56 to 6.96 log10 GC/L in effluent wastewater, showing higher mean concentration than targeted enteric viruses. Data obtained by PMAxx-RT-qPCR showed that crAssphage strongly correlated with norovirus GII (ρ = 0.67, p < 0.05) and weakly with HAstV and RV (ρ = 0.25–0.30, p < 0.05) in influent samples. In effluent wastewater, weak (ρ = 0.27–0.38, p < 0.05) to moderate (ρ = 0.47–0.48, p < 0.05) correlations between crAssphage and targeted viruses were observed. Overall, these results corroborate crAssphage as an indicator for fecal contamination in wastewater but a poor marker for either viral occurrence and viral integrity/infectivity. Despite the viral load reductions detected in effluent compared to influent wastewaters, the estimates of viral infectivity based on viability molecular methods might pose a concern for (re)-using of treated water.
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19
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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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20
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Monteiro S, Rente D, Cunha MV, Marques TA, Cardoso E, Vilaça J, Coelho N, Brôco N, Carvalho M, Santos R. Discrimination and surveillance of infectious severe acute respiratory syndrome Coronavirus 2 in wastewater using cell culture and RT-qPCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152914. [PMID: 34999067 PMCID: PMC8733236 DOI: 10.1016/j.scitotenv.2022.152914] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/10/2021] [Accepted: 12/31/2021] [Indexed: 05/04/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA has been extensively detected in raw wastewater in studies exploring wastewater-based epidemiology (WBE) for early warning purposes. Nonetheless, only a few limited studies investigated the presence of SARS-CoV-2 in treated wastewaters to determine the potential health risks across the water cycle. The detection of SARS-CoV-2 has been done mostly by RT-qPCR and ddPCR, which only provides information on the presence of nucleic acids rather than information on potential infectivity. In this study, we set to develop and evaluate the use of viability RT-qPCR for the selective discrimination and surveillance of infectious SARS-CoV-2 in secondary-treated wastewater. Enzymatic (nuclease) and viability dye (Reagent D) pretreatments were applied to infer infectivity through RT-qPCR using porcine epidemic diarrhea virus (PEDV) as a CoV surrogate. Infectivity tests were first performed on PEDV purified RNA, then on infectious and heat-inactivated PEDV, and finally on heat inactivated PEDV spiked in concentrated secondary-treated wastewater. The two viability RT-qPCR methods were then applied to 27 secondary-treated wastewater samples positive for SARS-CoV-2 RNA at the outlet of five large urban wastewater treatment plants in Portugal. Reagent D pretreatment showed similar behavior to cell culture for heat-inactivated PEDV and both viability RT-qPCR methods performed comparably to VERO E6 cell culture for SARS-CoV-2 present in secondary-treated wastewater, eliminating completely the RT-qPCR signal. Our study demonstrated the lack of infectious SARS-CoV-2 viral particles on secondary-treated wastewater through the application of two pretreatment methods for the rapid inference of infectivity through RT-qPCR, showing their potential application in environmental screening. This study addressed a knowledge gap on the public health risks of SARS-CoV-2 across the water cycle.
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Affiliation(s)
- Silvia Monteiro
- Laboratorio de Análises, Tecnico Lisboa, Universidade de Lisboa, Lisboa, Portugal.
| | - Daniela Rente
- Laboratorio de Análises, Tecnico Lisboa, Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St Andrews, St Andrews KY16 9LZ, Scotland; Centro de Estatística e Aplicações, Departamento de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Eugénia Cardoso
- Águas do Tejo Atlântico, Fábrica de Águas de Alcântara, Avenida de Ceuta, 1300-254 Lisboa, Portugal
| | - João Vilaça
- SIMDOURO, ETAR de Gaia Litoral, 4400-356 Canidelo, Portugal
| | | | - Nuno Brôco
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421 Lisboa, Portugal
| | - Marta Carvalho
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421 Lisboa, Portugal
| | - Ricardo Santos
- Laboratorio de Análises, Tecnico Lisboa, Universidade de Lisboa, Lisboa, Portugal
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21
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Canh VD, Torii S, Yasui M, Kyuwa S, Katayama H. Capsid integrity RT-qPCR for the selective detection of intact SARS-CoV-2 in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:148342. [PMID: 34139497 PMCID: PMC8184355 DOI: 10.1016/j.scitotenv.2021.148342] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 05/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes have been detected in wastewater worldwide. However, the assessment of SARS-CoV-2 infectivity in wastewater has been limited due to the stringent requirements of biosafety level 3. The main objective of this study is to investigate the applicability of capsid integrity RT-qPCR for the selective detection of intact SARS-CoV-2 in wastewater. Three capsid integrity reagents, namely ethidium monoazide (EMA, 0.1-100 μM), propidium monoazide (PMA, 0.1-100 μM), and cis-dichlorodiammineplatinum (CDDP, 0.1-1000 μM), were tested for their effects on different forms (including free genomes, intact and heat-inactivated) of murine hepatitis virus (MHV), which was used as a surrogate for SARS-CoV-2. CDDP at a concentration of 100 μM was identified as the most efficient reagent for the selective detection of infectious MHV by RT-qPCR (CDDP-RT-qPCR). Next, two common virus concentration methods including ultrafiltration (UF) and polyethylene glycol (PEG) precipitation were investigated for their compatibility with capsid integrity RT-qPCR. The UF method was more suitable than the PEG method since it recovered intact MHV (mean ± SD, 38% ± 29%) in wastewater much better than the PEG method did (0.013% ± 0.015%). Finally, CDDP-RT-qPCR was compared with RT-qPCR alone for the detection of SARS-CoV-2 in 16 raw wastewater samples collected in the Greater Tokyo Area. Five samples were positive for SARS-CoV-2 when evaluated by RT-qPCR alone. However, intact SARS-CoV-2 was detected in only three positive samples when determined by CDDP-RT-qPCR. Although CDDP-RT-qPCR was unable to determine the infectivity of SARS-CoV-2 in wastewater, this method could improve the interpretation of positive results of SARS-CoV-2 obtained by RT-qPCR.
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Affiliation(s)
- Vu Duc Canh
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Shotaro Torii
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Midori Yasui
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shigeru Kyuwa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroyuki Katayama
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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Shoults DC, Li Q, Petterson S, Rudko SP, Dlusskaya L, Leifels M, Scott C, Schlosser C, Ashbolt NJ. Pathogen performance testing of a natural swimming pool using a cocktail of microbiological surrogates and QMRA-derived management goals. JOURNAL OF WATER AND HEALTH 2021; 19:629-641. [PMID: 34371499 DOI: 10.2166/wh.2021.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In recent decades, natural swimming pools (NSPs) have gained popularity in Europe, especially in Germany and Austria. NSPs differ from swimming pools in that they utilize biological treatment processes based on wetland processes with no disinfection residual. However, data are missing on the specific log-reduction performance of NSPs to address enteric virus, bacteria, and parasitic protozoa removal considered necessary to meet the North American risk-based benchmark (<35 illnesses per 1,000 swimming events) set by the USEPA for voluntary swimming. In this study, we examined Canada's first NSP at Borden Park, Edmonton, Canada, to address the following three questions: (1) Given normal faecal shedding rates by bathers, what is the total log reduction (TLR) theoretically needed to meet the EPA benchmark? (2) what is the in-situ performance of the NSP based on spiking suitable microbial surrogates (MS2 coliphage, Enterococcus faecalis, and Saccharomyces cerevisiae [Baker's yeast])? and (3) how much time is required to reach acceptable bather risk levels under different representative volume-turnover rates? A reverse-quantitative microbial risk assessment (QMRA) revealed that of the four reference pathogens selected (Norovirus, Campylobacter, Cryptosporidium, and Giardia), only Norovirus was estimated to exceed the risk benchmark at the 50th, 75th, and 95th percentiles, while Campylobacter was the only other reference pathogen to exceed at the 95th percentile. Log-reduction values (LRVs) were similar to previous reports for bacterial indicators, and novel LRVs were estimated for the other two surrogates. A key finding was that more than 24 h treatment time would be necessary to provide acceptable bather protection following heavy bather use (378 bathers/day for main pool and 26 bathers/day for children's pool), due to the mixing dynamics of the treated water diluting out possible residual pool faecal contamination. The theoretical maximum number of people in the pool per day to be below USEPA's 35 gastro cases in 1,000 swimming events was 113, 47, and 8, at the 50th, 75th, and 95th percentiles. Further, the use of ultra-violet disinfection to the pool return flow had little effect on reducing the treatment time required.
