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Yang Y, Tan J, Wang F, Sun W, Shi H, Cheng Z, Xie Y, Zhou X. Preconcentration and detection of SARS-CoV-2 in wastewater: A comprehensive review. Biosens Bioelectron 2024; 263:116617. [PMID: 39094290 DOI: 10.1016/j.bios.2024.116617] [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: 05/22/2024] [Revised: 07/17/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
Severe acute respiratory syndrome coronaviruses 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) affected the health of human beings and the global economy. The patients with SARS-CoV-2 infection had viral RNA or live infectious viruses in feces. Thus, the possible transmission of SARS-CoV-2 through wastewater received great attentions. Moreover, SARS-CoV-2 in wastewater can serve as an early indicator of the infection within communities. We summarized the preconcentration and detection technology of SARS-CoV-2 in wastewater aiming at the complex matrices of wastewater and low virus concentration and compared their performance characteristics. We described the emerging tests that would be possible to realize the rapid detection of SARS-CoV-2 in fields and encourage academics to advance their technologies beyond conception. We concluded with a brief discussion on the outlook for integrating preconcentration and the detection of SARS-CoV-2 with emerging technologies.
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Affiliation(s)
- Yihan Yang
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jisui Tan
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Fan Wang
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Weiming Sun
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Hanchang Shi
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Zhao Cheng
- School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yangcun Xie
- Chinese Academy of Environmental Planning, Beijing, 100043, China.
| | - Xiaohong Zhou
- School of Environment, Tsinghua University, Beijing, 100084, China.
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Abney SE, Higham CA, Wilson AM, Ijaz MK, McKinney J, Reynolds KA, Gerba CP. Transmission of Viruses from Restroom Use: A Quantitative Microbial Risk Assessment. FOOD AND ENVIRONMENTAL VIROLOGY 2024; 16:65-78. [PMID: 38372960 DOI: 10.1007/s12560-023-09580-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/30/2023] [Indexed: 02/20/2024]
Abstract
Restroom use has been implicated in a number of viral outbreaks. In this study, we apply quantitative microbial risk assessment to quantify the risk of viral transmission by contaminated restroom fomites. We estimate risk from high-touch fomite surfaces (entrance/exit door, toilet seat) for three viruses of interest (SARS-CoV-2, adenovirus, norovirus) through eight exposure scenarios involving differing user behaviors, and the use of hand sanitizer following each scenario. We assessed the impacts of several sequences of fomite contacts in the restroom, reflecting the variability of human behavior, on infection risks for these viruses. Touching of the toilet seat was assumed to model adjustment of the seat (open vs. closed), a common touch point in single-user restrooms (home, small business, hospital). A Monte Carlo simulation was conducted for each exposure scenario (10,000 simulations each). Norovirus resulted in the highest probability of infection for all exposure scenarios with fomite surfaces. Post-restroom automatic-dispensing hand sanitizer use reduced the probability of infection for each virus by up to 99.75%. Handwashing within the restroom, an important risk-reduction intervention, was not found to be as effective as use of a non-touch hand sanitizer dispenser for reducing risk to near or below 1/1,000,000, a commonly used risk threshold for comparison.
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Affiliation(s)
- Sarah E Abney
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA
| | - Ciara A Higham
- EPSRC Centre for Doctoral Training in Fluid Dynamics, University of Leeds, Leeds, UK
| | - Amanda M Wilson
- Department of Community, Environment, & Policy, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - M Khalid Ijaz
- Global Research & Development for Lysol and Dettol, Reckitt Benckiser LLC, Montvale, NJ, USA
| | - Julie McKinney
- Global Research & Development for Lysol and Dettol, Reckitt Benckiser LLC, Montvale, NJ, USA
| | - Kelly A Reynolds
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA
- Department of Community, Environment, & Policy, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - Charles P Gerba
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA.
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Yan C, Hu YN, Gui ZC, Lai TN, Ali W, Wan NH, He SS, Liu S, Li X, Jin TX, Nasir ZA, Alcega SG, Coulon F. Quantitative SARS-CoV-2 exposure assessment for workers in wastewater treatment plants using Monte-Carlo simulation. WATER RESEARCH 2024; 248:120845. [PMID: 37976948 DOI: 10.1016/j.watres.2023.120845] [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: 05/03/2023] [Revised: 10/17/2023] [Accepted: 11/05/2023] [Indexed: 11/19/2023]
Abstract
Several studies on COVID-19 pandemic have shown that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originating from human stool are detected in raw sewage for several days, leading to potential health risks for workers due to the production of bioaerosols and droplets during wastewater treatment process. In this study, data of SARS-CoV-2 concentrations in wastewater were gathered from literatures, and a quantitative microbial risk assessment with Monte Carlo simulation was used to estimate the daily probability of infection risk through exposure to viable infectious viral airborne particles of the workers during four seasons and under six environmental conditions. Inhalation of bioaerosols and direct ingestion of wastewater droplets were selected as exposure pathways. Spearman rank correlation coefficients were used for sensitivity analysis to identify the variables with the greatest influence on the infection risk probability. It was found that the daily probability of infection risk decreased with temperature (T) and relative humidity (RH) increase. The probability of direct droplet ingestion exposure pathway was higher than that of the bioaerosol inhalation pathway. The sensitivity analysis indicated that the most sensitive variable for both exposure pathways was the concentration of SARS-CoV-2 in stool. So, appropriate aeration systems, covering facilities, and effective ventilation are suggested to implement in wastewater treatment plants (WWTPs) to reduce emission concentration. Further to this, the exposure time (t) had a larger variance contribution than T and RH for the bioaerosol inhalation pathway. Implementing measures such as adding more work shifts, mandating personal protective equipment for all workers, and implementing coverage for treatment processes can significantly reduce the risk of infection among workers at WWTPs. These measures are particularly effective during environmental conditions with low temperatures and humidity levels.
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Affiliation(s)
- Cheng Yan
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China; Hubei Key Laboratory of Environmental Water Science in the Yangtze River Basin, China University of Geosciences, Wuhan 430074, PR China.
| | - Yi-Ning Hu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China
| | - Zi-Cheng Gui
- CCDI (Suzhou) exploration and design consultant Co., Ltd., Suzhou 215123, PR China
| | - Tian-Nuo Lai
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China
| | - Wajid Ali
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, PR China
| | - Nian-Hong Wan
- Central & Southern China Municipal Engineering Design and Research Institute Co, Ltd., Wuhan 430010, PR China
| | - Shan-Shan He
- Central & Southern China Municipal Engineering Design and Research Institute Co, Ltd., Wuhan 430010, PR China
| | - Sai Liu
- CITIC Treated Water into River Engineering Investment Co., Ltd., Wuhan 430200, PR China
| | - Xiang Li
- Three Gorges Base Development Co., Ltd., Yichang 443002, PR China
| | - Ting-Xu Jin
- Department of Toxicology, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou 215123, PR China; School of Public Health, the Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang 550025, PR China
| | - Zaheer Ahmad Nasir
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Sonia Garcia Alcega
- School of Physical Sciences, The Open University, Walton Hall, Milton Keynes MK6 7AA, UK
| | - Frederic Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
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Esseili MA. In vitro digestion of SARS-CoV-2 contaminated berries reveals high inactivation of infectious virus during gastrointestinal passage. Appl Environ Microbiol 2023; 89:e0133923. [PMID: 37982639 PMCID: PMC10734541 DOI: 10.1128/aem.01339-23] [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: 08/04/2023] [Accepted: 09/28/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE During the pandemic, news outlets occasionally reported on the detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA on various foods, raising concerns over contaminated foods initiating infections. Coronavirus disease 2019 (COVID-19) patients often experience gastrointestinal symptoms and shed SARS-CoV-2 RNA in their feces. In addition, active virus replication in the gastrointestinal tract was shown; however, infectious viruses were rarely detected in feces. We previously showed that SARS-CoV-2 remained infectious on frozen berries for at least a month. Here, in vitro digestion models showed that SARS-CoV-2 on berries exhibits minimal inactivation at the oral phase and the virus may escape gastric inactivation early during feeding. However, high intestinal inactivation of the virus on berries suggested that SARS-CoV-2 was less likely to initiate infection in the small intestine. In contrast, the oral cavity is a potential site where infection might be initiated, providing more input for the gastrointestinal tract. High intestinal inactivation might explain the difficulty of detecting infectious SARS-CoV-2 in feces but not of virus RNA.
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Affiliation(s)
- Malak A. Esseili
- Department of Food Science and Technology, Center for Food Safety, University of Georgia, Griffin, Georgia, USA
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Termansen MB, Frische S. Fecal-oral transmission of SARS-CoV-2: A systematic review of evidence from epidemiological and experimental studies. Am J Infect Control 2023; 51:1430-1437. [PMID: 37121473 PMCID: PMC10141930 DOI: 10.1016/j.ajic.2023.04.170] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/21/2023] [Accepted: 04/21/2023] [Indexed: 05/02/2023]
Abstract
BACKGROUND SARS-CoV-2 ribonucleic acid (RNA) has been detected in feces, but RNA is not infectious. This systematic review aims to answer if fecal SARS-CoV-2 is experimentally infectious and if evidence of human fecal-oral SARS-CoV-2 transmission exists. METHODS On September 19, 2022, we searched PubMed, Embase, Web of Science, medRxiv, and bioRxiv. Biomedical studies inoculating SARS-CoV-2 from feces, rectal, or anal swabs in cells, tissue, organoids, or animals were included. Epidemiological studies of groups differing in exposure to fecal SARS-CoV-2 were included. Risk of bias was assessed using standardized tools. Results were summarized by vote counting, tabulation, and a harvest plot. PROSPERO registration no. CRD42020221719. RESULTS A total of 4,874 studies were screened; 26 studies were included; and 13 out of 23 biomedical studies (56.5%) succeeded in infection. Two (66.7%) epidemiological studies found limited evidence suggesting fecal-oral transmission. All studies had concerns about the risk of bias. CONCLUSIONS It is possible to experimentally infect cell cultures, organoids, and animals with fecal SARS-CoV-2. No strong epidemiologic evidence was found to support human fecal-oral transmission. We advise future research to study fecal infectivity at different time points during infection, apply appropriate controls, use in vivo models, and study fecal exposure as a risk factor of transmission in human populations.
