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Basanisi MG, Nobili G, La Bella G, D’Antuono AM, Coppola R, Damato AM, Scirocco T, Cilenti L, La Salandra G. One-year monitoring of potentially pathogenic microorganisms in the waters and sediments of the Lesina and Varano lagoons (South-East Italy). Ital J Food Saf 2024; 13:12218. [PMID: 38887590 PMCID: PMC11181116 DOI: 10.4081/ijfs.2024.12218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/11/2024] [Indexed: 06/20/2024] Open
Abstract
In this study, two Mediterranean coastal lagoons (Lesina and Varano) of southern Italy, located in the north of the Apulia region, were investigated for the presence of Shiga toxin Escherichia coli (STEC) and potentially enteropathogenic Vibrio species in parallel with norovirus (NoV), hepatitis A virus (HAV), hepatitis E virus (HEV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to evaluate the presence of potentially pathogenic bacteria and viruses in the water and sediments of these ecosystems. From March 2022 to February 2023, a total of 98 samples were collected: 49 water samples and 49 sediment samples. STEC strains were isolated in three samples (3.1%), of which one (2%) was water (stx1 and stx2 positive) and two (4.1%) were sediment (both stx2 positive) samples. Vibrio spp. were detected in twenty samples (20.4%), of which nine were water (18.4%) and eleven were sediment (22.4%) samples. The species detected included V. parahaemolyticus, V. cholerae, and V. vulnificus. NoV was detected in 25 (25.5%) samples, while none of the water or sediment samples were positive for HAV, HEV, and SARS-CoV-2. The results of this study provide an overview of the presence of potentially pathogenic microorganisms in areas influenced by anthropogenic pressure. Monitoring the circulation of these pathogens could be useful to evaluate the water flowing into the lagoons, in particular discharge waters (i.e., urban, agricultural, and livestock runoff), considering the presence of fish and shellfish farms in these sites.
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Affiliation(s)
| | - Gaia Nobili
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia
| | - Gianfranco La Bella
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia
| | | | - Rosa Coppola
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia
| | - Annita Maria Damato
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia
| | - Tommaso Scirocco
- Istituto per le Risorse Biologiche e le Biotecnologie Marine del Consiglio Nazionale delle Ricerche (IRBIM CNR), Lesina
| | - Lucrezia Cilenti
- Istituto di Scienze delle Produzioni Alimentari del Consiglio Nazionale delle Ricerche (ISPA CNR), Foggia, Italy
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Li J, Lyu C, An R, Wang D. Interaction Between SARS-CoV-2 Spike Protein S1 Subunit and Oyster Heat Shock Protein 70. FOOD AND ENVIRONMENTAL VIROLOGY 2024:10.1007/s12560-024-09599-y. [PMID: 38635140 DOI: 10.1007/s12560-024-09599-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024]
Abstract
There is growing evidence that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contaminates the marine environment and is bioaccumulated in filter-feeding shellfish. Previous study shows the Pacific oyster tissues can bioaccumulate the SARS-CoV-2, and the oyster heat shock protein 70 (oHSP70) may play as the primary attachment receptor to bind SARS-CoV-2's recombinant spike protein S1 subunit (rS1). However, detailed information about the interaction between rS1 and oHSP70 is still unknown. In this study, we confirmed that the affinity of recombinant oHSP70 (roHSP70) for rS1 (KD = 20.4 nM) is comparable to the receptor-binding affinity of rACE2 for rS1 (KD = 16.7 nM) by surface plasmon resonance (SPR)-based Biacore and further validated by enzyme-linked immunosorbent assay (ELISA). Three truncated proteins (roHSP70-N/C/M) and five mutated proteins (p.I229del, p.D457del, p.V491_K495del, p.K556I, and p.ΣroHSP70) were constructed according to the molecular docking results. All three truncated proteins have significantly lower affinity for rS1 than the full-length roHSP70, indicating that all three segments of roHSP70 are involved in binding to rS1. Further, the results of SPR and ELISA showed that all five mutant proteins had significantly lower affinity for rS1 than roHSP70, suggesting that amino acids at these sites are involved in binding to rS1. This study provides a preliminary theoretical basis for the bioaccumulation of SARS-CoV-2 in oyster tissues or using roHSP70 as the capture unit to selectively enrich virus particles for detection.
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Affiliation(s)
- Jingwen Li
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Chenang Lyu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Ran An
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Dapeng Wang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
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3
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González-Aravena M, Galbán-Malagón C, Castro-Nallar E, Barriga GP, Neira V, Krüger L, Adell AD, Olivares-Pacheco J. Detection of SARS-CoV-2 in Wastewater Associated with Scientific Stations in Antarctica and Possible Risk for Wildlife. Microorganisms 2024; 12:743. [PMID: 38674687 PMCID: PMC11051888 DOI: 10.3390/microorganisms12040743] [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: 02/01/2024] [Revised: 03/10/2024] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
Before December 2020, Antarctica had remained free of COVID-19 cases. The main concern during the pandemic was the limited health facilities available at Antarctic stations to deal with the disease as well as the potential impact of SARS-CoV-2 on Antarctic wildlife through reverse zoonosis. In December 2020, 60 cases emerged in Chilean Antarctic stations, disrupting the summer campaign with ongoing isolation needs. The SARS-CoV-2 RNA was detected in the wastewater of several scientific stations. In Antarctica, treated wastewater is discharged directly into the seawater. No studies currently address the recovery of infectious virus particles from treated wastewater, but their presence raises the risk of infecting wildlife and initiating new replication cycles. This study highlights the initial virus detection in wastewater from Antarctic stations, identifying viral RNA via RT-qPCR targeting various genomic regions. The virus's RNA was found in effluent from two wastewater plants at Maxwell Bay and O'Higgins Station on King George Island and the Antarctic Peninsula, respectively. This study explores the potential for the reverse zoonotic transmission of SARS-CoV-2 from humans to Antarctic wildlife due to the direct release of viral particles into seawater. The implications of such transmission underscore the need for continued vigilance and research.
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Affiliation(s)
| | - Cristóbal Galbán-Malagón
- GEMA, Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago 8580745, Chile;
- Anillo en Ciencia y Tecnología Antártica POLARIX, Santiago 8370146, Chile;
- Institute for Environment, Florida International University, Miami, FL 33199, USA
| | - Eduardo Castro-Nallar
- Anillo en Ciencia y Tecnología Antártica POLARIX, Santiago 8370146, Chile;
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Campus Talca, Talca 3481118, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Campus Talca, Talca 3460000, Chile
| | - Gonzalo P. Barriga
- Laboratorio de Virus Emergentes, Programa de Virología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile;
| | - Víctor Neira
- Medicina Preventiva Animal, Facultad de Ciencias Veterinarias, Universidad de Chile, Santiago 8820808, Chile;
| | - Lucas Krüger
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas 6200985, Chile;
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago 7750000, Chile
| | - Aiko D. Adell
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 9350841, Chile;
- Millennium Initiative for Collaborative Research on Bacterial Resistance, MICROB-R, Santiago 7550000, Chile
| | - Jorge Olivares-Pacheco
- Millennium Initiative for Collaborative Research on Bacterial Resistance, MICROB-R, Santiago 7550000, Chile
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales, GRABPA, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
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Fehrenbach GW, Murphy E, Pogue R, Carter F, Clifford E, Major I. Comprehensive analysis and assessment of exposure to enteric viruses and bacteria in shellfish. MARINE ENVIRONMENTAL RESEARCH 2024; 196:106404. [PMID: 38341981 DOI: 10.1016/j.marenvres.2024.106404] [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: 11/15/2023] [Revised: 01/30/2024] [Accepted: 02/07/2024] [Indexed: 02/13/2024]
Abstract
Shellfish species, including oysters, clams, and mussels, are extensively cultured in coastal waters. Its location is determined by factors such as nutrient availability, water temperature, tidal cycle, and the presence of contaminants such as Escherichia coli and enteric viruses. With the expansion and intensification of human activities at vicinities, the presence of anthropogenic contaminants has increased, threatening shellfish farms and consumer safety give the prevalent consumption of raw shellfish. This literature review aims to provide a comprehensive analysis of the dietary exposure and assess the risk associated with enteric viruses and bacteria detected in shellfish. The predominant bacteria and viruses detected in shellfish are reported, and the potential interrelation is discussed. The main characteristics of each contaminant and shellfish were reviewed for a more comprehensive understanding. To facilitate a direct estimation of exposure, the estimated daily intake (EDI) of bacteria was calculated based on the average levels of E. coli in shellfish, as reported in the literature. The mean daily ingestion of seafood in each of the five continents was considered. Asia exhibited the highest intake of contaminants, with an average of ±5.6 E. coli units/day.kg body weight in cockles. Simulations were conducted using recommended shellfish consumption levels established by state agencies, revealing significantly lower (p < 0.01) EDI for all continents compared to estimations based on recommended levels. This indicates a higher risk associated with healthy shellfish ingestion, potentially leading to increased intoxication incidents with a change in dietary habits. To promote a healthier lifestyle through increased shellfish consumptions, it is imperative to reduce the exposure of shellfish species to bacteria and enteric viruses. The conventional use of E. coli as the sole indicator for consumption safety and water quality in shellfish farms has been deemed insufficient. Instances where shellfish met E. coli limits established by state agencies were often found to be contaminated with human enteric viruses. Therefore, a holistic approach considering the entire production chain is necessary to support the shellfish industry and ensure food safety.