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Affiliation(s)
- David C Shoults
- Centre for Water Resources Studies, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Qiaozhi Li
- School of Public Health, University of Alberta, Edmonton, Alberta T6G 2G7, Canada E-mail:
| | - Susan Petterson
- Water & Health Pty Ltd, North Sydney, NSW 2060, Australia; School of Medicine, Griffith University, Gold Coast, QLD 4222, Australia
| | - Sydney P Rudko
- School of Public Health, University of Alberta, Edmonton, Alberta T6G 2G7, Canada E-mail:
| | - Lena Dlusskaya
- School of Public Health, University of Alberta, Edmonton, Alberta T6G 2G7, Canada E-mail:
| | - Mats Leifels
- Singapore Centre of Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Canada
| | - Candis Scott
- School of Public Health, University of Alberta, Edmonton, Alberta T6G 2G7, Canada E-mail:
| | - Cyndi Schlosser
- Borden Park, City of Edmonton, Edmonton, Alberta T5B 4W8, Canada
| | - Nicholas J Ashbolt
- School of Public Health, University of Alberta, Edmonton, Alberta T6G 2G7, Canada E-mail: ; Faculty of Science and Engineering, Southern Cross University, East Lismore, NSW 2480, Australia
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23
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Park JBK, Weaver L, Davies-Colley R, Stott R, Williamson W, Mackenzie M, McGill E, Lin S, Webber J, Craggs RJ. Comparison of faecal indicator and viral pathogen light and dark disinfection mechanisms in wastewater treatment pond mesocosms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 286:112197. [PMID: 33636629 DOI: 10.1016/j.jenvman.2021.112197] [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: 10/20/2020] [Revised: 02/01/2021] [Accepted: 02/13/2021] [Indexed: 06/12/2023]
Abstract
This study compared light and dark disinfection of faecal bacteria/viral indicator organisms (E. coli and MS2 (fRNA) bacteriophage) and human viruses (Echovirus and Norovirus) in Wastewater Treatment Pond (WTP) mesocosms. Stirred pond mesocosms were operated in either outdoor sunlight-exposed or laboratory dark conditions in two experiments during the austral summer. To investigate wavelength-dependence of sunlight disinfection, three optical filters were used: (1) polyethylene film (light control: transmitting all solar UV and visible wavelengths), (2) acrylic (removing most UVB <315 nm), and (3) polycarbonate (removing both UVB and UVA <400 nm). To assess different dark disinfection processes WTP effluent was treated before spiking with target microbes, by (a) 0.22 μm filtration to remove all but colloidal particles, (b) 0.22 μm filtration followed by heat treatment to destroy enzymes, and (c) addition of Cytochalasin B to supress protozoan grazing. Microbiological stocks containing E. coli, MS2 phage, Echovirus, and Norovirus were spiked into each mesocosm 10 min before the experiments commenced. The light control exposed to all sunlight wavelengths achieved >5-log E. coli and MS2 phage removal (from ~1.0 × 106 to <1 PFU/mL) within 3 h compared with up to 6 h in UV-filtered mesocosms. This result confirms that UVB contributes to inactivation of E. coli and viruses by direct sunlight inactivation. However, the very high attenuation with depth of UVB in WTP water (99% removal in the top 8 cm) suggests that UVB disinfection may be less important than other removal processes averaged over time and full-scale pond depth. Dark removal was appreciably slower than sunlight-mediated inactivation. The dark control typically achieved higher removal of E. coli and viruses than the 0.22 μm filtered (dark) mesocosms. This result suggests that adsorption of E. coli and viruses to WTP particles (e.g., algae and bacteria bio-flocs) is an important mechanism of dark disinfection, while bacteria and virus characteristics (e.g. surface charge) and environmental conditions can influence dark disinfection processes.
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Affiliation(s)
- Jason B K Park
- National Institute of Water and Atmospheric Research Ltd (NIWA), P. O. Box 11-115, Hamilton, New Zealand.
| | - Louise Weaver
- Environmental Science Research (ESR), Christchurch Science Centre, 27 CreykC Road, Ilam, PO Box 29181, Christchurch, 8540, New Zealand
| | - Rob Davies-Colley
- National Institute of Water and Atmospheric Research Ltd (NIWA), P. O. Box 11-115, Hamilton, New Zealand
| | - Rebecca Stott
- National Institute of Water and Atmospheric Research Ltd (NIWA), P. O. Box 11-115, Hamilton, New Zealand
| | - Wendy Williamson
- Environmental Science Research (ESR), Christchurch Science Centre, 27 CreykC Road, Ilam, PO Box 29181, Christchurch, 8540, New Zealand
| | - Margaret Mackenzie
- Environmental Science Research (ESR), Christchurch Science Centre, 27 CreykC Road, Ilam, PO Box 29181, Christchurch, 8540, New Zealand
| | - Erin McGill
- Environmental Science Research (ESR), Christchurch Science Centre, 27 CreykC Road, Ilam, PO Box 29181, Christchurch, 8540, New Zealand
| | - Susan Lin
- Environmental Science Research (ESR), Christchurch Science Centre, 27 CreykC Road, Ilam, PO Box 29181, Christchurch, 8540, New Zealand
| | - Judith Webber
- Environmental Science Research (ESR), Christchurch Science Centre, 27 CreykC Road, Ilam, PO Box 29181, Christchurch, 8540, New Zealand
| | - Rupert J Craggs
- National Institute of Water and Atmospheric Research Ltd (NIWA), P. O. Box 11-115, Hamilton, New Zealand
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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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25
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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
- Corresponding author.
