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Gad B, Kłosiewicz P, Oleksiak K, Krzysztoszek A, Toczyłowski K, Sulik A, Wieczorek T, Wieczorek M. Intensified Circulation of Echovirus 11 after the COVID-19 Pandemic in Poland: Detection of a Highly Pathogenic Virus Variant. Viruses 2024; 16:1011. [PMID: 39066174 PMCID: PMC11281687 DOI: 10.3390/v16071011] [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: 05/24/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
After the first phase of the COVID-19 pandemic in Europe, a new highly pathogenic variant of echovirus 11 (E11) was detected. The aim of this study was to analyze the genetic diversity of Polish E11 environmental and clinical strains circulating between 2017 and 2023 as well as compare them with E11 strains isolated from severe neonatal sepsis cases reported in Europe between 2022 and 2023. Additionally, the study explores the effectiveness of environmental monitoring in tracking the spread of new variants. For this purpose, the complete sequences of the VP1 capsid protein gene were determined for 266 E11 strains isolated in Poland from 2017 to 2023, and phylogenetic analysis was performed. In the years 2017-2023, a significant increase in the detection of E11 strains was observed in both environmental and clinical samples in Poland. The Polish E11 strains represented three different genotypes, C3, D5 and E, and were characterized by a high diversity. In Poland, the intensive circulation of the new variant E11, responsible for severe neonatal infections with a high mortality in Europe, was detected in the years 2022-2023. This investigation demonstrates the important role of environmental surveillance in the tracking of enteroviruses circulation, especially in settings with limited clinical surveillance.
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Affiliation(s)
- Beata Gad
- Department of Virology, National Institute of Public Health NIH—National Research Institute, Chocimska 24, 00-791 Warsaw, Poland; (B.G.); (P.K.); (K.O.); (A.K.)
| | - Paulina Kłosiewicz
- Department of Virology, National Institute of Public Health NIH—National Research Institute, Chocimska 24, 00-791 Warsaw, Poland; (B.G.); (P.K.); (K.O.); (A.K.)
| | - Kinga Oleksiak
- Department of Virology, National Institute of Public Health NIH—National Research Institute, Chocimska 24, 00-791 Warsaw, Poland; (B.G.); (P.K.); (K.O.); (A.K.)
| | - Arleta Krzysztoszek
- Department of Virology, National Institute of Public Health NIH—National Research Institute, Chocimska 24, 00-791 Warsaw, Poland; (B.G.); (P.K.); (K.O.); (A.K.)
| | - Kacper Toczyłowski
- Department of Pediatric Infectious Diseases, Medical University of Bialystok, Waszyngtona 17, 15-274 Bialystok, Poland; (K.T.); (A.S.)
| | - Artur Sulik
- Department of Pediatric Infectious Diseases, Medical University of Bialystok, Waszyngtona 17, 15-274 Bialystok, Poland; (K.T.); (A.S.)
| | - Tobiasz Wieczorek
- Faculty of Civil Engineering and Geodesy, Military University of Technology, Gen. S. Kaliskiego 2, 00-908 Warsaw, Poland;
| | - Magdalena Wieczorek
- Department of Virology, National Institute of Public Health NIH—National Research Institute, Chocimska 24, 00-791 Warsaw, Poland; (B.G.); (P.K.); (K.O.); (A.K.)
