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Vanderhoeven E, Paresque R, Mello I, Nates S, Vicentini F, Díaz A, Masachessi G. Circulation of picobirnavirus in Neotropical free-ranging mammals. Vet Res Commun 2024; 48:1097-1109. [PMID: 38114776 DOI: 10.1007/s11259-023-10282-z] [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: 08/03/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
Picobirnavirus (PBV) is a family of non-enveloped double-stranded RNA viruses with bisegmented genomes. Segment 1 encodes the capsid protein and segment 2 encodes RNA-dependent RNA polymerase. They exhibit high genomic heterogeneity and infect a wide range of vertebrate hosts, including humans. The objective of this study was to expand our knowledge of the circulation of PBV in free-living animals from two regions (Brazil and Argentina) of the Atlantic Forest. Fecal samples were analyzed from free-living animals: tapir, brocket deer, peccary, and different species of rodents and marsupials. A total of 133 samples were collected and analyzed by RT-PCR, of which 44 (33.08%) were PBV-positive. Nine amplicons were sequenced, five species from Argentina and four from Brazil, and phylogenetic analysis was performed. The nucleotide and amino acid identities of the PBV strains detected in animals from Argentina and Brazil were between 66.3% and 82.5% and between 55.3% and 74.2%, respectively. The analysed strains presented conserved nucleotide blocks without distinction of the host species. The phylogenetic tree showed that PBV strains from Atlantic Forest animals belonging to genogroup I were grouped into different clusters, without defining groups according to host species (human or animal) or the geographical area of detection. This is the first study on PBV in free-living animals in the Atlantic Forest. Our analysis suggested that PBV strains can infect different animal species, leading to PBV transmission between animals and humans. This reinforces the hypothesis of previous crossover points in the ecology and evolution of heterologous PBV strains.
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Affiliation(s)
- Ezequiel Vanderhoeven
- Instituto de Biología Subtropical, CONICET-Universidad Nacional de Misiones (UNaM), Puerto Iguazú, Misiones, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Roberta Paresque
- Programa de Pós Graduação Em Ciências Biológicas, Universidade Federal Do Espírito Santo BR, São Mateus, ES, Brazil
| | - Iago Mello
- Programa de Pós Graduação Em Ciências Biológicas, Universidade Federal Do Espírito Santo BR, São Mateus, ES, Brazil
| | - Silvia Nates
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | | | - Adrián Díaz
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Gisela Masachessi
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina
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Canh VD, Nga TTV, Lien NT, Katayama H. Development of a simple and low-cost method using Moringa seeds for efficient virus concentration in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167101. [PMID: 37716673 DOI: 10.1016/j.scitotenv.2023.167101] [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: 08/05/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023]
Abstract
Effective virus concentration methods are essential for detecting pathogenic viruses in environmental waters and play a crucial role in wastewater-based epidemiology. However, the current methods are often expensive, complicated, and time-consuming, which limits their practical application. In this study, a simple and low-cost method was developed using the extract of Moringa oleifera (MO) seeds (MO method) to recover both enveloped and non-enveloped viruses, including pepper mild mottle virus (PMMoV), murine norovirus (MNV), Aichivirus (AiV), murine hepatitis virus (MHV), and influenza A virus subtype H1N1[H1N1] in wastewater. The optimal conditions for the MO method were determined to be a concentration of MO extract at the UV280 value of 0.308 cm-1 and an elution buffer (0.05 M KH2PO4, 1 M NaCl, 0.1 % Tween80 [v/v]) for recovering the tested viruses in wastewater. Compared to other commonly used virus concentration methods such as InnovaPrep, HA, PEG, and Centricon, the MO method was found to be more efficient and cost-effective in recovering the tested viruses. Moreover, the MO method was successfully applied to detect various types of viruses (PMMoV, AiV, norovirus of genotype II [NoV II], enterovirus [EV], influenza A virus [matrix gene] [IAV], and SARS-CoV-2) in raw wastewater. Thus, the developed MO method could offer a simple, low-cost, and efficient tool to concentrate viruses in wastewater.
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Affiliation(s)
- Vu Duc Canh
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Tran Thi Viet Nga
- Faculty of Environmental Engineering, Hanoi University of Civil Engineering, 55 Giai Phong Road, Hai Ba Trung, Hanoi, Viet Nam
| | - Nguyen Thuy Lien
- Faculty of Environmental Engineering, Hanoi University of Civil Engineering, 55 Giai Phong Road, Hai Ba Trung, Hanoi, Viet Nam
| | - Hiroyuki Katayama
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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Dhiyebi HA, Abu Farah J, Ikert H, Srikanthan N, Hayat S, Bragg LM, Qasim A, Payne M, Kaleis L, Paget C, Celmer-Repin D, Folkema A, Drew S, Delatolla R, Giesy JP, Servos MR. Assessment of seasonality and normalization techniques for wastewater-based surveillance in Ontario, Canada. Front Public Health 2023; 11:1186525. [PMID: 37711234 PMCID: PMC10499178 DOI: 10.3389/fpubh.2023.1186525] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/04/2023] [Indexed: 09/16/2023] Open
Abstract
Introduction Wastewater-based surveillance is at the forefront of monitoring for community prevalence of COVID-19, however, continued uncertainty exists regarding the use of fecal indicators for normalization of the SARS-CoV-2 virus in wastewater. Using three communities in Ontario, sampled from 2021-2023, the seasonality of a viral fecal indicator (pepper mild mottle virus, PMMoV) and the utility of normalization of data to improve correlations with clinical cases was examined. Methods Wastewater samples from Warden, the Humber Air Management Facility (AMF), and Kitchener were analyzed for SARS-CoV-2, PMMoV, and crAssphage. The seasonality of PMMoV and flow rates were examined and compared by Season-Trend-Loess decomposition analysis. The effects of normalization using PMMoV, crAssphage, and flow rates were analyzed by comparing the correlations to clinical cases by episode date (CBED) during 2021. Results Seasonal analysis demonstrated that PMMoV had similar trends at Humber AMF and Kitchener with peaks in January and April 2022 and low concentrations (troughs) in the summer months. Warden had similar trends but was more sporadic between the peaks and troughs for PMMoV concentrations. Flow demonstrated similar trends but was not correlated to PMMoV concentrations at Humber AMF and was very weak at Kitchener (r = 0.12). Despite the differences among the sewersheds, unnormalized SARS-CoV-2 (raw N1-N2) concentration in wastewater (n = 99-191) was strongly correlated to the CBED in the communities (r = 0.620-0.854) during 2021. Additionally, normalization with PMMoV did not improve the correlations at Warden and significantly reduced the correlations at Humber AMF and Kitchener. Flow normalization (n = 99-191) at Humber AMF and Kitchener and crAssphage normalization (n = 29-57) correlations at all three sites were not significantly different from raw N1-N2 correlations with CBED. Discussion Differences in seasonal trends in viral biomarkers caused by differences in sewershed characteristics (flow, input, etc.) may play a role in determining how effective normalization may be for improving correlations (or not). This study highlights the importance of assessing the influence of viral fecal indicators on normalized SARS-CoV-2 or other viruses of concern. Fecal indicators used to normalize the target of interest may help or hinder establishing trends with clinical outcomes of interest in wastewater-based surveillance and needs to be considered carefully across seasons and sites.
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Affiliation(s)
- Hadi A. Dhiyebi
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Joud Abu Farah
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Heather Ikert
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | | | - Samina Hayat
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Leslie M. Bragg
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Asim Qasim
- Regional Municipality of York, Newmarket, ON, Canada
| | - Mark Payne
- Regional Municipality of York, Newmarket, ON, Canada
| | - Linda Kaleis
- Regional Municipality of York, Newmarket, ON, Canada
| | - Caitlyn Paget
- Regional Municipality of York, Newmarket, ON, Canada
| | | | | | - Stephen Drew
- Regional Municipality of Waterloo, Waterloo, ON, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - John P. Giesy
- Department of Biomedical Sciences and Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Environmental Science, Baylor University, Waco, TX, United States
| | - Mark R. Servos
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
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Andrianjakarivony FH, Bettarel Y, Desnues C. Searching for a Reliable Viral Indicator of Faecal Pollution in Aquatic Environments. J Microbiol 2023:10.1007/s12275-023-00052-6. [PMID: 37261715 DOI: 10.1007/s12275-023-00052-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/13/2023] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
The disposal of sewage in significant quantities poses a health hazard to aquatic ecosystems. These effluents can contain a wide range of pathogens, making faecal contamination a leading source of waterborne diseases around the world. Yet monitoring bacteria or viruses in aquatic environments is time consuming and expensive. The standard indicators of faecal pollution all have limitations, including difficulty in determining the source due to lack of host specificity, poor connection with the presence of non-bacterial pathogens, or low environmental persistence. Innovative monitoring techniques are sorely needed to provide more accurate and targeted solutions. Viruses are a promising alternative to faecal indicator bacteria for monitoring, as they are more persistent in ambient water, more abundant in faeces, and are extremely host-specific. Given the range of viruses found in diverse contexts, it is not easy to find one "ideal" viral indicator of faecal pollution; however, several are of interest. In parallel, the ongoing development of molecular techniques coupled with metagenomics and bioinformatics should enable improved ways to detect faecal contamination using viruses. This review examines the evolution of faecal contamination monitoring with the following aims (i) to identify the characteristics of the main viral indicators of faecal contamination, including human enteric viruses, bacteriophages, CRESS and plant viruses, (ii) to assess how these have been used to monitor water pollution in recent years, (iii) to evaluate the reliability of recent detection methods of such viruses, and (iv) to tentatively determine which viruses may be most effective as markers of faecal pollution.
