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Li Y, Miyani B, Faust RA, David RE, Xagoraraki I. A broad wastewater screening and clinical data surveillance for virus-related diseases in the metropolitan Detroit area in Michigan. Hum Genomics 2024; 18:14. [PMID: 38321488 PMCID: PMC10845806 DOI: 10.1186/s40246-024-00581-0] [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: 09/01/2023] [Accepted: 01/24/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Periodic bioinformatics-based screening of wastewater for assessing the diversity of potential human viral pathogens circulating in a given community may help to identify novel or potentially emerging infectious diseases. Any identified contigs related to novel or emerging viruses should be confirmed with targeted wastewater and clinical testing. RESULTS During the COVID-19 pandemic, untreated wastewater samples were collected for a 1-year period from the Great Lakes Water Authority Wastewater Treatment Facility in Detroit, MI, USA, and viral population diversity from both centralized interceptor sites and localized neighborhood sewersheds was investigated. Clinical cases of the diseases caused by human viruses were tabulated and compared with data from viral wastewater monitoring. In addition to Betacoronavirus, comparison using assembled contigs against a custom Swiss-Prot human virus database indicated the potential prevalence of other pathogenic virus genera, including: Orthopoxvirus, Rhadinovirus, Parapoxvirus, Varicellovirus, Hepatovirus, Simplexvirus, Bocaparvovirus, Molluscipoxvirus, Parechovirus, Roseolovirus, Lymphocryptovirus, Alphavirus, Spumavirus, Lentivirus, Deltaretrovirus, Enterovirus, Kobuvirus, Gammaretrovirus, Cardiovirus, Erythroparvovirus, Salivirus, Rubivirus, Orthohepevirus, Cytomegalovirus, Norovirus, and Mamastrovirus. Four nearly complete genomes were recovered from the Astrovirus, Enterovirus, Norovirus and Betapolyomavirus genera and viral species were identified. CONCLUSIONS The presented findings in wastewater samples are primarily at the genus level and can serve as a preliminary "screening" tool that may serve as indication to initiate further testing for the confirmation of the presence of species that may be associated with human disease. Integrating innovative environmental microbiology technologies like metagenomic sequencing with viral epidemiology offers a significant opportunity to improve the monitoring of, and predictive intelligence for, pathogenic viruses, using wastewater.
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Affiliation(s)
- Yabing Li
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI, 48823, USA
| | - Brijen Miyani
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI, 48823, USA
| | - Russell A Faust
- Oakland County Health Division, 1200 Telegraph Rd, Pontiac, MI, 48341, USA
| | - Randy E David
- School of Medicine, Wayne State University, Detroit, MI, 48282, USA
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, 1449 Engineering Research Ct, East Lansing, MI, 48823, USA.
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2
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Pörtner K, Wilking H, Frank C, Böhmer MM, Stark K, Tappe D. Risk factors for Borna disease virus 1 encephalitis in Germany - a case-control study. Emerg Microbes Infect 2023; 12:e2174778. [PMID: 36748319 PMCID: PMC9980402 DOI: 10.1080/22221751.2023.2174778] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In 2018, Borna Disease Virus 1 (BoDV-1) was confirmed as a human zoonotic pathogen causing rare but fatal encephalitis in Germany. While diagnostic procedures and the clinical picture have been described, epidemiology remains mysterious. Though endemic areas and a natural reservoir host have been identified with the shrew Crocidura leucodon shedding virus in secretions, transmission events, routes and risk factors are unclear. We performed the first comprehensive epidemiological study, combining a large case series with the first case-control study: We interviewed family members of 20 PCR-confirmed BoDV-1 encephalitis cases deceased in 1996-2021 with a standardized questionnaire covering medical history, housing environment, profession, animal contacts, outdoor activities, travel, and nutrition. Cases' median age was 51 (range 11-79) years, 12/20 were female, and 18/20 lived in the federal state of Bavaria in Southeastern Germany. None had a known relevant pre-existing medical condition. None of the interviews yielded a transmission event such as direct shrew contact, but peridomestic shrew presence was confirmed in 13 cases supporting environmental transmission. Residency in rural areas endemic for animal BoDV-1 was the common denominator of all cases. A subsequent individually matched case-control study revealed residence close to nature in a stand-alone location or on the fringe of the settlement as a risk factor for disease in multivariable analysis with an adjusted OR of 10.8 (95% CI 1.3-89.0). Other variables including keeping cats were not associated with disease. Targeted prevention, future post-exposure-prophylaxis, and timely diagnosis remain challenging.
