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Shaheen MNF, Ahmed NI, Elmahdy EM. Wastewater and Clinical Based Epidemiology for Viral Surveillance in the Nile Delta of Egypt. Curr Microbiol 2025; 82:296. [PMID: 40394397 DOI: 10.1007/s00284-025-04267-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2024] [Accepted: 04/29/2025] [Indexed: 05/22/2025]
Abstract
The release of inadequately treated wastewater, containing human viruses, into the water environment or agricultural use represent a major problem in public health. In this study, SYBR Green-based real-time polymerase chain (qPCR) was applied to evaluate the prevalence of human polyomavirus (HPyV), papillomavirus (HPV), hepatitis A virus (HAV), and hepatitis E virus (HEV) in urban sewage and among children with acute gastroenteritis. The seasonal distribution in wastewater and viral removal by wastewater treatment process were also evaluated, over the 2 year sampling period. HPyV, HPV, HAV, and HEV were detected in 68%, 39.6% 42.4%, and 33.3% of the raw sewage, respectively, with highest incidence in winter season. In treated sewage samples, HPyV, HPV, HAV, and HEV were detected in 21%, 9.4%, 18.7%, and 0%, respectively. Furthermore, among the 200 diarrheal stool samples, HPyV, HPV, HAV, and HEV were detected in 72.5%, 50%, 13%, and 5%, respectively. HPyV was more prevalent in both environmental and clinical samples. The mean concentration of these viruses in raw sewage, treated sewage, and stool samples was 3.62 × 106 GC/ml, 4.03 × 103 GC/ml, and 4.05 × 106 GC/g, respectively. Examination of wastewater treatment process efficiency based on mean concentration values at entry and exit observed an overall reduction of 49.5%, 47.9%, 41.2%, 100%, for HPyV, HPV, HAV, and HEV, respectively. This study showed the benefit of environmental monitoring as an additional tool to investigate the epidemiology of these viruses circulating in a given community.
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Affiliation(s)
- Mohamed Nasr Fathi Shaheen
- Environmental Virology Laboratory, Department of Water Pollution Research, Environment and Climate Change Research Institute, National Research Center, Dokki, Cairo, 12622, Egypt
| | - Nehal Ismail Ahmed
- Environmental Virology Laboratory, Department of Water Pollution Research, Environment and Climate Change Research Institute, National Research Center, Dokki, Cairo, 12622, Egypt
| | - Elmahdy Mohamed Elmahdy
- Environmental Virology Laboratory, Department of Water Pollution Research, Environment and Climate Change Research Institute, National Research Center, Dokki, Cairo, 12622, Egypt.
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2
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Fernandez-Sabatella C, Corrales G, Monzon L, Andrade E, Sica N, Cardozo E, Baccardatz N, Jacques J, Castro S, Castells M, Victoria M, Colina R. Wastewater-Based Epidemiology for Analysis of Human Papillomavirus Infections in a Uruguayan Urban Area. FOOD AND ENVIRONMENTAL VIROLOGY 2025; 17:27. [PMID: 40299146 DOI: 10.1007/s12560-025-09642-6] [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: 11/11/2024] [Accepted: 04/24/2025] [Indexed: 04/30/2025]
Abstract
Human papillomavirus (HPV) is primarily transmitted through sexual contact and is classified into high- and low-risk genotypes based on their association with cancer development. High-risk (HR) genotypes, such as 16 and 18, among others, have been identified as responsible for the development of cervical cancer while low-risk (LR) genotypes, such as 6 and 11, among others, cause anogenital warts. The aim of this study was to determine the presence of HPV genotypes in wastewater from the wastewater treatment plant of the city of Salto, Uruguay in order to analyze the circulating HPV strains in their population. These samples were subjected to qualitative PCR analysis, and genotypes were identified through sequencing of the DNA products. HPV 6, 16, 31, 66, 81, 84, and 145 were frequently detected in wastewater and HPV 6 and 16 were the prevalent in cytological samples. A great diversity of genotypes was evident in the wastewater of the city. The approach of wastewater-based epidemiology as a representation of the circulating HPV genotypes in the population is adequate and an important tool for molecular epidemiologic studies mainly in developing countries such as Uruguay where information concerning genotypes circulation is scarce.
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Affiliation(s)
- C Fernandez-Sabatella
- Laboratory of Molecular Virology, Department of Biological Sciences, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | - G Corrales
- Laboratory of Molecular Virology, Department of Biological Sciences, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | - L Monzon
- Regional Hospital of Salto, Public Health Service Administration (ASSE), Salto, Uruguay
| | - E Andrade
- Regional Hospital of Salto, Public Health Service Administration (ASSE), Salto, Uruguay
| | - N Sica
- Medical Center of Salto, Salto, Uruguay
| | - E Cardozo
- Medical Center of Salto, Salto, Uruguay
| | - N Baccardatz
- National Sanitation Authority (OSE), Salto, Uruguay
| | - J Jacques
- National Sanitation Authority (OSE), Salto, Uruguay
| | - S Castro
- Department of Mathematic and Statistic, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | - M Castells
- Laboratory of Molecular Virology, Department of Biological Sciences, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
| | - M Victoria
- Laboratory of Molecular Virology, Department of Biological Sciences, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay.
| | - R Colina
- Laboratory of Molecular Virology, Department of Biological Sciences, CENUR Litoral Norte, Universidad de la República, Salto, Uruguay
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Tiwari A, Radu E, Kreuzinger N, Ahmed W, Pitkänen T. Key considerations for pathogen surveillance in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:173862. [PMID: 38876348 DOI: 10.1016/j.scitotenv.2024.173862] [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: 04/09/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024]
Abstract
Wastewater surveillance (WWS) has received significant attention as a rapid, sensitive, and cost-effective tool for monitoring various pathogens in a community. WWS is employed to assess the spatial and temporal trends of diseases and identify their early appearances and reappearances, as well as to detect novel and mutated variants. However, the shedding rates of pathogens vary significantly depending on factors such as disease severity, the physiology of affected individuals, and the characteristics of pathogen. Furthermore, pathogens may exhibit differential fate and decay kinetics in the sewerage system. Variable shedding rates and decay kinetics may affect the detection of pathogens in wastewater. This may influence the interpretation of results and the conclusions of WWS studies. When selecting a pathogen for WWS, it is essential to consider it's specific characteristics. If data are not readily available, factors such as fate, decay, and shedding rates should be assessed before conducting surveillance. Alternatively, these factors can be compared to those of similar pathogens for which such data are available.