| | - 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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26
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da Silva PG, Nascimento MSJ, Soares RRG, Sousa SIV, Mesquita JR. Airborne spread of infectious SARS-CoV-2: Moving forward using lessons from SARS-CoV and MERS-CoV. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:142802. [PMID: 33071145 PMCID: PMC7543729 DOI: 10.1016/j.scitotenv.2020.142802] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 04/13/2023]
Abstract
BACKGROUND Although an increasing body of data reports the detection of SARS-CoV-2 RNA in air, this does not correlate to the presence of infectious viruses, thus not evaluating the risk for airborne COVID-19. Hence there is a marked knowledge gap that requires urgent attention. Therefore, in this systematic review, viability/stability of airborne SARS-CoV-2, SARS-CoV and MERS-CoV viruses is discussed. METHODS A systematic literature review was performed on PubMed/MEDLINE, Web of Science and Scopus to assess the stability and viability of SARS-CoV, MERS-CoV and SARS-CoV-2 on air samples. RESULTS AND DISCUSSION The initial search identified 27 articles. Following screening of titles and abstracts and removing duplicates, 11 articles were considered relevant. Temperatures ranging from 20 °C to 25 °C and relative humidity ranging from 40% to 50% were reported to have a protective effect on viral viability for airborne SARS-CoV and MERS-CoV. As no data is yet available on the conditions influencing viability for airborne SARS-CoV-2, and given the genetic similarity to SARS-CoV and MERS-CoV, one could extrapolate that the same conditions would apply. Nonetheless, the effect of these conditions seems to be residual considering the increasing number of cases in the south of USA, Brazil and India, where high temperatures and humidities have been observed. CONCLUSION Higher temperatures and high relative humidity can have a modest effect on SARS-CoV-2 viability in the environment, as reported in previous studies to this date. However, these studies are experimental, and do not support the fact that the virus has efficiently spread in the tropical regions of the globe, with other transmission routes such as the contact and droplet ones probably being responsible for the majority of cases reported in these regions, along with other factors such as human mobility patterns and contact rates. Further studies are needed to investigate the extent of aerosol transmission of SARS-CoV-2 as this would have important implications for public health and infection-control policies.
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Affiliation(s)
| | - Maria São José Nascimento
- Faculty of Pharmacy, University of Porto (FFUP), Porto, Portugal; Epidemiology Research Unit (EPIUnit), Institute of Public Health, University of Porto, Porto, Portugal
| | - Ruben R G Soares
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden; Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Sofia I V Sousa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
| | - João R Mesquita
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal; Epidemiology Research Unit (EPIUnit), Institute of Public Health, University of Porto, Porto, Portugal.
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27
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Razafimahefa RM, Ludwig-Begall LF, Le Guyader FS, Farnir F, Mauroy A, Thiry E. Optimisation of a PMAxx™-RT-qPCR Assay and the Preceding Extraction Method to Selectively Detect Infectious Murine Norovirus Particles in Mussels. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:93-106. [PMID: 33389671 DOI: 10.1007/s12560-020-09454-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
Human noroviruses are a major cause for gastroenteritis outbreaks. Filter-feeding bivalve molluscs, which accumulate noroviruses in their digestive tissues, are a typical vector for human infection. RT-qPCR, the established method for human norovirus detection in food, does not allow discrimination between infectious and non-infectious viruses and can overestimate potentially infectious viral loads. To develop a more accurate method of infectious norovirus load estimation, we combined intercalating agent propidium monoazide (PMAxx™)-pre-treatment with RT-qPCR assay using in vitro-cultivable murine norovirus. Three primer sets targeting different genome regions and diverse amplicon sizes were used to compare one-step amplification of a short genome fragment to three two-step long-range RT-qPCRs (7 kbp, 3.6 kbp and 2.3 kbp amplicons). Following initial assays performed on untreated infectious, heat-, or ultraviolet-inactivated murine noroviruses in PBS suspension, PMAxx™ RT-qPCRs were implemented to detect murine noroviruses subsequent to their extraction from mussel digestive tissues; virus extraction via anionic polymer-coated magnetic beads was compared with the proteinase K-dependent ISO norm. The long-range RT-qPCR process detecting fragments of more than 2.3 kbp allowed accurate estimation of the infectivity of UV-damaged murine noroviruses. While proteinase K extraction limited later estimation of PMAxx™ pre-treatment effects and was found to be unsuited to the assay, magnetic bead-captured murine noroviruses retained their infectivity. Genome copies of heat-inactivated murine noroviruses differed by 2.3 log10 between RT-qPCR and PMAxx™-RT-qPCR analysis in bivalve molluscs, the PMAxx™ pre-treatment allowing a closer approximation of infectious titres. The combination of bead-based virus extraction and PMAxx™ RT-qPCR thus provides a more accurate model for the estimation of noroviral bivalve mollusc contamination than the conjunction of proteinase K extraction and RT-qPCR and has the potential (once validated utilising infectious human norovirus) to provide an added measure of security to food safety authorities in the hazard assessment of potential bivalve mollusc contamination.
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Affiliation(s)
- Ravo M Razafimahefa
- Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, 4000, Liège, Belgium
| | - Louisa F Ludwig-Begall
- Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, 4000, Liège, Belgium
| | | | - Frédéric Farnir
- Biostatistics and Bioinformatics Applied To Veterinary Science, FARAH Research Centre, Faculty of Veterinary Medicine, University of Liège, 4000, Liège, Belgium
| | - Axel Mauroy
- Staff Direction for Risk Assessment, Control Policy, Federal Agency for the Safety of the Food Chain, Bld du Jardin Botanique 55, 1000, Brussels, Belgium
| | - Etienne Thiry
- Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liège University, B43b, Quartier Vallée 2, Avenue de Cureghem, 10, 4000, Liège, Belgium.
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28
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Trudel-Ferland M, Jubinville E, Jean J. Persistence of Hepatitis A Virus RNA in Water, on Non-porous Surfaces, and on Blueberries. Front Microbiol 2021; 12:618352. [PMID: 33613487 PMCID: PMC7890088 DOI: 10.3389/fmicb.2021.618352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/15/2021] [Indexed: 11/17/2022] Open
Abstract
Enteric viruses, such as human norovirus and hepatitis A virus (HAV), are the leading cause of transmissible foodborne illness. Fresh produce such as berries are often contaminated by infected food handlers, soiled water, or food contact surfaces. The gold-standard method for virus detection throughout the food chain is RT-qPCR, which detects portions of genomes including non-infectious viral particles and naked viral RNA. The aim of this study was to evaluate the persistence of heat-inactivated HAV in water, phosphate-buffered saline, on stainless steel and polyvinyl chloride, and on blueberries at −80°C, −20°C, 4°C, and room temperature. In water and phosphate-buffered saline, viral RNA could be detected for up to 90 days regardless of temperature when the initial load was 2.5 × 104 or 2.5 × 106 genome copies. It was detected on polyvinyl chloride and blueberries under most conditions. On stainless steel, the large initial load persisted for 90 days, while the medium-level load was detected only up to 16 days at room temperature or 60 days at 4°C. The detection of non-infectious viral RNA can confound investigations of gastroenteritis outbreaks. Pretreatments that discriminate between naked RNA, non-infectious virions and infectious virions need to be included in the RT-qPCR method in order to reduce the risk of positive results associated with non-infectious viral particles.