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Affiliation(s)
- Kirsten Pörtner
- Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany,Postgraduate Training for Applied Epidemiology (PAE), Robert Koch Institute, Berlin, Germany affiliated with the ECDC Fellowship Programme, Field Epidemiology path (EPIET), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden, Kirsten Pörtner Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany; Dennis Tappe Research Group Zoonoses, National Reference Centre for Tropical Pathogens, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Hendrik Wilking
- Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Christina Frank
- Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Merle M. Böhmer
- Department of Infectious Disease Epidemiology, Bavarian Health and Food Safety Authority, Munich, Germany,Institute of Social Medicine and Health Systems Research, Otto-von-Guericke-University, Magdeburg, Germany
| | - Klaus Stark
- Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Dennis Tappe
- Research Group Zoonoses, National Reference Centre for Tropical Pathogens, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany, Kirsten Pörtner Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany; Dennis Tappe Research Group Zoonoses, National Reference Centre for Tropical Pathogens, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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3
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Forés E, Rusiñol M, Itarte M, Martínez-Puchol S, Calvo M, Bofill-Mas S. Evaluation of a virus concentration method based on ultrafiltration and wet foam elution for studying viruses from large-volume water samples. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154431. [PMID: 35278558 DOI: 10.1016/j.scitotenv.2022.154431] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 06/14/2023]
Abstract
Assessing the presence of viruses in large-volume samples involves cumbersome methods that require specialized training and laboratory equipment. In this study, a large volume concentration (LVC) method, based on dead-end ultrafiltration (DEUF) and Wet Foam Elution™ technology, was evaluated in different type of waters and different microorganisms. Its recovery efficiency was evaluated through different techniques (infectivity assays and molecular detection) by spiking different viral surrogates (bacteriophages PhiX174 and MS2 and Coxsackie virus B5 (CVB5) and Escherichia coli (E. coli). Furthermore, the application of a secondary concentration step was evaluated and compared with skimmed milk flocculation. Viruses present in river water, seawater and groundwater samples were concentrated by applying LVC method and a centrifugal ultrafiltration device (CeUF), as a secondary concentration step and quantified with specific qPCR Human adenoviruses (HAdV) and noroviruses (NoVs). MS2 was used as process control, obtaining a mean viral recovery of 22.0 ± 12.47%. The presence of other viruses was also characterized by applying two different next-generation sequencing approaches. LVC coupled to a secondary concentration step based on CeUF allowed to detect naturally occurring viruses such as HAdV and NoVs in different water matrices. Using HAdV as a human fecal indicator, the highest viral pollution was found in river water samples (100% of positive samples), followed by seawater (83.33%) and groundwater samples (66.67%). The LVC method has also proven to be useful as a virus concentration method in the filed since HAdV and NoVs were detected in the river water and groundwater samples concentrated in the field. All in all, LVC method presents high concentration factor and a low limit of detection and provides viral concentrates useful for subsequent molecular analysis such as PCR and massive sequencing.