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Arienzo A, Gallo V, Tomassetti F, Pitaro N, Pitaro M, Antonini G. A narrative review of alternative transmission routes of COVID 19: what we know so far. Pathog Glob Health 2023; 117:681-695. [PMID: 37350182 PMCID: PMC10614718 DOI: 10.1080/20477724.2023.2228048] [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] [Indexed: 06/24/2023] Open
Abstract
The Coronavirus disease 19 (COVID-19) pandemics, caused by severe acute respiratory syndrome coronaviruses, SARS-CoV-2, represent an unprecedented public health challenge. Beside person-to-person contagion via airborne droplets and aerosol, which is the main SARS-CoV-2's route of transmission, alternative modes, including transmission via fomites, food and food packaging, have been investigated for their potential impact on SARS-CoV-2 diffusion. In this context, several studies have demonstrated the persistence of SARS-CoV-2 RNA and, in some cases, of infectious particles on exposed fomites, food and water samples, confirming their possible role as sources of contamination and transmission. Indeed, fomite-to-human transmission has been demonstrated in a few cases where person-to-person transmission had been excluded. In addition, recent studies supported the possibility of acquiring COVID-19 through the fecal-oro route; the occurrence of COVID-19 gastrointestinal infections, in the absence of respiratory symptoms, also opens the intriguing possibility that these cases could be directly related to the ingestion of contaminated food and water. Overall, most of the studies considered these alternative routes of transmission of low epidemiological relevance; however, it should be considered that they could play an important role, or even be prevalent, in settings characterized by different environmental and socio-economic conditions. In this review, we discuss the most recent findings regarding SARS-CoV-2 alternative transmission routes, with the aim to disclose what is known about their impact on COVID-19 spread and to stimulate research in this field, which could potentially have a great impact, especially in low-resource contexts.
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Affiliation(s)
| | | | | | | | - Michele Pitaro
- National Institute of Biostructures and Biosystems (INBB), Rome, Italy
| | - Giovanni Antonini
- National Institute of Biostructures and Biosystems (INBB), Rome, Italy
- Department of Science, Roma Tre University, Rome, Italy
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Kononova Y, Adamenko L, Kazachkova E, Solomatina M, Romanenko S, Proskuryakova A, Utkin Y, Gulyaeva M, Spirina A, Kazachinskaia E, Palyanova N, Mishchenko O, Chepurnov A, Shestopalov A. Features of SARS-CoV-2 Replication in Various Types of Reptilian and Fish Cell Cultures. Viruses 2023; 15:2350. [PMID: 38140591 PMCID: PMC10748073 DOI: 10.3390/v15122350] [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: 10/11/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND SARS-CoV-2 can enter the environment from the feces of COVID-19 patients and virus carriers through untreated sewage. The virus has shown the ability to adapt to a wide range of hosts, so the question of the possible involvement of aquafauna and animals of coastal ecosystems in maintaining its circulation remains open. METHODS the aim of this work was to study the tropism of SARS-CoV-2 for cells of freshwater fish and reptiles, including those associated with aquatic and coastal ecosystems, and the effect of ambient temperature on this process. In a continuous cell culture FHM (fathead minnow) and diploid fibroblasts CGIB (silver carp), SARS-CoV-2 replication was not maintained at either 25 °C or 29 °C. At 29 °C, the continuous cell culture TH-1 (eastern box turtle) showed high susceptibility to SARS-CoV-2, comparable to Vero E6 (development of virus-induced cytopathic effect (CPE) and an infectious titer of 7.5 ± 0.17 log10 TCID50/mL on day 3 after infection), and primary fibroblasts CNI (Nile crocodile embryo) showed moderate susceptibility (no CPE, infectious titer 4.52 ± 0.14 log10 TCID50/mL on day 5 after infection). At 25 °C, SARS-CoV-2 infection did not develop in TH-1 and CNI. CONCLUSIONS our results show the ability of SARS-CoV-2 to effectively replicate without adaptation in the cells of certain reptile species when the ambient temperature rises.
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Affiliation(s)
- Yulia Kononova
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Lyubov Adamenko
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Evgeniya Kazachkova
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Mariya Solomatina
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Svetlana Romanenko
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia; (S.R.); (A.P.); (Y.U.)
| | - Anastasia Proskuryakova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia; (S.R.); (A.P.); (Y.U.)
| | - Yaroslav Utkin
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia; (S.R.); (A.P.); (Y.U.)
| | - Marina Gulyaeva
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
- The Department of Natural Science, Novosibirsk State University, 2, Pirogova St., Novosibirsk 630090, Russia
| | - Anastasia Spirina
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Elena Kazachinskaia
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Natalia Palyanova
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Oksana Mishchenko
- 48 Central Research Institute of the Ministry of Defense of the Russian Federation, Moscow 141306, Russia;
| | - Alexander Chepurnov
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Alexander Shestopalov
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
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Khemiri H, Gdoura M, Ben Halima S, Krichen H, Cammà C, Lorusso A, Ancora M, Di Pasquale A, Cherni A, Touzi H, Sadraoui A, Meddeb Z, Hogga N, Ammi R, Triki H, Haddad-Boubaker S. SARS-CoV-2 excretion kinetics in nasopharyngeal and stool samples from the pediatric population. Front Med (Lausanne) 2023; 10:1226207. [PMID: 38020093 PMCID: PMC10643538 DOI: 10.3389/fmed.2023.1226207] [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: 05/20/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for serious respiratory infections in humans. Even in the absence of respiratory symptoms, gastrointestinal (GI) signs were commonly reported in adults and children. Thus, oral-fecal transmission was suspected as a possible route of infection. The objective of this study was to describe RNA shedding in nasopharyngeal and stool samples obtained from asymptomatic and symptomatic children and to investigate virus viability. Methods This study included 179 stool and 191 nasopharyngeal samples obtained from 71 children, which included symptomatic (n = 64) and asymptomatic (n = 7) ones. They were collected every 7 days from the onset of the infection until negativation. Viral RNA was detected by real-time RT-PCR, targeting the N and ORF1 genes. Whole-genome sequencing was performed for positive cases. Viral isolation was assessed on Vero cells, followed by molecular detection confirmation. Results All cases included in this study (n = 71) were positive in their nasopharyngeal samples. SARS-CoV-2 RNA was detected in 36 stool samples obtained from 15 out of 71 (21.1%) children; 13 were symptomatic and two were asymptomatic. Excretion periods varied from 7 to 21 days and 7 to 14 days in nasopharyngeal and fecal samples, respectively. Four variants were detected: Alpha (n = 3), B.1.160 (n = 3), Delta (n = 7), and Omicron (n = 1). Inoculation of stool samples on cell culture showed no specific cytopathic effect. All cell culture supernatants were negative for RT-qPCR. Conclusion Our study demonstrated nasopharyngeal and fecal shedding of SARS-CoV-2 RNA by children up to 21 and 14 days, respectively. Fecal shedding was recorded in symptomatic and asymptomatic children. Nevertheless, SARS-CoV-2 was not isolated from positive stool samples.
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Affiliation(s)
- Haifa Khemiri
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Mariem Gdoura
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Samar Ben Halima
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Henda Krichen
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Massimo Ancora
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Adriano Di Pasquale
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Asma Cherni
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Henda Touzi
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Amel Sadraoui
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Zina Meddeb
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nahed Hogga
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Radhia Ammi
- Service of External Consultants, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sondes Haddad-Boubaker
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for the EMR, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- LR 20 IPT 02 Laboratory of Virus, Host and Vectors, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
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Atoui A, Cordevant C, Chesnot T, Gassilloud B. SARS-CoV-2 in the environment: Contamination routes, detection methods, persistence and removal in wastewater treatment plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163453. [PMID: 37059142 PMCID: PMC10091716 DOI: 10.1016/j.scitotenv.2023.163453] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 06/01/2023]
Abstract
The present study reviewed the occurrence of SARS-CoV-2 RNA and the evaluation of virus infectivity in feces and environmental matrices. The detection of SARS-CoV-2 RNA in feces and wastewater samples, reported in several studies, has generated interest and concern regarding the possible fecal-oral route of SARS-CoV-2 transmission. To date, the presence of viable SARS-CoV-2 in feces of COVID-19 infected people is not clearly confirmed although its isolation from feces of six different patients. Further, there is no documented evidence on the infectivity of SARS-CoV-2 in wastewater, sludge and environmental water samples, although the viral genome has been detected in these matrices. Decay data revealed that SARS-CoV-2 RNA persisted longer than infectious particle in all aquatic environment, indicating that genome quantification of SARS-CoV-2 does not imply the presence of infective viral particles. In addition, this review also outlined the fate of SARS-CoV-2 RNA during the different steps in the wastewater treatment plant and focusing on the virus elimination along the sludge treatment line. Studies showed complete removal of SARS-CoV-2 during the tertiary treatment. Moreover, thermophilic sludge treatments present high efficiency in SARS-CoV-2 inactivation. Further studies are required to provide more evidence with respect to the inactivation behavior of infectious SARS-CoV-2 in different environmental matrices and to examine factors affecting SARS-CoV-2 persistence.