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Affiliation(s)
- Felana Harilanto Andrianjakarivony
- Microbes, Evolution, Phylogeny, and Infection (MEФI), IHU - Méditerranée Infection, 13005, Marseille, France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), 13009, Marseille, France
| | - Yvan Bettarel
- MARBEC, Marine Biodiversity, Exploitation and Conservation, University of Montpellier, CNRS, Ifremer, IRD, 34090, Montpellier, France.
| | - Christelle Desnues
- Microbes, Evolution, Phylogeny, and Infection (MEФI), IHU - Méditerranée Infection, 13005, Marseille, France
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Rainey AL, Liang S, Bisesi JH, Sabo-Attwood T, Maurelli AT. A multistate assessment of population normalization factors for wastewater-based epidemiology of COVID-19. PLoS One 2023; 18:e0284370. [PMID: 37043469 PMCID: PMC10096268 DOI: 10.1371/journal.pone.0284370] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/29/2023] [Indexed: 04/13/2023] Open
Abstract
Wastewater-based epidemiology (WBE) has become a valuable tool for monitoring SARS-CoV-2 infection trends throughout the COVID-19 pandemic. Population biomarkers that measure the relative human fecal contribution to normalize SARS-CoV-2 wastewater concentrations are needed for improved analysis and interpretation of community infection trends. The Centers for Disease Control and Prevention National Wastewater Surveillance System (CDC NWSS) recommends using the wastewater flow rate or human fecal indicators as population normalization factors. However, there is no consensus on which normalization factor performs best. In this study, we provided the first multistate assessment of the effects of flow rate and human fecal indicators (crAssphage, F+ Coliphage, and PMMoV) on the correlation of SARS-CoV-2 wastewater concentrations and COVID-19 cases using the CDC NWSS dataset of 182 communities across six U.S. states. Flow normalized SARS-CoV-2 wastewater concentrations produced the strongest correlation with COVID-19 cases. The correlation from the three human fecal indicators were significantly lower than flow rate. Additionally, using reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) significantly improved correlation values over samples that were analyzed with real-time reverse transcription quantitative polymerase chain reaction (rRT-qPCR). Our assessment shows that utilizing flow normalization with RT-ddPCR generate the strongest correlation between SARS-CoV-2 wastewater concentrations and COVID-19 cases.
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Affiliation(s)
- Andrew L. Rainey
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Song Liang
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Joseph H. Bisesi
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida, United States of America
| | - Tara Sabo-Attwood
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, Florida, United States of America
| | - Anthony T. Maurelli
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
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6
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Baldwin WM, Dayton RD, Bivins AW, Scott RS, Yurochko AD, Vanchiere JA, Davis T, Arnold CL, Asuncion JET, Bhuiyan MAN, Snead B, Daniel W, Smith DG, Goeders NE, Kevil CG, Carroll J, Murnane KS. Highly socially vulnerable communities exhibit disproportionately increased viral loads as measured in community wastewater. ENVIRONMENTAL RESEARCH 2023; 222:115351. [PMID: 36709030 PMCID: PMC9877155 DOI: 10.1016/j.envres.2023.115351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/12/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
Wastewater surveillance has proven to be a useful tool for evidence-based epidemiology in the fight against the SARS-CoV-2 virus. It is particularly useful at the population level where acquisition of individual test samples may be time or cost-prohibitive. Wastewater surveillance for SARS-CoV-2 has typically been performed at wastewater treatment plants; however, this study was designed to sample on a local level to monitor the spread of the virus among three communities with distinct social vulnerability indices in Shreveport, Louisiana, located in a socially vulnerable region of the United States. Twice-monthly grab samples were collected from September 30, 2020, to March 23, 2021, during the Beta wave of the pandemic. The goals of the study were to examine whether: 1) concentrations of SARS-CoV-2 RNA in wastewater varied with social vulnerability indices and, 2) the time lag of spikes differed during wastewater monitoring in the distinct communities. The size of the population contributing to each sample was assessed via the quantification of the pepper mild mottle virus (PMMoV), which was significantly higher in the less socially vulnerable community. We found that the communities with higher social vulnerability exhibited greater viral loads as assessed by wastewater when normalized with PMMoV (Kruskal-Wallis, p < 0.05). The timing of the spread of the virus through the three communities appeared to be similar. These results suggest that interconnected communities within a municipality experienced the spread of the SARS-CoV-2 virus at similar times, but areas of high social vulnerability experienced more intense wastewater viral loads.
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Affiliation(s)
- William M Baldwin
- Department of Pharmacology, Toxicology & Neuroscience, School of Graduate Studies, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Louisiana Addiction Research Center, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Center of Excellence for Emerging Viral Threats, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
| | - Robert D Dayton
- Department of Pharmacology, Toxicology & Neuroscience, School of Graduate Studies, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Louisiana Addiction Research Center, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Center of Excellence for Emerging Viral Threats, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
| | - Aaron W Bivins
- Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Rona S Scott
- Center of Excellence for Emerging Viral Threats, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Department of Microbiology and Immunology, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
| | - Andrew D Yurochko
- Louisiana Addiction Research Center, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Center of Excellence for Emerging Viral Threats, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Division of Health Disparities, Department of Medicine, School of Medicine, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
| | - John A Vanchiere
- Louisiana Addiction Research Center, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Center of Excellence for Emerging Viral Threats, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Division of Infectious Diseases, Department of Pediatrics, School of Medicine, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
| | - Terry Davis
- Louisiana Addiction Research Center, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Center of Excellence for Emerging Viral Threats, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Division of Health Disparities, Department of Medicine, School of Medicine, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
| | - Connie L Arnold
- Louisiana Addiction Research Center, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Center of Excellence for Emerging Viral Threats, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Division of Health Disparities, Department of Medicine, School of Medicine, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
| | - Jose E T Asuncion
- Department of Public Health, School of Allied Health Professions, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
| | - Mohammad A N Bhuiyan
- Louisiana Addiction Research Center, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Center of Excellence for Emerging Viral Threats, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Division of Clinical Informatics, Department of Medicine, School of Medicine, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
| | - Brandon Snead
- Department of Water and Sewage, City of Shreveport, Shreveport, Louisiana, USA
| | - William Daniel
- Department of Water and Sewage, City of Shreveport, Shreveport, Louisiana, USA
| | - Deborah G Smith
- Louisiana Addiction Research Center, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Department of Public Health, School of Allied Health Professions, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
| | - Nicholas E Goeders
- Department of Pharmacology, Toxicology & Neuroscience, School of Graduate Studies, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Louisiana Addiction Research Center, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Department of Psychiatry & Behavioral Medicine, School of Medicine, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
| | - Christopher G Kevil
- Louisiana Addiction Research Center, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Center of Excellence for Emerging Viral Threats, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Department of Pathology, School of Medicine, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Department of Molecular and Cellular Physiology, School of Graduate Studies, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Department of Cell Biology and Anatomy, School of Graduate Studies, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
| | - Jennifer Carroll
- Center of Excellence for Emerging Viral Threats, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA
| | - Kevin S Murnane
- Department of Pharmacology, Toxicology & Neuroscience, School of Graduate Studies, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Louisiana Addiction Research Center, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Center of Excellence for Emerging Viral Threats, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Department of Psychiatry & Behavioral Medicine, School of Medicine, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA; Department of Cell Biology and Anatomy, School of Graduate Studies, Louisiana State University Health Sciences Center at Shreveport, Shreveport, Louisiana, USA.