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Affiliation(s)
- Eva Forés
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Department at the University of Barcelona (UB), 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 Department at the University of Barcelona (UB), Barcelona, Catalonia, Spain; Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Catalonia, Spain.
| | - Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Department at the University of Barcelona (UB), Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Department at the University of Barcelona (UB), Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Miquel Calvo
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Department at the University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Department at the University of Barcelona (UB), Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
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4
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Xu X, Deng Y, Zheng X, Li S, Ding J, Yang Y, On HY, Yang R, Chui HK, Yau CI, Tun HM, Chin AWH, Poon LLM, Peiris M, Leung GM, Zhang T. Evaluation of RT-qPCR Primer-Probe Sets to Inform Public Health Interventions Based on COVID-19 Sewage Tests. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:8875-8884. [PMID: 35584232 PMCID: PMC9128008 DOI: 10.1021/acs.est.2c00974] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 05/02/2023]
Abstract
Sewage surveillance is increasingly employed as a supplementary tool for COVID-19 control. Experiences learnt from large-scale trials could guide better interpretation of the sewage data for public health interventions. Here, we compared the performance of seven commonly used primer-probe sets in RT-qPCR and evaluated the usefulness in the sewage surveillance program in Hong Kong. All selected primer-probe sets reliably detected SARS-CoV-2 in pure water at 7 copies per μL. Sewage matrix did not influence RT-qPCR determination of SARS-CoV-2 concentrated from a small-volume sewage (30 mL) but introduced inhibitory impacts on a large-volume sewage (920 mL) with a ΔCt of 0.2-10.8. Diagnostic performance evaluation in finding COVID-19 cases showed that N1 was the best single primer-probe set, while the ORF1ab set is not recommended. Sewage surveillance using the N1 set for over 3200 samples effectively caught the outbreak trend and, importantly, had a 56% sensitivity and a 96% specificity in uncovering the signal sources from new cases and/or convalescent patients in the community. Our study paves the way for selecting detection primer-probe sets in wider applications in responding to the COVID-19 pandemic.
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Affiliation(s)
- Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Xiawan Zheng
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Shuxian Li
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Jiahui Ding
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
| | - Hei Yin On
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
| | - Rong Yang
- Environmental Protection Department, The
Government of Hong Kong SAR, Tamar, Hong Kong SAR 999077,
China
| | - Ho-Kwong Chui
- Environmental Protection Department, The
Government of Hong Kong SAR, Tamar, Hong Kong SAR 999077,
China
| | - Chung In Yau
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
| | - Hein Min Tun
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
- HKU-Pasteur Research Pole,
Sassoon Road, Hong Kong SAR 999077, China
| | - Alex W. H. Chin
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
| | - Leo L. M. Poon
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
- HKU-Pasteur Research Pole,
Sassoon Road, Hong Kong SAR 999077, China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
- HKU-Pasteur Research Pole,
Sassoon Road, Hong Kong SAR 999077, China
| | - Gabriel M. Leung
- School of Public Health, Li Ka Shing Faculty of
Medicine, The University of Hong Kong, Sassoon Road, Hong Kong
SAR 999077, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology
Laboratory, Center for Environmental Engineering Research, Department of Civil
Engineering, The University of Hong Kong, Pokfulam Road, Hong
Kong SAR 999077, China
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5
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Gholipour S, Ghalhari MR, Nikaeen M, Rabbani D, Pakzad P, Miranzadeh MB. Occurrence of viruses in sewage sludge: A systematic review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153886. [PMID: 35182626 PMCID: PMC8848571 DOI: 10.1016/j.scitotenv.2022.153886] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/25/2022] [Accepted: 02/11/2022] [Indexed: 05/04/2023]
Abstract
Enteric viruses are of great importance in wastewater due to their high excretion from infected individuals, low removal in wastewater treatment processes, long-time survival in the environment, and low infectious dose. Among the other viruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surveillance in wastewater systems has received particular attention as a result of the current COVID-19 epidemic. Viruses adhering to solid particles in wastewater treatment processes will end up as sewage sludge, and therefore insufficient sludge treatment may result in viral particles dissemination into the environment. Here, we review data on viruses' presence in sewage sludge, their detection and concentration methods, and information on human health issues associated with sewage sludge land application. We used combinations of the following keywords in the Scopus, Web of Science (WOS), and PubMed databases, which were published between 2010 and January 21th, 2022: sludge (sewage sludge, biosolids, sewage solids, wastewater solids) and virus (enteric virus, viral particles, viral contamination, SARS-CoV-2, coronavirus). The sources were searched twice, once with and then without the common enteric virus names (adenovirus, rotavirus, norovirus, enterovirus, hepatitis A virus). Studies suggest adenovirus and norovirus as the most prevalent enteric viruses in sewage sludge. Indeed, other viruses include rotavirus, hepatitis A virus, and enterovirus were frequently found in sewage sludge samples. Untreated biological sludge and thickened sludge showed more viral contamination level than digested sludge and the lowest prevalence of viruses was reported in lime stabilized sludge. The review reveals that land application of sewage sludge may pose viral infection risks to people due to accidently ingestion of sludge or intake of crops grown in biosolids amended soil. Moreover, contamination of groundwater and/or surface water may occur due to land application of sewage sludge.