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Affiliation(s)
- Ali Atoui
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54 000 Nancy, France.
| | - Christophe Cordevant
- ANSES, Strategy and Programs Department, Research and Reference Division, Maisons-Alfort F-94 700, France
| | - Thierry Chesnot
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54 000 Nancy, France
| | - Benoît Gassilloud
- ANSES, Nancy Laboratory for Hydrology, Water Microbiology Unit, 40, rue Lionnois, 54 000 Nancy, France
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10
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Mendes-Correa MC, Salomão MC, Ghilardi F, Tozetto-Mendoza TR, Santos Villas-Boas L, de Paula AV, Paiao HGO, da Costa AC, Leal FE, Ferraz ADBC, Sales FCS, Claro IM, Ferreira NE, Pereira GM, da Silva AR, Freire W, Espinoza EPS, Manuli ER, Romano CM, de Jesus JG, Sabino EC, Witkin SS. SARS-CoV-2 Detection and Culture in Different Biological Specimens from Immunocompetent and Immunosuppressed COVID-19 Patients Infected with Two Different Viral Strains. Viruses 2023; 15:1270. [PMID: 37376568 DOI: 10.3390/v15061270] [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: 04/05/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 06/29/2023] Open
Abstract
Introduction-The dynamics of SARS-CoV-2 shedding and replication in humans remain incompletely understood. Methods-We analyzed SARS-CoV-2 shedding from multiple sites in individuals with an acute COVID-19 infection by weekly sampling for five weeks in 98 immunocompetent and 25 immunosuppressed individuals. Samples and culture supernatants were tested via RT-PCR for SARS-CoV-2 to determine viral clearance rates and in vitro replication. Results-A total of 2447 clinical specimens were evaluated, including 557 nasopharyngeal swabs, 527 saliva samples, 464 urine specimens, 437 anal swabs and 462 blood samples. The SARS-CoV-2 genome sequences at each site were classified as belonging to the B.1.128 (ancestral strain) or Gamma lineage. SARS-CoV-2 detection was highest in nasopharyngeal swabs regardless of the virus strain involved or the immune status of infected individuals. The duration of viral shedding varied between clinical specimens and individual patients. Prolonged shedding of potentially infectious virus varied from 10 days up to 191 days, and primarily occurred in immunosuppressed individuals. Virus was isolated in culture from 18 nasal swab or saliva samples collected 10 or more days after onset of disease. Conclusions-Our findings indicate that persistent SARS-CoV-2 shedding may occur in both competent or immunosuppressed individuals, at multiple clinical sites and in a minority of subjects is capable of in vitro replication.
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Affiliation(s)
- Maria Cássia Mendes-Correa
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, São Paulo 05403-010, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Matias Chiarastelli Salomão
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, São Paulo 05403-010, Brazil
- Rua Peixoto Gomide, 645, Sao Paulo 01409-002, Brazil
| | - Fábio Ghilardi
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Tania Regina Tozetto-Mendoza
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Lucy Santos Villas-Boas
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Anderson Vicente de Paula
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Heuder Gustavo Oliveira Paiao
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Antonio Charlys da Costa
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Fábio E Leal
- Faculdade de Medicina da, Universidade Municipal de Sao Caetano do Sul, São Paulo 09521-160, Brazil
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20230-130, Brazil
| | | | - Flavia C S Sales
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Ingra M Claro
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Noely E Ferreira
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Geovana M Pereira
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Almir Ribeiro da Silva
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Wilton Freire
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Evelyn Patricia Sánchez Espinoza
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Erika R Manuli
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Faculdade de Medicina da, Universidade Municipal de Sao Caetano do Sul, São Paulo 09521-160, Brazil
| | - Camila M Romano
- Hospital das Clínicas, Faculdade de Medicina, Universidade de Sao Paulo, São Paulo 05403-010, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Jaqueline G de Jesus
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
| | - Ester C Sabino
- Departamento de Molestias Infecciosas e Parasitarias, Aculdade de Medicina, Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar, n. 470, São Paulo 05403-000, Brazil
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Faculdade de Medicina da, Universidade Municipal de Sao Caetano do Sul, São Paulo 09521-160, Brazil
| | - Steven S Witkin
- Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo 05403-000, Brazil
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY 10065, USA
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11
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Lanzarini NM, Mannarino CF, Ribeiro AVC, Prado T, Vahia LS, Siqueira MM, Resende PC, Quintaes BR, Miagostovich MP. SARS-CoV-2 surveillance-based on municipal solid waste leachate in Brazil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:67368-67377. [PMID: 37101215 PMCID: PMC10132925 DOI: 10.1007/s11356-023-27019-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/10/2023] [Indexed: 05/25/2023]
Abstract
Municipal solid waste leachate-based epidemiology is an alternative viral tracking tool that applies fresh truck leachate as an early warning of public health emergencies. This study aimed to investigate the potential of SARS-CoV-2 surveillance based on solid waste fresh truck leachate. Twenty truck leachate samples were ultracentrifugated, nucleic acid extracted, and real-time RT-qPCR SARS-CoV-2 N1/N2 applied. Viral isolation, variant of concern (N1/N2) inference, and whole genome sequencing were also performed. SARS-CoV-2 was detected on 40% (8/20) of samples, with a concentration from 2.89 to 6.96 RNA Log10 100 mL-1. The attempt to isolate SARS-CoV-2 and recover the whole genome was not successful; however, positive samples were characterized as possible pre-variant of concern (pre-VOC), VOC Alpha (B.1.1.7) and variant of interest Zeta (P.2). This approach revealed an alternative tool to infer SARS-CoV-2 in the environment and may help the management of local surveillance, health, and social policies.
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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
- Department of Sanitation and Environmental Health, Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - André Vinicius Costa Ribeiro
- Department of Sanitation and Environmental Health, Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Tatiana Prado
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Leonardo Saboia Vahia
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, 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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12
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Scott G, Evens N, Porter J, Walker DI. The Inhibition and Variability of Two Different RT-qPCR Assays Used for Quantifying SARS-CoV-2 RNA in Wastewater. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:71-81. [PMID: 36790663 PMCID: PMC9930079 DOI: 10.1007/s12560-022-09542-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/01/2022] [Indexed: 06/18/2023]
Abstract
Faecal shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its subsequent detection in wastewater turned the spotlight onto wastewater-based epidemiology (WBE) for monitoring the coronavirus-disease 2019 (COVID-19) pandemic. WBE for SARS-CoV-2 has been deployed in 70 countries, providing insights into disease prevalence, forecasting and the spatiotemporal tracking and emergence of SARS-CoV-2 variants. Wastewater, however, is a complex sample matrix containing numerous reverse transcription quantitative PCR (RT-qPCR) inhibitors whose concentration and diversity are influenced by factors including population size, surrounding industry and agriculture and climate. Such differences in the RT-qPCR inhibitor profile are likely to impact the quality of data produced by WBE and potentially produce erroneous results.To help determine the possible impact of RT-qPCR assay on data quality, two assays employed by different laboratories within the UK's SARS-CoV-2 wastewater monitoring programme were assessed in the Cefas laboratory in Weymouth, UK. The assays were based on Fast Virus (FV) and qScript (qS) chemistries using the same primers and probes, but at different concentrations and under different cycling conditions. Bovine serum albumin and MgSO4 were also added to the FV assay reaction mixture. Two-hundred and eighty-six samples were analysed, and an external control RNA (EC RNA)-based method was used to measure RT-qPCR inhibition. Compared with qS, FV showed a 40.5% reduction in mean inhibition and a 57.0% reduction in inter-sample inhibition variability. A 4.1-fold increase in SARS-CoV-2 quantification was seen for FV relative to qS; partially due (1.5-fold) to differences in reverse transcription efficiency and the use of a dsDNA standard. Analytical variability was reduced by 51.2% using FV while qS increased the number of SARS-CoV-2 negative samples by 2.6-fold. This study indicates the importance of thorough method optimisation for RT-qPCR-based WBE which should be performed using a selection of samples which are representative of the physiochemical properties of wastewater. Furthermore, RT-qPCR inhibition, analytical variability and reverse transcription efficiency should be key considerations during assay optimisation. A standardised framework for the optimisation and validation of WBE procedures should be formed including concessions for emergency response situations that would allow flexibility in the process to address the difficult balance between the urgency of providing data and the availability of resources.