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González-Fernández A, Symonds EM, Gallard-Gongora JF, Mull B, Lukasik JO, Rivera Navarro P, Badilla Aguilar A, Peraud J, Mora Alvarado D, Cantor A, Breitbart M, Cairns MR, Harwood VJ. Risk of Gastroenteritis from Swimming at a Wastewater-Impacted Tropical Beach Varies across Localized Scales. Appl Environ Microbiol 2023; 89:e0103322. [PMID: 36847564 PMCID: PMC10057883 DOI: 10.1128/aem.01033-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 01/21/2023] [Indexed: 03/01/2023] Open
Abstract
Population growth and changing climate are expected to increase human exposure to pathogens in tropical coastal waters. We examined microbiological water quality in three rivers within 2.3 km of each other that impact a Costa Rican beach and in the ocean outside their plumes during the rainy and dry seasons. We performed quantitative microbial risk assessment (QMRA) to predict the risk of gastroenteritis associated with swimming and the amount of pathogen reduction needed to achieve safe conditions. Recreational water quality criteria based on enterococci were exceeded in >90% of river samples but in only 13% of ocean samples. Multivariate analysis grouped microbial observations by subwatershed and season in river samples but only by subwatershed in the ocean. The modeled median risk from all pathogens in river samples was between 0.345 and 0.577, 10-fold above the U.S. Environmental Protection Agency (U.S. EPA) benchmark of 0.036 (36 illnesses/1,000 swimmers). Norovirus genogroup I (NoVGI) contributed most to risk, but adenoviruses raised risk above the threshold in the two most urban subwatersheds. The risk was greater in the dry compared to the rainy season, due largely to the greater frequency of NoVGI detection (100% versus 41%). Viral log10 reduction needed to ensure safe swimming conditions varied by subwatershed and season and was greatest in the dry season (3.8 to 4.1 dry; 2.7 to 3.2 rainy). QMRA that accounts for seasonal and local variability of water quality contributes to understanding the complex influences of hydrology, land use, and environment on human health risk in tropical coastal areas and can contribute to improved beach management. IMPORTANCE This holistic investigation of sanitary water quality at a Costa Rican beach assessed microbial source tracking (MST) marker genes, pathogens, and indicators of sewage. Such studies are still rare in tropical climates. Quantitative microbial risk assessment (QMRA) found that rivers impacting the beach consistently exceeded the U.S. EPA risk threshold for gastroenteritis of 36/1,000 swimmers. The study improves upon many QMRA studies by measuring specific pathogens, rather than relying on surrogates (indicator organisms or MST markers) or estimating pathogen concentrations from the literature. By analyzing microbial levels and estimating the risk of gastrointestinal illness in each river, we were able to discern differences in pathogen levels and human health risks even though all rivers were highly polluted by wastewater and were located less than 2.5 km from one another. This variability on a localized scale has not, to our knowledge, previously been demonstrated.
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Affiliation(s)
| | - Erin M. Symonds
- College of Marine Science, University of South Florida, Saint Petersburg, Florida, USA
- Department of Anthropology, Southern Methodist University, Dallas, Texas, USA
| | | | - Bonnie Mull
- BCS Laboratories, Inc., Gainesville, Florida, USA
| | | | - Pablo Rivera Navarro
- Laboratorio Nacional de Aguas, Instituto Costarricense de Acueductos y Alcantarillados, Tres Ríos, Cartago, Costa Rica
| | - Andrei Badilla Aguilar
- Laboratorio Nacional de Aguas, Instituto Costarricense de Acueductos y Alcantarillados, Tres Ríos, Cartago, Costa Rica
| | - Jayme Peraud
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Darner Mora Alvarado
- Laboratorio Nacional de Aguas, Instituto Costarricense de Acueductos y Alcantarillados, Tres Ríos, Cartago, Costa Rica
| | - Allison Cantor
- Department of Anthropology, Southern Methodist University, Dallas, Texas, USA
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, Florida, USA
| | - Maryann R. Cairns
- Department of Anthropology, Southern Methodist University, Dallas, Texas, USA
| | - Valerie J. Harwood
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
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8
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Betancourt WQ. Waterborne Plant Viruses of Importance in Agriculture. Infect Dis (Lond) 2023. [DOI: 10.1007/978-1-0716-2463-0_1096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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9
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Standards to support an enduring capability in wastewater surveillance for public health: Where are we? CASE STUDIES IN CHEMICAL AND ENVIRONMENTAL ENGINEERING 2022; 6:100247. [PMID: 37520917 PMCID: PMC9376981 DOI: 10.1016/j.cscee.2022.100247] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 06/02/2023]
Abstract
The COVID-19 pandemic highlighted a wide range of public health system challenges for infectious disease surveillance. The discovery that the SARS-CoV-2 virus was shed in feces and can be characterized using PCR-based testing of sewage samples offers new possibilities and challenges for wastewater surveillance (WWS). However, WWS standardization of practices is needed to provide actionable data for a public health response. A workshop was convened consisting of academic, federal government, and industry stakeholders. The objective was to review WWS sampling protocols, testing methods, analyses, and data interpretation approaches for WWS employed nationally and identify opportunities for standardizing practices, including the development of documentary standards or reference materials in the case of SARS-CoV-2 surveillance. Other WWS potential future threats to public health were also discussed. Several aspects of WWS were considered and each offers the opportunity for standards development. These areas included sampling strategies, analytical methods, and data reporting practices. Each of these areas converged on a common theme, the challenge of results comparability across facilities and jurisdictions. For sampling, the consensus solution was the development of documentary standards to guide appropriate sampling practices. In contrast, the predominant opportunity for analytical methods was reference material development, such as PCR-based standards and surrogate recovery controls. For data reporting practices, the need for establishing the minimal required metadata, a metadata vocabulary, and standardizing data units of measure including measurement threshold definitions was discussed. Beyond SARS-CoV-2 testing, there was general agreement that the WWS platform will continue to be a valuable tool for a wide range of public health threats and that future cross-sector engagements are needed to guide an enduring WWS capability.
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Mendoza Grijalva L, Brown B, Cauble A, Tarpeh WA. Diurnal Variability of SARS-CoV-2 RNA Concentrations in Hourly Grab Samples of Wastewater Influent during Low COVID-19 Incidence. ACS ES&T WATER 2022; 2:2125-2133. [PMID: 37552729 PMCID: PMC9063989 DOI: 10.1021/acsestwater.2c00061] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/31/2022] [Accepted: 04/06/2022] [Indexed: 06/17/2023]
Abstract
Wastewater-based epidemiology (WBE) has been widely deployed during the COVID-19 pandemic, but with limited evaluation of the utility of discrete sampling for large sewersheds and low COVID-19 incidence. In this study, SARS-CoV-2 RNA was measured in 72 consecutive hourly influent grab samples collected at a wastewater treatment plant serving nearly 500 000 residents when incidence was low (approximately 20 cases per 100 000). We characterized diurnal variability and relationships between SARS-CoV-2 RNA detection and physicochemical covariates [flow rate, total ammonia nitrogen (TAN), and total solids (TS)]. The highest detection rate observed was 82% during the first peak flow, which occurred in the early afternoon (14:00). Higher detection rates were also observed when sampling above median TAN concentrations (71%; p < 0.01; median = 40.26 mg of NH4/L). SARS-CoV-2 RNA concentrations were weakly correlated with flow rate (Kendall's τ = 0.16; p < 0.01), TAN (τ = 0.19; p < 0.05), and TS (τ = 0.18; p < 0.01), suggesting generally low RNA sewer discharges as expected at low incidence. Our results elucidated sensible adjustments to maximize detection rates, including using multiple gene targets, collecting duplicate samples, and sampling during higher flow and TAN discharges. Optimizing the lower-incidence bounds of WBE can help assess its suitability for verifying COVID-19 reemergence or eradication.
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Affiliation(s)
- Lorelay Mendoza Grijalva
- Department of Civil and Environmental Engineering,
Stanford University, Stanford, California 94305,
United States
| | - Blake Brown
- Central Contra Costa Sanitary
District, Martinez, California 94553, United
States
| | - Amanda Cauble
- Central Contra Costa Sanitary
District, Martinez, California 94553, United
States
| | - William A. Tarpeh
- Department of Civil and Environmental Engineering,
Stanford University, Stanford, California 94305,
United States
- Department of Chemical Engineering,
Stanford University, Stanford, California 94305,
United States
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11
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Johnson W, Reeves K, Liebig J, Feula A, Butler C, Alkire M, Singh S, Litton S, O'Conor K, Jones K, Ortega N, Shimek T, Witteman J, Bjorkman KK, Mansfeldt C. Effectiveness of building-level sewage surveillance during both community-spread and sporadic-infection phases of SARS-CoV-2 in a university campus population. FEMS MICROBES 2022; 3:xtac024. [PMID: 37332508 PMCID: PMC10117889 DOI: 10.1093/femsmc/xtac024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/27/2022] [Accepted: 09/21/2022] [Indexed: 08/29/2023] Open
Abstract
Pathogen surveillance within wastewater rapidly progressed during the SARS-CoV-2 pandemic and informed public health management. In addition to the successful monitoring of entire sewer catchment basins at the treatment facility scale, subcatchment or building-level monitoring enabled targeted support of resource deployment. However, optimizing the temporal and spatial resolution of these monitoring programs remains complex due to population dynamics and within-sewer physical, chemical, and biological processes. To address these limitations, this study explores the advancement of the building-scale network that monitored the on-campus residential population at the University of Colorado Boulder between August 2020 and May 2021 through a daily SARS-CoV-2 surveillance campaign. During the study period, SARS-CoV-2 infection prevalence transitioned from robust community spread in Fall 2020 to sporadic infections in Spring 2021. Temporally, these distinct phases enabled investigating the effectiveness of resource commitment by exploring subsets of the original daily sampling data. Spatially, select sampling sites were installed along the flow path of the pipe network, enabling the exploration of the conservation of viral concentrations within the wastewater. Infection prevalence and resource commitment for informed action displayed an inverted relationship: higher temporal and spatial resolution surveillance is more imperative during sporadic infection phases than during high prevalence periods. This relationship was reinforced when norovirus (two minor clusters) and influenza (primarily absent) were additionally surveilled at a weekly frequency. Overall, resource commitment should scale to meet the objectives of the monitoring campaign-providing a general prevalence estimate requires fewer resources than an early-warning and targeted-action monitoring framework.