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Affiliation(s)
- Sahar Gholipour
- Department of Environmental Health Engineering, Faculty of Health, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohammad Rezvani Ghalhari
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahnaz Nikaeen
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Davarkhah Rabbani
- Department of Environmental Health Engineering, Faculty of Health, Kashan University of Medical Sciences, Kashan, Iran
| | - Parichehr Pakzad
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Bagher Miranzadeh
- Department of Environmental Health Engineering, Faculty of Health, Kashan University of Medical Sciences, Kashan, Iran.
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6
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Yang W, Cai C, Dai X. Interactions between virus surrogates and sewage sludge vary by viral analyte: Recovery, persistence, and sorption. WATER RESEARCH 2022; 210:117995. [PMID: 34998072 DOI: 10.1016/j.watres.2021.117995] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
Sewage sludge, as a reservoir of viruses, may pose threats to human health. Understanding how virus particles interact with sludge is the key to controlling virus exposure and transmission. In this study, we investigated the recovery, survivability, and sorption of four typical virus surrogates with different structures (Phi6, MS2, T4, and Phix174) in sewage sludge. The most effective elution method varies by viral analyte, while the ultrafiltration method could significantly reduce the recovery loss for all four viruses. Compared with nonenveloped viruses, the poor recoveries of Phi6 during elution (<15%) limited its efficient detection. The inactivation kinetics of four viruses in solid-containing sludge were significantly faster than those in solid-removed samples at 25 °C, indicating that the solid fraction of sludge played an important role in virus inactivation. Although enveloped Phi6 was more vulnerable in both solid-removed and solid-containing sludge samples, it could remain viable for several hours at 25 °C and several days at 4 °C, which may pose an infection risk during sludge collection, transportation, and treatment process. The adsorption and desorption behavior of viruses in sludge could be affected by virus envelope structure, capsid proteins, and virus particle size. Phi6 adsorption to sludge was great with log KF of 6.51 ± 0.53, followed by Phix174, MS2, and T4. Additionally, more than 95% of Phi6, MS2, and T4 adsorbed to sludge were strongly bound, and a considerable fraction of strongly-bound virus was confirmed to retain viability. These results shed light on the environmental behavior of viruses in sewage sludge and provide a theoretical basis for the risk assessment for sludge treatment and disposal.
