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Yang S, Jiao Y, Dong Q, Li S, Xu C, Liu Y, Sun L, Huang X. Evaluating approach uncertainties of quantitative detection of SARS-CoV-2 in wastewater: Concentration, extraction and amplification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175285. [PMID: 39102960 DOI: 10.1016/j.scitotenv.2024.175285] [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: 01/17/2024] [Revised: 06/10/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024]
Abstract
Substantial uncertainties pose challenges to the accuracy of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) quantification in wastewater. We conducted a comprehensive evaluation of two concentration methods, three nucleic acid extraction methods, and the amplification performance of eight primer-probe sets. Our results showed that the two concentration methods exhibited similar recovery rates. Specifically, using a 30 kDa cut-off ultrafilter and a centrifugal force of 2500 g achieved the highest virus recovery rates (27.32 ± 8.06 % and 26.37 ± 7.77 %, respectively), with lower corresponding quantification uncertainties of 29.51 % and 29.47 % in ultrafiltration methods. Similarly, a 15 % PEG concentration with 1.5 M NaCl markedly improved virus recovery (26.76 ± 5.92 % and 28.47 ± 6.74 %, respectively), and reducing variation to 22.16 % and 23.66 % in the PEG precipitation method. Additionally, employing a vigorous bead-beating approach at 6 m/s during viral RNA extraction significantly increased RNA yield, with an efficiency reaching up to 82.18 %. Among the evaluated eight primer-probe sets, the E_Sarbeco primer-probe set provided the most stable and consistent quantitative results across various sample matrices. These findings are crucial for establishing robust viral quantification protocols and enhancing methodological precision for effective wastewater surveillance, enabling sensitive and precise detection of SARS-CoV-2.
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Affiliation(s)
- Shaolin Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 10084, China
| | - Yang Jiao
- Beijing Chaoyang Center for Disease Control and Prevention, Beijing 100021, China
| | - Qian Dong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 10084, China
| | - Siqi Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 10084, China
| | - Chenyang Xu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 10084, China
| | - Yanchen Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 10084, China.
| | - Lingli Sun
- Beijing Chaoyang Center for Disease Control and Prevention, Beijing 100021, China.
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 10084, China.
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2
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Farkas K, Fletcher J, Oxley J, Ridding N, Williams RC, Woodhall N, Weightman AJ, Cross G, Jones DL. Implications of long-term sample storage on the recovery of viruses from wastewater and biobanking. WATER RESEARCH 2024; 265:122209. [PMID: 39126986 DOI: 10.1016/j.watres.2024.122209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024]
Abstract
Wastewater-based monitoring has been widely implemented worldwide for the tracking of SARS-CoV-2 outbreaks and other viral diseases. In many surveillance programmes, unprocessed and processed wastewater samples are often frozen and stored for long periods of time in case the identification and tracing of an emerging health threat becomes necessary. However, extensive sample bioarchives may be difficult to maintain due to limitations in ultra-freezer capacity and associated cost. Furthermore, the stability of viruses in such samples has not been systematically investigated and hence the usefulness of bioarchives is unknown. In this study, we assessed the stability of SARS-CoV-2, influenza viruses, noroviruses and the faecal indicator virus, crAssphage, in raw wastewater and purified nucleic aacid extracts stored at -80 °C for 6-24 months. We found that the isolated viral RNA and DNA showed little signs of degradation in storage over 8-24 months, whereas extensive decay viral and loss of qPCR signal was observed during the storage of raw unprocessed wastewater. The most stable viruses were noroviruses and crAssphage, followed by SARS-CoV-2 and influenza A virus. Based on our findings, we conclude that bioarchives comprised of nucleic acid extracts derived from concentrated wastewater samples may be archived long-term, for at least two years, whereas raw wastewater samples may be discarded after one year.