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Affiliation(s)
- Gustavo Waltzer Fehrenbach
- Materials Research Institute, Technological University of the Shannon, Midlands Campus, N37 HD68, Athlone, Ireland.
| | - Emma Murphy
- Materials Research Institute, Technological University of the Shannon, Midlands Campus, N37 HD68, Athlone, Ireland; LIFE - Health and Biosciences Research Institute, Technological University of the Shannon, Midwest Campus, V94 EC5T, Limerick, Ireland
| | - Robert Pogue
- Post-Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasilia, 71966-700, Brasilia, Brazil
| | - Frank Carter
- Coney Island Shellfish Ltd., F91 YH56, Sligo, Ireland
| | - Eoghan Clifford
- School of Engineering, National University of Ireland Galway, H91 HX31, Galway, Ireland; Ryan Institute, National University of Ireland Galway, H91 HX31, Galway, Ireland
| | - Ian Major
- Materials Research Institute, Technological University of the Shannon, Midlands Campus, N37 HD68, Athlone, Ireland
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La Rosa G, Mancini P, Iaconelli M, Veneri C, Bonanno Ferraro G, Del Giudice C, Suffredini E, Muratore A, Ferrara F, Lucentini L, Martuzzi M, Piccioli A. Tracing the footprints of SARS-CoV-2 in oceanic waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167343. [PMID: 37751837 DOI: 10.1016/j.scitotenv.2023.167343] [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: 07/15/2023] [Revised: 09/22/2023] [Accepted: 09/22/2023] [Indexed: 09/28/2023]
Abstract
The detection of SARS-CoV-2 in water environments has predominantly focused on wastewater, neglecting its presence in oceanic waters. This study aimed to fill this knowledge gap by investigating the occurrence of SARS-CoV-2 in remote sea and oceanic waters, at large distances from the coastline. Forty-three 500-liter samples were collected between May 2022 and January 2023 from the Atlantic Ocean, the Mediterranean Sea, the Arctic region, the Persian Gulf and the Red Sea. Using molecular detection methods including real-time RT-qPCR and nested PCR followed by sequencing, we successfully detected SARS-CoV-2 RNA in 7 of the 43 marine water samples (16.3 %), and specifically in samples taken from the Atlantic Ocean and the Mediterranean Sea. The estimated concentrations of SARS-CoV-2 genome copies in the positive samples ranged from 6 to 470 per 100 l. The presence of mutations characteristic of the Omicron variant was identified in these samples by amplicon sequencing. These findings provide evidence of the unforeseen presence of SARS-CoV-2 in marine waters even at distances of miles from the coastline and in open ocean waters. It is important to consider that these findings only display the occurrence of SARS-CoV-2 RNA, and further investigations are required to assess if infectious virus can be present in the marine environment.
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Affiliation(s)
- Giuseppina La Rosa
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy.
| | - P Mancini
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - C Veneri
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - G Bonanno Ferraro
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - C Del Giudice
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - A Muratore
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - F Ferrara
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - L Lucentini
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - M Martuzzi
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - A Piccioli
- Office of the Director General, Istituto Superiore di Sanità, Rome, Italy
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6
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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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7
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Lombardi A, Voli A, Mancusi A, Girardi S, Proroga YTR, Pierri B, Olivares R, Cossentino L, Suffredini E, La Rosa G, Fusco G, Pizzolante A, Porta A, Campiglia P, Torre I, Pennino F, Tosco A. SARS-CoV-2 RNA in Wastewater and Bivalve Mollusk Samples of Campania, Southern Italy. Viruses 2023; 15:1777. [PMID: 37632119 PMCID: PMC10459311 DOI: 10.3390/v15081777] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
SARS-CoV-2 can be detected in the feces of infected people, consequently in wastewater, and in bivalve mollusks, that are able to accumulate viruses due to their ability to filter large amounts of water. This study aimed to monitor SARS-CoV-2 RNA presence in 168 raw wastewater samples collected from six wastewater treatment plants (WWTPs) and 57 mollusk samples obtained from eight harvesting sites in Campania, Italy. The monitoring period spanned from October 2021 to April 2022, and the results were compared and correlated with the epidemiological situation. In sewage, the ORF1b region of SARS-CoV-2 was detected using RT-qPCR, while in mollusks, three targets-RdRp, ORF1b, and E-were identified via RT-dPCR. Results showed a 92.3% rate of positive wastewater samples with increased genomic copies (g.c.)/(day*inhabitant) in December-January and March-April 2022. In the entire observation period, 54.4% of mollusks tested positive for at least one SARS-CoV-2 target, and the rate of positive samples showed a trend similar to that of the wastewater samples. The lower SARS-CoV-2 positivity rate in bivalve mollusks compared to sewages is a direct consequence of the seawater dilution effect. Our data confirm that both sample types can be used as sentinels to detect SARS-CoV-2 in the environment and suggest their potential use in obtaining complementary information on SARS-CoV-2.
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Affiliation(s)
- Annalisa Lombardi
- Department of Public Health, University “Federico II”, Via Sergio Pansini 5, 80131 Naples, Italy; (A.L.)
| | - Antonia Voli
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (A.V.); (A.P.); (P.C.)
| | - Andrea Mancusi
- Department of Food Security Coordination, Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (A.M.); (S.G.); (Y.T.R.P.); (B.P.)
| | - Santa Girardi
- Department of Food Security Coordination, Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (A.M.); (S.G.); (Y.T.R.P.); (B.P.)
| | - Yolande Thérèse Rose Proroga
- Department of Food Security Coordination, Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (A.M.); (S.G.); (Y.T.R.P.); (B.P.)
| | - Biancamaria Pierri
- Department of Food Security Coordination, Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (A.M.); (S.G.); (Y.T.R.P.); (B.P.)
| | - Renato Olivares
- Campania Regional Environmental Protection Agency (ARPAC), Via Vicinale Santa Maria del Pianto, 80143 Naples, Italy; (R.O.); (L.C.)
| | - Luigi Cossentino
- Campania Regional Environmental Protection Agency (ARPAC), Via Vicinale Santa Maria del Pianto, 80143 Naples, Italy; (R.O.); (L.C.)
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Giovanna Fusco
- Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (G.F.); (A.P.)
| | - Antonio Pizzolante
- Zooprophylactic Institute of Southern Italy, Via Salute 2, 80055 Portici, Italy; (G.F.); (A.P.)
| | - Amalia Porta
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (A.V.); (A.P.); (P.C.)
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (A.V.); (A.P.); (P.C.)
| | - Ida Torre
- Department of Public Health, University “Federico II”, Via Sergio Pansini 5, 80131 Naples, Italy; (A.L.)
| | - Francesca Pennino
- Department of Public Health, University “Federico II”, Via Sergio Pansini 5, 80131 Naples, Italy; (A.L.)
| | - Alessandra Tosco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (A.V.); (A.P.); (P.C.)