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Affiliation(s)
- George Scott
- Centre for Environment, Fisheries and Aquaculture Science, The Nothe, Barrack Road, Weymouth, DT4 8UB, UK.
| | - Nicholas Evens
- Environment Agency, National Monitoring, Starcross, Exeter, EX6 8FD, UK
| | - Jonathan Porter
- Environment Agency, National Monitoring, Starcross, Exeter, EX6 8FD, UK
| | - David I Walker
- Centre for Environment, Fisheries and Aquaculture Science, The Nothe, Barrack Road, Weymouth, DT4 8UB, UK
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13
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[Viruses present in the environment: virological considerations and examples of their impact on human health]. REVUE FRANCOPHONE DES LABORATOIRES : RFL 2023; 2023:33-43. [PMID: 36879984 PMCID: PMC9978926 DOI: 10.1016/s1773-035x(23)00053-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Animal viruses are present in most human environments. Their viability in these media is very variable and the most important element that conditions this viability is the existence or not of a phospholipid envelope surrounding the nucleocapsid. After some general considerations on the structure of viruses, their multiplication cycle and their resistance to different physico-chemical agents, some examples of the impact of animal viruses present in the environment on human health will be presented. The situations that are related concern recent epidemiological events: circulation of type 2 polioviruses derived from the Sabin vaccine strain in the wastewater of New York, London and Jerusalem; risk of transmission of Sars-CoV-2 during the spreading of sludge from wastewater treatment plants on agricultural land in the era of the Covid-19 pandemic; « new » forms of food-borne poisoning of viral origin (hepatitis E, tick-borne encephalitis, Nipah virus infection); contamination by epidemic viruses of mobile phones used by pediatricians; role of fomites in the spread of orthopoxvirus infections (smallpox, cowpox, monkeypox). The risk attached to animal viruses present in the environment must be assessed in a measured way without overestimating or underestimating their potential consequences for human health.
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14
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Abstract
SARS-CoV-2 viral load and detection of infectious virus in the respiratory tract are the two key parameters for estimating infectiousness. As shedding of infectious virus is required for onward transmission, understanding shedding characteristics is relevant for public health interventions. Viral shedding is influenced by biological characteristics of the virus, host factors and pre-existing immunity (previous infection or vaccination) of the infected individual. Although the process of human-to-human transmission is multifactorial, viral load substantially contributed to human-to-human transmission, with higher viral load posing a greater risk for onward transmission. Emerging SARS-CoV-2 variants of concern have further complicated the picture of virus shedding. As underlying immunity in the population through previous infection, vaccination or a combination of both has rapidly increased on a global scale after almost 3 years of the pandemic, viral shedding patterns have become more distinct from those of ancestral SARS-CoV-2. Understanding the factors and mechanisms that influence infectious virus shedding and the period during which individuals infected with SARS-CoV-2 are contagious is crucial to guide public health measures and limit transmission. Furthermore, diagnostic tools to demonstrate the presence of infectious virus from routine diagnostic specimens are needed.
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Affiliation(s)
- Olha Puhach
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Benjamin Meyer
- Centre for Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Isabella Eckerle
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland.
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
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15
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Simple Wastewater Preparation Protocol Applied to Monitor the Emergence of the Omicron 21L/BA.2 Variant by Genome Sequencing. Viruses 2023; 15:v15020268. [PMID: 36851484 PMCID: PMC9965846 DOI: 10.3390/v15020268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/22/2022] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
Abstract
Detecting and monitoring viruses in wastewater samples have been reported as useful ways of tracking SARS-CoV-2 epidemic trends. However, there is currently no unanimously recognised method of processing samples to identify and quantify SARS-CoV-2 variants in wastewater. We aimed to implement a method that was as simple as possible in order to be used universally. In a study performed between January 2022 and June 2022 in the city of Marseille, France, we first evaluated the impact of the sample preservation strategy. We then compared ultracentrifugation to ultrafiltration and several steps of filtration to determine the optimal approach for virus concentration. As a proof-of-concept, the definitive protocol was applied to next-generation sequencing of SARS-CoV-2 in wastewater to monitor the emergence of the Omicron variant in the city. For sewage water to be processed in the week following the sampling, storage at +4 °C is sufficient, with less than 1 Ct loss. Filtration with a 5 µm syringe filter, then with a 0.8 µm filtration unit, followed by ultrafiltration was the optimal protocol, leading to an average increase of 3.24 Ct when the starting Ct was on average 38 in the wastewater. This made it possible to observe the emergence of the Omicron 21L/BA.2 variant after Omicron 21K/BA.1 by genome sequencing over a period ranging from 20 February to 10 April 2022 in agreement with observations based on patient data. To conclude, by using a simple method requiring only basic filters and a centrifuge as equipment, it is possible to accurately track the relative incidence rates and the emergence of SARS-CoV-2 variants based on sewage samples.
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Intestinal Shedding of SARS-CoV-2 in Children: No Evidence for Infectious Potential. Microorganisms 2022; 11:microorganisms11010033. [PMID: 36677323 PMCID: PMC9864026 DOI: 10.3390/microorganisms11010033] [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: 12/01/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The clinical courses of COVID-19 in children are often mild and may remain undiagnosed, but prolonged intestinal virus shedding has been documented, thus potentially enabling fecal-oral transmission. However, the infectious potential of SARS-CoV-2 viruses excreted with feces has remained unclear. Here, we investigated 247 stool specimens from 213 pediatric patients to assess the prevalence of intestinal SARS-CoV-2 shedding in hospitalized children without or with COVID-19 and determined the infectious capacity of stool-borne viruses. Upon RT-qPCR screening, the infectivity of virus-positive samples was tested in cell culture using the Vero-E6 permissive cell line. SARS-CoV-2 RNA was detected by RT-qPCR in 32 (13%) stool specimens, but the analysis of virus-positive samples in cell culture revealed no cytopathic effects attributable to SARS-CoV-2-related cell damage. Our findings do not support the notion of potential fecal-oral SARS-CoV-2 spreading, thus questioning the role of hygienic measures designed to prevent this mode of viral transmission.
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17
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Stoll ML. Therapeutic alteration of the microbiota in rheumatic diseases: Hype or potential? Best Pract Res Clin Rheumatol 2022; 36:101806. [PMID: 36564273 DOI: 10.1016/j.berh.2022.101806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Multiple studies have demonstrated abnormalities in the contents of the fecal microbiota in patients with a variety of forms of arthritis. This has prompted interest in microbial-altering therapy as a therapeutic tool. While antibiotics as a long-term therapeutic tool have largely fallen out of favor, there have been multiple studies evaluating probiotics in rheumatoid arthritis, spondyloarthritis, or systemic sclerosis; a small number of studies have tested fecal microbial transplantation (FMT) in rheumatic diseases. Although probiotics were well tolerated, few studies detected meaningful clinical benefit regardless of indication. Likewise, one of the two randomized studies evaluating FMT showed minimal clinical benefit, while the other demonstrated worsening compared to sham treatment. In this review article, I summarize the literature on probiotics and FMT in rheumatic diseases, discuss potential reasons for the absence of demonstrable benefit, and suggest avenues of future direction of research.
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Affiliation(s)
- Matthew L Stoll
- University of Alabama at Birmingham, 1600 7th Avenue South, Children's Park Place Suite G10, Birmingham, AL 35233 UK.
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18
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Clerbaux LA, Mayasich SA, Muñoz A, Soares H, Petrillo M, Albertini MC, Lanthier N, Grenga L, Amorim MJ. Gut as an Alternative Entry Route for SARS-CoV-2: Current Evidence and Uncertainties of Productive Enteric Infection in COVID-19. J Clin Med 2022; 11:5691. [PMID: 36233559 PMCID: PMC9573230 DOI: 10.3390/jcm11195691] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/17/2022] [Accepted: 09/20/2022] [Indexed: 12/15/2022] Open
Abstract
The gut has been proposed as a potential alternative entry route for SARS-CoV-2. This was mainly based on the high levels of SARS-CoV-2 receptor expressed in the gastrointestinal (GI) tract, the observations of GI disorders (such as diarrhea) in some COVID-19 patients and the detection of SARS-CoV-2 RNA in feces. However, the underlying mechanisms remain poorly understood. It has been proposed that SARS-CoV-2 can productively infect enterocytes, damaging the intestinal barrier and contributing to inflammatory response, which might lead to GI manifestations, including diarrhea. Here, we report a methodological approach to assess the evidence supporting the sequence of events driving SARS-CoV-2 enteric infection up to gut adverse outcomes. Exploring evidence permits to highlight knowledge gaps and current inconsistencies in the literature and to guide further research. Based on the current insights on SARS-CoV-2 intestinal infection and transmission, we then discuss the potential implication on clinical practice, including on long COVID. A better understanding of the GI implication in COVID-19 is still needed to improve disease management and could help identify innovative therapies or preventive actions targeting the GI tract.