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Hotta C, Fujinuma Y, Ogawa T, Akita M, Ogawa T. Surveillance of Wastewater to Monitor the Prevalence of Gastroenteritis Viruses in Chiba Prefecture (2014-2019). J Epidemiol 2024; 34:195-202. [PMID: 37211397 PMCID: PMC10918334 DOI: 10.2188/jea.je20220305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/11/2023] [Indexed: 05/23/2023] Open
Abstract
BACKGROUND In Japan, sentinel surveillance is used to monitor the trend of infectious gastroenteritis. Another method of pathogen surveillance, wastewater-based epidemiology, has been used recently because it can help to monitor infectious disease without relying on patient data. Here, we aimed to determine the viral trends reflected in the number of reported patients and number of gastroenteritis virus-positive samples. We focused on gastroenteritis viruses present in wastewater and investigated the usefulness of wastewater surveillance for the surveillance of infectious gastroenteritis. METHODS Real-time polymerase chain reaction was used for viral gene detection in wastewater. The number of reported patients per pediatric sentinel site and number of viral genome copies were compared for correlation potential. The number of gastroenteritis virus-positive samples reported by National Epidemiological Surveillance of Infectious Disease (NESID) and the status of gastroenteritis viruses detected in wastewater were also evaluated. RESULTS Genes of norovirus genotype I, norovirus genotype II, sapovirus, astrovirus, rotavirus group A, and rotavirus group C were detected in wastewater samples. Viruses were detected in wastewater during periods when no gastroenteritis virus-positive samples were reported to NESID. CONCLUSION Norovirus genotype II and other gastroenteritis viruses were detected in wastewater even during periods when no gastroenteritis virus-positive samples were found. Therefore, surveillance using wastewater can complement sentinel surveillance and is an effective tool for the surveillance of infectious gastroenteritis.
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Affiliation(s)
- Chiemi Hotta
- Division of Virology and Medical Zoology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Yuki Fujinuma
- Division of Virology and Medical Zoology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Takashi Ogawa
- Division of Virology and Medical Zoology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Mamiko Akita
- Division of Virology and Medical Zoology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Tomoko Ogawa
- Division of Virology and Medical Zoology, Chiba Prefectural Institute of Public Health, Chiba, Japan
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Huang S, Zhang Y, Zhang W, Chen M, Li C, Guo X, Zhu S, Zeng H, Fang L, Ke B, Li H, Yoshida H, Xu W, Deng X, Zheng H. Prevalence of Non-Polio Enteroviruses in the Sewage of Guangzhou City, China, from 2013 to 2021. Microbiol Spectr 2023; 11:e0363222. [PMID: 36995241 PMCID: PMC10269821 DOI: 10.1128/spectrum.03632-22] [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: 09/14/2022] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
Continuous surveillance of enteroviruses (EVs) in urban domestic sewage can timely reflect the circulation of EVs in the environment and crowds, and play a predictive and early warning role in EV-related diseases. To better understand the long-term epidemiological trends of circulating EVs and EV-related diseases, we conducted a 9-year (2013 to 2021) surveillance study of non-polio EVs (NPEVs) in urban sewage in Guangzhou city, China. After concentrating and isolating the viruses from the sewage samples, NPEVs were detected and molecular typing was performed. Twenty-one different NPEV serotypes were identified. The most isolated EVs were echovirus 11 (E11), followed by coxsackievirus (CV) B5, E6, and CVB3. EV species B prevailed in sewage samples, but variations in the annual frequency of different serotypes were also observed in different seasons, due to spatial and temporal factors. E11 and E6 were detected continuously before 2017, and the number of isolates was relatively stable during the surveillance period. However, after their explosive growth in 2018 and 2019, their numbers suddenly decreased significantly. CVB3 and CVB5 had alternating trends; CVB5 was most frequently detected in 2013 to 2014 and 2017 to 2018, while CVB3 was most frequently detected in 2015 to 2016 and 2020 to 2021. Phylogenetic analysis showed that at least two different transmission chains of CVB3 and CVB5 were prevalent in Guangzhou City. Our results show that in the absence of a comprehensive and systematic EV-related disease surveillance system in China, environmental surveillance is a powerful and effective tool to strengthen and further investigate the invisible transmission of EVs in the population. IMPORTANCE This study surveilled urban sewage samples from north China for 9 years to monitor enteroviruses. Samples were collected, processed, and viral identification and molecular typing were performed. We detected 21 different non-polio enteroviruses (NPEVs) with yearly variations in prevalence and peak seasons. In addition, this study is very important for understanding the epidemiology of EVs during the COVID-19 pandemic, as the detection frequency and serotypes of EVs in sewage changed considerably around 2020. We believe that our study makes a significant contribution to the literature because our results strongly suggest that environmental surveillance is an exceptionally important tool, which can be employed to detect and monitor organisms of public health concern, which would otherwise be missed and under-reported by case-based surveillance systems alone.