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Affiliation(s)
- Mathilde Trudel-Ferland
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Eric Jubinville
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
| | - Julie Jean
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Quebec City, QC, Canada
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29
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Canh VD, Torii S, Furumai H, Katayama H. Application of Capsid Integrity (RT-)qPCR to Assessing Occurrence of Intact Viruses in Surface Water and Tap Water in Japan. WATER RESEARCH 2021; 189:116674. [PMID: 33279831 DOI: 10.1016/j.watres.2020.116674] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/29/2020] [Accepted: 11/23/2020] [Indexed: 05/05/2023]
Abstract
Capsid integrity (RT-)qPCR has recently been developed to discriminate between intact forms from inactivated forms of viruses, but its applicability to identifying integrity of viruses in drinking water has remained limited. In this study, we investigated the application of capsid integrity (RT-)qPCR using cis-dichlorodiammineplatinum (CDDP) with sodium deoxycholate (SD) pretreatment (SD-CDDP-(RT-)qPCR) to detect intact viruses in surface water and tap water. A total of 63 water samples (surface water, n = 20; tap water, n = 43) were collected in the Kanto region in Japan and quantified by conventional (RT)-qPCR and SD-CDDP-(RT-)qPCR for pepper mild mottle virus (PMMoV) and seven other viruses pathogenic to humans (Aichivirus (AiV), noroviruses of genotypes I and II, enterovirus, adenovirus type 40 and 41, and JC and BK polyomaviruses). In surface water, PMMoV (100%) was more frequently detected than other human pathogenic viruses (30%-60%), as determined by conventional (RT-)qPCR. SD-CDDP-(RT-)qPCR also revealed that intact PMMoV (95%) was more common than intact human pathogenic viruses (20%-45%). In the tap water samples, most of the target viruses were not detected by conventional (RT-)qPCR, except for PMMoV (9%) and AiV (5%). PMMoV remained positive (5%), whereas no AiV was detected when tested by SD-CDDP-(RT-)qPCR, indicating that some PMMoV had an intact capsid, whereas AiV had damaged capsids. The presence of AiV in the absence of PMMoV in tap water produced from groundwater may demonstrate the limitation of PMMoV as a viral indicator in groundwater. In addition to being abundant in surface water, PMMoV was detected in tap water, including PMMoV with intact capsids. Thus, the absence of intact PMMoV may be used to guarantee the viral safety of tap water produced from surface water.
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Affiliation(s)
- Vu Duc Canh
- Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Shotaro Torii
- Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroaki Furumai
- Research Center for Water Environment Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroyuki Katayama
- Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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30
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How to Evaluate Non-Growing Cells-Current Strategies for Determining Antimicrobial Resistance of VBNC Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10020115. [PMID: 33530321 PMCID: PMC7912045 DOI: 10.3390/antibiotics10020115] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 12/17/2022] Open
Abstract
Thanks to the achievements in sanitation, hygiene practices, and antibiotics, we have considerably improved in our ongoing battle against pathogenic bacteria. However, with our increasing knowledge about the complex bacterial lifestyles and cycles and their plethora of defense mechanisms, it is clear that the fight is far from over. One of these resistance mechanisms that has received increasing attention is the ability to enter a dormancy state termed viable but non-culturable (VBNC). Bacteria that enter the VBNC state, either through unfavorable environmental conditions or through potentially lethal stress, lose their ability to grow on standard enrichment media, but show a drastically increased tolerance against antimicrobials including antibiotics. The inability to utilize traditional culture-based methods represents a considerable experimental hurdle to investigate their increased antimicrobial resistance and impedes the development and evaluation of effective treatments or interventions against bacteria in the VBNC state. Although experimental approaches were developed to detect and quantify VBNCs, only a few have been utilized for antimicrobial resistance screening and this review aims to provide an overview of possible methodological approaches.
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31
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Shirasaki N, Matsushita T, Matsui Y, Koriki S. Suitability of pepper mild mottle virus as a human enteric virus surrogate for assessing the efficacy of thermal or free-chlorine disinfection processes by using infectivity assays and enhanced viability PCR. WATER RESEARCH 2020; 186:116409. [PMID: 32942179 DOI: 10.1016/j.watres.2020.116409] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/02/2020] [Accepted: 09/06/2020] [Indexed: 05/05/2023]
Abstract
Evaluating the efficacy of disinfection processes to inactivate human enteric viruses is important for the prevention and control of waterborne diseases caused by exposure to those viruses via drinking water. Here, we evaluated the inactivation of two representative human enteric viruses (adenovirus type 40 [AdV] and coxsackievirus B5 [CV]) by thermal or free-chlorine disinfection. In addition, we compared the infectivity reduction ratio of a plant virus (pepper mild mottle virus [PMMoV], a recently proposed novel surrogate for human enteric viruses for the assessment of virus removal by coagulation‒rapid sand filtration and membrane filtration) with that of the two human enteric viruses to assess the suitability of PMMoV as a human enteric virus surrogate for use in thermal and free-chlorine disinfection processes. Finally, we examined whether conventional or enhanced viability polymerase chain reaction (PCR) analysis using propidium monoazide (PMA) or improved PMA (PMAxx) with or without an enhancer could be used as alternatives to infectivity assays (i.e., plaque-forming unit method for AdV and CV; local lesion count assay for PMMoV) for evaluating virus inactivation by disinfection processes. We found that PMMoV was more resistant to heat treatment than AdV and CV, suggesting that PMMoV is a potential surrogate for these two enteric viruses with regard to thermal disinfection processes. However, PMMoV was much more resistant to chlorine treatment compared with AdV and CV (which is chlorine-resistant) (CT value for 4-log10 inactivation: PMMoV, 84.5 mg-Cl2·min/L; CV, 1.15-1.19 mg-Cl2·min/L), suggesting that PMMoV is not useful as a surrogate for these enteric viruses with regard to free-chlorine disinfection processes. For thermal disinfection, the magnitude of the signal reduction observed with PMAxx-Enhancer-PCR was comparable with the magnitude of reduction in infectivity, indicating that PMAxx-Enhancer-PCR is a potential alternative to infectivity assay. However, for free-chlorine disinfection, the magnitude of the signal reduction observed with PMAxx-Enhancer-PCR was smaller than the magnitude of the reduction in infectivity, indicating that PMAxx-Enhancer-PCR underestimated the efficacy of virus inactivation (i.e., overestimated the infectious virus concentration) by chlorine treatment. Nevertheless, among the PCR approaches examined in the present study (PCR alone, PMA-PCR or PMAxx-PCR either with or without enhancer), PMAxx-Enhancer-PCR provided the most accurate assessment of the efficacy of virus inactivation by thermal or free chlorine disinfection processes.
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Affiliation(s)
- N Shirasaki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan.
| | - T Matsushita
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan
| | - Y Matsui
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan
| | - S Koriki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, N13W8, Sapporo, 060-8628, Japan
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Puente H, Randazzo W, Falcó I, Carvajal A, Sánchez G. Rapid Selective Detection of Potentially Infectious Porcine Epidemic Diarrhea Coronavirus Exposed to Heat Treatments Using Viability RT-qPCR. Front Microbiol 2020; 11:1911. [PMID: 32973701 PMCID: PMC7472829 DOI: 10.3389/fmicb.2020.01911] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/21/2020] [Indexed: 12/24/2022] Open
Abstract
Coronaviruses (CoVs) cause severe respiratory, enteric, and systemic infections in a wide range of hosts, including humans and animals. Porcine epidemic diarrhea virus (PEDV), a member of the Coronaviridae family, is the etiological agent of porcine epidemic diarrhea (PED), a highly contagious intestinal disease affecting pigs of all ages. In this study, we optimized a viability real-time reverse transcriptase polymerase chain reaction (RT-qPCR) for the selective detection of infectious and heat-inactivated PEDV. PEMAX™, EMA™, and PMAxx™ photoactivable dyes along with PtCl4 and CDDP platinum compounds were screened as viability markers using two RT-qPCR assays: firstly, on PEDV purified RNA, and secondly on infectious and thermally inactivated virus suspensions. Furthermore, PMAxx™ pretreatment matched the thermal inactivation pattern obtained by cell culture better than other viability markers. Finally, we further optimized the pretreatment by coupling viability markers with Triton X-100 in inoculated serum resulting in a better estimation of PEDV infectivity than RT-qPCR alone. Our study has provided a rapid analytical tool based on viability RT-qPCR to infer PEDV infectivity with potential application for feed and feed ingredients monitoring in swine industry. This development would allow for greater accuracy in epidemiological surveys and outbreak investigations.