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Affiliation(s)
| | - Sally A. Mayasich
- University of Wisconsin-Madison Aquatic Sciences Center at US EPA, Duluth, MN 55804, USA
| | - Amalia Muñoz
- European Commission, Joint Research Centre (JRC), 2440 Geel, Belgium
| | - Helena Soares
- Laboratory of Human Immunobiology and Pathogenesis, iNOVA4Health, Faculdade de Ciências Médicas—Nova Medical School, Universidade Nova de Lisboa, 1099-085 Lisbon, Portugal
| | | | | | - Nicolas Lanthier
- Laboratory of Hepatogastroenterology, Service d’Hépato-Gastroentérologie, Cliniques Universitaires Saint-Luc, UCLouvain, 1200 Brussels, Belgium
| | - Lucia Grenga
- Département Médicaments et Technologies pour la Santé, Commissariat à l’Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay, 91190 Paris, France
| | - Maria-Joao Amorim
- Instituto Gulbenkian de Ciência, 2780-156 Lisbon, Portugal
- Católica Biomedical Research Centre, Católica Medical School, Universidade Católica Portuguesa, 1649-023 Lisbon, Portugal
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19
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Dallner M, Harlow J, Nasheri N. Efficacy of washing produce in removing human coronavirus OC43 and murine norovirus. J Appl Microbiol 2022; 133:1800-1807. [PMID: 35702940 PMCID: PMC9545982 DOI: 10.1111/jam.15667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/07/2022] [Accepted: 06/11/2022] [Indexed: 11/27/2022]
Abstract
AIMS Fresh produce is often a vehicle for the transmission of foodborne pathogens such as human norovirus. Thus, it is recommended to wash the surface of produce before consumption, and one of the most common ways to wash produce is by rinsing under running tap water. This study determined the effectiveness of removal of human coronavirus-OC43 (HCoV-OC43), as a surrogate for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and murine norovirus-1 (MNV-1), as a surrogate for human norovirus, from contaminated lettuce, apples and cucumbers. METHODS AND RESULTS The produce surfaces were artificially inoculated in conjunction with faecal material to represent natural contamination. Rinsing under tap water for 10 s at 40 ml/s removed 1.94 ± 0.44, 1.42 ± 0.00 and 1.42 ± 0.42 log of HCoV-OC43 from apple, cucumber and lettuce respectively. The same washing technique removed 1.77 ± 0.17, 1.42 ± 0.07 and 1.79 ± 0.14 log of MNV-1 from apple, cucumber and lettuce respectively. This washing technique was effective at reducing a significant amount of viral contamination, however, it was not enough to eliminate the entire contamination. There was no significant difference in the reduction of viral load between the two viruses, nor between the three surfaces tested in this study. CONCLUSIONS Our data suggest that washing under tap water would be an efficient way of reducing the risk of foodborne viral transmission only if the level of contamination is less than 2 log PFU. SIGNIFICANCE AND IMPACT OF STUDY This study demonstrates that running tap water was effective at reducing the amount of infectious HCoV-OC43 and MNV on produce surfaces, and washing produce continues to be an important task to perform prior to consumption to avoid infection by foodborne viruses, particularly for foods which are eaten raw.
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Affiliation(s)
- Matthew Dallner
- National Food Virology Reference CentreBureau of Microbial Hazards, Health CanadaOttawaOntarioCanada
| | - Jennifer Harlow
- National Food Virology Reference CentreBureau of Microbial Hazards, Health CanadaOttawaOntarioCanada
| | - Neda Nasheri
- National Food Virology Reference CentreBureau of Microbial Hazards, Health CanadaOttawaOntarioCanada
- Department of BiochemistryMicrobiology and Immunology, Faculty of Medicine, University of OttawaOttawaOntarioCanada
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20
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Wurtzer S, Lacote S, Murri S, Marianneau P, Monchatre-Leroy E, Boni M, Ferraris O, Maday Y, Kébé O, Dia N, Peyrefitte C, Sokol H, Moulin L, Maréchal V. Reduction in SARS-CoV-2 Virus Infectivity in Human and Hamster Feces. Viruses 2022; 14:v14081777. [PMID: 36016399 PMCID: PMC9415851 DOI: 10.3390/v14081777] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/05/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022] Open
Abstract
Objective: There is extensive evidence that SARS-CoV-2 replicates in the gastrointestinal tract. However, the infectivity of virions in feces is poorly documented. Although the primary mode of transmission is airborne, the risk of transmission from contaminated feces remains to be assessed. Design: The persistence of SARS-CoV-2 (infectivity and RNA) in human and animal feces was evaluated by virus isolation on cell culture and RT-qPCR, respectively. The exposure of golden Syrian hamsters to experimentally contaminated feces through intranasal inoculation has also been tested to assess the fecal-oral transmission route. Results: For periods that are compatible with average intestinal transit, the SARS-CoV-2 genome was noticeably stable in human and animal feces, contrary to the virus infectivity that was reduced in a time- and temperature-dependent manner. In human stools, this reduction was variable depending on the donors. Viral RNA was excreted in the feces of infected hamsters, but exposure of naïve hamsters to feces of infected animals did not lead to any productive infection. Conversely, hamsters could be experimentally infected following exposure to spiked fresh feces. Conclusion: Infection following exposure to naturally contaminated feces has been suspected but has not been established so far. The present work demonstrates that SARS-CoV-2 rapidly lost infectivity in spiked or naturally infected feces. Although the possibility of persistent viral particles in human or animal feces cannot be fully ruled out, SARS-CoV-2 transmission after exposure to contaminated feces is unlikely.
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Affiliation(s)
- Sébastien Wurtzer
- Research and Development Department, Eau de Paris, 33 Avenue Jean Jaurès, 94200 Ivry-sur-Seine, France
- Correspondence:
| | - Sandra Lacote
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France
| | - Severine Murri
- ANSES—Laboratoire de Lyon, Unité Virologie, 69007 Lyon, France
| | | | | | - Mickaël Boni
- French Armed Forces Biomedical Research Institute, 91220 Brétigny-sur-Orge, France
| | - Olivier Ferraris
- French Armed Forces Biomedical Research Institute, 91220 Brétigny-sur-Orge, France
| | - Yvon Maday
- Laboratoire Jacques-Louis Lions (LJLL), CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France
- Institut Universitaire de France, 75005 Paris, France
| | | | - Ndongo Dia
- Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Christophe Peyrefitte
- Institut Pasteur de Dakar, Dakar 12900, Senegal
- Institut Pasteur de la Guyane, 97300 Cayenne, France
| | - Harry Sokol
- INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Sorbonne Université, 75571 Paris, France
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, 75571 Paris, France
- INRAe, UMR1319 Micalis and AgroParisTech, 78350 Jouy en Josas, France
| | | | - Laurent Moulin
- Research and Development Department, Eau de Paris, 33 Avenue Jean Jaurès, 94200 Ivry-sur-Seine, France
| | - Vincent Maréchal
- INSERM U938, Centre de Recherche Saint-Antoine, Sorbonne Université, 75012 Paris, France
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21
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A Methodological Approach to Water Concentration to Investigate the Presence of SARS-CoV-2 RNA in Surface Freshwaters. Pathogens 2022; 11:pathogens11080845. [PMID: 36014966 PMCID: PMC9415985 DOI: 10.3390/pathogens11080845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
During the COVID-19 public health emergency, an increasing number of studies reported the occurrence of SARS-CoV-2 in wastewaters worldwide, but little is known about the presence of the virus in surface freshwaters. The aim of the current study was to develop and validate an appropriate and scalable methodological approach for the concentration and detection of SARS-CoV-2 from surface freshwater samples, collected within the Milan rural network subjected to flood spillways activity. Overall, both surface water and distilled water samples spiked with inactivated SARS-CoV-2 were used to validate the concentration method for pathogens determination. Two pre-filtration systems, filter paper and Sartolab® P20 (Sartorius, Germany) and two concentration methods, two-phase (PEG-dextran method) separation and tangential flow ultrafiltration (UF), were compared. The effects of pre-filtration and concentration on viral nucleic acid recovery were assessed through real time RT-PCR targeting SARS-CoV-2 and the internal viral control PMMoV (Pepper Mild Mottle Virus). Our results showed that UF is more sensitive than the PEG-dextran method in viral acid nucleic recovery from surface water samples. Better results were obtained pre-filtering samples with Sartolab® P20 and extracting the nucleic acids with undiluted silica, rather than diluted as required by the standard protocol. The proposed method will be used for the monitoring of surface waters in the Milan area.
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22
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Arnaboldi S, Mangeri L, Galuppini E, Righi F, Tilola M, Scarazzato A, Bertasi B, Finazzi G, Varisco G, Filipello V, Losio MN. Is SARS-CoV-2 a Concern for Food Safety? A Very Low Prevalence from a Food Survey during the COVID-19 Pandemic in Northern Italy. Foods 2022; 11:foods11142096. [PMID: 35885339 PMCID: PMC9324013 DOI: 10.3390/foods11142096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/08/2022] [Accepted: 07/13/2022] [Indexed: 02/04/2023] Open
Abstract
In 2019, SARS-CoV-2 was identified as the cause of an easily transmissible disease that was declared as a world pandemic. Foodborne transmission was never reported. However, early studies suggested that food could be involved in SARS-CoV-2 entry in the human gastrointestinal tract leading to possible infection, and highlighting the importance of further studies to inspect possible issues linked to food consumption. In this perspective, this work aimed at monitoring SARS-CoV-2 presence in some food and mains water samples in Northern Italy during the COVID-19 pandemic (2020–2022). A total of 1806 foods, 112 mains water samples, and 580 swabs on meat and dairy product surfaces were analyzed for SARS-CoV-2 RNA detection by Real-time PCR. All the analyzed samples were negative to viral RNA detection with the exception of one vegetable sample. Even if data on foodborne coronavirus transmission suggested a limited importance of this pathway, the impact of the current pandemic in Northern Italy deserved a rigorous investigation to rule out such possibility. Indeed, gaining insight on all SARS-CoV-2 possible transmission pathways, including the foodborne route, seemed of interest to maintain consumers’ confidence and trust in food safety, and for the effective management of the current, and future, possible pandemics.