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Affiliation(s)
- Wan Yang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Chen Cai
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
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7
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A SYSTEMATIC REVIEW AND NARRATIVE SYNTHESIS OF THE USE OF ENVIRONMENTAL SAMPLES FOR THE SURVEILLANCE OF AVIAN INFLUENZA VIRUSES IN WILD WATERBIRDS. J Wildl Dis 2021; 57:1-18. [PMID: 33635994 DOI: 10.7589/jwd-d-20-00082] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/25/2020] [Indexed: 11/20/2022]
Abstract
Wild waterbirds are reservoir hosts for avian influenza viruses (AIV), which can cause devastating outbreaks in multiple species, making them a focus for surveillance efforts. Traditional AIV surveillance involves direct sampling of live or dead birds, but environmental substrates present an alternative sample for surveillance. Environmental sampling analyzes AIV excreted by waterbirds into the environment and complements direct bird sampling by minimizing financial, logistic, permitting, and spatial-temporal constraints associated with traditional surveillance. Our objectives were to synthesize the literature on environmental AIV surveillance, to compare and contrast the different sample types, and to identify key themes and recommendations to aid in the implementation of AIV surveillance using environmental samples. The four main environmental substrates for AIV surveillance are feces, feathers, water, and sediment or soil. Feces were the most common environmental substrate collected. The laboratory analysis of water and sediment provided challenges, such as low AIV concentration, heterogenous AIV distribution, or presence of PCR inhibitors. There are a number of abiotic and biotic environmental factors, including temperature, pH, salinity, or presence of filter feeders, that can influence the presence and persistence of AIV in environmental substrates; however, the nature of this influence is poorly understood in field settings, and field data from southern, coastal, and tropical ecosystems are underrepresented. Similarly, there are few studies comparing the performance of environmental samples to each other and to samples collected in wild waterbirds, and environmental surveillance workflows have yet to be validated or optimized. Environmental samples, particularly when used in combination with new technology such as environmental DNA and next generation sequencing, provided information on trends in AIV detection rates and circulating subtypes that complemented traditional, direct waterbird sampling. The use of environmental samples for AIV surveillance also shows significant promise for programs whose goal is early warning of high-risk subtypes.
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8
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Graham KE, Loeb SK, Wolfe MK, Catoe D, Sinnott-Armstrong N, Kim S, Yamahara KM, Sassoubre LM, Mendoza Grijalva LM, Roldan-Hernandez L, Langenfeld K, Wigginton KR, Boehm AB. SARS-CoV-2 RNA in Wastewater Settled Solids Is Associated with COVID-19 Cases in a Large Urban Sewershed. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:488-498. [PMID: 33283515 PMCID: PMC7737534 DOI: 10.1021/acs.est.0c06191] [Citation(s) in RCA: 229] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 05/11/2023]
Abstract
Wastewater-based epidemiology may be useful for informing public health response to viral diseases like COVID-19 caused by SARS-CoV-2. We quantified SARS-CoV-2 RNA in wastewater influent and primary settled solids in two wastewater treatment plants to inform the preanalytical and analytical approaches and to assess whether influent or solids harbored more viral targets. The primary settled solids samples resulted in higher SARS-CoV-2 detection frequencies than the corresponding influent samples. Likewise, SARS-CoV-2 RNA was more readily detected in solids using one-step digital droplet (dd)RT-PCR than with two-step RT-QPCR and two-step ddRT-PCR, likely owing to reduced inhibition with the one-step ddRT-PCR assay. We subsequently analyzed a longitudinal time series of 89 settled solids samples from a single plant for SARS-CoV-2 RNA as well as coronavirus recovery (bovine coronavirus) and fecal strength (pepper mild mottle virus) controls. SARS-CoV-2 RNA targets N1 and N2 concentrations correlated positively and significantly with COVID-19 clinically confirmed case counts in the sewershed. Together, the results demonstrate that measuring SARS-CoV-2 RNA concentrations in settled solids may be a more sensitive approach than measuring SARS-CoV-2 in influent.