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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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9
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Bioaccumulation Pattern of the SARS-CoV-2 Spike Proteins in Pacific Oyster Tissues. Appl Environ Microbiol 2023; 89:e0210622. [PMID: 36815797 PMCID: PMC10057954 DOI: 10.1128/aem.02106-22] [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: 02/24/2023] Open
Abstract
There is mounting evidence of the contamination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the sewage, surface water, and even marine environment. Various studies have confirmed that bivalve mollusks can bioaccumulate SARS-CoV-2 RNA to detectable levels. However, these results do not provide sufficient evidence for the presence of infectious viral particles. To verify whether oysters can bind the viral capsid and bioaccumulate the viral particles, Pacific oysters were artificially contaminated with the recombinant SARS-CoV-2 spike protein S1 subunit (rS1). The bioaccumulation pattern of the rS1 in different tissues was investigated by immunohistological assays. The results revealed that the rS1 was bioaccumulated predominately in the digestive diverticula. The rS1 was also present in the epithelium of the nondigestive tract tissues, including the gills, mantle, and heart. In addition, three potential binding ligands, including angiotensin-converting enzyme 2 (ACE 2)-like substances, A-type histo-blood group antigen (HBGA)-like substances, and oyster heat shock protein 70 (oHSP 70), were confirmed to bind rS1 and were distributed in tissues with various patterns. The colocalization analysis of rS1 and those potential ligands indicated that the distributions of rS1 are highly consistent with those of ACE 2-like substances and oHSP 70. Both ligands are distributed predominantly in the secretory absorptive cells of the digestive diverticula and may serve as the primary ligands to bind rS1. Therefore, oysters are capable of bioaccumulating the SARS-CoV-2 capsid readily by filter-feeding behavior assisted by specific binding ligands, especially in digestive diverticula. IMPORTANCE This is the first article to investigate the SARS-CoV-2 spike protein bioaccumulation pattern and mechanism in Pacific oysters by the histochemical method. Oysters can bioaccumulate SARS-CoV-2 capsid readily by filter-feeding behavior assisted by specific binding ligands. The new possible foodborne transmission route may change the epidemic prevention strategies and reveal some outbreaks that current conventional epidemic transmission routes cannot explain. This original and interdisciplinary paper advances a mechanistic understanding of the bioaccumulation of SARS-CoV-2 in oysters inhabiting contaminated surface water.
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10
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Danielli Bastos de Sousa F. The impact of plastic during the COVID-19 pandemic: The point of view of the environmental science literature. MATERIALS TODAY. PROCEEDINGS 2023; 80:1448-1455. [PMID: 36743883 PMCID: PMC9889263 DOI: 10.1016/j.matpr.2023.01.268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/15/2023] [Accepted: 01/24/2023] [Indexed: 02/04/2023]
Abstract
COVID-19 is the official name of the disease provoked by a coronavirus called SARS-CoV-2. Since the advent of the first cases of the new coronavirus, our society has been completely changed. Due to the changes, new environmental challenges were imposed, principally due to the considerable growth in using plastic materials in packages and personal protective equipment such as face masks. The impact of plastic during the COVID-19 pandemic was discussed in the present work from the point of view of the environmental science area. Bibliometric analysis and mapping were performed based on Scopus database search results. Emphasis was placed on analyzing the authors' keywords of the publications. The main concern of the research area concerning the use of plastic during the COVID-19 pandemic is the pollution of water bodies by plastic.
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Affiliation(s)
- Fabiula Danielli Bastos de Sousa
- Technology Development Center, Universidade Federal de Pelotas, Rua Gomes Carneiro, 1, 96010-610, Pelotas, RS, Brazil,Center of Engineering, Modeling and Applied Social Science, Universidade Federal do ABC, Avenida dos Estados, 5001, 09210-580, Santo André, SP, Brazil,Corresponding author
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11
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Ransome E, Hobbs F, Jones S, Coleman CM, Harris ND, Woodward G, Bell T, Trew J, Kolarević S, Kračun-Kolarević M, Savolainen V. Evaluating the transmission risk of SARS-CoV-2 from sewage pollution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159161. [PMID: 36191696 PMCID: PMC9525188 DOI: 10.1016/j.scitotenv.2022.159161] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 06/02/2023]
Abstract
The presence of SARS-CoV-2 in untreated sewage has been confirmed in many countries but its incidence and infection risk in contaminated waters is poorly understood. The River Thames in the UK receives untreated sewage from 57 Combined Sewer Overflows (CSOs), with many discharging dozens of times per year. This study investigated if such discharges provide a pathway for environmental transmission of SARS-CoV-2. Samples of wastewater, surface water, and sediment collected close to six CSOs on the River Thames were assayed over eight months for SARS-CoV-2 RNA and infectious virus. Bivalves were also sampled as an indicator species of viral bioaccumulation. Sediment and water samples from the Danube and Sava rivers in Serbia, where raw sewage is also discharged in high volumes, were assayed as a positive control. No evidence of SARS-CoV-2 RNA or infectious virus was found in UK samples, in contrast to RNA positive samples from Serbia. Furthermore, this study shows that infectious SARS-CoV-2 inoculum is stable in Thames water and sediment for <3 days, while SARS-CoV-2 RNA is detectable for at least seven days. This indicates that dilution of wastewater likely limits environmental transmission, and that detection of viral RNA alone is not an indication of pathogen spillover.
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Affiliation(s)
- E Ransome
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK.
| | - F Hobbs
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - S Jones
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - C M Coleman
- Wolfson Centre for Global Virus Research, Department of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - N D Harris
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - G Woodward
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - T Bell
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - J Trew
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - S Kolarević
- University of Belgrade, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, Department of Hydroecology and Water Protection, Bulevar despota Stefana 142, 11000 Belgrade, Serbia
| | - M Kračun-Kolarević
- University of Belgrade, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, Department of Hydroecology and Water Protection, Bulevar despota Stefana 142, 11000 Belgrade, Serbia
| | - V Savolainen
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
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12
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Ekanayake A, Rajapaksha AU, Hewawasam C, Anand U, Bontempi E, Kurwadkar S, Biswas JK, Vithanage M. Environmental challenges of COVID-19 pandemic: resilience and sustainability - A review. ENVIRONMENTAL RESEARCH 2023; 216:114496. [PMID: 36257453 PMCID: PMC9576205 DOI: 10.1016/j.envres.2022.114496] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/14/2022] [Accepted: 10/01/2022] [Indexed: 05/05/2023]
Abstract
The emergence of novel respiratory disease (COVID-19) caused by SARS-CoV-2 has become a public health emergency worldwide and perturbed the global economy and ecosystem services. Many studies have reported the presence of SARS-CoV-2 in different environmental compartments, its transmission via environmental routes, and potential environmental challenges posed by the COVID-19 pandemic. None of these studies have comprehensively reviewed the bidirectional relationship between the COVID-19 pandemic and the environment. For the first time, we explored the relationship between the environment and the SARS-CoV-2 virus/COVID-19 and how they affect each other. Supporting evidence presented here clearly demonstrates the presence of SARS-CoV-2 in soil and water, denoting the role of the environment in the COVID-19 transmission process. However, most studies fail to determine if the viral genomes they have discovered are infectious, which could be affected by the environmental factors in which they are found.The potential environmental impact of the pandemic, including water pollution, chemical contamination, increased generation of non-biodegradable waste, and single-use plastics have received the most attention. For the most part, efficient measures have been used to address the current environmental challenges from COVID-19, including using environmentally friendly disinfection technologies and employing measures to reduce the production of plastic wastes, such as the reuse and recycling of plastics. Developing sustainable solutions to counter the environmental challenges posed by the COVID-19 pandemic should be included in national preparedness strategies. In conclusion, combating the pandemic and accomplishing public health goals should be balanced with environmentally sustainable measures, as the two are closely intertwined.