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Affiliation(s)
- Sara Arnaboldi
- Food Safety Department, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via A. Bianchi 9, 25124 Brescia, Italy; (L.M.); (E.G.); (F.R.); (M.T.); (A.S.); (B.B.); (G.F.); (G.V.); (V.F.); (M.-N.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via Celoria 12, 20133 Milan, Italy
- Correspondence: ; Tel.: +39-0302290381
| | - Lucia Mangeri
- Food Safety Department, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via A. Bianchi 9, 25124 Brescia, Italy; (L.M.); (E.G.); (F.R.); (M.T.); (A.S.); (B.B.); (G.F.); (G.V.); (V.F.); (M.-N.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via Celoria 12, 20133 Milan, Italy
| | - Elisa Galuppini
- Food Safety Department, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via A. Bianchi 9, 25124 Brescia, Italy; (L.M.); (E.G.); (F.R.); (M.T.); (A.S.); (B.B.); (G.F.); (G.V.); (V.F.); (M.-N.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via Celoria 12, 20133 Milan, Italy
| | - Francesco Righi
- Food Safety Department, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via A. Bianchi 9, 25124 Brescia, Italy; (L.M.); (E.G.); (F.R.); (M.T.); (A.S.); (B.B.); (G.F.); (G.V.); (V.F.); (M.-N.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via Celoria 12, 20133 Milan, Italy
| | - Michela Tilola
- Food Safety Department, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via A. Bianchi 9, 25124 Brescia, Italy; (L.M.); (E.G.); (F.R.); (M.T.); (A.S.); (B.B.); (G.F.); (G.V.); (V.F.); (M.-N.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via Celoria 12, 20133 Milan, Italy
| | - Annalisa Scarazzato
- Food Safety Department, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via A. Bianchi 9, 25124 Brescia, Italy; (L.M.); (E.G.); (F.R.); (M.T.); (A.S.); (B.B.); (G.F.); (G.V.); (V.F.); (M.-N.L.)
| | - Barbara Bertasi
- Food Safety Department, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via A. Bianchi 9, 25124 Brescia, Italy; (L.M.); (E.G.); (F.R.); (M.T.); (A.S.); (B.B.); (G.F.); (G.V.); (V.F.); (M.-N.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via Celoria 12, 20133 Milan, Italy
| | - Guido Finazzi
- Food Safety Department, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via A. Bianchi 9, 25124 Brescia, Italy; (L.M.); (E.G.); (F.R.); (M.T.); (A.S.); (B.B.); (G.F.); (G.V.); (V.F.); (M.-N.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via Celoria 12, 20133 Milan, Italy
| | - Giorgio Varisco
- Food Safety Department, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via A. Bianchi 9, 25124 Brescia, Italy; (L.M.); (E.G.); (F.R.); (M.T.); (A.S.); (B.B.); (G.F.); (G.V.); (V.F.); (M.-N.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via Celoria 12, 20133 Milan, Italy
| | - Virginia Filipello
- Food Safety Department, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via A. Bianchi 9, 25124 Brescia, Italy; (L.M.); (E.G.); (F.R.); (M.T.); (A.S.); (B.B.); (G.F.); (G.V.); (V.F.); (M.-N.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via Celoria 12, 20133 Milan, Italy
| | - Marina-Nadia Losio
- Food Safety Department, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via A. Bianchi 9, 25124 Brescia, Italy; (L.M.); (E.G.); (F.R.); (M.T.); (A.S.); (B.B.); (G.F.); (G.V.); (V.F.); (M.-N.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), Via Celoria 12, 20133 Milan, Italy
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23
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Le Targa L, Wurtz N, Lacoste A, Penant G, Jardot P, Annessi A, Colson P, La Scola B, Aherfi S. SARS-CoV-2 Testing of Aircraft Wastewater Shows That Mandatory Tests and Vaccination Pass before Boarding Did Not Prevent Massive Importation of Omicron Variant into Europe. Viruses 2022; 14:v14071511. [PMID: 35891491 PMCID: PMC9319773 DOI: 10.3390/v14071511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Most new SARS-CoV-2 epidemics in France occurred following the importation from abroad of emerging viral variants. Currently, the risk of new variants being imported is controlled based on a negative screening test (PCR or antigenic) and proof of up-to-date vaccine status, such as the International Air Transport Association travel pass. METHODS The wastewater from two planes arriving in Marseille (France) from Addis Ababa (Ethiopia) in December 2021 was tested by RT-PCR to detect SARS-CoV2 and screen for variants. These tests were carried out between landing and customs clearance and were then sequenced by MiSeq Illumina. Antigenic tests and sequencing by NovaSeq were carried out on respiratory samples collected from the 56 passengers on the second flight. RESULTS SARS-CoV-2 RNA suspected of being from the Omicron BA.1 variant was detected in the aircraft's wastewater. SARS-CoV2 RNA was detected in 11 [20%) passengers and the Omicron BA.1 variant was identified. CONCLUSION Our work shows the efficiency of aircraft wastewater testing to detect SARS-CoV-2 cases among travellers and to identify the viral genotype. It also highlights the low efficacy of the current control strategy for flights entering France from outside Europe, which combines a requirement to produce a vaccine pass and proof of a negative test before boarding.
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Affiliation(s)
- Lorlane Le Targa
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Biosellal, 27 Chemin des Peupliers, 69570 Lyon, France
| | - Nathalie Wurtz
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Alexandre Lacoste
- Bataillon des Marins Pompiers de la ville de Marseille, 13005 Marseille, France; (A.L.); (A.A.)
| | - Gwilherm Penant
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Priscilla Jardot
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Alexandre Annessi
- Bataillon des Marins Pompiers de la ville de Marseille, 13005 Marseille, France; (A.L.); (A.A.)
| | - Philippe Colson
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Bernard La Scola
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Correspondence: (B.L.S.); (S.A.); Tel.: +33-413-732-401 (B.L.S. & S.A.); Fax: +33-413-732-402 (B.L.S.); +33-413-732-052 (S.A.)
| | - Sarah Aherfi
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Correspondence: (B.L.S.); (S.A.); Tel.: +33-413-732-401 (B.L.S. & S.A.); Fax: +33-413-732-402 (B.L.S.); +33-413-732-052 (S.A.)
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24
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Harlow J, Dallner M, Nasheri N. Protective Effect of Food Against Inactivation of Human Coronavirus OC43 by Gastrointestinal Fluids. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:212-216. [PMID: 35320506 PMCID: PMC8941299 DOI: 10.1007/s12560-022-09520-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
The involvement of the gastrointestinal (GI) tract in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection has been reported in multiple studies. Since it has been demonstrated that human intestinal epithelial cells support productive viral replication and that a substantial portion of infected individuals shed the virus in feces, the possibility of fecal-oral and fecal-respiratory modes of transmission have been proposed for SARS-CoV-2. In order to establish viral replication in the intestine, enteric viruses need to retain their infectivity in often low pH gastric fluids, and in intestinal fluids, which contain digestive enzymes and bile salts. In this study, we examined whether human coronaviruses OC43 (HCoV-OC43) can remain infectious in simulated GI fluids that models human fasting-state and fed-state, in the presence or absence of food. We demonstrated that except for fasting-state gastric fluid (pH 1.6), the virus can remain infectious in all other gastrointestinal fluids for 1 h. Furthermore, we demonstrated that presence of food could significantly improve viral survival in gastric fluids. Therefore, this study provides evidence that ingestion with food could protect the virus against inactivation by the GI fluids.
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Affiliation(s)
- Jennifer Harlow
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Health Canada, Ottawa, ON, Canada
| | - Matthew Dallner
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Health Canada, Ottawa, ON, Canada
| | - Neda Nasheri
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Health Canada, Ottawa, ON, Canada.
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
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25
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Osman IO, Garrec C, de Souza GAP, Zarubica A, Belhaouari DB, Baudoin JP, Lepidi H, Mege JL, Malissen B, Scola BL, Devaux CA. Control of CDH1/E-Cadherin Gene Expression and Release of a Soluble Form of E-Cadherin in SARS-CoV-2 Infected Caco-2 Intestinal Cells: Physiopathological Consequences for the Intestinal Forms of COVID-19. Front Cell Infect Microbiol 2022; 12:798767. [PMID: 35601094 PMCID: PMC9114883 DOI: 10.3389/fcimb.2022.798767] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/22/2022] [Indexed: 12/19/2022] Open
Abstract
COVID-19 is the biggest pandemic the world has seen this century. Alongside the respiratory damage observed in patients with severe forms of the disease, gastrointestinal symptoms have been frequently reported. These symptoms (e.g., diarrhoea), sometimes precede the development of respiratory tract illnesses, as if the digestive tract was a major target during early SARS-CoV-2 dissemination. We hypothesize that in patients carrying intestinal SARS-CoV-2, the virus may trigger epithelial barrier damage through the disruption of E-cadherin (E-cad) adherens junctions, thereby contributing to the overall gastrointestinal symptoms of COVID-19. Here, we use an intestinal Caco-2 cell line of human origin which expresses the viral receptor/co-receptor as well as the membrane anchored cell surface adhesion protein E-cad to investigate the expression of E-cad after exposure to SARS-CoV-2. We found that the expression of CDH1/E-cad mRNA was significantly lower in cells infected with SARS-CoV-2 at 24 hours post-infection, compared to virus-free Caco-2 cells. The viral receptor ACE2 mRNA expression was specifically down-regulated in SARS-CoV-2-infected Caco-2 cells, while it remained stable in HCoV-OC43-infected Caco-2 cells, a virus which uses HLA class I instead of ACE2 to enter cells. It is worth noting that SARS-CoV-2 induces lower transcription of TMPRSS2 (involved in viral entry) and higher expression of B0AT1 mRNA (that encodes a protein known to co-express with ACE2 on intestinal cells). At 48 hours post-exposure to the virus, we also detected a small but significant increase of soluble E-cad protein (sE-cad) in the culture supernatant of SARS-CoV-2-infected Caco-2 cells. The increase of sE-cad release was also found in the intestinal HT29 cell line when infected by SARS-CoV-2. Beside the dysregulation of E-cad, SARS-CoV-2 infection of Caco-2 cells also leads to the dysregulation of other cell adhesion proteins (occludin, JAMA-A, zonulin, connexin-43 and PECAM-1). Taken together, these results shed light on the fact that infection of Caco-2 cells with SARS-CoV-2 affects tight-, adherens-, and gap-junctions. Moreover, intestinal tissues damage was associated to the intranasal SARS-CoV-2 infection in human ACE2 transgenic mice.