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Affiliation(s)
- Ananda Tiwari
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Helsinki, Finland.
| | - Elena Radu
- Institute for Water Quality and Resource Management, Vienna University of Technology, Karlsplatz 13/226, 1040 Vienna, Austria; Stefan S. Nicolau Institute of Virology, Department of Cellular and Molecular Pathology, 285 Mihai Bravu Avenue, 030304 Bucharest, Romania; University of Medicine and Pharmacy Carol Davila, Department of Virology, 37 Dionisie Lupu Street, 020021 Bucharest, Romania.
| | - Norbert Kreuzinger
- Institute for Water Quality and Resource Management, Vienna University of Technology, Karlsplatz 13/226, 1040 Vienna, Austria.
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Department of Health Security, Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Helsinki, Finland.
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Peng L, Yang F, Shi J, Liu Y, Pan L, Mao D, Luo Y. Insights into the panorama of multiple DNA viruses in municipal wastewater and recycled sludge in Tianjin, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 355:124215. [PMID: 38797349 DOI: 10.1016/j.envpol.2024.124215] [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: 02/04/2024] [Revised: 05/06/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Environmental viruses in wastewater and sludge are widely recognized for their roles in waterborne diseases. However, previous studies mainly focused on RNA viruses, and little is known about the diversity of DNA viral communities and their driving factors in municipal wastewater treatment environments. Herein, we conducted a pilot study to explore DNA virus profiles in municipal wastewater and recycled sludge by metagenomics method, and track their temporal changes in northern China. Results showed that 467 viral species were co-shared among all the samples. We identified six families of human viruses with a prevalence of 0.1%, which were rare but relatively stable in wastewater and sludge for six months. Adenoviridae, Parvoviridae, and Herpersviridae were the most dominant human viral families in municipal wastewater and recycled sludge. A time series of samples revealed that the dynamic changes of human DNA viruses were stable based on qPCR results, particularly for high-risk fecal-oral transmission viruses of adenovirus, bocavirus, polyomavirus, human gamma herpesvirus, human papillomavirus, and hepatitis B virus. Concentrations of Adenovirus (5.39-7.48 log10 copies/L) and bocavirus (4.36-7.48 log10 copies/L) were observed to be the highest in these samples compared to other viruses. Our findings demonstrated the DNA viruses' high prevalence and persistence in municipal wastewater treatment environments, highlighting the value of enhancing public health responses based on wastewater-based epidemiology.
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Affiliation(s)
- Liang Peng
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Jingliang Shi
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China
| | - YiXin Liu
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Liuzhu Pan
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210093, China.
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Haghi Navand A, Jalilian S, Ahmadi Angali K, Karimi Babaahmadi M, Talaiezadeh A, Makvandi M. A new evaluation of the rearranged non-coding control region of JC virus in patients with colorectal cancer. BMC Cancer 2024; 24:1001. [PMID: 39134946 PMCID: PMC11320957 DOI: 10.1186/s12885-024-12684-x] [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: 04/06/2024] [Accepted: 07/24/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Several studies have reported the presence of JC virus (JCV) in human tumors, The association of JCV and CRC remains controversial. This study aimed to evaluate the rearranged NCCR region of the detected JCV DNA in CRC patients' tissue samples. METHODS In this case-control study, tumor tissues (n = 60), adjacent normal tissues (n = 60), and urine samples (n = 60) of the CRC patients were collected. The nested PCR was employed to detect the VP1 and NCCR regions of the JCV genome. The positive JCV PCR products were sequenced and a phylogenetic tree was constructed to determine the JCV genotypes. After extracting RNA and preparing cDNA, the expression of JCV LTAg was examined in 60 tumor tissues and 60 adjacent normal tissues. The analysis of JCV LTAg expression was performed using GraphPad Prism software version 8. RESULTS The analysis reveals that JCV DNA was detected in 35/60 (58.3%) tumor tissues, while 36/60 (60.0%) of adjacent normal tissues (p = 0.85). JCV DNA was detected in 42/60 (70.0%) urine samples when compared to 35/60 (58.3%) tumor tissues of CRC patients and was not found significant (P = 0.25). The phylogenetic tree analysis showed the dominant JCV genotype 3, followed by genotype 2D was distributed in tumor tissue, normal tissue, and urine samples of the CRC patients. Analysis of randomly selected NCCR sequences from JCV regions in tumor tissue samples revealed the presence of rearranged NCCR blocks of different lengths.: 431 bp, 292 bp, 449 bp, and 356 bp. These rearranged NCCR blocks differ from the rearranged NCCR blocks described in PML-type Mad-1, Mad-4, Mad-7, and Mad-8 prototypes. The expression of JCV LTAg was significantly different in tumor tissue compared to normal tissue, with a p-value of less than 0.002. CONCLUSION A significant proportion of 35%> of the tumor tissue and urine samples of the CRC patients was found to be positive for JCV DNA (P = 0.25). The parallel analysis of tumor and urine samples for JCV DNA further supports the potential for non-invasive screening tools. This study provides new insights into Rearranged NCCR variant isolates from patients with CRC. The significant difference in JCV LTAg expression between tumor and normal tissue indicates a latent JCV status potentially leading to cancer development.