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Affiliation(s)
- William Johnson
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, 1111 Engineering Drive, Boulder, CO 80309, United States
- Environmental Engineering Program, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO 80303, United States
| | - Katelyn Reeves
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, 1111 Engineering Drive, Boulder, CO 80309, United States
- Environmental Engineering Program, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO 80303, United States
| | - Jennifer Liebig
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80303, United States
| | - Antonio Feula
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80303, United States
| | - Claire Butler
- Environmental Engineering Program, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO 80303, United States
| | - Michaela Alkire
- Environmental Engineering Program, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO 80303, United States
| | - Samiha Singh
- Environmental Engineering Program, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO 80303, United States
| | - Shelby Litton
- Environmental Engineering Program, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO 80303, United States
| | - Kerry O'Conor
- Environmental Engineering Program, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO 80303, United States
| | - Keaton Jones
- Environmental Engineering Program, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO 80303, United States
| | - Nikolas Ortega
- Environmental Engineering Program, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO 80303, United States
| | - Trace Shimek
- Environmental Engineering Program, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO 80303, United States
| | - Julia Witteman
- Environmental Engineering Program, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO 80303, United States
| | - Kristen K Bjorkman
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80303, United States
| | - Cresten Mansfeldt
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, 1111 Engineering Drive, Boulder, CO 80309, United States
- Environmental Engineering Program, University of Colorado Boulder, 4001 Discovery Drive, Boulder, CO 80303, United States
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12
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Sharma A, Mangla D, Choudhry A, Sajid M, Ali Chaudhry S. Facile synthesis, physico-chemical studies of Ocimum sanctum magnetic nanocomposite and its adsorptive application against Methylene blue. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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13
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Mailepessov D, Arivalan S, Kong M, Griffiths J, Low SL, Chen H, Hapuarachchi HC, Gu X, Lee WL, Alm EJ, Thompson J, Wuertz S, Gin K, Ng LC, Wong JCC. Development of an efficient wastewater testing protocol for high-throughput country-wide SARS-CoV-2 monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 826:154024. [PMID: 35217043 PMCID: PMC8860745 DOI: 10.1016/j.scitotenv.2022.154024] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 05/04/2023]
Abstract
Wastewater-based surveillance has been widely used as a non-intrusive tool to monitor population-level transmission of COVID-19. Although various approaches are available to concentrate viruses from wastewater samples, scalable methods remain limited. Here, we sought to identify and evaluate SARS-CoV-2 virus concentration protocols for high-throughput wastewater testing. A total of twelve protocols for polyethylene glycol (PEG) precipitation and four protocols for ultrafiltration-based approaches were evaluated across two phases. The first phase entailed an initial evaluation using a small sample set, while the second phase further evaluated five protocols using wastewater samples of varying SARS-CoV-2 concentrations. Permutations in the pre-concentration, virus concentration and RNA extraction steps were evaluated. Among PEG-based methods, SARS-CoV-2 virus recovery was optimal with 1) the removal of debris prior to processing, 2) 2 h to 24 h incubation with 8% PEG at 4 °C, 3) 4000 xg or 14,000 xg centrifugation, and 4) a column-based RNA extraction method, yielding virus recovery of 42.4-52.5%. Similarly, the optimal protocol for ultrafiltration included 1) the removal of debris prior to processing, 2) ultrafiltration, and 3) a column-based RNA extraction method, yielding a recovery of 38.2%. This study also revealed that SARS-CoV-2 RNA recovery for samples with higher virus concentration were less sensitive to changes in the PEG method, but permutations in the PEG protocol could significantly impact virus yields when wastewater samples with lower SARS-CoV-2 RNA were used. Although both PEG precipitation and ultrafiltration methods resulted in similar SARS-CoV-2 RNA recoveries, the former method is more cost-effective while the latter method provided operational efficiency as it required a shorter turn-around-time (PEG precipitation, 9-23 h; Ultrafiltration, 5 h). The decision on which method to adopt will thus depend on the use-case for wastewater testing, and the need for cost-effectiveness, sensitivity, operational feasibility and scalability.
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Affiliation(s)
- Diyar Mailepessov
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way #06-05/08, Helios Block, Singapore 138667, Singapore
| | - Sathish Arivalan
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way #06-05/08, Helios Block, Singapore 138667, Singapore
| | - Marcella Kong
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way #06-05/08, Helios Block, Singapore 138667, Singapore
| | - Jane Griffiths
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way #06-05/08, Helios Block, Singapore 138667, Singapore
| | - Swee Ling Low
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way #06-05/08, Helios Block, Singapore 138667, Singapore
| | - Hongjie Chen
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore 138602, Singapore
| | | | - Xiaoqiong Gu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore 138602, Singapore
| | - Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore 138602, Singapore
| | - Eric J Alm
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore 138602, Singapore; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore 138602, Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore 637459, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Karina Gin
- Department of Civil and Environmental Engineering, Faculty of Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way #06-05/08, Helios Block, Singapore 138667, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
| | - Judith Chui Ching Wong
- Environmental Health Institute, National Environment Agency, 11 Biopolis Way #06-05/08, Helios Block, Singapore 138667, Singapore.
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14
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Cuevas-Ferrando E, Pérez-Cataluña A, Falcó I, Randazzo W, Sánchez G. Monitoring Human Viral Pathogens Reveals Potential Hazard for Treated Wastewater Discharge or Reuse. Front Microbiol 2022; 13:836193. [PMID: 35464930 PMCID: PMC9026171 DOI: 10.3389/fmicb.2022.836193] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/21/2022] [Indexed: 01/22/2023] Open
Abstract
Wastewater discharge to the environment or its reuse after sanitization poses a concern for public health given the risk of transmission of human viral diseases. However, estimating the viral infectivity along the wastewater cycle presents technical challenges and still remains underexplored. Recently, human-associated crAssphage has been investigated to serve as viral pathogen indicator to monitor fecal impacted water bodies, even though its assessment as biomarker for infectious enteric viruses has not been explored yet. To this end, the occurrence of potentially infectious norovirus genogroup I (GI), norovirus GII, hepatitis A virus (HAV), rotavirus A (RV), and human astrovirus (HAstV) along with crAssphage was investigated in influent and effluent water sampled in four wastewater treatment plants (WWTPs) over 1 year by a PMAxx-based capsid integrity RT-qPCR assay. Moreover, influent and effluent samples of a selected WWTP were additionally assayed by an in situ capture RT-qPCR assay (ISC-RT-qPCR) as estimate for viral infectivity in alternative to PMAxx-RT-qPCR. Overall, our results showed lower viral occurrence and concentration assessed by ISC-RT-qPCR than PMAxx-RT-qPCR. Occurrence of potentially infectious enteric virus was estimated by PMAxx-RT-qPCR as 88–94% in influent and 46–67% in effluent wastewaters with mean titers ranging from 4.77 to 5.89, and from 3.86 to 4.97 log10 GC/L, with the exception of HAV that was sporadically detected. All samples tested positive for crAssphage at concentration ranging from 7.41 to 9.99 log10 GC/L in influent and from 4.56 to 6.96 log10 GC/L in effluent wastewater, showing higher mean concentration than targeted enteric viruses. Data obtained by PMAxx-RT-qPCR showed that crAssphage strongly correlated with norovirus GII (ρ = 0.67, p < 0.05) and weakly with HAstV and RV (ρ = 0.25–0.30, p < 0.05) in influent samples. In effluent wastewater, weak (ρ = 0.27–0.38, p < 0.05) to moderate (ρ = 0.47–0.48, p < 0.05) correlations between crAssphage and targeted viruses were observed. Overall, these results corroborate crAssphage as an indicator for fecal contamination in wastewater but a poor marker for either viral occurrence and viral integrity/infectivity. Despite the viral load reductions detected in effluent compared to influent wastewaters, the estimates of viral infectivity based on viability molecular methods might pose a concern for (re)-using of treated water.
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15
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Evaluating the Use of Alternative Normalization Approaches on SARS-CoV-2 Concentrations in Wastewater: Experiences from Two Catchments in Northern Sweden. ENVIRONMENTS 2022. [DOI: 10.3390/environments9030039] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The detection of SARS-CoV-2 RNA fragments in feces has paved the way for wastewater-based epidemiology to contribute to COVID-19 mitigation measures, with its use in a public health context still under development. As a way to facilitate data comparison, this paper explores the impact of using alternative normalization approaches (wastewater treatment plant (WWTP) flow, population size estimates (derived using total nitrogen (TN), total phosphorus (TP) and census data) and pepper mild mottle virus (PMMoV)) on the relationship between viral wastewater data and clinical case numbers. Influent wastewater samples were collected at two WWTPs in Luleå, northern Sweden, between January and March 2021. TN and TP were determined upon sample collection, with RNA analysis undertaken on samples after one freeze–thaw cycle. The strength of the correlation between normalization approaches and clinical cases differed between WWTPs (r ≤ 0.73 or r ≥ 0.78 at the larger WWTP and r ≤ 0.23 or r ≥ 0.43 at the smaller WWTP), indicating that the use of wastewater as an epidemiological tool is context-dependent. Depending on the normalization approach utilized, time-shifted analyses imply that wastewater data on SARS-CoV-2 RNA pre-dated a rise in clinical cases by 0–2 and 5–8 days, for the lager and smaller WWTPs, respectively. SARS-CoV-2 viral loads normalized to the population or PMMoV better reflect the number of clinical cases when comparing wastewater data between sewer catchments.