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Affiliation(s)
- Kata Farkas
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
| | - Jessica Fletcher
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - James Oxley
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Nicola Ridding
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Rachel C Williams
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Nick Woodhall
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Andrew J Weightman
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Gareth Cross
- Science Evidence Advice Division, Health and Social Services Group, Welsh Government, Cathays Park, Cardiff, CF10 3NQ, UK
| | - Davey L Jones
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
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3
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Shaheen MNF, Elmahdy EM. Seasonal Prevalence and Detection of Enteric and Respiratory Viruses in Wastewater and Hospitalized Children with Acute Gastroenteritis. Curr Microbiol 2024; 81:337. [PMID: 39223408 DOI: 10.1007/s00284-024-03841-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/11/2024] [Indexed: 09/04/2024]
Abstract
Human enteric and some respiratory viruses are identified to be involved with acute gastroenteritis that can be shed in feces of infected persons into the environment. Understanding the abundance of these viruses in wastewater is significant when assessing the public health impacts associated with discharge of wastewater into the environment. This study aimed to investigate the prevalence and seasonal variation of human enteric adenovirus (HAdV), Aichi virus (AiV-1), bocavirus (HBoV), and respiratory syndrome coronavirus 2 virus (SARS-CoV-2) in wastewater as well as their prevalence among hospitalized children with acute gastroenteritis. The viruses were detected and quantified with real-time PCR. HAdV was the most detected virus in raw sewage (88.5%), treated sewage (28%), and stool gastroenteritis (74%), followed by HBoV (45.8% for raw sewage, 14.6% for treated sewage, and 55.3% for stool samples). The detection rate of AiV-1 was 59.4%, 19.8%, and 62.6% in raw sewage, treated sewage, and stool samples, respectively. The rate of SARS-CoV-2 detection in raw sewage, treated sewage, and stool samples was 33.3%, 7.3%, and 20.6%, respectively. The viral concentrations ranged between 4.50 × 101 and 8.75 × 107 GC/ml in raw sewage samples, 1.20 × 101 and 5.43 × 106 GC/ml in treated sewage samples, and 4.80 × 101 and 9.88 × 108 GC/gram in stool samples. The overall log means of virus reduction during the wastewater treatment process ranged from 1.68 log10 (HAdV) to 3.31 log10 (AiV-1). The peak prevalence of the four viruses in raw sewage samples occurred during the winter season. This study showed the high detection rates of the four targeted viruses in wastewater and demonstrated that virological surveillance of wastewater in local wastewater treatment plants is a suitable model for epidemiological monitoring of diarrheal and respiratory diseases in middle- and low-resource countries.
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Affiliation(s)
- Mohamed Nasr Fathi Shaheen
- Environmental Virology Laboratory, Department of Water Pollution Research, Environment and Climate Change Research Institute, National Research Centre, Al-Buhouth Street, Dokki, 12622, Cairo, Egypt.
| | - Elmahdy Mohamed Elmahdy
- Environmental Virology Laboratory, Department of Water Pollution Research, Environment and Climate Change Research Institute, National Research Centre, Al-Buhouth Street, Dokki, 12622, Cairo, Egypt
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4
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Oyervides-Muñoz MA, Aguayo-Acosta A, de los Cobos-Vasconcelos D, Carrillo-Reyes J, Espinosa-García AC, Campos E, Driver EM, Lucero-Saucedo SL, Armenta-Castro A, de la Rosa O, Martínez-Ruiz M, Barragán-Trinidad M, Vázquez-Salvador N, Silva-Magaña MA, Zavala-Méndez M, Iqbal HM, Mazari-Hiriart M, Velazco H, Buitrón G, Noyola A, Halden RU, Sosa-Hernández JE, Parra-Saldívar R. Inter-institutional laboratory standardization for SARS-CoV-2 surveillance through wastewater-based epidemiology applied to Mexico City. IJID REGIONS 2024; 12:100429. [PMID: 39318545 PMCID: PMC11419891 DOI: 10.1016/j.ijregi.2024.100429] [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: 03/06/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 09/26/2024]
Abstract
Objectives Wastewater-based surveillance applied to SARS-CoV-2 viral load quantification for COVID-19 has become one of the most relevant complementary tools in epidemiologic prevention programs worldwide. However, this valuable decision-making tool still requires fine-tuning to produce comparable results between laboratories, especially when applied to the surveillance of megacities. Methods Six laboratories across Mexico and one from the United States executed an interlaboratory study to set up a singular standardized protocol considering method cost, installed infrastructure, materials available, and supply availability for SARS-CoV-2 quantification from five Mexico City sampling sites across this megacity. Results Comparable data from processing outcomes in the Mexican laboratories and in the external international laboratory serve as a validating data source. The Bland-Altman comparison showed consistency, with cycle threshold values within ±1.96 SD of SARS-CoV-2 genetic copies for the standard curve quantification, with a mismatch of two laboratories. In addition, MS2 bacteriophage recovery rates varied between 35% and 67% among all participating laboratories. Finally, the efficiency of viral genetic material recovered from all participating laboratories varied between 65% and 93% for the participating laboratories. Conclusion This work lays the foundation for extensive and continuous wastewater-based surveillance application across independent Mexican laboratories in a time- and resource-effective manner.