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Affiliation(s)
- Anusha Ekanayake
- Ecosphere Resilience Research Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | - Anushka Upamali Rajapaksha
- Ecosphere Resilience Research Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka; Instrument Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka.
| | - Choolaka Hewawasam
- Faculty of Technology, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka
| | - Uttpal Anand
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion, 8499000, Israel
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, University of Brescia, via Branze 38, 25123 Brescia, Italy
| | - Sudarshan Kurwadkar
- Department of Civil and Environmental Engineering, California State University, 800 N. State College Blvd., Fullerton, CA, 92831, USA
| | - Jayanta Kumar Biswas
- Department of Ecological Studies & International Centre for Ecological Engineering, University of Kalyani, Kalyani, Nadia, 741235, West Bengal, India
| | - Meththika Vithanage
- Ecosphere Resilience Research Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, 10250, Sri Lanka; Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand, 248007, India
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13
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Focus on Marine Animal Safety and Marine Bioresources in Response to the SARS-CoV-2 Crisis. Int J Mol Sci 2022; 23:ijms232315136. [PMID: 36499463 PMCID: PMC9737530 DOI: 10.3390/ijms232315136] [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: 10/18/2022] [Revised: 11/18/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
SARS-CoV-2 as a zoonotic virus has significantly affected daily life and social behavior since its outbreak in late 2019. The concerns over its transmission through different media directly or indirectly have evoked great attention about the survival of SARS-CoV-2 virions in the environment and its potential infection of other animals. To evaluate the risk of infection by SARS-CoV-2 and to counteract the COVID-19 disease, extensive studies have been performed to understand SARS-CoV-2 biogenesis and its pathogenesis. This review mainly focuses on the molecular architecture of SARS-CoV-2, its potential for infecting marine animals, and the prospect of drug discovery using marine natural products to combat SARS-CoV-2. The main purposes of this review are to piece together progress in SARS-CoV-2 functional genomic studies and antiviral drug development, and to raise our awareness of marine animal safety on exposure to SARS-CoV-2.
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14
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do Nascimento LG, Sarmento SK, Leonardo R, Gutierrez MB, Malta FC, de Oliveira JM, Guerra CR, Coutinho R, Miagostovich MP, Fumian TM. Detection and Molecular Characterization of Enteric Viruses in Bivalve Mollusks Collected in Arraial do Cabo, Rio de Janeiro, Brazil. Viruses 2022; 14:v14112359. [PMID: 36366459 PMCID: PMC9695388 DOI: 10.3390/v14112359] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 01/31/2023] Open
Abstract
Viral bivalve contamination is a recognized food safety hazard. Therefore, this study investigated the detection rates, seasonality, quantification, and genetic diversity of enteric viruses in bivalve samples (mussels and oysters). We collected 97 shellfish samples between March 2018 and February 2020. The screening of samples by qPCR or RT-qPCR revealed the detection of norovirus (42.3%), rotavirus A (RVA; 16.5%), human adenovirus (HAdV; 24.7%), and human bocavirus (HBoV; 13.4%). There was no detection of hepatitis A virus. In total, 58.8% of shellfish samples tested positive for one or more viruses, with 42.1% of positive samples contaminated with two or more viruses. Norovirus showed the highest median viral load (3.3 × 106 GC/g), followed by HAdV (median of 3.5 × 104 GC/g), RVA (median of 1.5 × 103 GC/g), and HBoV (median of 1.3 × 103 GC/g). Phylogenetic analysis revealed that norovirus strains belonged to genotype GII.12[P16], RVA to genotype I2, HAdV to types -C2, -C5, and -F40, and HBoV to genotypes -1 and -2. Our results demonstrate the viral contamination of bivalves, emphasizing the need for virological monitoring programs to ensure the quality and safety of shellfish for human consumption and as a valuable surveillance tool to monitor emerging viruses and novel variants.
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Affiliation(s)
- Lilian Gonçalves do Nascimento
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
| | - Sylvia Kahwage Sarmento
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
| | - Raphael Leonardo
- Laboratory of Viral Morphology and Morphogenesis, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
| | - Meylin Bautista Gutierrez
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
| | - Fábio Correia Malta
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
| | - Jaqueline Mendes de Oliveira
- Laboratory of Technological Development in Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
| | - Caroline Rezende Guerra
- Laboratory of Marine Genetics, Department of Marine Biotechnology, Sea Studies Institute Admiral Paulo Moreira (IEAPM), Arraial do Cabo 28930-000, RJ, Brazil
| | - Ricardo Coutinho
- Laboratory of Marine Genetics, Department of Marine Biotechnology, Sea Studies Institute Admiral Paulo Moreira (IEAPM), Arraial do Cabo 28930-000, RJ, Brazil
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
| | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
- Correspondence: ; Tel.: +55-21-2562-1817
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15
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Yamazaki Y, Thongchankaew-Seo U, Yamazaki W. Very low likelihood that cultivated oysters are a vehicle for SARS-CoV-2: 2021-2022 seasonal survey at supermarkets in Kyoto, Japan. Heliyon 2022; 8:e10864. [PMID: 36217407 PMCID: PMC9535880 DOI: 10.1016/j.heliyon.2022.e10864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/03/2022] [Accepted: 09/28/2022] [Indexed: 11/25/2022] Open
Abstract
The pandemic caused by novel coronavirus disease of 2019 (COVID-19) is a global threat. Wastewater surveillance in Japan and abroad has led to the detection of SARS-CoV-2, causing concern that SARS-CoV-2 in the feces of infected persons may contaminate the aquatic environment. Bivalves such as oysters cultivated in coastal areas are known to filter and concentrate viruses such as norovirus present in seawater in their bodies; however, whether they do so with SARS-CoV-2 is unknown. Therefore, we examined cultivated oysters sold in Japan for the presence of SARS-CoV-2 between October 2021 and April 2022 to clarify the extent of viral contamination and evaluate the risk of food-borne transmission of SARS-CoV-2. Porcine epidemic diarrhea virus (PEDV), known as pig coronavirus, was used to spike midgut-gland samples as a whole process control. The presence of SARS-CoV-2 and PEDV was investigated using a modified polyethylene glycol precipitation method and RT-qPCR. While all samples spiked with the whole process control were positive, no SARS-CoV-2 was detected in any of the 145 raw oyster samples surveyed, despite a marked increase in infections caused by the Omicron variant from January to April 2022 in Japan. Therefore, our results suggest that with well-developed sewage treatment facilities, consumption of oysters cultivated in coastal areas may not be a risk factor for SARS-CoV-2 outbreaks.
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Affiliation(s)
- Yasuko Yamazaki
- Center for Southeast Asian Studies, Kyoto University, 46 Shimoadachicho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Uraiwan Thongchankaew-Seo
- Center for Southeast Asian Studies, Kyoto University, 46 Shimoadachicho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Wataru Yamazaki
- Center for Southeast Asian Studies, Kyoto University, 46 Shimoadachicho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan,Kyoto University School of Public Health, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8303, Japan,Corresponding author.
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16
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Li Q, Bergquist R, Grant L, Song JX, Feng XY, Zhou XN. Consideration of COVID-19 beyond the human-centred approach of prevention and control: the ONE-HEALTH perspective. Emerg Microbes Infect 2022; 11:2520-2528. [PMID: 36102336 PMCID: PMC9621238 DOI: 10.1080/22221751.2022.2125343] [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] [Indexed: 11/27/2022]
Abstract
Most of the new emerging and re-emerging zoonotic virus outbreaks in recent years stem from close interaction with dead or alive infected animals. Since late 2019, the coronavirus disease 2019 (COVID-19) has spread into 221 countries and territories resulting in close to 300 million known infections and 5.4 million deaths in addition to a huge impact on both public health and the world economy. This paper reviews the COVID-19 prevalence in animals, raise concerns about animal welfare and discusses the role of environment in the transmission of COVID-19. Attention is drawn to the One Health concept as it emphasizes the environment in connection with the risk of transmission and establishment of diseases shared between animals and humans. Considering the importance of One Health for an effective response to the dissemination of infections of pandemic character, some unsettled issues with respect to COVID-19 are highlighted.