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Affiliation(s)
- Héctor Puente
- Department of Animal Health, Faculty of Veterinary Medicine, Universidad de León, León, Spain
| | - Walter Randazzo
- Department of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Irene Falcó
- Department of Preservation and Food Safety Technologies, Instituto de Agroquímica y Tecnología de Alimentos - Consejo Superior de Investigaciones Científicas (IATA-CSIC), Valencia, Spain
| | - Ana Carvajal
- Department of Animal Health, Faculty of Veterinary Medicine, Universidad de León, León, Spain
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Instituto de Agroquímica y Tecnología de Alimentos - Consejo Superior de Investigaciones Científicas (IATA-CSIC), Valencia, Spain
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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: 9] [Impact Index Per Article: 2.3] [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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Sangsanont J, Kurisu F, Furumai H, Katayama H. Ozone disinfection kinetics of poliovirus 1 determined by cell culture assay, RT-qPCR and ethidium monoazide qPCR reduction in a continuous quench-flow reactor. J Appl Microbiol 2020; 129:1530-1540. [PMID: 32681543 DOI: 10.1111/jam.14787] [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: 12/16/2018] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 11/26/2022]
Abstract
AIMS A continuous quench-flow (CQF) reactor was developed to collect samples at the reaction times of less than one second. The reactor is applied to determine ozone disinfection kinetics of poliovirus and to study whether EMA-qPCR can assess the viral infectivity after ozone disinfection. METHODS Ozone disinfection of poliovirus was conducted in the developed CQF, and the disinfection kinetics were tested in the range of 0·7-5·0 s at ozone concentration of 0·08 and 0·25 mg l-1 . Inactivation, damage on viral genome and damage on capsid integrity were determined by plaque assay, quantitative reverse transcription polymerase chain reaction (RT-qPCR) and ethidium monoazide treatment coupled with RT-qPCR (EMA-qPCR), respectively. RESULTS By using CQF, 2·18 and 2·76 log10 reductions were observed at the reaction time of 0·7 s and ozone concentration of 0·08 and 0·25 mg l-1 , respectively, followed by tailing. Ozone disinfection kinetics of poliovirus 1 were better fit by the efficiency factor Hom model than by the Chick-Watson model, or the modified Chick-Watson model. Kinetics observed were similar between RT-qPCR and EMA-qPCR assays at the reaction times of <2·0 s and ozone concentrations of 0·08 and 0·25 mg l-1 . At reaction times > 5 s, viral concentration evaluated by EMA-qPCR was reduced in comparison to stable RT-qPCR results. Both assays still underestimated the virus inactivation. CONCLUSION The simple developed reactor can be used to investigate viral ozone disinfection kinetics and to elucidate inactivation characteristics or mechanisms at very short exposure times. SIGNIFICANCE AND IMPACT OF THE STUDY The developed CQF reactor is beneficial for better understanding of virus inactivation by ozone, and the reactor can be used to better elucidate disinfection kinetics and mechanisms for future research. This work constitutes an important contribution to the existing knowledge of the application and limitation of the EMA/PMA-qPCR to assess virus infectivity after ozone disinfection.
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Affiliation(s)
- J Sangsanont
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan.,Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand
| | - F Kurisu
- Research Center for Water Environment Technology, The University of Tokyo, Tokyo, Japan
| | - H Furumai
- Research Center for Water Environment Technology, The University of Tokyo, Tokyo, Japan
| | - H Katayama
- Department of Urban Engineering, The University of Tokyo, Tokyo, Japan
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Quantum Leap from Gold and Silver to Aluminum Nanoplasmonics for Enhanced Biomedical Applications. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10124210] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nanotechnology has been used in many biosensing and medical applications, in the form of noble metal (gold and silver) nanoparticles and nanostructured substrates. However, the translational clinical and industrial applications still need improvements of the efficiency, selectivity, cost, toxicity, reproducibility, and morphological control at the nanoscale level. In this review, we highlight the recent progress that has been made in the replacement of expensive gold and silver metals with the less expensive aluminum. In addition to low cost, other advantages of the aluminum plasmonic nanostructures include a broad spectral range from deep UV to near IR, providing additional signal enhancement and treatment mechanisms. New synergistic treatments of bacterial infections, cancer, and coronaviruses are envisioned. Coupling with gain media and quantum optical effects improve the performance of the aluminum nanostructures beyond gold and silver.
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Hügle M, Behrmann O, Raum M, Hufert FT, Urban GA, Dame G. A lab-on-a-chip for free-flow electrophoretic preconcentration of viruses and gel electrophoretic DNA extraction. Analyst 2020; 145:2554-2561. [DOI: 10.1039/c9an02333j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A lab-on-a-chip for FFE preconcentration of viruses and gel electrophoretic DNA extraction: complete preparation of amplifiable DNA from dilute specimens.
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Affiliation(s)
- Matthias Hügle
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
| | - Ole Behrmann
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
| | - Madlen Raum
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
| | - Frank T. Hufert
- Institute of Microbiology and Virology
- Brandenburg Medical School Theodor Fontane
- Neuruppin
- Germany
| | - Gerald A. Urban
- Laboratory for Sensors
- Department of Microsystems Engineering (IMTEK)
- University of Freiburg
- Freiburg
- Germany
| | - Gregory Dame
- Institute of Microbiology and Virology
- Brandenburg Medical School Theodor Fontane
- Neuruppin
- Germany
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Anfruns-Estrada E, Bottaro M, Pintó RM, Guix S, Bosch A. Effectiveness of Consumers Washing with Sanitizers to Reduce Human Norovirus on Mixed Salad. Foods 2019; 8:E637. [PMID: 31817024 PMCID: PMC6963976 DOI: 10.3390/foods8120637] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 12/13/2022] Open
Abstract
Human norovirus (HuNoV) is a foremost cause of domestically acquired foodborne acute gastroenteritis and outbreaks. Despite industrial efforts to control HuNoV contamination of foods, its prevalence in foodstuffs at retail is significant. HuNoV infections are often associated with the consumption of contaminated produce, including ready-to-eat (RTE) salads. Decontamination of produce by washing with disinfectants is a consumer habit which could significantly contribute to mitigate the risk of infection. The aim of our study was to measure the effectiveness of chemical sanitizers in inactivating genogroup I and II HuNoV strains on mixed salads using a propidium monoazide (PMAxx)-viability RTqPCR assay. Addition of sodium hypochlorite, peracetic acid, or chlorine dioxide significantly enhanced viral removal as compared with water alone. Peracetic acid provided the highest effectiveness, with log10 reductions on virus levels of 3.66 ± 0.40 and 3.33 ± 0.19 for genogroup I and II, respectively. Chlorine dioxide showed lower disinfection efficiency. Our results provide information useful to the food industry and final consumers for improving the microbiological safety of fresh products in relation to foodborne viruses.