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Affiliation(s)
- Shufen Huang
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Panyu District, Guangzhou, China
- School of Public Health, Southern Medical University, Baiyun District, Guangzhou, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory and Ministry of Health Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Wei Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Panyu District, Guangzhou, China
| | - Meizhong Chen
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Panyu District, Guangzhou, China
- School of Public Health, Southern Medical University, Baiyun District, Guangzhou, China
| | - Caixia Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Panyu District, Guangzhou, China
| | - Xue Guo
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Panyu District, Guangzhou, China
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory and Ministry of Health Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Hanri Zeng
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Panyu District, Guangzhou, China
| | - Ling Fang
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Panyu District, Guangzhou, China
| | - Bixia Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Panyu District, Guangzhou, China
| | - Hui Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Panyu District, Guangzhou, China
| | - Hiromu Yoshida
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory and Ministry of Health Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Xiaoling Deng
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Panyu District, Guangzhou, China
| | - Huanying Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Panyu District, Guangzhou, China
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Kilaru P, Hill D, Anderson K, Collins MB, Green H, Kmush BL, Larsen DA. Wastewater Surveillance for Infectious Disease: A Systematic Review. Am J Epidemiol 2022; 192:305-322. [PMID: 36227259 PMCID: PMC9620728 DOI: 10.1093/aje/kwac175] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 08/25/2022] [Accepted: 10/05/2022] [Indexed: 02/07/2023] Open
Abstract
Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been shown to be a valuable source of information regarding SARS-CoV-2 transmission and coronavirus disease 2019 (COVID-19) cases. Although the method has been used for several decades to track other infectious diseases, there has not been a comprehensive review outlining all of the pathogens that have been surveilled through wastewater. Herein we identify the infectious diseases that have been previously studied via wastewater surveillance prior to the COVID-19 pandemic. Infectious diseases and pathogens were identified in 100 studies of wastewater surveillance across 38 countries, as were themes of how wastewater surveillance and other measures of disease transmission were linked. Twenty-five separate pathogen families were identified in the included studies, with the majority of studies examining pathogens from the family Picornaviridae, including polio and nonpolio enteroviruses. Most studies of wastewater surveillance did not link what was found in the wastewater to other measures of disease transmission. Among those studies that did, the value reported varied by study. Wastewater surveillance should be considered as a potential public health tool for many infectious diseases. Wastewater surveillance studies can be improved by incorporating other measures of disease transmission at the population-level including disease incidence and hospitalizations.
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Affiliation(s)
- Pruthvi Kilaru
- Department of Public Health, Syracuse University, Syracuse, New York, United States,Des Moines University College of Osteopathic Medicine, Des Moines, Iowa, United States
| | - Dustin Hill
- Department of Public Health, Syracuse University, Syracuse, New York, United States,Graduate Program in Environmental Science, State University of New York College of Environmental Science and Forestry, Syracuse, New York, United States
| | - Kathryn Anderson
- Department of Medicine, State University of New York Upstate Medical University, Syracuse, New York, United States
| | - Mary B Collins
- Department of Environmental Studies, State University of New York College of Environmental Science, Syracuse, New York, United States
| | - Hyatt Green
- Department of Environmental Biology, State University of New York College of Environmental Science, Syracuse, New York, United States
| | - Brittany L Kmush
- Department of Public Health, Syracuse University, Syracuse, New York, United States
| | - David A Larsen
- Correspondence to Dr. Dave Larsen, Department of Public Health, Syracuse University, 430C White Hall, Syracuse, NY 13244 ()