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Affiliation(s)
- Qin Li
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai 20025, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, China
| | - Robert Bergquist
- Ingerod, Brastad, Sweden (formerly at the UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Liz Grant
- Global Health, The University of Edinburgh, Edinburgh, UK
| | - Jun-Xia Song
- Food and Agriculture Organization of United Nations, Rome, Italy
| | - Xin-Yu Feng
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai 20025, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, China
- Department of Biology, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Xiao-Nong Zhou
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai 20025, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research); NHC Key Laboratory of Parasite and Vector Biology; WHO Collaborating Centre for Tropical Diseases; National Center for International Research on Tropical Diseases, China
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17
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Shaheen MNF, Elmahdy EM, Shahein YE. The first detection of SARS-CoV-2 RNA in urban wastewater in Giza, Egypt. JOURNAL OF WATER AND HEALTH 2022; 20:1212-1222. [PMID: 36044190 DOI: 10.2166/wh.2022.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The new coronavirus (SARS-CoV-2) is a respiratory virus causing coronavirus disease (COVID-19). Individuals with COVID-19 can shed the viral genome in their feces, even if they do not have symptoms, and the virus can be detected in wastewater. The current study provides the first surveillance of SARS-CoV-2 RNA genome in the wastewater in Egypt. To study this aim, untreated influent (n = 48) and treated effluent (n = 48) samples were collected between January and December 2021 from the wastewater treatment plant in Giza. The viral RNA genome was determined by reverse transcription-polymerase chain reaction (RT-PCR) (S, E, and N target regions) and real-time quantitative reverse transcription-PCR (RT-qPCR) (N1 and N2 target regions). The RT-PCR assay failed to detect SARS-CoV-2 RNA in all samples analyzed, whereas RT-qPCR succeeded in the detection of N gene of SARS-CoV-2 in 62.5% of untreated influent samples. The RT-qPCR Ct values of those samples tested positive ranged from 19.9 to 30.1 with a mean of 23. The treated effluent samples were negative for viral RNA detected by both RT-PCR and RT-qPCR, indicating the efficiency of the sewage treatment plant in degrading SARS-CoV-2. Our preliminary findings provide evidence for the value of wastewater epidemiology approach for the surveillance of SARS-CoV-2 in the population to assist in the responses of public health to COVID-19 outbreak.
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Affiliation(s)
- Mohamed N F Shaheen
- Environmental Virology Laboratory, Water Pollution Research Department, Environment and Climate Change Research Institute, National Research Centre, Dokki 12622, Giza, Egypt E-mail: ,
| | - Elmahdy M Elmahdy
- Environmental Virology Laboratory, Water Pollution Research Department, Environment and Climate Change Research Institute, National Research Centre, Dokki 12622, Giza, Egypt E-mail: ,
| | - Yasser E Shahein
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, 12622 Dokki, Cairo, Egypt
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18
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Sabar MA, Honda R, Haramoto E. CrAssphage as an indicator of human-fecal contamination in water environment and virus reduction in wastewater treatment. WATER RESEARCH 2022; 221:118827. [PMID: 35820313 DOI: 10.1016/j.watres.2022.118827] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/03/2022] [Accepted: 07/04/2022] [Indexed: 05/14/2023]
Abstract
Viral indicators of human-fecal contamination in wastewaters and environmental waters have been getting much attention in the past decade. Cross-assembly phage (crAssphage) is the most abundant DNA virus in human feces. Recently, the usefulness of crAssphage as a microbial source tracking and water quality monitoring tool for human-fecal contamination has been highlighted. Here, we conducted a comprehensive review on crAssphage in water, focusing on detection methodology, concentration range in various waters and wastewaters, specificity to human-fecal contamination, and reduction in wastewater treatment systems. This review highlights that crAssphage is globally distributed in wastewaters and various fecal-contaminated water bodies at high concentrations without seasonal fluctuations. CrAssphage is highly specific to human-fecal contamination and is rarely found in animal feces. It also has a good potential as a performance indicator to ensure virus reduction in wastewater treatment systems. Accordingly, crAssphage could be an effective tool for monitoring of human-fecal contamination and potential presence of fecal pathogenic microbes in environmental waters. Bridging the research gaps highlighted in this review would make crAssphage a powerful tool to support the control of water-related health risks.
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Affiliation(s)
| | - Ryo Honda
- Faculty of Geoscience and Civil Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Eiji Haramoto
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Japan
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19
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Bukha KK, Sharif EA, Eldaghayes IM. The One Health concept for the threat of severe acute respiratory syndrome coronavirus-2 to marine ecosystems. INTERNATIONAL JOURNAL OF ONE HEALTH 2022. [DOI: 10.14202/ijoh.2022.48-57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global health threat. This virus is the causative agent for coronavirus disease 2019 (COVID-19). Pandemic prevention is best addressed through an integrated One Health (OH) approach. Understanding zoonotic pathogen fatality and spillover from wildlife to humans are effective for controlling and preventing zoonotic outbreaks. The OH concept depends on the interface of humans, animals, and their environment. Collaboration among veterinary medicine, public health workers and clinicians, and veterinary public health is necessary for rapid response to emerging zoonotic pathogens. SARS-CoV-2 affects aquatic environments, primarily through untreated sewage. Patients with COVID-19 discharge the virus in urine and feces into residential wastewater. Thus, marine organisms may be infected with SARS-CoV-2 by the subsequent discharge of partially treated or untreated wastewater to marine waters. Viral loads can be monitored in sewage and surface waters. Furthermore, shellfish are vulnerable to SARS-CoV-2 infection. Filter-feeding organisms might be monitored to protect consumers. Finally, the stability of SARS-CoV-2 to various environmental factors aids in viral studies. This article highlights the presence and survival of SARS-CoV-2 in the marine environment and its potential to enter marine ecosystems through wastewater. Furthermore, the OH approach is discussed for improving readiness for successive outbreaks. This review analyzes information from public health and epidemiological monitoring tools to control COVID-19 transmission.
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Affiliation(s)
- Khawla K. Bukha
- Department of Poultry and Fish Diseases, Faculty of Veterinary Medicine, University of Tripoli, Tripoli, Libya
| | - Ehab A. Sharif
- Department of Poultry and Fish Diseases, Faculty of Veterinary Medicine, University of Tripoli, Tripoli, Libya
| | - Ibrahim M. Eldaghayes
- Department of Microbiology and Parasitology, Faculty of Veterinary Medicine, University of Tripoli, Tripoli, Libya
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20
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Brnić D, Lojkić I, Škoko I, Krešić N, Šimić I, Keros T, Ganjto M, Štefanac D, Viduka B, Karšaj D, Štiler D, Habrun B, Jemeršić L. SARS-CoV-2 circulation in Croatian wastewaters and the absence of SARS-CoV-2 in bivalve molluscan shellfish. ENVIRONMENTAL RESEARCH 2022; 207:112638. [PMID: 34990611 PMCID: PMC8721915 DOI: 10.1016/j.envres.2021.112638] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/25/2021] [Accepted: 12/26/2021] [Indexed: 05/07/2023]
Abstract
The circulation of SARS-CoV-2 in the environment has been confirmed numerous times, whilst research on the bioaccumulation in bivalve molluscan shellfish (BMS) has been rather scarce. The present study aimed to fulfil the knowledge gap on SARS-CoV-2 circulation in wastewaters and surface waters in this region and to extend the current knowledge on potential presence of SARS-CoV-2 contamination in BMS. The study included 13 archive wastewater and surface water samples from the start of epidemic and 17 influents and effluents from nine wastewater treatment plants (WWTP) of different capacity and treatment stage, sampled during the second epidemic wave. From that period are the most of 77 collected BMS samples, represented by mussels, oysters and warty venus clams harvested along the Dalmatian coast. All samples were processed according to EN ISO 15216-1 2017 using Mengovirus as a whole process control. SARS-CoV-2 detection was performed by real-time and conventional RT-PCR assays targeting E, N and nsp14 protein genes complemented with nsp14 partial sequencing. Rotavirus A (RVA) real-time RT-PCR assay was implemented as an additional evaluation criterion of virus concentration techniques. The results revealed the circulation of SARS-CoV-2 in nine influents and two secondary treatment effluents from eight WWTPs, while all samples from the start of epidemic (wastewaters, surface waters) were negative which was influenced by sampling strategy. All tertiary effluents and BMS were SARS-CoV-2 negative. The results of RVA amplification were beneficial in evaluating virus concentration techniques and provided insights into RVA dynamics within the environment and community. In conclusion, the results of the present study confirm SARS-CoV-2 circulation in Croatian wastewaters during the second epidemic wave while extending the knowledge on wastewater treatment potential in SARS-CoV-2 removal. Our findings represent a significant contribution to the current state of knowledge that considers BMS of a very low food safety risk regarding SARS-CoV-2.