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Affiliation(s)
- Ikram Omar Osman
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Marseille, France
| | - Clémence Garrec
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Marseille, France
| | - Gabriel Augusto Pires de Souza
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Ana Zarubica
- Centre d’Immunophénomique (CIPHE), Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), CELPHEDIA, PHENOMIN, Marseille, France
| | - Djamal Brahim Belhaouari
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Marseille, France
| | - Jean-Pierre Baudoin
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Hubert Lepidi
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
- Assitance Publique Hôpitaux de Marseille (APHM), Marseille, France
| | - Jean-Louis Mege
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Marseille, France
- Assitance Publique Hôpitaux de Marseille (APHM), Marseille, France
| | - Bernard Malissen
- Centre d’Immunophénomique (CIPHE), Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), CELPHEDIA, PHENOMIN, Marseille, France
| | - Bernard La Scola
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Christian Albert Devaux
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Marseille, France
- Centre National de la Recherche Scientifique (CNRS), Marseille, France
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FERCHICHI S, FATNASSI N, DHAOUADI A, ATTIA EL HILI H. [The hazards of SARS-COV-2 for aquatic ecosystems]. MEDECINE TROPICALE ET SANTE INTERNATIONALE 2022; 2:mtsi.v2i1.2022.228. [PMID: 35685840 PMCID: PMC9128476 DOI: 10.48327/mtsi.v2i1.2022.228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 02/14/2022] [Indexed: 11/24/2022]
Abstract
Introduction The current COVID-19 pandemic is due to a new emerging coronavirus SARS-CoV-2, belonging to the Coronaviridae family and to the Orthocoronavirinae subfamily. This virus was first reported in December 2019 in China. Although reported by several countries in several animal species, COVID-19 is a disease transmitted from human to human. Moreover, SARS-CoV-2 virus and its RNA were detected in body excretions besides saliva, such as urine and fecal matter discharged into sewage. Bibliographic review Within this framework, this article aims to synthesize the bibliographical reviews on SARS-CoV-2 in aquatic environment. It will underline the generalities on SARS-CoV-2, the possible sources of potential contaminations of SARS-CoV-2 in water environment, the viability of SARS-CoV-2 in aquatic environment, the receptive species and the impacts of SARS-CoV-2 on the aquatic ecosystems. Conclusion We compile key information about SARS-CoV-2 that are considered important to remember and highlight the importance of further research in this area in order to assess the hazards of SARS-CoV-2 on aquatic ecosystems.
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Affiliation(s)
- Salma FERCHICHI
- Centre national de veille zoosanitaire, 33 avenue Charles Nicolle, Tunis, Tunisie
| | - Naouel FATNASSI
- Centre national de veille zoosanitaire, 33 avenue Charles Nicolle, Tunis, Tunisie
| | - Anissa DHAOUADI
- Centre national de veille zoosanitaire, 33 avenue Charles Nicolle, Tunis, Tunisie
| | - Hédia ATTIA EL HILI
- Centre national de veille zoosanitaire, 33 avenue Charles Nicolle, Tunis, Tunisie
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Groenewegen B, van Lingen E, Ooijevaar RE, Wessels E, Feltkamp MCW, Boeije-Koppenol E, Verspaget HW, Kuijper EJ, van Prehn J, Keller JJ, Terveer EM. How to prepare stool banks for an appropriate response to the ongoing COVID-19 pandemic: Experiences in the Netherlands and a retrospective comparative cohort study for faecal microbiota transplantation. PLoS One 2022; 17:e0265426. [PMID: 35298520 PMCID: PMC8929558 DOI: 10.1371/journal.pone.0265426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/02/2022] [Indexed: 12/02/2022] Open
Abstract
Background Faecal microbiota transplantation (FMT) is an efficacious treatment for patients with recurrent Clostridioides difficile infections (rCDI). Stool banks facilitate FMT by providing screened faecal suspensions from highly selected healthy donors. Due to the ongoing coronavirus disease 2019 (COVID-19) pandemic and the potential risk of SARS coronavirus-2 (SARS-CoV-2) transmission via FMT, many stool banks were forced to temporarily halt and adjust donor activities. Goal The evaluation of a strategy to effectively continue stool banking activities during the ongoing COVID-19 pandemic. Study To restart our stool banking activities after an initial halt, we implemented periodic SARS-CoV-2 screening in donor faeces and serum, and frequent donor assessment for COVID-19 related symptoms. FMT donor and recipient data obtained before (2016–2019) and during the COVID-19 pandemic (March 2020-August 2021) were compared to assess stool banking efficacy. Results Two out of ten donors developed COVID-19. No differences during versus before the COVID-19 pandemic were observed in the number of approved faeces donations (14 vs 22/month, p = 0.06), FMT requests for rCDI (3.9 vs 4.3/month, p = 0.6); rCDI patients eligible for FMT (80.6% vs 73.3%, p = 0.2); rCDI cure rate (90.3% vs 89.2%, p = 0.9); CDI-free survival (p = 0.7); the number of non-rCDI patients treated with FMT (0.5/month vs 0.4/month), and the number of possibly FMT related adverse events (9.5% vs 7.8%, p = 0.7). Two FMTs for rCDI were delayed due to COVID-19. Conclusions There is a continued need for FMT treatment of rCDI during the COVID-19 pandemic. Appropriate donor screening and SARS-CoV-2 infection prevention measures can be implemented in existing protocols without increasing the burden for donors, and allow safe, effective and efficient FMT during the ongoing COVID-19 pandemic. Stool banks should evaluate their SARS-CoV-2 donor screening protocols for long-term sustainability and efficacy, and share their experiences to help the utilisation, standardisation and improvement of stool banks worldwide.
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Affiliation(s)
- Bas Groenewegen
- Department of Medical Microbiology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Emilie van Lingen
- Department of Gastroenterology and Hepatology, LUMC, Leiden, The Netherlands
| | - Rogier E. Ooijevaar
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, VU University Medical Center, Amsterdam, The Netherlands
| | - Els Wessels
- Department of Medical Microbiology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Mariet C. W. Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Eline Boeije-Koppenol
- Department of Medical Microbiology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Hein W. Verspaget
- Department of Gastroenterology and Hepatology, LUMC, Leiden, The Netherlands
- Department of Biobanking, LUMC, Leiden, The Netherlands
| | - Ed J. Kuijper
- Department of Medical Microbiology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Reference Laboratory for C. difficile, LUMC and RIVM (Center for Infectious Disease Control, National Institute for Public Health and the Environment), Bilthoven, The Netherlands
| | - Joffrey van Prehn
- Department of Medical Microbiology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Josbert J. Keller
- Department of Gastroenterology and Hepatology, LUMC, Leiden, The Netherlands
- Department of Gastroenterology, Haaglanden Medical Center, Den Haag, The Netherlands
| | - Elisabeth M. Terveer
- Department of Medical Microbiology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- * E-mail:
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Mancusi A, Capuano F, Girardi S, Di Maro O, Suffredini E, Di Concilio D, Vassallo L, Cuomo MC, Tafuro M, Signorelli D, Pierri A, Pizzolante A, Cerino P, La Rosa G, Proroga YTR, Pierri B. Detection of SARS-CoV-2 RNA in Bivalve Mollusks by Droplet Digital RT-PCR (dd RT-PCR). INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:943. [PMID: 35055765 PMCID: PMC8776039 DOI: 10.3390/ijerph19020943] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 12/12/2022]
Abstract
Bivalve shellfish are readily contaminated by human pathogens present in waters impacted by municipal sewage, and the detection of SARS-CoV-2 in feces of infected patients and in wastewater has drawn attention to the possible presence of the virus in bivalves. The aim of this study was to collect data on SARS-CoV-2 prevalence in bivalve mollusks from harvesting areas of Campania region. A total of 179 samples were collected between September 2019 and April 2021 and were tested using droplet digital RT-PCR (dd RT-PCR) and real-time RT-PCR. Combining results obtained with different assays, SARS-CoV-2 presence was detected in 27/179 (15.1%) of samples. A median viral concentration of 1.1 × 102 and 1.4 × 102 g.c./g was obtained using either Orf1b nsp14 or RdRp/gene E, respectively. Positive results were unevenly distributed among harvesting areas and over time, positive samples being more frequent after January 2021. Partial sequencing of the spike region was achieved for five samples, one of which displaying mutations characteristic of the Alpha variant (lineage B.1.1.7). This study confirms that bivalve mollusks may bioaccumulate SARS-CoV-2 to detectable levels and that they may represent a valuable approach to track SARS-CoV-2 in water bodies and to monitor outbreak trends and viral diversity.
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Affiliation(s)
- Andrea Mancusi
- Department of Food Security Coordination, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (A.M.); (F.C.); (S.G.); (O.D.M.)
| | - Federico Capuano
- Department of Food Security Coordination, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (A.M.); (F.C.); (S.G.); (O.D.M.)
| | - Santa Girardi
- Department of Food Security Coordination, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (A.M.); (F.C.); (S.G.); (O.D.M.)
| | - Orlandina Di Maro
- Department of Food Security Coordination, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (A.M.); (F.C.); (S.G.); (O.D.M.)