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Affiliation(s)
- Katherine E. Graham
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford 94305,
California, United States
| | - Stephanie K. Loeb
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford 94305,
California, United States
| | - Marlene K. Wolfe
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford 94305,
California, United States
| | - David Catoe
- Joint Initiative for Metrology in Biology,
SLAC National Accelerator Laboratory, Stanford 94305,
California, United States
| | - Nasa Sinnott-Armstrong
- Department of Genetics, Stanford University
School of Medicine, Stanford 94305, California, United
States
- Emmett Interdisciplinary Program in Environment and
Resources, Stanford University, Stanford 94305, California,
United States
| | - Sooyeol Kim
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford 94305,
California, United States
| | - Kevan M. Yamahara
- Monterey Bay Aquarium Research
Institute, Moss Landing 95039, California, United
States
| | - Lauren M. Sassoubre
- Department of Engineering, University of San
Francisco, San Francisco 94117, California, United
States
| | - Lorelay M. Mendoza Grijalva
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford 94305,
California, United States
| | - Laura Roldan-Hernandez
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford 94305,
California, United States
| | - Kathryn Langenfeld
- Department of Civil and Environmental Engineering,
University of Michigan, Ann Arbor 48109, Michigan,
United States
| | - Krista R. Wigginton
- Department of Civil and Environmental Engineering,
University of Michigan, Ann Arbor 48109, Michigan,
United States
| | - Alexandria B. Boehm
- Department of Civil and Environmental Engineering,
Stanford University, 473 Via Ortega, Stanford 94305,
California, United States
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9
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Hood G, Roche X, Brioudes A, von Dobschuetz S, Fasina FO, Kalpravidh W, Makonnen Y, Lubroth J, Sims L. A literature review of the use of environmental sampling in the surveillance of avian influenza viruses. Transbound Emerg Dis 2021; 68:110-126. [PMID: 32652790 PMCID: PMC8048529 DOI: 10.1111/tbed.13633] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 05/07/2020] [Accepted: 05/13/2020] [Indexed: 02/05/2023]
Abstract
This literature review provides an overview of use of environmental samples (ES) such as faeces, water, air, mud and swabs of surfaces in avian influenza (AI) surveillance programs, focussing on effectiveness, advantages and gaps in knowledge. ES have been used effectively for AI surveillance since the 1970s. Results from ES have enhanced understanding of the biology of AI viruses in wild birds and in markets, of links between human and avian influenza, provided early warning of viral incursions, allowed assessment of effectiveness of control and preventive measures, and assisted epidemiological studies in outbreaks, both avian and human. Variation exists in the methods and protocols used, and no internationally recognized guidelines exist on the use of ES and data management. Few studies have performed direct comparisons of ES versus live bird samples (LBS). Results reported so far demonstrate reliance on ES will not be sufficient to detect virus in all cases when it is present, especially when the prevalence of infection/contamination is low. Multiple sample types should be collected. In live bird markets, ES from processing/selling areas are more likely to test positive than samples from bird holding areas. When compared to LBS, ES is considered a cost-effective, simple, rapid, flexible, convenient and acceptable way of achieving surveillance objectives. As a non-invasive technique, it can minimize effects on animal welfare and trade in markets and reduce impacts on wild bird communities. Some limitations of environmental sampling methods have been identified, such as the loss of species-specific or information on the source of virus, and taxonomic-level analyses, unless additional methods are applied. Some studies employing ES have not provided detailed methods. In others, where ES and LBS are collected from the same site, positive results have not been assigned to specific sample types. These gaps should be remedied in future studies.
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Affiliation(s)
- Grace Hood
- Food and Agriculture Organization of the United NationsRomeItaly
| | - Xavier Roche
- Food and Agriculture Organization of the United NationsRomeItaly
| | - Aurélie Brioudes
- Food and Agriculture Organization of the United NationsRegional Office for Asia and the PacificBangkokThailand
| | | | | | | | - Yilma Makonnen
- Food and Agriculture Organization of the United Nations, Sub-Regional Office for Eastern AfricaAddis AbabaEthiopia
| | - Juan Lubroth
- Food and Agriculture Organization of the United NationsRomeItaly
| | - Leslie Sims
- Asia Pacific Veterinary Information ServicesMelbourneAustralia
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TARGETED RESEQUENCING OF WETLAND SEDIMENT AS A TOOL FOR AVIAN INFLUENZA VIRUS SURVEILLANCE. J Wildl Dis 2020. [DOI: 10.7589/2019-05-135] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Horm SV, Sorn S, Allal L, Buchy P. Influenza A(H5N1) virus surveillance at live poultry markets, Cambodia, 2011. Emerg Infect Dis 2013; 19:305-8. [PMID: 23347451 PMCID: PMC3559060 DOI: 10.3201/eid1902.121201] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In Cambodia, influenza A(H5N1) virus surveillance at live poultry markets (LPMs) relies on virus isolation from poultry specimens; however, virus is rarely detected by this method. We tested 502 environmental LPM samples: 90 were positive by PCR, 10 by virus isolation. Virus circulation could be better monitored by environmental sampling of LPMs.