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16
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Peng J, Yin Y, Liang H, Lu Y, Zheng H, Wu G, Rao S, Chen J, Yan F, Hu J. Tumor Microenvironment Responsive Pepper Mild Mottle Virus-Based Nanotubes for Targeted Delivery and Controlled Release of Paclitaxel. Front Bioeng Biotechnol 2021; 9:763661. [PMID: 34660562 PMCID: PMC8514841 DOI: 10.3389/fbioe.2021.763661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
Plant virus nanoparticles (PVNPs) have been widely used for drug delivery, antibody development and medical imaging because of their good biodegradation and biocompatibility. Particles of pepper mild mottle virus (PMMoV) are elongated and may be useful as drug carriers because their shape favours long circulation, preferential distribution and increased cellular uptake. Moreover, its effective degradation in an acidic microenvironment enables a pH-responsive release of the encapsulated drug. In this study, genetic engineering techniques were used to form rod-shaped structures of nanoparticles (PMMoV) and folated-modified PMMoV nanotubes were prepared by polyethylene glycol (PEG) to provide targeted delivery of paclitaxel (PTX). FA@PMMoV@PTX nanotubes were designed to selectively target tumor cells and to release the encapsulated PTX in response to pH. Efficient cell uptake of FA@PMMoV@PTX nanotubes was observed when incubated with tumor cells, and FA@PMMoV@PTX nanotubes had superior cytotoxicity to free PTX, as reflected by cell survival and apoptosis. This system is a strong candidate for use in developing improved strategies for targeted treatment of tumors.
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Affiliation(s)
- Jiejun Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Yueyan Yin
- College of Plant Protection, Yunnan Agricultural University, Kunming, China.,Institute of Alpine Economic Plants, Yunnan Academy of Agricultural Sciences, Lijiang, China
| | - Hongze Liang
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, China
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Guanwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Shaofei Rao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jingbo Hu
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, China
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17
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Zero-Valent Iron Filtration Reduces Microbial Contaminants in Irrigation Water and Transfer to Raw Agricultural Commodities. Microorganisms 2021; 9:microorganisms9102009. [PMID: 34683330 PMCID: PMC8541138 DOI: 10.3390/microorganisms9102009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
Groundwater depletion is a critical agricultural irrigation issue, which can be mitigated by supplementation with water of higher microbiological risk, including surface and reclaimed waters, to support irrigation needs in the United States. Zero-valent iron (ZVI) filtration may be an affordable and effective treatment for reducing pathogen contamination during crop irrigation. This study was performed to determine the effects of ZVI filtration on the removal and persistence of Escherichia coli, and pepper mild mottle virus (PMMoV) in irrigation water. Water was inoculated with E. coli TVS 353, filtered through a ZVI filtration unit, and used to irrigate cucurbit and cruciferous crops. Water (n = 168), leaf (n = 40), and soil (n = 24) samples were collected, the E. coli were enumerated, and die-off intervals were calculated for bacteria in irrigation water. Variable reduction of PMMoV was observed, however E. coli levels were consistently and significantly (p < 0.05) reduced in the filtered (9.59 lnMPN/mL), compared to unfiltered (13.13 lnMPN/mL) water. The die-off intervals of the remaining bacteria were significantly shorter in the filtered (−1.50 lnMPN/day), as compared to the unfiltered (−0.48 lnMPN/day) water. E. coli transfer to crop leaves and soils was significantly reduced (p < 0.05), as expected. The reduction of E. coli in irrigation water and its transfer to crops, by ZVI filtration is indicative of its potential to reduce pathogens in produce pre-harvest environments.
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Greenwald HD, Kennedy LC, Hinkle A, Whitney ON, Fan VB, Crits-Christoph A, Harris-Lovett S, Flamholz AI, Al-Shayeb B, Liao LD, Beyers M, Brown D, Chakrabarti AR, Dow J, Frost D, Koekemoer M, Lynch C, Sarkar P, White E, Kantor R, Nelson KL. Tools for interpretation of wastewater SARS-CoV-2 temporal and spatial trends demonstrated with data collected in the San Francisco Bay Area. WATER RESEARCH X 2021; 12:100111. [PMID: 34373850 DOI: 10.1101/2021.05.04.21256418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/30/2021] [Accepted: 07/25/2021] [Indexed: 05/26/2023]
Abstract
Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can be integrated with COVID-19 case data to inform timely pandemic response. However, more research is needed to apply and develop systematic methods to interpret the true SARS-CoV-2 signal from noise introduced in wastewater samples (e.g., from sewer conditions, sampling and extraction methods, etc.). In this study, raw wastewater was collected weekly from five sewersheds and one residential facility. The concentrations of SARS-CoV-2 in wastewater samples were compared to geocoded COVID-19 clinical testing data. SARS-CoV-2 was reliably detected (95% positivity) in frozen wastewater samples when reported daily new COVID-19 cases were 2.4 or more per 100,000 people. To adjust for variation in sample fecal content, four normalization biomarkers were evaluated: crAssphage, pepper mild mottle virus, Bacteroides ribosomal RNA (rRNA), and human 18S rRNA. Of these, crAssphage displayed the least spatial and temporal variability. Both unnormalized SARS-CoV-2 RNA signal and signal normalized to crAssphage had positive and significant correlation with clinical testing data (Kendall's Tau-b (τ)=0.43 and 0.38, respectively), but no normalization biomarker strengthened the correlation with clinical testing data. Locational dependencies and the date associated with testing data impacted the lead time of wastewater for clinical trends, and no lead time was observed when the sample collection date (versus the result date) was used for both wastewater and clinical testing data. This study supports that trends in wastewater surveillance data reflect trends in COVID-19 disease occurrence and presents tools that could be applied to make wastewater signal more interpretable and comparable across studies.
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Affiliation(s)
- Hannah D Greenwald
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Berkeley Water Center, University of California, Berkeley, CA, USA
| | - Lauren C Kennedy
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Berkeley Water Center, University of California, Berkeley, CA, USA
| | - Adrian Hinkle
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Berkeley Water Center, University of California, Berkeley, CA, USA
| | - Oscar N Whitney
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Vinson B Fan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | | | - Avi I Flamholz
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Lauren D Liao
- School of Public Health, University of California, Berkeley, CA, USA
| | - Matt Beyers
- Alameda County Public Health Department, San Leandro, CA, USA
| | | | | | - Jason Dow
- Central Marin Sanitation Agency, San Rafael, CA, USA
| | - Dan Frost
- Central Contra Costa Sanitary District, Martinez, CA, USA
| | | | - Chris Lynch
- Contra Costa Health Services, Martinez, CA, USA
| | - Payal Sarkar
- San José-Santa Clara Regional Wastewater Facility, San José, CA, USA
| | - Eileen White
- East Bay Municipal Utility District, Oakland, CA, USA
| | - Rose Kantor
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Berkeley Water Center, University of California, Berkeley, CA, USA
| | - Kara L Nelson
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Berkeley Water Center, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
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19
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Sala-Comorera L, Reynolds LJ, Martin NA, O'Sullivan JJ, Meijer WG, Fletcher NF. Decay of infectious SARS-CoV-2 and surrogates in aquatic environments. WATER RESEARCH 2021; 201:117090. [PMID: 34111729 PMCID: PMC8005746 DOI: 10.1016/j.watres.2021.117090] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 05/03/2023]
Abstract
The introduction of SARS-CoV-2 containing human stool and sewage into water bodies may raise public health concerns. However, assessment of public health risks by faecally contaminated water is limited by a lack of knowledge regarding the persistence of infectious SARS-CoV-2 in water. In the present study the decay rates of viable infectious SARS-CoV-2 and SARS-CoV-2 RNA were determined in river and seawater at 4 and 20°C. These decay rates were compared to S. typhimurium bacteriophage MS2 and pepper mild mottle virus (PMMoV). Persistence of viable SARS-CoV-2 was temperature dependent, remaining infectious for significantly longer periods of time in both freshwater and seawater at 4°C than at 20°C. T90 for infectious SARS-CoV-2 in river water was 2.3 days and 3.8 days at 20°C and 4°C, respectively. The T90 values were 1.1 days and 2.2 days in seawater at 20°C and 4°C, respectively. In contrast to the rapid inactivation of infectious SARS-CoV-2 in river and sea water, viral RNA was relatively stable. The RNA decay rates were increased in non-sterilised river and seawater, presumably due to the presence of microbiota. The decay rates of infectious MS2, MS2 RNA and PMMoV RNA differed significantly from the decay rate of SARS-CoV-2 RNA, suggesting that their use as surrogate markers for the persistence of SARS-CoV-2 in the environment is limited.