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Grants
- NO. CRC-0113 Cancer, Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- NO. CRC-0113 Cancer, Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- NO. CRC-0113 Cancer, Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- NO. CRC-0113 Cancer, Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- NO. CRC-0113 Cancer, Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- NO. CRC-0113 Cancer, Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Affiliation(s)
- Azadeh Haghi Navand
- Cancer, Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shahram Jalilian
- Cancer, Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Kambiz Ahmadi Angali
- Biostatistics and Epidemiology Department, Health School, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Karimi Babaahmadi
- Department of Medical Biotechnology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Manoochehr Makvandi
- Cancer, Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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Javadi M, Jalilian S, Kanani M, Kia V, Talaiezadeh A, Angali KA, Ahmadi MKB, Makvandi M. Time to take HPV infection in colorectal cancer patients more seriously. Front Med (Lausanne) 2024; 11:1418359. [PMID: 39050539 PMCID: PMC11266041 DOI: 10.3389/fmed.2024.1418359] [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: 04/16/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Background The association between viral infections and colorectal cancer (CRC) remains an enigma in cancer research. Certain types of Human Papillomaviruses (hr-HPVs), known for their oncogenic properties, have been observed in particular CRC biopsies, further adding to the enigma surrounding this association. Materials and methods This cross-sectional study was conducted on 40 confirmed cases of CRC adenocarcinoma. The presence and genotyping of HPV DNA in colorectal fresh tissue and urine samples was assessed using an HPV DNA hybridization kit. A subset of serum samples from both CRC cases and healthy volunteers was randomly chosen and subjected to western blot to investigate the presence of HPV16 E6/E7 oncoproteins carried by exosomes. Results It was observed that 26/40 HPV-positive CRC patients demonstrated 7 times more chance to develop colorectal cancer when compared to those 8/40 normal tissue (odds ratio [OR] = 7.4; confidence interval [CI] 95% = 0.483156-0.793718; p < 0.001). Of 26 HPV-positive CRC patients, 14 urine samples were also showed HPV DNA positivity (p = 0.013). High-risk HPV16 was the most prevalent genotype detected in both 24/40 tumor and 12/40 urine samples (p < 0.001). The tumor sample of a male was HPV45, while another male's urine sample was HPV31. A female CRC patient had HPV83 in tumor and HPV56 in urine. Here, was the first detection of HPV83 in a CRC patient. Notably among 20 randomly selected serum exosome samples, one serum sample concurrently tested positive for both HPV16 E6 and E7 oncoproteins, and one sample tested positive for HPV16 E7 oncoprotein. Conclusion High risk HPV DNA detection in CRC urine samples supports non-invasive screening tools. Detection of HPV16 E6 and E7 oncoproteins in exosomes from serum samples shows potential for non-invasive diagnostics. HPV's potential role in CRC development is also underscored. HPV vaccination should be implemented in low- and middle-income countries to prevent cancer.
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Affiliation(s)
- Mahsa Javadi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Virology Department, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shahram Jalilian
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Virology Department, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Malek Kanani
- Department of Pathology, Imam Khomeini Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Vahid Kia
- Department of Medical Biotechnology, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | | | - Kambiz Ahmadi Angali
- Department of Biostatistics and Epidemiology, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Karimi Baba Ahmadi
- Department of Medical Biotechnology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Manoochehr Makvandi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Virology Department, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Morecchiato F, Coppi M, Niccolai C, Antonelli A, Di Gloria L, Calà P, Mancuso F, Ramazzotti M, Lotti T, Lubello C, Rossolini GM. Evaluation of different molecular systems for detection and quantification of SARS-CoV-2 RNA from wastewater samples. J Virol Methods 2024; 328:114956. [PMID: 38796134 DOI: 10.1016/j.jviromet.2024.114956] [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: 11/29/2023] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024]
Abstract
Wastewater-based epidemiology has proved to be a suitable approach for tracking the spread of epidemic agents including SARS-CoV-2 RNA. Different protocols have been developed for quantitative detection of SARS-CoV-2 RNA from wastewater samples, but little is known on their performance. In this study we compared three protocols based on Reverse Transcription Real Time-PCR (RT-PCR) and one based on Droplet Digital PCR (ddPCR) for SARS-CoV-2 RNA detection from 35 wastewater samples. Overall, SARS-CoV-2 RNA was detected by at least one method in 85.7 % of samples, while 51.4 %, 22.8 % and 8.6 % resulted positive with two, three or all four methods, respectively. Protocols based on commercial RT-PCR assays and on Droplet Digital PCR showed an overall higher sensitivity vs. an in-house assay. The use of more than one system, targeting different genes, could be helpful to increase detection sensitivity.
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Affiliation(s)
- Fabio Morecchiato
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Marco Coppi
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Claudia Niccolai
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy
| | - Leandro Di Gloria
- Department of Experimental Biomedical and Clinical Sciences "Mario Serio" (SBSC), University of Florence, Viale Morgagni, 50, Firenze (FI) 50134, Italy
| | - Piergiuseppe Calà
- Tuscany Region, Department of Prevention Local Health Authority Tuscany Center, Via S. Salvi, 12, Firenze (FI) 50135, Italy
| | - Fabrizio Mancuso
- Ingegnerie Toscane - Area R&D, Via Bellatalla, 1, Pisa (PI) 56121, Italy
| | - Matteo Ramazzotti
- Department of Experimental Biomedical and Clinical Sciences "Mario Serio" (SBSC), University of Florence, Viale Morgagni, 50, Firenze (FI) 50134, Italy
| | - Tommaso Lotti
- Department of Civil and Environmental Engineering (DICEA), University of Florence, Via di S. Marta, 3, Firenze (FI) 50139, Italy
| | - Claudio Lubello
- Department of Civil and Environmental Engineering (DICEA), University of Florence, Via di S. Marta, 3, Firenze (FI) 50139, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine (DMSC), University of Florence, Largo Brambilla, 3, Firenze (FI) 50134, Italy; Microbiology and Virology Unit, Careggi University Hospital, Largo Brambilla, 3, Firenze (FI) 50134, Italy.