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Affiliation(s)
- Eduard Anfruns-Estrada
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, 08028 Barcelona, Spain; (E.A.-E.); (M.B.); (R.M.P.); (A.B.)
- Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Santa Coloma de, 08921 Gramenet, Spain
| | - Marilisa Bottaro
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, 08028 Barcelona, Spain; (E.A.-E.); (M.B.); (R.M.P.); (A.B.)
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Bari, Italy
| | - Rosa M. Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, 08028 Barcelona, Spain; (E.A.-E.); (M.B.); (R.M.P.); (A.B.)
- Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Santa Coloma de, 08921 Gramenet, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, 08028 Barcelona, Spain; (E.A.-E.); (M.B.); (R.M.P.); (A.B.)
- Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Santa Coloma de, 08921 Gramenet, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, 08028 Barcelona, Spain; (E.A.-E.); (M.B.); (R.M.P.); (A.B.)
- Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Santa Coloma de, 08921 Gramenet, Spain
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Boehm AB, Silverman AI, Schriewer A, Goodwin K. Systematic review and meta-analysis of decay rates of waterborne mammalian viruses and coliphages in surface waters. WATER RESEARCH 2019; 164:114898. [PMID: 31404902 DOI: 10.1016/j.watres.2019.114898] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/04/2019] [Accepted: 07/21/2019] [Indexed: 05/04/2023]
Abstract
Surface waters are essential natural resources. They are also receiving waters for a variety of anthropogenic waste streams that carry a myriad of pollutants including pathogens. Watershed and fate and transport models can help inform the spatial and temporal extent of microbial pollution from point and non-point sources and thus provide useful information for managing surface waters. Viruses are particularly important water-related pathogens because they often have a low infectious dose, which means that ingestion of even a small volume of water containing a low concentration of virions has the potential to cause disease. We conducted a systematic review of the literature, following best practices, to gather decay rate constants (k) of mammalian waterborne viruses (enteroviruses, adenoviruses, noroviruses, astroviruses, rotaviruses, and hepatitis A viruses) and coliphages in raw surface waters to aid in the parameterization of virus fate and transport models. We identified 562 k values from the literature, with the largest number identified for enteroviruses and coliphages and the smallest for astrovirus, hepatitis A virus, and norovirus. Average k values for each virus varied from 0.07 to 0.9 per day, in order from smallest to largest: Norwalk virus (i.e., noroviruses) < Human astrovirus < Mastadenovirus (i.e., adenoviruses) < Hepatovirus A (i.e., hepatitis A viruses) < Rotavirus A < coliphages < Enterovirus. A meta-analysis investigated how k varied among viruses for experiments conducted with different virus serotypes or species at different temperatures, salinities, and sunlight exposures, and for experiments that enumerated viruses using different methodologies. Virus species or serotype did not affect k among decay experiments. k values were generally larger for experiments conducted at higher temperatures, in sunlight, and in estuarine waters, and enumerated using culture methods. k values were statistically different between virus types with Norwalk virus, Hepatovirus A, and Mastadenovirus having smaller k values than other viruses, controlling for experimental condition and enumeration method. While F+ coliphage k values were similar to those of Enterovirus, Human astrovirus, and Rotavirus A, they were different from those of the other mammalian viruses. This compilation of coliphage and mammalian virus k values provides essential information for researchers and risk assessors who model virus fate and transport in surface waters and identifies avenues for future research to fill knowledge gaps.
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Affiliation(s)
- Alexandria B Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, 94305, USA.
| | - Andrea I Silverman
- Department of Civil and Urban Engineering, Tandon School of Engineering, New York University, Brooklyn, NY, 11201, USA; College of Global Public Health, New York University, New York, NY, 10012, USA
| | - Alexander Schriewer
- Weston Solutions, Inc., 5817 Dryden Place Suite 101, Carlsbad, CA, 92008, USA
| | - Kelly Goodwin
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration (stationed at NOAA/NMFS/SWFSC, La Jolla, CA), Miami, FL, USA
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Capsid Integrity qPCR—An Azo-Dye Based and Culture-Independent Approach to Estimate Adenovirus Infectivity after Disinfection and in the Aquatic Environment. WATER 2019. [DOI: 10.3390/w11061196] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recreational, reclaimed and drinking source waters worldwide are under increasing anthropogenic pressure, and often contain waterborne enteric bacterial, protozoan, and viral pathogens originating from non-point source fecal contamination. Recently, the capsid integrity (ci)-qPCR, utilizing the azo-dyes propidium monoazide (PMA) or ethidium monoazide (EMA), has been shown to reduce false-positive signals under laboratory conditions as well as in food safety applications, thus improving the qPCR estimation of virions of public health significance. The compatibility of two widely used human adenovirus (HAdV) qPCR protocols was evaluated with the addition of a PMA/EMA pretreatment using a range of spiked and environmental samples. Stock suspensions of HAdV were inactivated using heat, UV, and chlorine before being quantified by cell culture, qPCR, and ci-qPCR. Apparent inactivation of virions was detected for heat and chlorine treated HAdV while there was no significant difference between ci-qPCR and qPCR protocols after disinfection by UV. In a follow-up comparative analysis under more complex matrix conditions, 51 surface and 24 wastewater samples pre/post UV treatment were assessed for enteric waterborne HAdV to evaluate the ability of ci-qPCR to reduce the number of false-positive results when compared to conventional qPCR and cell culture. Azo-dye pretreatment of non-UV inactivated samples was shown to improve the ability of molecular HAdV quantification by reducing signals from virions with an accessible genome, thereby increasing the relevance of qPCR results for public health purposes, particularly suited to resource-limited low and middle-income settings.
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40
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Gyawali P, Kc S, Beale DJ, Hewitt J. Current and Emerging Technologies for the Detection of Norovirus from Shellfish. Foods 2019; 8:foods8060187. [PMID: 31159220 PMCID: PMC6617275 DOI: 10.3390/foods8060187] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 12/14/2022] Open
Abstract
Reports of norovirus infections associated with the consumption of contaminated bivalve molluscan shellfish negatively impact both consumers and commercial shellfish operators. Current virus recovery and PCR detection methods can be expensive and time consuming. Due to the lack of rapid, user-friendly and onsite/infield methods, it has been difficult to establish an effective virus monitoring regime that is able to identify contamination points across the production line (i.e., farm-to-plate) to ensure shellfish quality. The focus of this review is to evaluate current norovirus detection methods and discuss emerging approaches. Recent advances in omics-based detection approaches have the potential to identify novel biomarkers that can be incorporated into rapid detection kits for onsite use. Furthermore, some omics techniques have the potential to simultaneously detect multiple enteric viruses that cause human disease. Other emerging technologies discussed include microfluidic, aptamer and biosensor-based detection methods developed to detect norovirus with high sensitivity from a simple matrix. Many of these approaches have the potential to be developed as user-friendly onsite detection kits with minimal costs. However, more collaborative efforts on research and development will be required to commercialize such products. Once developed, these emerging technologies could provide a way forward that minimizes public health risks associated with shellfish consumption.
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Affiliation(s)
- Pradip Gyawali
- Institute of Environmental Science and Research Ltd. (ESR), Porirua 5240, New Zealand.
| | - Sanjaya Kc
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - David J Beale
- Commonwealth Scientific and Industrial Research Organization, Ecoscience Precinct, Dutton Park, QLD 4102, Australia.
| | - Joanne Hewitt
- Institute of Environmental Science and Research Ltd. (ESR), Porirua 5240, New Zealand.