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Affiliation(s)
- Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Liam J Reynolds
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Niamh A Martin
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - John J O'Sullivan
- UCD School of Civil Engineering, UCD Dooge Centre for Water Resources Research and UCD Earth Institute, University College Dublin, Dublin 4, Ireland
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
| | - Nicola F Fletcher
- UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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20
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Greenwald HD, Kennedy LC, Hinkle A, Whitney ON, Fan VB, Crits-Christoph A, Harris-Lovett S, Flamholz AI, Al-Shayeb B, Liao LD, Beyers M, Brown D, Chakrabarti AR, Dow J, Frost D, Koekemoer M, Lynch C, Sarkar P, White E, Kantor R, Nelson KL. Tools for interpretation of wastewater SARS-CoV-2 temporal and spatial trends demonstrated with data collected in the San Francisco Bay Area. WATER RESEARCH X 2021; 12:100111. [PMID: 34373850 PMCID: PMC8325558 DOI: 10.1016/j.wroa.2021.100111] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/30/2021] [Accepted: 07/25/2021] [Indexed: 05/18/2023]
Abstract
Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can be integrated with COVID-19 case data to inform timely pandemic response. However, more research is needed to apply and develop systematic methods to interpret the true SARS-CoV-2 signal from noise introduced in wastewater samples (e.g., from sewer conditions, sampling and extraction methods, etc.). In this study, raw wastewater was collected weekly from five sewersheds and one residential facility. The concentrations of SARS-CoV-2 in wastewater samples were compared to geocoded COVID-19 clinical testing data. SARS-CoV-2 was reliably detected (95% positivity) in frozen wastewater samples when reported daily new COVID-19 cases were 2.4 or more per 100,000 people. To adjust for variation in sample fecal content, four normalization biomarkers were evaluated: crAssphage, pepper mild mottle virus, Bacteroides ribosomal RNA (rRNA), and human 18S rRNA. Of these, crAssphage displayed the least spatial and temporal variability. Both unnormalized SARS-CoV-2 RNA signal and signal normalized to crAssphage had positive and significant correlation with clinical testing data (Kendall's Tau-b (τ)=0.43 and 0.38, respectively), but no normalization biomarker strengthened the correlation with clinical testing data. Locational dependencies and the date associated with testing data impacted the lead time of wastewater for clinical trends, and no lead time was observed when the sample collection date (versus the result date) was used for both wastewater and clinical testing data. This study supports that trends in wastewater surveillance data reflect trends in COVID-19 disease occurrence and presents tools that could be applied to make wastewater signal more interpretable and comparable across studies.
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Affiliation(s)
- Hannah D. Greenwald
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Berkeley Water Center, University of California, Berkeley, CA, USA
| | - Lauren C. Kennedy
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Berkeley Water Center, University of California, Berkeley, CA, USA
| | - Adrian Hinkle
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Berkeley Water Center, University of California, Berkeley, CA, USA
| | - Oscar N. Whitney
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Vinson B. Fan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | | | - Avi I. Flamholz
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Lauren D. Liao
- School of Public Health, University of California, Berkeley, CA, USA
| | - Matt Beyers
- Alameda County Public Health Department, San Leandro, CA, USA
| | | | | | - Jason Dow
- Central Marin Sanitation Agency, San Rafael, CA, USA
| | - Dan Frost
- Central Contra Costa Sanitary District, Martinez, CA, USA
| | | | - Chris Lynch
- Contra Costa Health Services, Martinez, CA, USA
| | - Payal Sarkar
- San José-Santa Clara Regional Wastewater Facility, San José, CA, USA
| | - Eileen White
- East Bay Municipal Utility District, Oakland, CA, USA
| | - Rose Kantor
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Berkeley Water Center, University of California, Berkeley, CA, USA
| | - Kara L. Nelson
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Berkeley Water Center, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
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21
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Leifels M, Cheng D, Sozzi E, Shoults DC, Wuertz S, Mongkolsuk S, Sirikanchana K. Capsid integrity quantitative PCR to determine virus infectivity in environmental and food applications - A systematic review. WATER RESEARCH X 2021; 11:100080. [PMID: 33490943 DOI: 10.1101/2020.05.08.20095364] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 11/08/2020] [Accepted: 12/06/2020] [Indexed: 05/19/2023]
Abstract
Capsid integrity quantitative PCR (qPCR), a molecular detection method for infectious viruses combining azo dye pretreatment with qPCR, has been widely used in recent years; however, variations in pretreatment conditions for various virus types can limit the efficacy of specific protocols. By identifying and critically synthesizing forty-one recent peer-reviewed studies employing capsid integrity qPCR for viruses in the last decade (2009-2019) in the fields of food safety and environmental virology, we aimed to establish recommendations for the detection of infectious viruses. Intercalating dyes are effective measures of viability in PCR assays provided the viral capsid is damaged; viruses that have been inactivated by other causes, such as loss of attachment or genomic damage, are less well detected using this approach. Although optimizing specific protocols for each virus is recommended, we identify a framework for general assay conditions. These include concentrations of ethidium monoazide, propidium monoazide or its derivates between 10 and 200 μM; incubation on ice or at room temperature (20 - 25 °C) for 5-120 min; and dye activation using LED or high light (500-800 Watts) exposure for periods ranging from 5 to 20 min. These simple steps can benefit the investigation of infectious virus transmission in routine (water) monitoring settings and during viral outbreaks such as the current COVID-19 pandemic or endemic diseases like dengue fever.
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Affiliation(s)
- Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Dan Cheng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Emanuele Sozzi
- Gilling's School of Global Public Health, Department of Environmental Science and Engineering, University of North Carolina at Chapel Hill, NC, USA
| | - David C Shoults
- Civil and Resource Engineering, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- School of Civil and Environmental Engineering, NTU, Singapore
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand
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22
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Leifels M, Cheng D, Sozzi E, Shoults DC, Wuertz S, Mongkolsuk S, Sirikanchana K. Capsid integrity quantitative PCR to determine virus infectivity in environmental and food applications - A systematic review. WATER RESEARCH X 2021; 11:100080. [PMID: 33490943 PMCID: PMC7811166 DOI: 10.1016/j.wroa.2020.100080] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 11/08/2020] [Accepted: 12/06/2020] [Indexed: 05/19/2023]
Abstract
Capsid integrity quantitative PCR (qPCR), a molecular detection method for infectious viruses combining azo dye pretreatment with qPCR, has been widely used in recent years; however, variations in pretreatment conditions for various virus types can limit the efficacy of specific protocols. By identifying and critically synthesizing forty-one recent peer-reviewed studies employing capsid integrity qPCR for viruses in the last decade (2009-2019) in the fields of food safety and environmental virology, we aimed to establish recommendations for the detection of infectious viruses. Intercalating dyes are effective measures of viability in PCR assays provided the viral capsid is damaged; viruses that have been inactivated by other causes, such as loss of attachment or genomic damage, are less well detected using this approach. Although optimizing specific protocols for each virus is recommended, we identify a framework for general assay conditions. These include concentrations of ethidium monoazide, propidium monoazide or its derivates between 10 and 200 μM; incubation on ice or at room temperature (20 - 25 °C) for 5-120 min; and dye activation using LED or high light (500-800 Watts) exposure for periods ranging from 5 to 20 min. These simple steps can benefit the investigation of infectious virus transmission in routine (water) monitoring settings and during viral outbreaks such as the current COVID-19 pandemic or endemic diseases like dengue fever.
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Affiliation(s)
- Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Dan Cheng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Emanuele Sozzi
- Gilling's School of Global Public Health, Department of Environmental Science and Engineering, University of North Carolina at Chapel Hill, NC, USA
| | - David C. Shoults
- Civil and Resource Engineering, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- School of Civil and Environmental Engineering, NTU, Singapore
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology, CHE, Ministry of Education, Bangkok, Thailand
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23
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Whitney O, Kennedy LC, Fan VB, Hinkle A, Kantor R, Greenwald H, Crits-Christoph A, Al-Shayeb B, Chaplin M, Maurer AC, Tjian R, Nelson KL. Sewage, Salt, Silica, and SARS-CoV-2 (4S): An Economical Kit-Free Method for Direct Capture of SARS-CoV-2 RNA from Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:4880-4888. [PMID: 33759506 PMCID: PMC8009096 DOI: 10.1021/acs.est.0c08129] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/01/2021] [Accepted: 03/11/2021] [Indexed: 05/19/2023]
Abstract
Wastewater-based epidemiology is an emerging tool to monitor COVID-19 infection levels by measuring the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. There remains a need to improve wastewater RNA extraction methods' sensitivity, speed, and reduce reliance on often expensive commercial reagents to make wastewater-based epidemiology more accessible. We present a kit-free wastewater RNA extraction method, titled "Sewage, Salt, Silica and SARS-CoV-2" (4S), that employs the abundant and affordable reagents sodium chloride (NaCl), ethanol, and silica RNA capture matrices to recover sixfold more SARS-CoV-2 RNA from wastewater than an existing ultrafiltration-based method. The 4S method concurrently recovered pepper mild mottle virus (PMMoV) and human 18S ribosomal subunit rRNA, which have been proposed as fecal concentration controls. The SARS-CoV-2 RNA concentrations measured in three sewersheds corresponded to the relative prevalence of COVID-19 infection determined via clinical testing. Lastly, controlled experiments indicate that the 4S method prevented RNA degradation during storage of wastewater samples, was compatible with heat pasteurization, and in our experience, 20 samples can be processed by one lab technician in approximately 2 h. Overall, the 4S method is promising for effective, economical, and accessible wastewater-based epidemiology for SARS-CoV-2, providing another tool to fight the global pandemic.