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Al-Hazmi HE, Mohammadi A, Hejna A, Majtacz J, Esmaeili A, Habibzadeh S, Saeb MR, Badawi M, Lima EC, Mąkinia J. Wastewater reuse in agriculture: Prospects and challenges. ENVIRONMENTAL RESEARCH 2023; 236:116711. [PMID: 37487927 DOI: 10.1016/j.envres.2023.116711] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/11/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023]
Abstract
Sustainable water recycling and wastewater reuse are urgent nowadays considering water scarcity and increased water consumption through human activities. In 2015, United Nations Sustainable Development Goal 6 (UN SDG6) highlighted the necessity of recycling wastewater to guarantee water availability for individuals. Currently, wastewater irrigation (WWI) of crops and agricultural land appears essential. The present work overviews the quality of treated wastewater in terms of soil microbial activities, and discusses challenges and benefits of WWI in line with wastewater reuse in agriculture and aquaculture irrigation. Combined conventional-advanced wastewater treatment processes are specifically deliberated, considering the harmful impacts on human health arising from WWI originating from reuse of contaminated water (salts, organic pollutants, toxic metals, and microbial pathogens i.e., viruses and bacteria). The comprehensive literature survey revealed that, in addition to the increased levels of pathogen and microbial threats to human wellbeing, poorly-treated wastewater results in plant and soil contamination with toxic organic/inorganic chemicals, and microbial pathogens. The impact of long-term emerging pollutants like plastic nanoparticles should also be established in further studies, with the development of standardized analytical techniques for such hazardous chemicals. Likewise, the reliable, long-term and extensive judgment on heavy metals threat to human beings's health should be explored in future investigations.
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Affiliation(s)
- Hussein E Al-Hazmi
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Ali Mohammadi
- Department of Engineering and Chemical Sciences, Karlstad University, 65188, Karlstad, Sweden.
| | - Aleksander Hejna
- Institute of Materials Technology, Poznan University of Technology, Poznań, Poland
| | - Joanna Majtacz
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Amin Esmaeili
- Department of Chemical Engineering, School of Engineering Technology and Industrial Trades, University of Doha for Science and Technology (UDST), 24449, Arab League St, Doha, Qatar
| | - Sajjad Habibzadeh
- Surface Reaction and Advanced Energy Materials Laboratory, Chemical Engineering Department, Amirkabir University of Technology (Tehran Polytechnic), Tehran, Iran
| | - Mohammad Reza Saeb
- Department of Polymer Technology, Faculty of Chemistry, Gdańsk University of Technology, G. Narutowicza 11/12, 80-233, Gdańsk, Poland.
| | - Michael Badawi
- Laboratoire de Physique et Chimie Théoriques UMR CNRS 7019, Université de Lorraine, Nancy, France
| | - Eder C Lima
- Institute of Chemistry, Federal University of Rio Grande Do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Jacek Mąkinia
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233, Gdańsk, Poland
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Victoria M, Moller A, Salvo M, Baccardatz N, Colina R. High abundance of high-risk Human Papillomavirus genotypes in wastewater in Uruguay. JOURNAL OF WATER AND HEALTH 2022; 20:1748-1754. [PMID: 36573677 DOI: 10.2166/wh.2022.330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The aim of this study was to determine the frequency of Human Papillomavirus (HPV) genotypes in wastewater of Salto city, Uruguay, in order to obtain a general overview of the circulating genotypes in their population. HPV was detected in 34% (32/93) of the wastewater samples collected and analyzed during 2020/21 in Salto city, Uruguay. Thirty-three genotypes were observed, of which 16 presented read abundance higher than 1%, including both high-risk (HR) and low-risk (LR) genotypes. HR genotypes 31, 16, 58, 52, 33 and 59 were detected representing 40% (163,220 reads) of the total read abundance, with genotypes 31 (64,365), 16 (39,337) and 58 (36,332) being the most abundant. LR genotypes 72, 6, 11 and 40 were also detected in a high frequency, accounting for 37% (148,359) of the HPV reads. This study highlights the high frequency of HR genotypes of HPV, circulating in the population of Salto city which is a burden in public health mainly due to the devastating impact of cervical cancer in women.