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Amdiouni H, Soukri A, Nourlil J, Maunula L. Preliminary Study to Assess the Performance of Mengovirus Elution from Sludge. FOOD AND ENVIRONMENTAL VIROLOGY 2013; 5:180-183. [PMID: 23797496 DOI: 10.1007/s12560-013-9116-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Accepted: 06/13/2013] [Indexed: 05/21/2023]
Abstract
In the virus detection protocol for sludge, the viral elution step from solids to solution is critical. In this study, mengoviruses were detected in artificially contaminated sludge with a qRT-PCR assay. The viral yields ranged between 19 and 66 % for 60 % sludge. This study demonstrates that mengovirus can be used as a sample process control for analysis of sewage sludge.
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Affiliation(s)
- Hasna Amdiouni
- Medical Virology & BSL3 Laboratory, Institut Pasteur du Maroc. 1, Place Louis Pasteur, 20360, Casablanca, Morocco,
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Horm VS, Gutiérrez RA, Nicholls JM, Buchy P. Highly pathogenic influenza A(H5N1) virus survival in complex artificial aquatic biotopes. PLoS One 2012; 7:e34160. [PMID: 22514622 PMCID: PMC3325971 DOI: 10.1371/journal.pone.0034160] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 02/27/2012] [Indexed: 11/24/2022] Open
Abstract
Background Very little is known regarding the persistence of Highly Pathogenic Avian Influenza (HPAI) H5N1 viruses in aquatic environments in tropical countries, although environmental materials have been suggested to play a role as reservoirs and sources of transmission for H5N1 viruses. Methodology/Principal Findings The survival of HPAI H5N1 viruses in experimental aquatic biotopes (water, mud, aquatic flora and fauna) relevant to field conditions in Cambodia was investigated. Artificial aquatic biotopes, including simple ones containing only mud and water, and complex biotopes involving the presence of aquatic flora and fauna, were set up. They were experimentally contaminated with H5N1 virus. The persistence of HPAI H5N1 virus (local avian and human isolates) was determined by virus isolation in embryonated chicken eggs and by real-time reverse-polymerase chain reaction. Persistence of infectious virus did not exceed 4 days, and was only identified in rain water. No infectious virus particles were detected in pond and lake water or mud even when high inoculum doses were used. However, viral RNA persisted up to 20 days in rain water and 7 days in pond or lake water. Viral RNA was also detected in mud samples, up to 14 days post-contamination in several cases. Infectious virus and viral RNA was detected in few cases in the aquatic fauna and flora, especially in bivalves and labyrinth fish, although these organisms seemed to be mostly passive carriers of the virus rather than host allowing virus replication. Conclusions/Significance Although several factors for the survival and persistence of HPAI viruses in the environment are still to be elucidated, and are particularly hard to control in laboratory conditions, our results, along with previous data, support the idea that environmental surveillance is of major relevance for avian influenza control programs.
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Affiliation(s)
- Viseth Srey Horm
- Virology Unit, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur, Phnom Penh, Cambodia
| | - Ramona A. Gutiérrez
- Virology Unit, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur, Phnom Penh, Cambodia
| | - John M. Nicholls
- Department of Pathology, University of Hong Kong, Pokfulam, Hong Kong, Hong Kong SAR
| | - Philippe Buchy
- Virology Unit, Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur, Phnom Penh, Cambodia
- * E-mail:
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