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Affiliation(s)
- Oscar
N. Whitney
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720-1710, United States
| | - Lauren C. Kennedy
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Vinson B. Fan
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720-1710, United States
| | - Adrian Hinkle
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Rose Kantor
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Hannah Greenwald
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Alexander Crits-Christoph
- Department
of Plant and Microbial Biology, University
of California, Berkeley, California 94720-1710, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - Basem Al-Shayeb
- Department
of Plant and Microbial Biology, University
of California, Berkeley, California 94720-1710, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - Mira Chaplin
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Anna C. Maurer
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720-1710, United States
| | - Robert Tjian
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720-1710, United States
- The
Howard Hughes Medical Institute, University
of California Berkeley, Berkeley, California 94720, United States
| | - Kara L. Nelson
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
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24
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Whitney ON, Kennedy LC, Fan VB, Hinkle A, Kantor R, Greenwald H, Crits-Christoph A, Al-Shayeb B, Chaplin M, Maurer AC, Tjian R, Nelson KL. Sewage, Salt, Silica, and SARS-CoV-2 (4S): An Economical Kit-Free Method for Direct Capture of SARS-CoV-2 RNA from Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021. [PMID: 33759506 DOI: 10.17504/protocols.io.biwfkfbn] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Wastewater-based epidemiology is an emerging tool to monitor COVID-19 infection levels by measuring the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. There remains a need to improve wastewater RNA extraction methods' sensitivity, speed, and reduce reliance on often expensive commercial reagents to make wastewater-based epidemiology more accessible. We present a kit-free wastewater RNA extraction method, titled "Sewage, Salt, Silica and SARS-CoV-2" (4S), that employs the abundant and affordable reagents sodium chloride (NaCl), ethanol, and silica RNA capture matrices to recover sixfold more SARS-CoV-2 RNA from wastewater than an existing ultrafiltration-based method. The 4S method concurrently recovered pepper mild mottle virus (PMMoV) and human 18S ribosomal subunit rRNA, which have been proposed as fecal concentration controls. The SARS-CoV-2 RNA concentrations measured in three sewersheds corresponded to the relative prevalence of COVID-19 infection determined via clinical testing. Lastly, controlled experiments indicate that the 4S method prevented RNA degradation during storage of wastewater samples, was compatible with heat pasteurization, and in our experience, 20 samples can be processed by one lab technician in approximately 2 h. Overall, the 4S method is promising for effective, economical, and accessible wastewater-based epidemiology for SARS-CoV-2, providing another tool to fight the global pandemic.
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Affiliation(s)
- Oscar N Whitney
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
| | - Lauren C Kennedy
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Vinson B Fan
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
| | - Adrian Hinkle
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Rose Kantor
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Hannah Greenwald
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-1710, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
| | - Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-1710, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
| | - Mira Chaplin
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Anna C Maurer
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
- The Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, United States
| | - Kara L Nelson
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
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25
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Whitney ON, Kennedy LC, Fan VB, Hinkle A, Kantor R, Greenwald H, Crits-Christoph A, Al-Shayeb B, Chaplin M, Maurer AC, Tjian R, Nelson KL. Sewage, Salt, Silica, and SARS-CoV-2 (4S): An Economical Kit-Free Method for Direct Capture of SARS-CoV-2 RNA from Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021. [PMID: 33759506 DOI: 10.17504/protocols.io.biwekfbe] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Wastewater-based epidemiology is an emerging tool to monitor COVID-19 infection levels by measuring the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. There remains a need to improve wastewater RNA extraction methods' sensitivity, speed, and reduce reliance on often expensive commercial reagents to make wastewater-based epidemiology more accessible. We present a kit-free wastewater RNA extraction method, titled "Sewage, Salt, Silica and SARS-CoV-2" (4S), that employs the abundant and affordable reagents sodium chloride (NaCl), ethanol, and silica RNA capture matrices to recover sixfold more SARS-CoV-2 RNA from wastewater than an existing ultrafiltration-based method. The 4S method concurrently recovered pepper mild mottle virus (PMMoV) and human 18S ribosomal subunit rRNA, which have been proposed as fecal concentration controls. The SARS-CoV-2 RNA concentrations measured in three sewersheds corresponded to the relative prevalence of COVID-19 infection determined via clinical testing. Lastly, controlled experiments indicate that the 4S method prevented RNA degradation during storage of wastewater samples, was compatible with heat pasteurization, and in our experience, 20 samples can be processed by one lab technician in approximately 2 h. Overall, the 4S method is promising for effective, economical, and accessible wastewater-based epidemiology for SARS-CoV-2, providing another tool to fight the global pandemic.
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Affiliation(s)
- Oscar N Whitney
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
| | - Lauren C Kennedy
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Vinson B Fan
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
| | - Adrian Hinkle
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Rose Kantor
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Hannah Greenwald
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-1710, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
| | - Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-1710, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
| | - Mira Chaplin
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Anna C Maurer
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
- The Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, United States
| | - Kara L Nelson
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
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26
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Koonin EV, Dolja VV, Krupovic M. The healthy human virome: from virus-host symbiosis to disease. Curr Opin Virol 2021; 47:86-94. [PMID: 33652230 DOI: 10.1016/j.coviro.2021.02.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 02/07/2023]
Abstract
Viruses are ubiquitous, essential components of any ecosystem, and of multicellular organism holobionts. Numerous viruses cause acute infection, killing the host or being cleared by immune system. In many other cases, viruses coexist with the host as symbionts, either temporarily or for the duration of the host's life. Apparently, virus-host relationships span the entire range from aggressive parasitism to mutualism. Here we attempt to delineate the healthy human virome, that is, the entirety of viruses that are present in a healthy human body. The bulk of the healthy virome consists of bacteriophages infecting bacteria in the intestine and other locations. However, a variety of viruses, such as anelloviruses and herpesviruses, and the numerous endogenous retroviruses, persist by replicating in human cells, and these are our primary focus. Crucially, the boundary between symbiotic and pathogenic viruses is fluid such that members of the healthy virome can become pathogens under changing conditions.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
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27
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Filipić A, Dobnik D, Tušek Žnidarič M, Žegura B, Štern A, Primc G, Mozetič M, Ravnikar M, Žel J, Gutierrez Aguirre I. Inactivation of Pepper Mild Mottle Virus in Water by Cold Atmospheric Plasma. Front Microbiol 2021; 12:618209. [PMID: 33584622 PMCID: PMC7877120 DOI: 10.3389/fmicb.2021.618209] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/04/2021] [Indexed: 11/18/2022] Open
Abstract
Water scarcity is one of the greatest threats for human survival and quality of life, and this is increasingly contributing to the risk of human, animal and plant infections due to waterborne viruses. Viruses are transmitted through polluted water, where they can survive and cause infections even at low concentrations. Plant viruses from the genus Tobamovirus are highly mechanically transmissible, and cause considerable damage to important crops, such as tomato. The release of infective tobamoviruses into environmental waters has been reported, with the consequent risk for arid regions, where these waters are used for irrigation. Virus inactivation in water is thus very important and cold atmospheric plasma (CAP) is emerging in this field as an efficient, safe, and sustainable alternative to classic waterborne virus inactivation methods. In the present study we evaluated CAP-mediated inactivation of pepper mild mottle virus (PMMoV) in water samples. PMMoV is a very resilient water-transmissible tobamovirus that can survive transit through the human digestive tract. The efficiency of PMMoV inactivation was characterized for infectivity and virion integrity, and at the genome level, using test plant infectivity assays, transmission electron microscopy, and molecular methods, respectively. Additionally, the safety of CAP treatment was determined by testing the cytotoxic and genotoxic properties of CAP-treated water on the HepG2 cell line. 5-min treatment with CAP was sufficient to inactivate PMMoV without introducing any cytotoxic or genotoxic effects in the in-vitro cell model system. These data on inactivation of such stable waterborne virus, PMMoV, will encourage further examination of CAP as an alternative for treatment of potable and irrigation waters, and even for other water sources, with emphasis on inactivation of various viruses including enteric viruses.
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Affiliation(s)
- Arijana Filipić
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Bojana Žegura
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Alja Štern
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Gregor Primc
- Department of Surface Engineering, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Miran Mozetič
- Department of Surface Engineering, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,University of Nova Gorica, Nova Gorica, Slovenia
| | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Ion Gutierrez Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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28
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Yang W, Zhao J, Huang D, Guan H, Wang Z, Lan Q, Zhang L, Yu J, Zhang S, Wang L. Immobilization of ZnO into polychlorotrifluoroethylene-co-acrylate matrix as hybrid film photocatalyst for effective degradation of methylene blue. J PHOTOPOLYM SCI TEC 2021. [DOI: 10.2494/photopolymer.34.597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Weiguang Yang
- The Marine Biomedical Research Institute, Guangdong Medical University
| | - Jin Zhao
- Department of Chemistry, Lishui University
| | | | | | | | | | - Ling Zhang
- Department of Chemistry, Lishui University
| | - Jian Yu
- Department of Chemistry, Lishui University
| | | | - Lingnan Wang
- Wenzhou Institute, University of Chinese Academy of Sciences
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29
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Ko S, Kim NK, Lee HJ, Ryu TH, Hong JS, Jeong RD. Detection of Plant Pathogenic Viruses in Commercial Gochujang (Fermented Red Pepper Paste) from Korea. THE PLANT PATHOLOGY JOURNAL 2020; 36:503-508. [PMID: 33082735 PMCID: PMC7542032 DOI: 10.5423/ppj.nt.06.2020.0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 01/01/2020] [Accepted: 01/01/2020] [Indexed: 06/11/2023]
Abstract
The potential transmission of plant pathogenic viruses through processed foods could be a source of concern for global crop production; however, there is a lack of supporting evidence. The present study was conducted to investigate the presence of plant pathogenic viruses in five samples of gochujang (fermented red pepper paste) manufactured in Korea. Several viruses infecting pepper were detected by reverse transcriptionpolymerase chain reaction, among which the pepper mild mottle virus (PMMoV) was detected in all five samples, at concentrations ranging from 2.8 to 7.0 (log10 copies/ml). In addition, PMMoV was observed by transmission electron microscopy in all five samples. The samples exhibited viral pathogenicity to Nicotiana benthamiana plants, indicating that global trade of processed products could be a possible source of the transmission of plant viruses.