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Zhang Y, Qu S, Xu L. Progress in the study of virus detection methods: The possibility of alternative methods to validate virus inactivation. Biotechnol Bioeng 2019; 116:2095-2102. [PMID: 31038205 DOI: 10.1002/bit.27003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/21/2019] [Accepted: 04/25/2019] [Indexed: 11/09/2022]
Abstract
Virus inactivation validation studies have been widely applied in the risk assessment of biogenic material-based medical products, such as biological products, animal tissue-derived biomaterials, and allogeneic biomaterials, to decrease the risk of virus transmission. Traditional virus detection methods in an inactivation validation study utilize cell culture as a tool to quantify the infectious virus by observing cytopathic effects (CPEs) after virus inactivation. However, this is susceptible to subjective factors because CPEs must be observed by experts under a microscope during virus titration. In addition, this method is costly and time- and labor-consuming. Molecular biological technologies such as quantitative polymerase chain reaction (qPCR) have been widely used for virus detection but cannot distinguish infectious and noninfectious viruses. Therefore, qPCR cannot be directly applied to virus inactivation validation studies. In this paper, methods to detect viruses and progress in the challenge of differentiating infectious and noninfectious viruses with the combination of pretreatment and qPCR techniques such as the integrated cell culture-qPCR (ICC-qPCR) method are reviewed. In addition, the advantages and disadvantages of each new method, as well as its prospect in virus inactivation validation studies, are discussed.
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Affiliation(s)
- Yu Zhang
- Institute for Medical Devices Control, National Institutes for Food and Drug Control, Beijing, China.,School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Shuxin Qu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Liming Xu
- Institute for Medical Devices Control, National Institutes for Food and Drug Control, Beijing, China
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42
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Microbiological Constraints for Use of Reclaimed and Reconditioned Water in Food Production and Processing Operations. Food Microbiol 2019. [DOI: 10.1128/9781555819972.ch41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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43
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Fenaux H, Chassaing M, Berger S, Gantzer C, Bertrand I, Schvoerer E. Transmission of hepatitis E virus by water: An issue still pending in industrialized countries. WATER RESEARCH 2019; 151:144-157. [PMID: 30594083 DOI: 10.1016/j.watres.2018.12.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 06/09/2023]
Abstract
Hepatitis E virus (HEV) is an enteric virus divided into eight genotypes. Genotype 1 (G1) and G2 are specific to humans; G3, G4 and G7 are zoonotic genotypes infecting humans and animals. Transmission to humans through water has been demonstrated for G1 and G2, mainly in developing countries, but is only suspected for the zoonotic genotypes. Thus, the water-related HEV hazard may be due to human and animal faeces. The high HEV genetic variability allows considering the presence in wastewater of not only different genotypes, but also quasispecies adding even greater diversity. Moreover, recent studies have demonstrated that HEV particles may be either quasi-enveloped or non-enveloped, potentially implying differential viral behaviours in the environment. The presence of HEV has been demonstrated at the different stages of the water cycle all over the world, especially for HEV G3 in Europe and the USA. Concerning HEV survival in water, the virus does not have higher resistance to inactivating factors (heat, UV, chlorine, physical removal), compared to viral indicators (MS2 phage) or other highly resistant enteric viruses (Hepatitis A virus). But the studies did not take into account genetic (genogroups, quasispecies) or structural (quasi- or non-enveloped forms) HEV variability. Viral variability could indeed modify HEV persistence in water by influencing its interaction with the environment, its infectivity and its pathogenicity, and subsequently its transmission by water. The cell culture methods used to study HEV survival still have drawbacks (challenging virus cultivation, time consuming, lack of sensitivity). As explained in the present review, the issue of HEV transmission to humans through water is similar to that of other enteric viruses because of their similar or lower survival. HEV transmission to animals through water and how the virus variability affects its survival and transmission remain to be investigated.
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Affiliation(s)
- H Fenaux
- Laboratoire de Virologie, CHRU de Nancy Brabois, F-54511 Vandoeuvre lès Nancy, France; Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement, LCPME UMR 7564 CNRS-UL, F-54600 Villers lès Nancy, France
| | - M Chassaing
- Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement, LCPME UMR 7564 CNRS-UL, F-54600 Villers lès Nancy, France
| | - S Berger
- Laboratoire de Virologie, CHRU de Nancy Brabois, F-54511 Vandoeuvre lès Nancy, France
| | - C Gantzer
- Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement, LCPME UMR 7564 CNRS-UL, F-54600 Villers lès Nancy, France
| | - I Bertrand
- Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement, LCPME UMR 7564 CNRS-UL, F-54600 Villers lès Nancy, France
| | - E Schvoerer
- Laboratoire de Virologie, CHRU de Nancy Brabois, F-54511 Vandoeuvre lès Nancy, France; Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement, LCPME UMR 7564 CNRS-UL, F-54600 Villers lès Nancy, France.
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44
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Canh VD, Kasuga I, Furumai H, Katayama H. Viability RT-qPCR Combined with Sodium Deoxycholate Pre-treatment for Selective Quantification of Infectious Viruses in Drinking Water Samples. FOOD AND ENVIRONMENTAL VIROLOGY 2019; 11:40-51. [PMID: 30680674 DOI: 10.1007/s12560-019-09368-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/18/2019] [Indexed: 05/22/2023]
Abstract
The presence of pathogenic viruses in drinking water is a major public health concern. Although viability RT-qPCR methods were developed to quantify infectious viruses, they may not always reflect viral infectivity, therefore leading to false-positive results. In this study, sodium deoxycholate (SD) pre-treatment was used to improve the efficiency of viability RT-qPCR methods with respect to exclusive quantification of infectious viruses. The ability of SD pre-treatment to enhance the penetration of three viability markers, namely, ethidium monoazide (EMA, 100 µM), propidium monoazide (PMA, 100 µM), and cis-dichlorodiammineplatinum (CDDP, 1000 µM), into heat-treated (90 °C for 1 min) Aichi virus at various concentrations (0.01-0.5%) was evaluated. The optimal SD concentration was found to be 0.1% for all markers. EMA/PMA/CDDP-RT-qPCR with 0.1% SD pre-treatment was significantly more effective than without SD pre-treatment in determining AiV inactivation after heat (50, 60, 70, 80, or 90 °C for 1 min) or chlorine treatment (1 mgCl2/L for 1, 2, 5, or 10 min). Among the viability RT-qPCR methods tested, CDDP-RT-qPCR with SD pre-treatment (SD-CDDP-RT-qPCR) was the most effective in reflecting viral infectivity. Performance testing of SD-CDDP-RT-qPCR in concentrated drinking water samples did not reveal any significant effects of SD-CDDP treatment. Thus, SD-CDDP-RT-qPCR could be a useful tool for monitoring infectious virus presence in drinking water.