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Tao Z, Lin X, Liu Y, Ji F, Wang S, Xiong P, Zhang L, Xu Q, Xu A, Cui N. Detection of multiple human astroviruses in sewage by next generation sequencing. WATER RESEARCH 2022; 218:118523. [PMID: 35525029 DOI: 10.1016/j.watres.2022.118523] [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: 02/17/2022] [Revised: 04/09/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Human astrovirus (HAstV) composes of classic HAstV serotypes 1-8 and recently discovered novel HAstV-MLB and HAstV-VA strains. A number of studies have demonstrated that wastewater analysis is an effective approach to understand the prevalence and diversity of enteric viruses in local population. However, a comprehensive analysis of classic and novel HAstVs in sewage is still lacking. In this study, sewage samples were collected monthly from Jinan, China during 2018-2019. Quantification of HAstV genomes was performed by real-time quantitative PCR. Different from previous studies which focused on partial ORF1b or ORF2 gene, complete ORF2 region of HAstV was amplified from sewage concentrates, and amplicons were subjected to next generation sequencing (NGS) and genetic analysis. This methodology allowed detection of 18 astroviruses, of which 7 (HAstV-1, -2, -4, -5, VA1, VA2, and VA3) were detected in all sewage samples. A new strain VA6 mapped to the HMO clade was identified in 20.8% of samples, with 82.4%-83.3% nucleotide identities to the closest strain VA5. The viral load of classic, MLB and VA clades in sewage samples ranged from 3.7 × 104 to 4.6 × 107, 3.4 × 104 to 3.9 × 106, and 3.3 × 104 to 4.1 × 106 copies per liter, respectively. Phylogenetic analysis based on complete ORF2 region reflected local HAstVs within each genotype constituted multiple co-circulating lineages. Existence of several new lineages composed exclusively or predominantly of Chinese sequences was observed as well. These results demonstrate sewage contains astroviruses with considerable high diversities. NGS based environmental surveillance greatly improves the understanding of HAstV circulation and should be encouraged.
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Affiliation(s)
- Zexin Tao
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Xiaojuan Lin
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Yao Liu
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Feng Ji
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Suting Wang
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Ping Xiong
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Li Zhang
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Qing Xu
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China
| | - Aiqiang Xu
- Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Jinan 250014, China.
| | - Ning Cui
- Shandong University of Traditional Chinese Medicine, 4655 Daxue Road, Jinan 250355, China.
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Rmadi Y, Elargoubi A, González-Sanz R, Mastouri M, Cabrerizo M, Aouni M. Molecular characterization of enterovirus detected in cerebrospinal fluid and wastewater samples in Monastir, Tunisia, 2014-2017. Virol J 2022; 19:45. [PMID: 35303921 PMCID: PMC8932122 DOI: 10.1186/s12985-022-01770-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/23/2022] [Indexed: 11/10/2022] Open
Abstract
Background Enteroviruses (EVs) are considered the main causative agents responsible for aseptic meningitis worldwide. This study was conducted in the Monastir region of Tunisia in order to know the prevalence of EV infections in children with meningitis symptoms. Detected EV types were compared to those identified in wastewater samples.
Methods Two hundred CSF samples collected from hospitalized patients suspected of having aseptic meningitis for an EV infection between May 2014 and May 2017 and 80 wastewater samples collected in the same time-period were analyzed. EV detection and genotyping were performed using PCR methods followed by sequencing. Phylogenetic analyses in the 3′-VP1 region were also carried-out. Results EVs were detected in 12% (24/200) CSF and in 35% (28/80) wastewater samples. EV genotyping was reached in 50% (12/24) CSF-positive samples and in 64% (18/28) sewage. Most frequent types detected in CSF were CVB3, E-30 and E-9 (25% each). In wastewater samples, the same EVs were identified, but also other types non-detected in CSF samples, such as E-17,CVA9 and CVB1 from EV species B, and EV-A71 and CVA8 from EV-A, suggesting their likely lower pathogenicity. Phylogenetic analysis showed that within the same type, different strains circulate in Tunisia. For some of the EV types such as E-9, E-11 or CVB3, the same strains were detected in CSF and wastewater samples. Conclusions Epidemiological studies are important for the surveillance of the EV infections and to better understand the emergence of certain types and variants.