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Affiliation(s)
- Matías Victoria
- Laboratory of Molecular Virology, Centro Universitario Regional Litoral Norte, Universidad de la República, Salto, Rivera 1350, CP 50000, Uruguay E-mail:
| | - Ana Moller
- Laboratory of Molecular Virology, Centro Universitario Regional Litoral Norte, Universidad de la República, Salto, Rivera 1350, CP 50000, Uruguay E-mail:
| | - Matías Salvo
- Laboratory of Molecular Virology, Centro Universitario Regional Litoral Norte, Universidad de la República, Salto, Rivera 1350, CP 50000, Uruguay E-mail: ; Water Department, Centro Universitario Regional Litoral Norte, Universidad de la República, Salto, Rivera 1350, CP 50000, Uruguay
| | | | - Rodney Colina
- Laboratory of Molecular Virology, Centro Universitario Regional Litoral Norte, Universidad de la República, Salto, Rivera 1350, CP 50000, Uruguay E-mail:
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Bonanno Ferraro G, Veneri C, Mancini P, Iaconelli M, Suffredini E, Bonadonna L, Lucentini L, Bowo-Ngandji A, Kengne-Nde C, Mbaga DS, Mahamat G, Tazokong HR, Ebogo-Belobo JT, Njouom R, Kenmoe S, La Rosa G. A State-of-the-Art Scoping Review on SARS-CoV-2 in Sewage Focusing on the Potential of Wastewater Surveillance for the Monitoring of the COVID-19 Pandemic. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:315-354. [PMID: 34727334 PMCID: PMC8561373 DOI: 10.1007/s12560-021-09498-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/21/2021] [Indexed: 05/07/2023]
Abstract
The outbreak of coronavirus infectious disease-2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has rapidly spread throughout the world. Several studies have shown that detecting SARS-CoV-2 in untreated wastewater can be a useful tool to identify new outbreaks, establish outbreak trends, and assess the prevalence of infections. On 06 May 2021, over a year into the pandemic, we conducted a scoping review aiming to summarize research data on SARS-CoV-2 in sewage. Papers dealing with raw sewage collected at wastewater treatment plants, sewer networks, septic tanks, and sludge treatment facilities were included in this review. We also reviewed studies on sewage collected in community settings such as private or municipal hospitals, healthcare facilities, nursing homes, dormitories, campuses, airports, aircraft, and cruise ships. The literature search was conducted using the electronic databases PubMed, EMBASE, and Web Science Core Collection. This comprehensive research yielded 1090 results, 66 of which met the inclusion criteria and are discussed in this review. Studies from 26 countries worldwide have investigated the occurrence of SARS-CoV-2 in sewage of different origin. The percentage of positive samples in sewage ranged from 11.6 to 100%, with viral concentrations ranging from ˂LOD to 4.6 × 108 genome copies/L. This review outlines the evidence currently available on wastewater surveillance: (i) as an early warning system capable of predicting COVID-19 outbreaks days or weeks before clinical cases; (ii) as a tool capable of establishing trends in current outbreaks; (iii) estimating the prevalence of infections; and (iv) studying SARS-CoV-2 genetic diversity. In conclusion, as a cost-effective, rapid, and reliable source of information on the spread of SARS-CoV-2 and its variants in the population, wastewater surveillance can enhance genomic and epidemiological surveillance with independent and complementary data to inform public health decision-making during the ongoing pandemic.
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Affiliation(s)
- G Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | | | - P Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - L Bonadonna
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - L Lucentini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - A Bowo-Ngandji
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - C Kengne-Nde
- Research Monitoring and Planning Unit, National Aids Control Committee, Douala, Cameroon
| | - D S Mbaga
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - G Mahamat
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - H R Tazokong
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - J T Ebogo-Belobo
- Medical Research Centre, Institute of Medical Research and Medicinal Plants Studies, Yaounde, Cameroon
| | - R Njouom
- Virology Department, Centre Pasteur of Cameroon, Yaounde, Cameroon
| | - S Kenmoe
- Virology Department, Centre Pasteur of Cameroon, Yaounde, Cameroon
| | - G La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy.
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Stolbikov AS, Salyaev RK, Nurminsky VN, Chernyshov MY. Investigation of the Presence of DNA of Highly Pathogenic Human Papillomaviruses in Water Bodies of the Lake Baikal Natural Territory. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:258-266. [PMID: 35932447 DOI: 10.1007/s12560-022-09529-w] [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: 03/05/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
Human papillomaviruses (HPVs) are extremely widespread throughout the world. There are more than 100 types of HPVs, of which at least 14 types represent high oncogenic risk viruses (World Health Organization, 2020). Numerous attempts were made to analyze various water sources in order to (i) reveal the presence of DNA of pathogenic human papillomaviruses in them and (ii) assess the potential risks of occurrence of epidemics caused by HPV. With time, the necessity to solve these important problems stimulated the formation of a new direction in the world medical and environmental investigations.This paper contains the investigation of the presence of DNA of highly dangerous types of human papillomaviruses (HPV6, HPV11, HPV16 and HPV18) in water bodies of the Baikal natural territory, in particular in the water reservoirs in and near the villages of Listvyanka, Bolshiye Koty, Kultuk and the cities of Baikalsk and Slyudyanka. In course of our work, the conditions good for the study of the biological material obtained from water samples by the PCR technique to reveal the presence of DNA of HPV6, HPV11, HPV16 and HPV18 papillomaviruses were chosen. PCR analysis was conducted with the aid of both the already well-known universal primers GP5 + /6 + and the primers developed by our team to be applied to the conservative domains of nucleotide sequences encoding the main capsid protein L1 of human papillomaviruses HPV6, HPV11 (these types of the virus contribute to the occurrence of anogenital condylomatosis and the development of respiratory papillomatosis) and HPV16, HPV16 (these types of virus contribute to the occurrence of cervical cancer).The analyzes conducted by our team have revealed the presence of DNA of the four types of HPVs (6, 11, 16 and 18) in the samples taken from various water sources of the Baikal natural territory.
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Affiliation(s)
- A S Stolbikov
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of Russian Academy of Sciences, 132 Lermontov st, Irkutsk, 664033, Russia.