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Affiliation(s)
- Dragan Brnić
- Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia.
| | - Ivana Lojkić
- Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia
| | - Ines Škoko
- Croatian Veterinary Institute, Veterinary Department Split, Poljička cesta 33, 21000, Split, Croatia
| | - Nina Krešić
- Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia
| | - Ivana Šimić
- Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia; Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Tomislav Keros
- Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia
| | - Marin Ganjto
- Zagreb Wastewater Ltd., Čulinečka cesta 287, 10040, Zagreb, Croatia
| | - Dario Štefanac
- Vodovod i kanalizacija d.o.o., Gažanski trg 8, 47000, Karlovac, Croatia
| | - Branka Viduka
- Odvodnja d.o.o., Hrvatskog sabora 2D, 23000, Zadar, Croatia
| | - Dario Karšaj
- Vodovod d.o.o., Nikole Zrinskog 25, 35000, Slavonski brod, Croatia
| | - Darko Štiler
- Vinkovački vodovod i kanalizacija d.o.o., Ulica Dragutina Žanića Karle 47a, 32100, Vinkovci, Croatia
| | - Boris Habrun
- Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia
| | - Lorena Jemeršić
- Croatian Veterinary Institute, Savska cesta 143, 10000, Zagreb, Croatia.
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21
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Monteiro S, Rente D, Cunha MV, Marques TA, Cardoso E, Vilaça J, Coelho N, Brôco N, Carvalho M, Santos R. Discrimination and surveillance of infectious severe acute respiratory syndrome Coronavirus 2 in wastewater using cell culture and RT-qPCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152914. [PMID: 34999067 PMCID: PMC8733236 DOI: 10.1016/j.scitotenv.2022.152914] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/10/2021] [Accepted: 12/31/2021] [Indexed: 05/04/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA has been extensively detected in raw wastewater in studies exploring wastewater-based epidemiology (WBE) for early warning purposes. Nonetheless, only a few limited studies investigated the presence of SARS-CoV-2 in treated wastewaters to determine the potential health risks across the water cycle. The detection of SARS-CoV-2 has been done mostly by RT-qPCR and ddPCR, which only provides information on the presence of nucleic acids rather than information on potential infectivity. In this study, we set to develop and evaluate the use of viability RT-qPCR for the selective discrimination and surveillance of infectious SARS-CoV-2 in secondary-treated wastewater. Enzymatic (nuclease) and viability dye (Reagent D) pretreatments were applied to infer infectivity through RT-qPCR using porcine epidemic diarrhea virus (PEDV) as a CoV surrogate. Infectivity tests were first performed on PEDV purified RNA, then on infectious and heat-inactivated PEDV, and finally on heat inactivated PEDV spiked in concentrated secondary-treated wastewater. The two viability RT-qPCR methods were then applied to 27 secondary-treated wastewater samples positive for SARS-CoV-2 RNA at the outlet of five large urban wastewater treatment plants in Portugal. Reagent D pretreatment showed similar behavior to cell culture for heat-inactivated PEDV and both viability RT-qPCR methods performed comparably to VERO E6 cell culture for SARS-CoV-2 present in secondary-treated wastewater, eliminating completely the RT-qPCR signal. Our study demonstrated the lack of infectious SARS-CoV-2 viral particles on secondary-treated wastewater through the application of two pretreatment methods for the rapid inference of infectivity through RT-qPCR, showing their potential application in environmental screening. This study addressed a knowledge gap on the public health risks of SARS-CoV-2 across the water cycle.
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Affiliation(s)
- Silvia Monteiro
- Laboratorio de Análises, Tecnico Lisboa, Universidade de Lisboa, Lisboa, Portugal.
| | - Daniela Rente
- Laboratorio de Análises, Tecnico Lisboa, Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Tiago A Marques
- Centre for Research into Ecological and Environmental Modelling, The Observatory, University of St Andrews, St Andrews KY16 9LZ, Scotland; Centro de Estatística e Aplicações, Departamento de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Eugénia Cardoso
- Águas do Tejo Atlântico, Fábrica de Águas de Alcântara, Avenida de Ceuta, 1300-254 Lisboa, Portugal
| | - João Vilaça
- SIMDOURO, ETAR de Gaia Litoral, 4400-356 Canidelo, Portugal
| | | | - Nuno Brôco
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421 Lisboa, Portugal
| | - Marta Carvalho
- AdP VALOR, Serviços Ambientais, S.A., Rua Visconde de Seabra, 3, 1700-421 Lisboa, Portugal
| | - Ricardo Santos
- Laboratorio de Análises, Tecnico Lisboa, Universidade de Lisboa, Lisboa, Portugal
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Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject to false-negative and -positive results, affecting its precision, especially for the detection of low viral loads in samples. In contrast, digital PCR (dPCR), the third generation of PCR, has been shown to be more effective than the gold standard, RT-qPCR, in detecting low viral loads in samples. In this review article, we selected publications to show the broad-spectrum applications of dPCR, including the development of assays and reference standards, environmental monitoring, mutation detection, and clinical diagnosis of SARS-CoV-2, while comparing it analytically to the gold standard, RT-qPCR. In summary, it is evident that the specificity, sensitivity, reproducibility, and detection limits of RT-dPCR are generally unaffected by common factors that may affect RT-qPCR. As this is the first time that dPCR is being tested in an outbreak of such a magnitude, knowledge of its applications will help chart a course for future diagnosis and monitoring of infectious disease outbreaks.
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23
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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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24
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Cuevas-Ferrando E, Girón-Guzmán I, Falcó I, Pérez-Cataluña A, Díaz-Reolid A, Aznar R, Randazzo W, Sánchez G. Discrimination of non-infectious SARS-CoV-2 particles from fomites by viability RT-qPCR. ENVIRONMENTAL RESEARCH 2022; 203:111831. [PMID: 34352235 PMCID: PMC8327643 DOI: 10.1016/j.envres.2021.111831] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/01/2021] [Accepted: 08/01/2021] [Indexed: 05/05/2023]
Abstract
The ongoing coronavirus 2019 (COVID-19) pandemic constitutes a concerning global threat to public health and economy. In the midst of this pandemic scenario, the role of environment-to-human COVID-19 spread is still a matter of debate because mixed results have been reported concerning SARS-CoV-2 stability on high-touch surfaces in real-life scenarios. Up to now, no alternative and accessible procedures for cell culture have been applied to evaluate SARS-CoV-2 infectivity on fomites. Several strategies based on viral capsid integrity have latterly been developed using viability markers to selectively remove false-positive qPCR signals resulting from free nucleic acids and damaged viruses. These have finally allowed an estimation of viral infectivity. The present study aims to provide a rapid molecular-based protocol for detection and quantification of viable SARS-CoV-2 from fomites based on the discrimination of non-infectious SARS-CoV-2 particles by platinum chloride (IV) (PtCl4) viability RT-qPCR. An initial assessment compared two different swabbing procedures to recover inactivated SARS-CoV-2 particles from fomites coupled with two RNA extraction methods. Procedures were validated with human (E229) and porcine (PEDV) coronavirus surrogates, and compared with inactivated SARS-CoV-2 suspensions on glass, steel and plastic surfaces. The viability RT-qPCR efficiently removed the PCR amplification signals from heat and gamma-irradiated inactivated SARS-CoV-2 suspensions that had been collected from specified surfaces. This study proposes a rapid viability RT-qPCR that discriminates non-infectious SARS-CoV-2 particles on surfaces thus helping researchers to better understand the risk of contracting COVID-19 through contact with fomites and to develop more efficient epidemiological measures.
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Affiliation(s)
- Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Inés Girón-Guzmán
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain; Department of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Irene Falcó
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Azahara Díaz-Reolid
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Rosa Aznar
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain; Department of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, Paterna, 46980, Valencia, Spain.