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Affiliation(s)
- Yosra Rmadi
- Faculty of Pharmacy, Laboratory of Infectious Diseases and Biological Agents, University of Monastir, LR99-ES27, 5000, Monastir, Tunisia
| | - Aida Elargoubi
- Laboratory of Microbiology, Fattouma Bourguiba University Hospital, Monastir, Tunisia
| | - Rubén González-Sanz
- Enterovirus and Viral Gastrointestinal Unit, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Maha Mastouri
- Faculty of Pharmacy, Laboratory of Infectious Diseases and Biological Agents, University of Monastir, LR99-ES27, 5000, Monastir, Tunisia.,Laboratory of Microbiology, Fattouma Bourguiba University Hospital, Monastir, Tunisia
| | - Maria Cabrerizo
- Enterovirus and Viral Gastrointestinal Unit, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain.
| | - Mahjoub Aouni
- Faculty of Pharmacy, Laboratory of Infectious Diseases and Biological Agents, University of Monastir, LR99-ES27, 5000, Monastir, Tunisia
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Mousazadeh M, Ashoori R, Paital B, Kabdaşlı I, Frontistis Z, Hashemi M, Sandoval MA, Sherchan S, Das K, Emamjomeh MM. Wastewater Based Epidemiology Perspective as a Faster Protocol for Detecting Coronavirus RNA in Human Populations: A Review with Specific Reference to SARS-CoV-2 Virus. Pathogens 2021; 10:1008. [PMID: 34451472 PMCID: PMC8401392 DOI: 10.3390/pathogens10081008] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/21/2022] Open
Abstract
Wastewater-based epidemiology (WBE) has a long history of identifying a variety of viruses from poliovirus to coronaviruses, including novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The presence and detection of SARS-CoV-2 in human feces and its passage into the water bodies are significant public health challenges. Hence, the hot issue of WBE of SARS-CoV-2 in the coronavirus respiratory disease (COVID-19) pandemic is a matter of utmost importance (e.g., SARS-CoV-1). The present review discusses the background, state of the art, actual status, and prospects of WBE, as well as the detection and quantification protocols of SARS-CoV-2 in wastewater. The SARS-CoV-2 detection studies have been performed in different water matrixes such as influent and effluent of wastewater treatment plants, suburban pumping stations, hospital wastewater, and sewer networks around the globe except for Antarctica. The findings revealed that all WBE studies were in accordance with clinical and epidemiological data, which correlates the presence of SARS-CoV-2 ribonucleic acid (RNA) with the number of new daily positive cases officially reported. This last was confirmed via Reverse Transcriptase-quantitative Polymerase Chain Reaction (RT-qPCR) testing which unfortunately is not suitable for real-time surveillance. In addition, WBE concept may act as a faster protocol to alert the public health authorities to take administrative orders (possible re-emerging infections) due to the impracticality of testing all citizens in a short time with limited diagnostic facilities. A comprehensive and integrated review covering all steps starting from sampling to molecular detection of SARS-CoV-2 in wastewater has been made to guide for the development well-defined and reliable protocols.