- Irkutsk State University, 1 Karl Marx st, Irkutsk, 664003, Russia.
| | - R K Salyaev
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of Russian Academy of Sciences, 132 Lermontov st, Irkutsk, 664033, Russia
| | - V N Nurminsky
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of Russian Academy of Sciences, 132 Lermontov st, Irkutsk, 664033, Russia
| | - M Yu Chernyshov
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of Russian Academy of Sciences, 132 Lermontov st, Irkutsk, 664033, Russia
- Presidium of Irkutsk Scientific Center, Siberian Branch of Russian Academy of Sciences, 134 Lermontov st, Irkutsk, 664033, Russia
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12
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Chen C, Guo L, Yang Y, Oguma K, Hou LA. Comparative effectiveness of membrane technologies and disinfection methods for virus elimination in water: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149678. [PMID: 34416607 PMCID: PMC8364419 DOI: 10.1016/j.scitotenv.2021.149678] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/20/2021] [Accepted: 08/11/2021] [Indexed: 05/22/2023]
Abstract
The pandemic of the 2019 novel coronavirus disease (COVID-19) has brought viruses into the public horizon. Since viruses can pose a threat to human health in a low concentration range, seeking efficient virus removal methods has been the research hotspots in the past few years. Herein, a total of 1060 research papers were collected from the Web of Science database to identify technological trends as well as the research status. Based on the analysis results, this review elaborates on the state-of-the-art of membrane filtration and disinfection technologies for the treatment of virus-containing wastewater and drinking water. The results evince that membrane and disinfection methods achieve a broad range of virus removal efficiency (0.5-7 log reduction values (LRVs) and 0.09-8 LRVs, respectively) that is attributable to the various interactions between membranes or disinfectants and viruses having different susceptibility in viral capsid protein and nucleic acid. Moreover, this review discusses the related challenges and potential of membrane and disinfection technologies for customized virus removal in order to prevent the dissemination of the waterborne diseases.
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Affiliation(s)
- Chao Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No.19, Xinjiekouwai Street, Haidian District, Beijing 100875, China.
| | - Lihui Guo
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No.19, Xinjiekouwai Street, Haidian District, Beijing 100875, China.
| | - Yu Yang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No.19, Xinjiekouwai Street, Haidian District, Beijing 100875, China.
| | - Kumiko Oguma
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Li-An Hou
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, No.19, Xinjiekouwai Street, Haidian District, Beijing 100875, China; Xi'an High-Tech Institute, Xi'an 710025, China.
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13
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NGS Techniques Reveal a High Diversity of RNA Viral Pathogens and Papillomaviruses in Fresh Produce and Irrigation Water. Foods 2021; 10:foods10081820. [PMID: 34441597 PMCID: PMC8394881 DOI: 10.3390/foods10081820] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/22/2021] [Accepted: 07/31/2021] [Indexed: 02/07/2023] Open
Abstract
Fresh fruits and vegetables are susceptible to microbial contamination at every stage of the food production chain, and as a potential source of pathogens, irrigation water quality is a critical factor. Next-generation sequencing (NGS) techniques have been flourishing and expanding to a wide variety of fields. However, their application in food safety remains insufficiently explored, and their sensitivity requires improvement. In this study, quantitative polymerase chain reaction (qPCR) assays showed low but frequent contamination of common circulating viral pathogens, which were found in 46.9% of samples of fresh produce: 6/12 lettuce samples, 4/12 strawberries samples, and 5/8 parsley samples. Furthermore, the application of two different NGS approaches, target enrichment sequencing (TES) for detecting viruses that infect vertebrates and amplicon deep sequencing (ADS), revealed a high diversity of viral pathogens, especially Norovirus (NoV) and Human Papillomavirus (HPV), in fresh produce and irrigation water. All NoV and HPV types found in fresh fruit and vegetable samples were also detected in irrigation water sources, indicating that these viruses are common circulating pathogens in the population and that irrigation water may be the most probable source of viral pathogens in food samples.
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Ali W, Zhang H, Wang Z, Chang C, Javed A, Ali K, Du W, Niazi NK, Mao K, Yang Z. Occurrence of various viruses and recent evidence of SARS-CoV-2 in wastewater systems. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125439. [PMID: 33684818 PMCID: PMC7894103 DOI: 10.1016/j.jhazmat.2021.125439] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/11/2021] [Accepted: 02/13/2021] [Indexed: 05/17/2023]
Abstract
Viruses are omnipresent and persistent in wastewater, which poses a risk to human health. In this review, we summarise the different qualitative and quantitative methods for virus analysis in wastewater and systematically discuss the spatial distribution and temporal patterns of various viruses (i.e., enteric viruses, Caliciviridae (Noroviruses (NoVs)), Picornaviridae (Enteroviruses (EVs)), Hepatitis A virus (HAV)), and Adenoviridae (Adenoviruses (AdVs))) in wastewater systems. Then we critically review recent SARS-CoV-2 studies to understand the ongoing COVID-19 pandemic through wastewater surveillance. SARS-CoV-2 genetic material has been detected in wastewater from France, the Netherlands, Australia, Italy, Japan, Spain, Turkey, India, Pakistan, China, and the USA. We then discuss the utility of wastewater-based epidemiology (WBE) to estimate the occurrence, distribution, and genetic diversity of these viruses and generate human health risk assessment. Finally, we not only promote the prevention of viral infectious disease transmission through wastewater but also highlight the potential use of WBE as an early warning system for public health assessment.