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Le Guernic A, Palos Ladeiro M, Boudaud N, Do Nascimento J, Gantzer C, Inglard JC, Mouchel JM, Pochet C, Moulin L, Rocher V, Waldman P, Wurtzer S, Geffard A. First evidence of SARS-CoV-2 genome detection in zebra mussel (Dreissena polymorpha). JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 301:113866. [PMID: 34624574 PMCID: PMC9467573 DOI: 10.1016/j.jenvman.2021.113866] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/10/2021] [Accepted: 09/26/2021] [Indexed: 05/26/2023]
Abstract
The uses of bivalve molluscs in environmental biomonitoring have recently gained momentum due to their ability to indicate and concentrate human pathogenic microorganisms. In the context of the health crisis caused by the COVID-19 epidemic, the objective of this study was to determine if the SARS-CoV-2 ribonucleic acid genome can be detected in zebra mussels (Dreissena polymorpha) exposed to raw and treated urban wastewaters from two separate plants to support its interest as bioindicator of the SARS-CoV-2 genome contamination in water. The zebra mussels were exposed to treated wastewater through caging at the outlet of two plants located in France, as well as to raw wastewater in controlled conditions. Within their digestive tissues, our results showed that SARS-CoV-2 genome was detected in zebra mussels, whether in raw and treated wastewaters. Moreover, the detection of the SARS-CoV-2 genome in such bivalve molluscans appeared even with low concentrations in raw wastewaters. This is the first detection of the SARS-CoV-2 genome in the tissues of a sentinel species exposed to raw and treated urban wastewaters. Despite the need for development for quantitative approaches, these results support the importance of such invertebrate organisms, especially zebra mussel, for the active surveillance of pathogenic microorganisms and their indicators in environmental waters.
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Affiliation(s)
- Antoine Le Guernic
- Université de Reims Champagne-Ardenne, UMR-I02 SEBIO, Moulin de la Housse, BP1039, 51687, Reims, France.
| | - Mélissa Palos Ladeiro
- Université de Reims Champagne-Ardenne, UMR-I02 SEBIO, Moulin de la Housse, BP1039, 51687, Reims, France
| | | | - Julie Do Nascimento
- Université de Reims Champagne-Ardenne, UMR-I02 SEBIO, Moulin de la Housse, BP1039, 51687, Reims, France
| | - Christophe Gantzer
- Université de Lorraine, LCPME, Laboratoire de Chimie Physique et Microbiologie pour l'Environnement, UMR 7564, Institut Jean Barriol, Faculté des Sciences et Technologies, Vandœuvre-lès-Nancy, F-54506, France
| | - Jean-Christophe Inglard
- Grand Reims Communauté Urbaine, Direction de l'eau et de l'assainissement, CS 80036, 51722, Reims, Cedex, France
| | - Jean-Marie Mouchel
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, E-LTER Zone Atelier Seine, Paris, F-75005, France
| | - Cécile Pochet
- Grand Reims Communauté Urbaine, Direction de l'eau et de l'assainissement, CS 80036, 51722, Reims, Cedex, France
| | - Laurent Moulin
- Eau de Paris. Direction de la Recherche, du Développement et de la Qualité de l'Eau, 94200, Ivry-sur-Seine, France
| | - Vincent Rocher
- Syndicat Interdépartemental pour l'Assainissement de l'Agglomération Parisienne (SIAAP), Direction de l'Innovation, 82 avenue Kléber, Colombes, 92700, France
| | - Prunelle Waldman
- Sorbonne Université, CNRS, EPHE, UMR 7619 Metis, E-LTER Zone Atelier Seine, Paris, F-75005, France
| | - Sébastien Wurtzer
- Eau de Paris. Direction de la Recherche, du Développement et de la Qualité de l'Eau, 94200, Ivry-sur-Seine, France
| | - Alain Geffard
- Université de Reims Champagne-Ardenne, UMR-I02 SEBIO, Moulin de la Housse, BP1039, 51687, Reims, France
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26
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Bonny P, Schaeffer J, Besnard A, Desdouits M, Ngang JJE, Le Guyader FS. Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams. Front Microbiol 2021; 12:770385. [PMID: 34917052 PMCID: PMC8669915 DOI: 10.3389/fmicb.2021.770385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Many recent pandemics have been recognized as zoonotic viral diseases. While their origins remain frequently unknown, environmental contamination may play an important role in emergence. Thus, being able to describe the viral diversity in environmental samples contributes to understand the key issues in zoonotic transmission. This work describes the use of a metagenomic approach to assess the diversity of eukaryotic RNA viruses in river clams and identify sequences from human or potentially zoonotic viruses. Clam samples collected over 2years were first screened for the presence of norovirus to verify human contamination. Selected samples were analyzed using metagenomics, including a capture of sequences from viral families infecting vertebrates (VirCapSeq-VERT) before Illumina NovaSeq sequencing. The bioinformatics analysis included pooling of data from triplicates, quality filtering, elimination of bacterial and host sequences, and a deduplication step before de novo assembly. After taxonomic assignment, the viral fraction represented 0.8–15% of reads with most sequences (68–87%) remaining un-assigned. Yet, several mammalian RNA viruses were identified. Contigs identified as belonging to the Astroviridae were the most abundant, with some nearly complete genomes of bastrovirus identified. Picobirnaviridae sequences were related to strains infecting bats, and few others to strains infecting humans or other hosts. Hepeviridae sequences were mostly related to strains detected in sponge samples but also strains from swine samples. For Caliciviridae and Picornaviridae, most of identified sequences were related to strains infecting bats, with few sequences close to human norovirus, picornavirus, and genogroup V hepatitis A virus. Despite a need to improve the sensitivity of our method, this study describes a large diversity of RNA virus sequences from clam samples. To describe all viral contaminants in this type of food, and being able to identify the host infected by viral sequences detected, may help to understand some zoonotic transmission events and alert health authorities of possible emergence.
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Affiliation(s)
- Patrice Bonny
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France.,Département de Microbiologie, Université de Yaoundé I, Yaoundé, Cameroon.,Centre de Recherche en Alimentation et Nutrition, IMPM, Yaoundé, Cameroon
| | - Julien Schaeffer
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
| | - Alban Besnard
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
| | - Marion Desdouits
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
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Cuevas-Ferrando E, Randazzo W, Pérez-Cataluña A, Falcó I, Navarro D, Martin-Latil S, Díaz-Reolid A, Girón-Guzmán I, Allende A, Sánchez G. Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples. Sci Rep 2021; 11:18120. [PMID: 34518622 PMCID: PMC8438079 DOI: 10.1038/s41598-021-97700-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023] Open
Abstract
Isolation, contact tracing and restrictions on social movement are being globally implemented to prevent and control onward spread of SARS-CoV-2, even though the infection risk modelled on RNA detection by RT-qPCR remains biased as viral shedding and infectivity are not discerned. Thus, we aimed to develop a rapid viability RT-qPCR procedure to infer SARS-CoV-2 infectivity in clinical specimens and environmental samples. We screened monoazide dyes and platinum compounds as viability molecular markers on five SARS-CoV-2 RNA targets. A platinum chloride-based viability RT-qPCR was then optimized using genomic RNA, and inactivated SARS-CoV-2 particles inoculated in buffer, stool, and urine. Our results were finally validated in nasopharyngeal swabs from persons who tested positive for COVID-19 and in wastewater samples positive for SARS-CoV-2 RNA. We established a rapid viability RT-qPCR that selectively detects potentially infectious SARS-CoV-2 particles in complex matrices. In particular, the confirmed positivity of nasopharyngeal swabs following the viability procedure suggests their potential infectivity, while the complete prevention of amplification in wastewater indicated either non-infectious particles or free RNA. The viability RT-qPCR approach provides a more accurate ascertainment of the infectious viruses detection and it may complement analyses to foster risk-based investigations for the prevention and control of new or re-occurring outbreaks with a broad application spectrum.
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Affiliation(s)
- Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain.