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Affiliation(s)
- Milad Mousazadeh
- Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran;
- Department of Environmental Health Engineering, School of Health, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Razieh Ashoori
- Department of Environmental Health Engineering, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran;
| | - Biswaranjan Paital
- Redox Regulation Laboratory, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar 751003, India;
| | - Işık Kabdaşlı
- Environmental Engineering Department, Civil Engineering Faculty, Ayazağa Campus, İstanbul Technical University, İstanbul 34469, Turkey;
| | - Zacharias Frontistis
- Department of Chemical Engineering, University of Western Macedonia, 50132 Kozani, Greece;
| | - Marjan Hashemi
- Environmental and Occupational Hazards Control Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran;
| | - Miguel A. Sandoval
- Laboratorio de Electroquímica Medio Ambiental LEQMA, Departamento de Química de los Materiales, Facultad de Química y Biología, Universidad de Santiago de Chile USACH, Casilla 40, Correo 33, Santiago 9170022, Chile;
- Departamento de Ingeniería Química, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - Samendra Sherchan
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 7011, USA;
| | - Kabita Das
- Department of Philosophy, Utkal University, Bhubaneswar 751004, India;
| | - Mohammad Mahdi Emamjomeh
- Social Determinants of Health Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
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Hillary LS, Farkas K, Maher KH, Lucaci A, Thorpe J, Distaso MA, Gaze WH, Paterson S, Burke T, Connor TR, McDonald JE, Malham SK, Jones DL. Monitoring SARS-CoV-2 in municipal wastewater to evaluate the success of lockdown measures for controlling COVID-19 in the UK. WATER RESEARCH 2021; 200:117214. [PMID: 34058486 PMCID: PMC8105641 DOI: 10.1016/j.watres.2021.117214] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/19/2021] [Accepted: 04/30/2021] [Indexed: 05/18/2023]
Abstract
SARS-CoV-2 and the resulting COVID-19 pandemic represents one of the greatest recent threats to human health, wellbeing and economic growth. Wastewater-based epidemiology (WBE) of human viruses can be a useful tool for population-scale monitoring of SARS-CoV-2 prevalence and epidemiology to help prevent further spread of the disease, particularly within urban centres. Here, we present a longitudinal analysis (March-July 2020) of SARS-CoV-2 RNA prevalence in sewage across six major urban centres in the UK (total population equivalent 3 million) by q(RT-)PCR and viral genome sequencing. Our results demonstrate that levels of SARS-CoV-2 RNA generally correlated with the abundance of clinical cases recorded within the community in large urban centres, with a marked decline in SARS-CoV-2 RNA abundance following the implementation of lockdown measures. The strength of this association was weaker in areas with lower confirmed COVID-19 case numbers. Further, sequence analysis of SARS-CoV-2 from wastewater suggested that multiple genetically distinct clusters were co-circulating in the local populations covered by our sample sites, and that the genetic variants observed in wastewater reflected similar SNPs observed in contemporaneous samples from cases tested in clinical diagnostic laboratories. We demonstrate how WBE can be used for both community-level detection and tracking of SARS-CoV-2 and other virus' prevalence, and can inform public health policy decisions. Although, greater understanding of the factors that affect SARS-CoV-2 RNA concentration in wastewater are needed for the full integration of WBE data into outbreak surveillance. In conclusion, our results lend support to the use of routine WBE for monitoring of SARS-CoV-2 and other human pathogenic viruses circulating in the population and assessment of the effectiveness of disease control measures.
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Affiliation(s)
- Luke S Hillary
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, United Kingdom.
| | - Kata Farkas
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, United Kingdom; School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, LL59 5AB, United Kingdom
| | - Kathryn H Maher
- NERC Environmental Omics Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Anita Lucaci
- NERC Environmental Omics Facility, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Jamie Thorpe
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, United Kingdom; School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, LL59 5AB, United Kingdom
| | - Marco A Distaso
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, United Kingdom
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, ESI, Penryn Campus, TR10 9FE United Kingdom
| | - Steve Paterson
- NERC Environmental Omics Facility, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
| | - Terry Burke
- NERC Environmental Omics Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom; Public Health Wales, University Hospital of Wales, Cardiff, CF14 4XW, United Kingdom
| | - James E McDonald
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, United Kingdom
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, LL59 5AB, United Kingdom
| | - David L Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, United Kingdom; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
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Song K, Lin X, Liu Y, Ji F, Zhang L, Chen P, Zhao C, Song Y, Tao Z, Xu A. Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:270-280. [PMID: 33755873 PMCID: PMC7985922 DOI: 10.1007/s12560-021-09469-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Human sapovirus (SaV) is an important causative agent of nonbacterial gastroenteritis in humans. However, little is known about its circulation in China. To study the prevalence and diversity of human SaV genotypes circulating in eastern China, a 3-year environmental surveillance combined with next generation sequencing (NGS) technology was conducted. A total of 36 raw sewage samples were collected from January 2017 to December 2019 in Jinan and processed. Thirty-five (97.22%) samples were positive for human SaV genome in quantitative RT-PCR assay; 33 (91.67%) samples were positive in nested RT-PCR assay on partial capsid VP1 sequence and all amplicons were further analyzed separately by NGS. Among those, ten genotypes belonging to the genogroups of GI, GII, GIV, and GV were identified by NGS, including 4 major genotypes (GI.2, GI.1, GV.1 and GI.3) and 6 uncommon genotypes (GII.5, GII.1, GII.NA1, GII.3, GI.6 and GIV.1). A temporal switch of predominant genotype was observed from GI.2 to GI.1 around June 2019. Local and foreign sequences clustered together in some branches according to phylogenetic analysis, indicating frequent transmission of various lineages in different regions of the world. Environmental surveillance provides a comprehensive picture of human SaV in China. NGS-based environmental surveillance improves our knowledge on human SaV circulating in communities greatly and should be encouraged as a sensitive surveillance tool.