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Affiliation(s)
- Waqar Ali
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Hua Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China.
| | - Zhenglu Wang
- Key Laboratory of Marine Hazards Forecasting, Ministry of Natural Resources, College of Oceanography, Hohai University, Nanjing 210098, PR China
| | - Chuanyu Chang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Asif Javed
- Department of Earth and Environmental Sciences, Bahria University Islamabad, Pakistan
| | - Kamran Ali
- Institute of Environmental Sciences and Engineering (IESE), School of Civil and Environmental Engineering (SCEE), National University of Science and Technology (NUST), Islamabad 44000, Pakistan
| | - Wei Du
- Key Laboratory of Geographic Information Science of the Ministry of Education, School of Geographic Sciences, East China Normal University, Shanghai 200241, PR China
| | - Nabeel Khan Niazi
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan
| | - Kang Mao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China.
| | - Zhugen Yang
- Cranfield Water Science Institute, Cranfield University, Cranfield MK43 0AL, United Kingdom
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15
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Farkas K, Walker DI, Adriaenssens EM, McDonald JE, Hillary LS, Malham SK, Jones DL. Viral indicators for tracking domestic wastewater contamination in the aquatic environment. WATER RESEARCH 2020; 181:115926. [PMID: 32417460 PMCID: PMC7211501 DOI: 10.1016/j.watres.2020.115926] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 05/13/2023]
Abstract
Waterborne enteric viruses are an emerging cause of disease outbreaks and represent a major threat to global public health. Enteric viruses may originate from human wastewater and can undergo rapid transport through aquatic environments with minimal decay. Surveillance and source apportionment of enteric viruses in environmental waters is therefore essential for accurate risk management. However, individual monitoring of the >100 enteric viral strains that have been identified as aquatic contaminants is unfeasible. Instead, viral indicators are often used for quantitative assessments of wastewater contamination, viral decay and transport in water. An ideal indicator for tracking wastewater contamination should be (i) easy to detect and quantify, (ii) source-specific, (iii) resistant to wastewater treatment processes, and (iv) persistent in the aquatic environment, with similar behaviour to viral pathogens. Here, we conducted a comprehensive review of 127 peer-reviewed publications, to critically evaluate the effectiveness of several viral indicators of wastewater pollution, including common enteric viruses (mastadenoviruses, polyomaviruses, and Aichi viruses), the pepper mild mottle virus (PMMoV), and gut-associated bacteriophages (Type II/III FRNA phages and phages infecting human Bacteroides species, including crAssphage). Our analysis suggests that overall, human mastadenoviruses have the greatest potential to indicate contamination by domestic wastewater due to their easy detection, culturability, and high prevalence in wastewater and in the polluted environment. Aichi virus, crAssphage and PMMoV are also widely detected in wastewater and in the environment, and may be used as molecular markers for human-derived contamination. We conclude that viral indicators are suitable for the long-term monitoring of viral contamination in freshwater and marine environments and that these should be implemented within monitoring programmes to provide a holistic assessment of microbiological water quality and wastewater-based epidemiology, improve current risk management strategies and protect global human health.
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Affiliation(s)
- Kata Farkas
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK; School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, LL59 5AB, UK.
| | - David I Walker
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, DT4 8UB, UK
| | | | - James E McDonald
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Luke S Hillary
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, LL59 5AB, UK
| | - Davey L Jones
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, UK; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
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16
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Martínez-Puchol S, Rusiñol M, Fernández-Cassi X, Timoneda N, Itarte M, Andrés C, Antón A, Abril JF, Girones R, Bofill-Mas S. Characterisation of the sewage virome: comparison of NGS tools and occurrence of significant pathogens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 713:136604. [PMID: 31955099 DOI: 10.1016/j.scitotenv.2020.136604] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 04/14/2023]
Abstract
NGS techniques are excellent tools to monitor and identify viral pathogens circulating among the population with some limitations that need to be overcome, especially in complex matrices. Sewage contains a high amount of other microorganisms that could interfere when trying to sequence viruses for which random PCR amplifications are needed before NGS. The selection of appropriate NGS tools is important for reliable identification of viral diversity among the population. We have compared different NGS methodologies (Untargeted Viral Metagenomics, Target Enrichment Sequencing and Amplicon Deep Sequencing) for the detection and characterisation of viruses in urban sewage, focusing on three important human pathogens: papillomaviruses, adenoviruses and enteroviruses. A full picture of excreted viruses was obtained by applying Untargeted Viral Metagenomics, which detected members of four different vertebrate viral families in addition to bacteriophages, plant viruses and viruses infecting other hosts. Target Enrichment Sequencing, using specific vertebrate viral probes, allowed the detection of up to eight families containing human viruses, with high variety of types within the families and with a high genome coverage. By applying Amplicon Deep Sequencing, the diversity of enteroviruses, adenoviruses and papillomaviruses observed was higher than when applying the other two strategies and this technique allowed the subtyping of an enterovirus A71 C1 strain related to a brainstem encephalitis outbreak occurring at the same time in the sampling area. From the data obtained, we concluded that the different strategies studied provided different levels of analysis: TES is the best strategy to obtain a broad picture of human viruses present in complex samples such as sewage. Other NGS strategies are useful for studying the virome of complex samples when also targeting viruses infecting plants, bacteria, invertebrates or fungi (Untargeted Viral Metagenomics) or when observing the variety within a sole viral family is the objective of the study (Amplicon Deep Sequencing).