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Irene Falcó
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
- Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - Sandra Martin-Latil
- ANSES Laboratory for Food Safety, Université Paris-Est, 94700, Maisons-Alfort, France
| | - Azahara Díaz-Reolid
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Inés Girón-Guzmán
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Ana Allende
- Research Group on Quality and Safety of Fruits and Vegetables, Department of Food Science and Technology, CEBAS-CSIC, Campus Universitario de Espinardo, 25, 30100, Murcia, Spain
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
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28
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Cuevas-Ferrando E, Randazzo W, Pérez-Cataluña A, Falcó I, Navarro D, Martin-Latil S, Díaz-Reolid A, Girón-Guzmán I, Allende A, Sánchez G. Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples. Sci Rep 2021; 11:18120. [PMID: 34518622 DOI: 10.1101/2021.03.22.21253818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/24/2021] [Indexed: 05/21/2023] Open
Abstract
Isolation, contact tracing and restrictions on social movement are being globally implemented to prevent and control onward spread of SARS-CoV-2, even though the infection risk modelled on RNA detection by RT-qPCR remains biased as viral shedding and infectivity are not discerned. Thus, we aimed to develop a rapid viability RT-qPCR procedure to infer SARS-CoV-2 infectivity in clinical specimens and environmental samples. We screened monoazide dyes and platinum compounds as viability molecular markers on five SARS-CoV-2 RNA targets. A platinum chloride-based viability RT-qPCR was then optimized using genomic RNA, and inactivated SARS-CoV-2 particles inoculated in buffer, stool, and urine. Our results were finally validated in nasopharyngeal swabs from persons who tested positive for COVID-19 and in wastewater samples positive for SARS-CoV-2 RNA. We established a rapid viability RT-qPCR that selectively detects potentially infectious SARS-CoV-2 particles in complex matrices. In particular, the confirmed positivity of nasopharyngeal swabs following the viability procedure suggests their potential infectivity, while the complete prevention of amplification in wastewater indicated either non-infectious particles or free RNA. The viability RT-qPCR approach provides a more accurate ascertainment of the infectious viruses detection and it may complement analyses to foster risk-based investigations for the prevention and control of new or re-occurring outbreaks with a broad application spectrum.
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Affiliation(s)
- Enric Cuevas-Ferrando
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain.
| | - Walter Randazzo
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Alba Pérez-Cataluña
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Irene Falcó
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
- Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - Sandra Martin-Latil
- ANSES Laboratory for Food Safety, Université Paris-Est, 94700, Maisons-Alfort, France
| | - Azahara Díaz-Reolid
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Inés Girón-Guzmán
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
| | - Ana Allende
- Research Group on Quality and Safety of Fruits and Vegetables, Department of Food Science and Technology, CEBAS-CSIC, Campus Universitario de Espinardo, 25, 30100, Murcia, Spain
| | - Gloria Sánchez
- Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Av. Agustín Escardino 7, 46980, Paterna, Valencia, Spain
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Islam A, Sayeed MA, Kalam MA, Ferdous J, Rahman MK, Abedin J, Islam S, Shano S, Saha O, Shirin T, Hassan MM. Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally. Microorganisms 2021; 9:1696. [PMID: 34442775 PMCID: PMC8401355 DOI: 10.3390/microorganisms9081696] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/27/2021] [Accepted: 08/03/2021] [Indexed: 01/01/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swamped the global environment greatly in the current pandemic. Wastewater-based epidemiology (WBE) effectively forecasts the surge of COVID-19 cases in humans in a particular region. To understand the genomic characteristics/footprints and diversity of SARS-CoV-2 in the environment, we analyzed 807 SARS-CoV-2 sequences from 20 countries deposited in GISAID till 22 May 2021. The highest number of sequences (n = 638) were reported in Austria, followed by the Netherlands, China, and Bangladesh. Wastewater samples were highest (40.0%) to successfully yield the virus genome followed by a 24 h composite wastewater sample (32.6%) and sewage (18.5%). Phylogenetic analysis revealed that SARS-CoV-2 environmental strains are a close congener with the strains mostly circulating in the human population from the same region. Clade GRY (32.7%), G (29.2%), GR (25.3%), O (7.2%), GH (3.4%), GV (1.4%), S (0.5%), and L (0.4%) were found in environmental samples. Various lineages were identified in environmental samples; nevertheless, the highest percentages (49.4%) of the alpha variant (B.1.1.7) were detected in Austria, Liechtenstein, Slovenia, Czech Republic, Switzerland, Germany, and Italy. Other prevalent lineages were B.1 (18.2%), B.1.1 (9.2%), and B.1.160 (3.9%). Furthermore, a significant number of amino acid substitutions were found in environmental strains where the D614G was found in 83.8% of the sequences. However, the key mutations-N501Y (44.6%), S982A (44.4%), A570D (43.3%), T716I (40.4%), and P681H (40.1%) were also recorded in spike protein. The identification of the environmental belvedere of SARS-CoV-2 and its genetic signature is crucial to detect outbreaks, forecast pandemic harshness, and prepare with the appropriate tools to control any impending pandemic. We recommend genomic environmental surveillance to trace the emerging variants and diversity of SARS-CoV-2 viruses circulating in the community. Additionally, proper disposal and treatment of wastewater, sewage, and medical wastes are important to prevent environmental contamination.
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Affiliation(s)
- Ariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (M.A.S.); (J.F.); (M.K.R.); (J.A.); (S.I.); (S.S.)
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Burwood, VIC 3216, Australia
| | - Md. Abu Sayeed
- EcoHealth Alliance, New York, NY 10001-2320, USA; (M.A.S.); (J.F.); (M.K.R.); (J.A.); (S.I.); (S.S.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | | | - Jinnat Ferdous
- EcoHealth Alliance, New York, NY 10001-2320, USA; (M.A.S.); (J.F.); (M.K.R.); (J.A.); (S.I.); (S.S.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Md. Kaisar Rahman
- EcoHealth Alliance, New York, NY 10001-2320, USA; (M.A.S.); (J.F.); (M.K.R.); (J.A.); (S.I.); (S.S.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Josefina Abedin
- EcoHealth Alliance, New York, NY 10001-2320, USA; (M.A.S.); (J.F.); (M.K.R.); (J.A.); (S.I.); (S.S.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Shariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (M.A.S.); (J.F.); (M.K.R.); (J.A.); (S.I.); (S.S.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Shahanaj Shano
- EcoHealth Alliance, New York, NY 10001-2320, USA; (M.A.S.); (J.F.); (M.K.R.); (J.A.); (S.I.); (S.S.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh;
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Mohammad Mahmudul Hassan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh;
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30
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De Rijcke M, Shaikh HM, Mees J, Nauwynck H, Vandegehuchte MB. Environmental stability of porcine respiratory coronavirus in aquatic environments. PLoS One 2021; 16:e0254540. [PMID: 34260643 PMCID: PMC8279332 DOI: 10.1371/journal.pone.0254540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/28/2021] [Indexed: 12/23/2022] Open
Abstract
Coronaviruses (CoVs) are a family of viruses that are best known as the causative agents of human diseases like the common cold, Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS) and COVID-19. CoVs spread by human-to-human transmission via droplets or direct contact. There is, however, concern about potential waterborne transmission of SARS-CoV-2, the virus responsible for COVID-19, as it has been found in wastewater facilities and rivers. To date, little is known about the stability of SARS-CoV-2 or any other free coronavirus in aquatic environments. The inactivation of terrestrial CoVs in seawater is rarely studied. Here, we use a porcine respiratory coronavirus (PRCV) that is commonly found in animal husbandry as a surrogate to study the stability of CoVs in natural water. A series of experiments were conducted in which PRCV (strain 91V44) was added to filtered and unfiltered fresh- and saltwater taken from the river Scheldt and the North Sea. Virus titres were then measured by TCID50-assays using swine testicle cell cultures after various incubation times. The results show that viral inactivation of PRCV in filtered seawater can be rapid, with an observed 99% decline in the viral load after just two days, which may depend on temperature and the total suspended matter concentration. PRCV degraded much slower in filtered water from the river Scheldt, taking over 15 days to decline by 99%, which was somewhat faster than the PBS control treatment (T99 = 19.2 days). Overall, the results suggest that terrestrial CoVs are not likely to accumulate in marine environments. Studies into potential interactions with exudates (proteases, nucleases) from the microbial food web are, however, recommended.
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Affiliation(s)
- Maarten De Rijcke
- Flanders Marine Institute (VLIZ), InnovOcean Site, Oostende, Belgium
| | | | - Jan Mees
- Flanders Marine Institute (VLIZ), InnovOcean Site, Oostende, Belgium
- Marine Biology Research Group, Ghent University, Faculty of Sciences, Ghent, Belgium
| | - Hans Nauwynck
- Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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