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Denise Di Concilio
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Lucia Vassallo
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Maria Concetta Cuomo
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Maria Tafuro
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Daniel Signorelli
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Andrea Pierri
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Antonio Pizzolante
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Pellegrino Cerino
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Yolande Thérèse Rose Proroga
- Department of Food Security Coordination, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (A.M.); (F.C.); (S.G.); (O.D.M.)
| | - Biancamaria Pierri
- Centro di Referenza Nazionale per l’Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute No. 2, 80055 Portici, Italy; (D.D.C.); (L.V.); (M.C.C.); (M.T.); (D.S.); (A.P.); (A.P.); (P.C.); (B.P.)
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Prednisone/tacrolimus. REACTIONS WEEKLY 2022. [PMCID: PMC8795322 DOI: 10.1007/s40278-022-09505-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Rutter H, Parker S, Stahl-Timmins W, Noakes C, Smyth A, Macbeth R, Fitzgerald S, Freeman ALJ. Visualising SARS-CoV-2 transmission routes and mitigations. BMJ 2021; 375:e065312. [PMID: 34853080 DOI: 10.1136/bmj-2021-065312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Simon Parker
- Defence Science and Technology Laboratory, Salisbury, UK
| | | | | | | | | | - Shaun Fitzgerald
- Centre for Climate Repair at Cambridge, University of Cambridge, UK
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Vilibic-Cavlek T, Stevanovic V, Brlek-Gorski D, Ferencak I, Ferenc T, Ujevic-Bosnjak M, Tabain I, Janev-Holcer N, Perkovic I, Anticevic M, Bekavac B, Kaic B, Mrzljak A, Ganjto M, Zmak L, Mauric Maljkovic M, Jelicic P, Bucic L, Barbic L. Emerging Trends in the Epidemiology of COVID-19: The Croatian 'One Health' Perspective. Viruses 2021; 13:2354. [PMID: 34960623 PMCID: PMC8707935 DOI: 10.3390/v13122354] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 02/07/2023] Open
Abstract
During the four pandemic waves, a total of 560,504 cases and 10,178 deaths due to COVID-19 were reported in Croatia. The Alpha variant, dominant from March 2021 (>50% of positive samples), was rapidly replaced by Delta variants (>90%) by August 2021. Several seroprevalence studies were conducted in different populations (general population, children/adolescents, professional athletes, healthcare workers, veterinarians) and in immunocompromised patients (hemodialysis patients, liver/kidney transplant recipients). After the first pandemic wave, seroprevalence rates of neutralizing (NT) antibodies were reported to be 0.2-5.5%. Significantly higher seropositivity was detected during/after the second wave, 2.6-18.7%. Two studies conducted in pet animals (February-June 2020/July-December 2020) reported SARS-CoV-2 NT antibodies in 0.76% of cats and 0.31-14.69% of dogs, respectively. SARS-CoV-2 NT antibodies were not detected in wildlife. Environmental samples taken in the households of COVID-19 patients showed high-touch personal objects as most frequently contaminated (17.3%), followed by surfaces in patients' rooms (14.6%), kitchens (13.3%) and bathrooms (8.3%). SARS-CoV-2 RNA was also detected in 96.8% affluent water samples, while all effluent water samples tested negative. Detection of SARS-CoV-2 in humans, animals and the environment suggests that the 'One Health' approach is critical to controlling COVID-19 and future pandemics.
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Affiliation(s)
- Tatjana Vilibic-Cavlek
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (I.F.); (I.T.)
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Vladimir Stevanovic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine University of Zagreb, 10000 Zagreb, Croatia;
| | - Diana Brlek-Gorski
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
| | - Ivana Ferencak
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (I.F.); (I.T.)
| | - Thomas Ferenc
- Clinical Department of Diagnostic and Interventional Radiology, Merkur University Hospital, 10000 Zagreb, Croatia;
| | - Magdalena Ujevic-Bosnjak
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
| | - Irena Tabain
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (I.F.); (I.T.)
| | - Natasa Janev-Holcer
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
- Department of Social Medicine and Epidemiology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Ivana Perkovic
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
| | - Mario Anticevic
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
| | - Barbara Bekavac
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
| | - Bernard Kaic
- Department of Epidemiology, Croatian Institute of Public Health, 10000 Zagreb, Croatia;
| | - Anna Mrzljak
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
- Department of Gastroenterology and Hepatology, University Hospital Center Zagreb, 10000 Zagreb, Croatia
| | - Marin Ganjto
- Zagreb Wastewater-Management and Operation Ltd., 10000 Zagreb, Croatia;
| | - Ljiljana Zmak
- Department for Tuberculosis, Croatian Institute of Public Health, 10000 Zagreb, Croatia;
| | - Maja Mauric Maljkovic
- Department for Animal Breeding and Livestock Production, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Pavle Jelicic
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
| | - Lovro Bucic
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
| | - Ljubo Barbic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine University of Zagreb, 10000 Zagreb, Croatia;
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Wurtz N, Revol O, Jardot P, Giraud-Gatineau A, Houhamdi L, Soumagnac C, Annessi A, Lacoste A, Colson P, Aherfi S, Scola BL. Monitoring the Circulation of SARS-CoV-2 Variants by Genomic Analysis of Wastewater in Marseille, South-East France. Pathogens 2021. [PMID: 34451505 DOI: 10.3390/pathogens10081042.pmid:34451505;pmcid:pmc8401729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to a succession of epidemic waves. It thus appears that monitoring the presence of SARS-CoV-2 in wastewater alone is insufficient, and it may be important in the future to also monitor the evolution of these variants. We used a real-time RT-PCR screening test for variants in the wastewater of our city to assess the effectiveness of direct SARS-CoV-2 sequencing from the same wastewater. We compared the genome sequencing results obtained over the large RS network and the smaller B7 network with the different distributions of the variants observed by RT-PCR screening. The prevalence of the "UK variant" in the RS and B7 networks was estimated to be 70% and 8% using RT-PCR screening compared to 95% and 64% using genome sequencing, respectively. The latter values were close to the epidemiology observed in patients of the corresponding area, which were 91% and 58%, respectively. Genome sequencing in sewage identified SARS-CoV-2 of lineage B.1.525 in B7 at 27% (37% in patients), whereas it was completely missed by RT-PCR. We thus determined that direct sequencing makes it possible to observe, in wastewater, a distribution of the variants comparable to that revealed by genomic monitoring in patients and that this method is more accurate than RT-PCR. It also shows that, rather than a single large sample, it would be preferable to analyse several targeted samples if we want to more appropriately assess the geographical distribution of the different variants. In conclusion, this work supports the wider surveillance of SARS-CoV-2 variants in wastewater by genome sequencing and targeting small areas on the condition of having a sequencing capacity and, when this is not the case, to developing more precise screening tests based on the multiplexed detection of the mutations of interest.
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Affiliation(s)
- Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Océane Revol
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Priscilla Jardot
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | - Audrey Giraud-Gatineau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Linda Houhamdi
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | | | | | | | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
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Wurtz N, Revol O, Jardot P, Giraud-Gatineau A, Houhamdi L, Soumagnac C, Annessi A, Lacoste A, Colson P, Aherfi S, Scola BL. Monitoring the Circulation of SARS-CoV-2 Variants by Genomic Analysis of Wastewater in Marseille, South-East France. Pathogens 2021; 10:1042. [PMID: 34451505 PMCID: PMC8401729 DOI: 10.3390/pathogens10081042] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022] Open
Abstract
The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to a succession of epidemic waves. It thus appears that monitoring the presence of SARS-CoV-2 in wastewater alone is insufficient, and it may be important in the future to also monitor the evolution of these variants. We used a real-time RT-PCR screening test for variants in the wastewater of our city to assess the effectiveness of direct SARS-CoV-2 sequencing from the same wastewater. We compared the genome sequencing results obtained over the large RS network and the smaller B7 network with the different distributions of the variants observed by RT-PCR screening. The prevalence of the "UK variant" in the RS and B7 networks was estimated to be 70% and 8% using RT-PCR screening compared to 95% and 64% using genome sequencing, respectively. The latter values were close to the epidemiology observed in patients of the corresponding area, which were 91% and 58%, respectively. Genome sequencing in sewage identified SARS-CoV-2 of lineage B.1.525 in B7 at 27% (37% in patients), whereas it was completely missed by RT-PCR. We thus determined that direct sequencing makes it possible to observe, in wastewater, a distribution of the variants comparable to that revealed by genomic monitoring in patients and that this method is more accurate than RT-PCR. It also shows that, rather than a single large sample, it would be preferable to analyse several targeted samples if we want to more appropriately assess the geographical distribution of the different variants. In conclusion, this work supports the wider surveillance of SARS-CoV-2 variants in wastewater by genome sequencing and targeting small areas on the condition of having a sequencing capacity and, when this is not the case, to developing more precise screening tests based on the multiplexed detection of the mutations of interest.
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Affiliation(s)
- Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Océane Revol
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Priscilla Jardot
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Audrey Giraud-Gatineau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Linda Houhamdi
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Christophe Soumagnac
- Bataillon de Marins-Pompiers de Marseille, 13003 Marseille, France; (C.S.); (A.A.); (A.L.)
| | - Alexandre Annessi
- Bataillon de Marins-Pompiers de Marseille, 13003 Marseille, France; (C.S.); (A.A.); (A.L.)
| | - Alexandre Lacoste
- Bataillon de Marins-Pompiers de Marseille, 13003 Marseille, France; (C.S.); (A.A.); (A.L.)
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
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