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Affiliation(s)
- Ke Song
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China
| | - Xiaojuan Lin
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Yao Liu
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Feng Ji
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Li Zhang
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
| | - Peng Chen
- School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, 44-1 Wenhuaxi Road, Jinan, 250012, People's Republic of China
| | - Chenxu Zhao
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China
| | - Yanyan Song
- Department of Microbiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China.
| | - Zexin Tao
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China.
| | - Aiqiang Xu
- Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan, 250014, People's Republic of China
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, No. 44 Wenhuaxi Road, Jinan, 250012, People's Republic of China
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Kitamura K, Sadamasu K, Muramatsu M, Yoshida H. Efficient detection of SARS-CoV-2 RNA in the solid fraction of wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 763:144587. [PMID: 33360957 PMCID: PMC7746508 DOI: 10.1016/j.scitotenv.2020.144587] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 05/16/2023]
Abstract
In the context of the coronavirus disease 2019 (COVID-19) pandemic, environmental surveillance for the detection of SARS-CoV-2 has become increasingly important. Studies have demonstrated that the SARS-CoV-2 RNA is present in the feces of infected individuals; further, its presence in wastewater has been reported. However, an optimized method for its detection in sewage has not yet been adequately investigated. Therefore, in this study, the efficient detection of SARS-CoV-2 RNA in the solid fraction of wastewater was investigated using two quantitative PCR assays. In particular, wastewater samples were collected from a manhole located in the commercial district of a metropolitan region in Japan, where COVID-19 is highly prevalent, and two wastewater treatment plants (WWTPs). The samples were concentrated using four separate methods, namely, electronegative membrane adsorption, polyethylene glycol precipitation, ultrafiltration, and solid precipitation. Each method revealed a significant concentration of pepper mild mottle virus (PMMoV) RNA, which is an indicator virus for wastewater. As expected, non-enveloped PMMoV RNA was enriched in the supernatant fraction such that relatively low concentrations were detected in the solid fraction of the wastewater samples. In contrast, higher SARS-CoV-2 RNA concentrations were consistently detected in the solid fractions compared with the supernatant fractions based on the other methods that were investigated in this study. Spearman's correlation tests showed that the SARS-CoV-2 RNA concentrations in wastewater samples from the WWTP were significantly correlated with the number of COVID-19 cases recorded during the data collection period. These results demonstrate that viral recovery from the solid fraction is an effective method for SARS-CoV-2 RNA surveillance in an aqueous environment.
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Affiliation(s)
- Kouichi Kitamura
- Department of Virology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-murayama, Tokyo 208-0011, Japan.
| | - Kenji Sadamasu
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunin-cho, Shinjuku-ku, Tokyo 169-0073, Japan
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-murayama, Tokyo 208-0011, Japan
| | - Hiromu Yoshida
- Department of Virology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-murayama, Tokyo 208-0011, Japan
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