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Affiliation(s)
- Seoyeon Ko
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 685, Korea
| | - Na-Kyeong Kim
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 685, Korea
| | - Hyo-Jeong Lee
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 685, Korea
| | - Tae-Ho Ryu
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 685, Korea
| | - Jin-Sung Hong
- Department of Applied Biology, College of Agriculture and Life Science, Kangwon National University, Chuncheon 4341, Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 685, Korea
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30
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Tandukar S, Sherchan SP, Haramoto E. Reduction of Pathogenic and Indicator Viruses at a Drinking Water Treatment Plant in Southern Louisiana, USA. FOOD AND ENVIRONMENTAL VIROLOGY 2020; 12:269-273. [PMID: 32666473 DOI: 10.1007/s12560-020-09436-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
Monthly sampling was conducted at a drinking water treatment plant (DWTP) in Southern Louisiana, USA from March 2017 to February 2018 to determine the prevalence and reduction efficiency of pathogenic and indicator viruses. Water samples were collected from the DWTP at three different treatment stages (raw, secondary-treated, and chlorinated drinking water) and subjected to quantification of seven pathogenic viruses and three indicator viruses [pepper mild mottle virus (PMMoV), tobacco mosaic virus (TMV), and crAssphage] based on quantitative polymerase chain reaction. Among the seven pathogenic viruses tested, only Aichi virus 1 (AiV-1) (7/12, 58%) and noroviruses of genogroup II (NoVs-GII) (2/12, 17%) were detected in the raw water samples. CrAssphage had the highest positive ratio at 78% (28/36), and its concentrations were significantly higher than those of the other indicator viruses for all three water types (P < 0.05). The reduction ratios of AiV-1 (0.7 ± 0.5 log10; n = 7) during the whole treatment process were the lowest among the tested viruses, followed by crAssphage (1.1 ± 1.9 log10; n = 9), TMV (1.3 ± 0.9 log10; n = 8), PMMoV (1.7 ± 0.8 log10; n = 12), and NoVs-GII (3.1 ± 0.1 log10; n = 2). Considering the high abundance and relatively low reduction, crAssphage was judged to be an appropriate process indicator during drinking water treatment. To the best of our knowledge, this is the first study to assess the reduction of crAssphage and TMV during drinking water treatment.
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Affiliation(s)
- Sarmila Tandukar
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi, 400-8511, Japan
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA, 70112, USA
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi, 400-8511, Japan.
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31
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Bačnik K, Kutnjak D, Pecman A, Mehle N, Tušek Žnidarič M, Gutiérrez Aguirre I, Ravnikar M. Viromics and infectivity analysis reveal the release of infective plant viruses from wastewater into the environment. WATER RESEARCH 2020; 177:115628. [PMID: 32299020 DOI: 10.1016/j.watres.2020.115628] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 05/06/2023]
Abstract
Viruses represent one of the most important threats to agriculture. Several viral families include highly stable pathogens, which remain infective and can be transported long distances in water. The diversity of plant viruses in wastewater remains understudied; however, their potential impact is increasing with the increased irrigation usage of reclaimed wastewater. To determine the abundance, diversity and biological relevance of plant viruses in wastewater influents and effluents we applied an optimized virus concentration method followed by high-throughput sequencing and infectivity assays. We detected representatives of 47 plant virus species, including emerging crop threats. We also demonstrated infectivity for pathogenic and economically relevant plant viruses from the genus Tobamovirus (family Virgaviridae), which remain infective even after conventional wastewater treatment. These results demonstrate the potential of metagenomics to capture the diversity of plant viruses circulating in the environment and expose the potential risk of the uncontrolled use of reclaimed water for irrigation.
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Affiliation(s)
- Katarina Bačnik
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Denis Kutnjak
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Anja Pecman
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Nataša Mehle
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Ion Gutiérrez Aguirre
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia; University of Nova Gorica, Vipavska cesta, 5000, Nova Gorica, Slovenia.
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32
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Ahmed W, Payyappat S, Cassidy M, Harrison N, Besley C. Sewage-associated marker genes illustrate the impact of wet weather overflows and dry weather leakage in urban estuarine waters of Sydney, Australia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 705:135390. [PMID: 31838427 DOI: 10.1016/j.scitotenv.2019.135390] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/03/2019] [Accepted: 11/04/2019] [Indexed: 05/18/2023]
Abstract
This study investigates the impact of wet weather overflows (WWOs) at three estuarine locations in Sydney, NSW, Australia. WWOs can occur when infiltration of stormwater leads to an excess volume of flow within the sewerage system, resulting in the release of diluted sewage into the environment. Sewage contamination poses a risk to human health due to the presence of pathogens. The magnitude of sewage contamination was monitored using established and novel sewage-associated marker genes, Bacteroides HF183, pepper mild mottle virus (PMMoV), crAssphage CPQ_056, Lachnospiraceae (Lachno3) marker genes along with culturable fecal indicator bacteria (FIB) Escherichia coli (E. coli) and enterococci. Water samples were collected at two water depths (0.5 m below the water surface and 1 m above the bottom surface) during one dry weather and two storm events. Analysis of sewage-associated marker genes showed greater (i.e., 3-5 orders of magnitude) concentrations in water samples collected during the storm events compared to dry weather event. Water samples were also analysed for four animal feces-associated marker genes targeting avian (GFD), dog (BacCan-UCD), cow (cowM2) and horse (HoF597) species to determine the extent of animal fecal contamination. Among the four marker genes, cowM2 and HoF597 could not be detected, while GFD marker gene was consistently present and BacCan-UCD was occasionally detected. Overall results suggested that after rainfall, untreated sewage from WWOs was present at sampling locations. In addition, microbial source tracking (MST) monitoring was able to distinguish the presence of a leaking sewer impacting on the recreational area during dry weather condition. This study demonstrated the capability of the MST monitoring approach to understand sources (sewage or animal) of fecal contamination. This capability will greatly enhance management decisions assisting in the prioritisation of remediation efforts of the sewerage system to improve estuarine bathing water quality and diminish human health risk.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Michele Cassidy
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Nathan Harrison
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Colin Besley
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
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33
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Ahmed W, Payyappat S, Cassidy M, Besley C. Enhanced insights from human and animal host-associated molecular marker genes in a freshwater lake receiving wet weather overflows. Sci Rep 2019; 9:12503. [PMID: 31467317 PMCID: PMC6715810 DOI: 10.1038/s41598-019-48682-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023] Open
Abstract
This study investigated the magnitude of wet weather overflow (WWO)-driven sewage pollution in an urban lake (Lake Parramatta) located in Sydney, New South Wales, Australia. Water samples were collected during a dry weather period and after two storm events, and tested for a range of novel and established sewage- [Bacteroides HF183, crAssphage CPQ_056 and pepper mild mottle virus (PMMoV)] and animal feces-associated (Bacteroides BacCan-UCD, cowM2 and Helicobacter spp. associated GFD) microbial source tracking marker genes along with the enumeration of culturable fecal indicator bacteria (FIB), namely Escherichia coli (E. coli) and Enterococcus spp. The magnitude of general and source-specific fecal pollution was low in water samples collected during dry weather compared to storm events. The levels of HF183, crAssphage and PMMoV in water samples collected during storm events were as high as 6.39, 6.33 and 5.27 log10 GC/L of water, respectively. Moderate to strong positive correlations were observed among the quantitative occurrence of sewage-associated marker genes. The concentrations of HF183 and PMMoV in most storm water samples exceeded the risk benchmark threshold values established in the literature for primary contact recreators. None of the samples tested was positive for the cowM2 (cow) marker gene, while BacCan-UCD (dog) and GFD (avian) animal-associated markers were sporadically detected in water samples collected from both dry weather and storm events. Based on the results, the ongoing advice that swimming should be avoided for several days after storm events appears appropriate. Further research to determine the decay rates of sewage-associated marker genes in relation to each other and enteric viruses would help refine current advice. Microbial source tracking approaches employed in this study provided insights into sources of contamination over currently used FIB.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD, 4102, Australia.
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW, 2150, Australia
| | - Michele Cassidy
- Sydney Water, 1 Smith Street, Parramatta, NSW, 2150, Australia
| | - Colin Besley
- Sydney Water, 1 Smith Street, Parramatta, NSW, 2150, Australia
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