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Affiliation(s)
- Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology &Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA); Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | - Marta Rusiñol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology &Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA); Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Xavier Fernández-Cassi
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology &Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Natàlia Timoneda
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology &Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; Computational Genomics Lab, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona, Institut de Biomedicina (IBUB), Barcelona, Catalonia, Spain
| | - Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology &Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA); Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Cristina Andrés
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep F Abril
- Computational Genomics Lab, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona, Institut de Biomedicina (IBUB), Barcelona, Catalonia, Spain
| | - Rosina Girones
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology &Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA); Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology &Statistics Dept., Universitat de Barcelona, Barcelona, Catalonia, Spain; The Water Research Institute (IdRA); Universitat de Barcelona, Barcelona, Catalonia, Spain
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17
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Wu Z, Greaves J, Arp L, Stone D, Bibby K. Comparative fate of CrAssphage with culturable and molecular fecal pollution indicators during activated sludge wastewater treatment. ENVIRONMENT INTERNATIONAL 2020; 136:105452. [PMID: 31931347 DOI: 10.1016/j.envint.2019.105452] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/23/2019] [Accepted: 12/25/2019] [Indexed: 05/04/2023]
Abstract
Wastewater treatment plants are typically monitored using fecal indicator bacteria to ensure adequate microbial water quality of the treated effluent. Fecal indicator bacteria exhibit poor correlation with virus fate in the environment, including during wastewater treatment. Viral-based microbial source tracking methods have the potential to overcome this limitation. The recently discovered human gut bacteriophage crAssphage is a promising viral human fecal indicator. In this current study, primary influent, primary effluent, secondary effluent, and final effluent of a conventional activated sludge wastewater treatment plant were analyzed for a suite of fecal indicators to evaluate the suitability of crAssphage as a wastewater process indicator for virus removal. CrAssphage was the most abundant fecal indicator measured through the wastewater treatment process. Culturable and molecular bacterial fecal pollution indicators showed higher removal than viral fecal pollution indicators, including crAssphage, confirming the necessity of a viral-specific fecal monitoring target. CrAssphage was strongly correlated with adenovirus and polyomavirus molecular indicators through the wastewater treatment process. Literature comparison demonstrated site-specific removal of molecular fecal indicators during wastewater treatment highlighting the need for local performance validation. The high abundance of crAssphage and correlation with pathogenic viruses suggests the potential suitability of crAssphage as a viral fecal pollution process indicator during wastewater treatment.
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Affiliation(s)
- Zhenyu Wu
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, South Bend, IN, 46556, USA
| | - Justin Greaves
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, South Bend, IN, 46556, USA
| | - Lillian Arp
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, South Bend, IN, 46556, USA
| | - Daniel Stone
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, South Bend, IN, 46556, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, South Bend, IN, 46556, USA.
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18
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Hamza H, Rizk NM, Gad MA, Hamza IA. Pepper mild mottle virus in wastewater in Egypt: a potential indicator of wastewater pollution and the efficiency of the treatment process. Arch Virol 2019; 164:2707-2713. [PMID: 31456085 DOI: 10.1007/s00705-019-04383-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/24/2019] [Indexed: 02/03/2023]
Abstract
There is increasing evidence that the fecal indicator bacteria that are routinely used for testing water quality are inadequate for ensuring protection of the public health. Pepper mild mottle virus (PMMoV) has recently been suggested as an alternative indicator of human fecal contamination in water; however, in Egypt there are no data available about its occurrence and concentration in aquatic environment. The concentration of PMMoV in the influent and effluent of three wastewater treatment plants was measured using qRT-PCR over a period of one year and compared to that of human adenovirus (HAdV), which is considered an indicator for human fecal contamination. PMMoV was detected in ~ 94% of the influent samples and 78% of the effluent samples, with concentrations ranging from 3.9 × 104 to 3.3 × 108 genome copies/l (GC/l) in the influent and 3.9 × 104 to 1.2 × 107 GC/l in the effluent. Similarly, HAdV was identified in 88% and 78% of the influent and effluent samples, respectively. The HAdV concentration ranged between 1.5 × 104 and 1.5 × 107 GC/l for the influent and 2.6 × 104 and 4.4 × 106 GC/l for the effluent. No significant difference was found between the removal ratio of PMMoV and HAdV. Viral reduction of 0.2-1.9 log10 and 0.2- 2.3 log10 by the treatment process was observed for PMMoV and HAdV, respectively. Both viruses showed no clear seasonality. Our data support the use of PMMoV as a fecal indicator of wastewater contamination and a process indicator for the performance of the treatment process.
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Affiliation(s)
- Hazem Hamza
- Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, Cairo, Egypt
| | - Neveen Magdy Rizk
- Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, Cairo, Egypt
| | - Mahmoud Afw Gad
- Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, Cairo, Egypt
| | - Ibrahim Ahmed Hamza
- Environmental Virology Laboratory, Department of Water Pollution Research, National Research Centre, Cairo, Egypt.
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19
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Karbalaie Niya MH, Safarnezhad Tameshkel F, Alemrajabi M, Taherizadeh M, Keshavarz M, Rezaee M, Keyvani H. Molecular survey on Merkel cell polyomavirus in patients with colorectal cancer. MEDICAL JOURNAL OF INDONESIA 2018. [DOI: 10.13181/mji.v27i4.2759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Background: Merkel cell polyomavirus (MCV) has been associated with Merkel cell carcinoma (MCC) in humans, and its role in other human cancers is under investigation. The aim of this study was to investigate MCV genome infection in patients with colorectal cancer (CRC).Methods: This retrospective, case-control study used archived formalin-fixed, paraffin-embedded (FFPE) tissue samples from colorectal cancer patients (cases) and matched healthy subjects (controls) diagnosed by an expert pathologist from hospitals affiliated with Iran University of Medical Sciences, Tehran, Iran from 2011 to 2016. After DNA extraction with a QIAamp® DNA FFPE Tissue Kit, real-time polymerase chain reaction (PCR) was used for diagnosis. A positive control was produced by cloning with the Generay Biotechnology system. SPSS v.22 was used for analysis of demographic variables.Results: There were 157 participants included in the study: 66 were cases and 91 were controls. Their mean ages (±SD) were 59.35±14.48 and 57.21±14.66, respectively. The proportion of males was 57.6% in the case group and 57.1% in the control group. None of the samples were positive for MCV expression by real-time PCR assay. Association was detected between males with CRC and tumor location in the rectum and between males with CRC and the mucinous tumor type.Conclusion: None of the tissues from the CRC or non-cancerous control groups were positive for MCV genome infection, although a low viral load, the sample type, or the method of use should not be neglected. Further studies are recommended to obtain more comprehensive results.
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