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Affiliation(s)
- Vu Duc Canh
- Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Ikuro Kasuga
- Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Hiroaki Furumai
- Research Center for Water Environment Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Hiroyuki Katayama
- Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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45
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Cooksey EM, Singh G, Scott LC, Aw TG. Detection of coliphages and human adenoviruses in a subtropical estuarine lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 649:1514-1521. [PMID: 30308919 DOI: 10.1016/j.scitotenv.2018.08.322] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 06/08/2023]
Abstract
Fecal indicator bacteria (FIB) have been used to assess fecal contamination in recreational water. However, enteric viruses have been shown to be more persistent in the environment and resistant to wastewater treatment than bacteria. Recently, U.S Environmental Protection Agency has proposed the use of coliphages as viral indicators to better protect against viral waterborne outbreaks. This study aimed to detect and determine correlation between coliphages (F-specific and somatic), fecal indicator bacteria (enterococci and fecal coliforms), and human enteric viruses (human adenovirus) in a subtropical brackish estuarine lake. Water samples were collected from 9 estuarine recreation sites on Lake Pontchartrain in southeast Louisiana. Water samples (n = 222, collected weekly) were analyzed for coliphages and fecal indicator bacteria using culture-based methods and large volume water samples (n = 54, collected monthly) were analyzed for human adenovirus using quantitative PCR. Somatic coliphage and F-specific coliphage were found in 93.7 and 65.2% of samples with geometric mean concentrations of 30 and 3 plaque forming units (PFU) per 100 mL, respectively. Enterococci, fecal coliforms, and adenovirus were found in all samples with geometric mean concentrations of 27 most probable number (MPN), 77 MPN, and 3.0 × 104 gene copies per 100 mL, respectively. Watersheds in suburban areas exhibited significantly higher concentrations of coliphages and fecal indicator bacteria, indicating potential fecal contamination from septic systems. There was no significant correlation (p > 0.05) observed between the presence of adenoviruses and fecal indicator bacteria and coliphages. The presence of human adenovirus in Lake Pontchartrain poses a significant public health problem for both recreational use and seafood harvesting as it increases exposure risks. This study demonstrated the lack of relationship between fecal indicators and human viral pathogen in Lake Pontchartrain supporting an alternative microbial surveillance system such as direct pathogen detection.
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Affiliation(s)
- Emily M Cooksey
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, United States of America
| | - Gulshan Singh
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, United States of America
| | - Laura C Scott
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, United States of America
| | - Tiong Gim Aw
- Department of Global Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, United States of America.
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46
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Hamza IA, Bibby K. Critical issues in application of molecular methods to environmental virology. J Virol Methods 2019; 266:11-24. [PMID: 30659861 DOI: 10.1016/j.jviromet.2019.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
Abstract
Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable viruses, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.
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Affiliation(s)
- Ibrahim Ahmed Hamza
- Department of Water Pollution Research, National Research Centre, Cairo, Egypt.
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, USA
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47
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Lee S, Bae S. Molecular viability testing of viable but non-culturable bacteria induced by antibiotic exposure. Microb Biotechnol 2018; 11:1008-1016. [PMID: 29243404 PMCID: PMC6196391 DOI: 10.1111/1751-7915.13039] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/20/2017] [Accepted: 11/28/2017] [Indexed: 12/16/2022] Open
Abstract
Nucleic acid amplification-based methods are limited by their inability to discriminate between viable and dead cells. To overcome this drawback, propidium monoazide (PMA) combined with qPCR has been used to differentiate viable from nonviable cells in environmental samples. However, assessing bacterial physiology using PMA-qPCR remains a challenge due to its incapability of detecting metabolic activities, leading to overestimation of the viable bacteria population under an inactivation condition (e.g. antibiotic treatments). A recent advanced technique to amplify ribosomal RNA precursors (pre-rRNA) has been shown to detect viable cells because pre-rRNAs are intermediates in rRNA synthesis. This study investigated the effect of different types of antibiotics on the bacterial viability or viable but non-culturable (VBNC) state using both PMA-qPCR and pre-rRNA analyses with Pseudomonas aeruginosa. This study demonstrated that P. aeruginosa was more sensitive to colistin than it was to carbenicillin, gentamicin and levofloxacin. We could discriminate VBNCP. aeruginosa cells using PMA-qPCR when antibiotic pressure induced the VBNC state. Also, pre-rRNA was able to distinguish viable cells from colistin-inactivated bacteria cells, and it could detect the presence of VBNC and persister cells. Our results showed that these two molecular methods could successfully eliminate false-positive signals derived from antibiotics-inactivated cells.
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Affiliation(s)
- Seunguk Lee
- Department of Civil and Environmental EngineeringNational University of Singapore1 Engineering Drive 2Singapore117576Singapore
| | - Sungwoo Bae
- Department of Civil and Environmental EngineeringNational University of Singapore1 Engineering Drive 2Singapore117576Singapore
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48
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López-Gálvez F, Randazzo W, Vásquez A, Sánchez G, Decol LT, Aznar R, Gil MI, Allende A. Irrigating Lettuce with Wastewater Effluent: Does Disinfection with Chlorine Dioxide Inactivate Viruses? JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:1139-1145. [PMID: 30272803 DOI: 10.2134/jeq2017.12.0485] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Reclaimed water obtained from urban wastewater is currently being used as irrigation water in water-scarce regions in Spain. However, wastewater can contain enteric viruses that water reclamation treatment cannot remove or inactivate completely. In the present study, greenhouse-grown baby lettuce ( L.) was irrigated with secondary treatment effluent from a wastewater treatment plant untreated and treated using chlorine dioxide (ClO). The effect of ClO treatment on the physicochemical characteristics and the presence of enteric viruses in irrigation water and lettuce was assessed. The presence of human noroviruses genogroups I and II (NoV GI and NoV GII), and human astroviruses (HAstV), was analyzed by real-time polymerase chain reaction (RT-qPCR). Additionally, to check for the loss of infectivity induced by the disinfection treatment, positive samples were re-analyzed after pretreatment with the intercalating dye PMAxx before RNA extraction and RT-qPCR. There were no significant differences in the proportion of positive samples and the concentration of enteric viruses between treated and untreated reclaimed water without PMAxx pretreatment ( > 0.05). A significantly lower concentration of NoV GI was detected in ClO-treated water when samples were pretreated with PMAxx ( < 0.05), indicating that inactivation was due to the disinfection treatment. Laboratory-scale validation tests indicated the suitability of PMAxx-RT-qPCR for discrimination between potentially infectious and ClO-damaged viruses. Although the applied ClO treatment was not able to significantly reduce the enteric virus load of the secondary effluent from the wastewater treatment plant, none of the lettuce samples analyzed ( = 36) was positive for the presence of NoV or HAstV.
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49
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Detection of Infectious Noroviruses from Wastewater and Seawater Using PEMAXTM Treatment Combined with RT-qPCR. WATER 2018. [DOI: 10.3390/w10070841] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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50
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Abstract
Viruses represent the most abundant and diverse of the biological entities in environmental waters, including the seas and probably also freshwater systems. They are important players in ecological networks in waters and influence global biochemical cycling and community composition dynamics. Among the many diverse viruses from terrestrial environments found in environmental waters, some are plant, animal, and/or human pathogens. The majority of pathogenic viral species found in waters are very stable and can survive outside host cells for long periods. The occurrence of such viruses in environmental waters has raised concerns because of the confirmation of the infectivity of waterborne viruses even at very low concentrations. This chapter focuses mainly on the survival of human, animal, and plant pathogenic viruses in aqueous environments, the possibility of their water-mediated transmission, the ecological implications of viruses in water, the methods adapted for detecting such viruses, and how to minimize the risk of viruses spreading through water.
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