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Affiliation(s)
- Mariel Araceli Oyervides-Muñoz
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Alberto Aguayo-Acosta
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Daniel de los Cobos-Vasconcelos
- Grupo de Investigación en Procesos Anaerobios, Coordinación de Ingeniería Ambiental, Instituto de Ingeniería, Campus CU, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Julián Carrillo-Reyes
- Laboratory for Research on Advanced Processes for Water Treatment, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Ana C. Espinosa-García
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eneida Campos
- Laboratorio de Ingeniería de Bioprocesos, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Erin M. Driver
- Biodesign Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, Tempe, USA
| | | | - Arnoldo Armenta-Castro
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
| | - Orlando de la Rosa
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Manuel Martínez-Ruiz
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Martín Barragán-Trinidad
- Laboratory for Research on Advanced Processes for Water Treatment, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Nallely Vázquez-Salvador
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Miguel A Silva-Magaña
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Marcela Zavala-Méndez
- Laboratory for Research on Advanced Processes for Water Treatment, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Hafiz M.N. Iqbal
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Marisa Mazari-Hiriart
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Hugo Velazco
- Laboratorio de Ingeniería de Bioprocesos, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - German Buitrón
- Laboratory for Research on Advanced Processes for Water Treatment, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Adalberto Noyola
- Grupo de Investigación en Procesos Anaerobios, Coordinación de Ingeniería Ambiental, Instituto de Ingeniería, Campus CU, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Rolf U. Halden
- Biodesign Center for Environmental Health Engineering, The Biodesign Institute, Arizona State University, Tempe, USA
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, USA
| | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
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Subroyen S, Pillay L, Bux F, Kumari S. Evaluating storage conditions and enhancement strategies on viral biomarker recovery for WBE applications. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2024; 90:213-224. [PMID: 39007315 DOI: 10.2166/wst.2024.203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/31/2024] [Indexed: 07/16/2024]
Abstract
Wastewater-based epidemiology (WBE) is a valuable disease surveillance tool. However, little is known on how factors such as transportation, storage, and wastewater characteristics influence the accuracy of the quantification methods. Hence, this study investigated the impact of storage temperatures and physicochemical characteristics of wastewater on SARS-CoV-2 and influenza A stability using droplet digital PCR. Additionally, strategies to enhance viral recovery were explored. Municipal influent wastewater stored between ±25 and -80 °C was assessed for a period of 84 days to determine viral degradation. Degradation up to 94.1% of influenza A and SARS-CoV-2 was observed in all samples with the highest at ±25 °C. Viral degradation was correlated to the changes in wastewater physicochemical characteristics. The low degradation observed of SARS-CoV-2 in the spiked pellets were indicative of viral adhesion to wastewater solids, which correlated with changes in pH. Ultrasonication frequencies ranging from 4 to 16 kHz, increased SARS-CoV-2 concentrations in the supernatant between 3.30 and 35.65%, indicating viral RNA attachment to wastewater solids. These results highlight the importance of additional pretreatment methods for maximizing RNA recovery from wastewater samples. Based on these findings, it was deduced that wastewater preservation studies are essential, and pretreatment should be included in the WBE methodology.
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Affiliation(s)
- Sueyanka Subroyen
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Leanne Pillay
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa E-mail:
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Goitom E, Ariano S, Gilbride K, Yang MI, Edwards EA, Peng H, Dannah N, Farahbakhsh F, Hataley E, Sarvi H, Sun J, Waseem H, Oswald C. Identification of environmental and methodological factors driving variability of Pepper Mild Mottle Virus (PMMoV) across three wastewater treatment plants in the City of Toronto. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:172917. [PMID: 38701931 DOI: 10.1016/j.scitotenv.2024.172917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
PMMoV has been widely used to normalize the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA, influenza, and respiratory syncytial virus (RSV) to account for variations in the fecal content of wastewater. PMMoV is also used as an internal RNA recovery control for wastewater-based epidemiology (WBE) tests. While potentially useful for the interpretation of WBE data, previous studies have suggested that PMMoV concentration can be affected by various physico-chemical characteristics of wastewater. There is also the possibility that laboratory methods, particularly the variability in centrifugation steps to remove supernatant from pellets can cause PMMoV variability. The goal of this study is to improve our understanding of the main drivers of PMMoV variability by assessing the relationship between PMMoV concentration, the physico-chemical characteristics of wastewater, and the methodological approach for concentrating wastewater samples. We analyzed 24-hour composite wastewater samples collected from the influent stream of three wastewater treatment plants (WWTPs) located in the City of Toronto, Ontario, Canada. Samples were collected 3 to 5 times per week starting from the beginning of March 2021 to mid-July 2023. The influent flow rate was used to partition the data into wet and dry weather conditions. Physico-chemical characteristics (e.g., total suspended solids (TSS), biological oxygen demand (BOD), alkalinity, electrical conductivity (EC), and ammonia (NH3)) of the raw wastewater were measured, and PMMoV was quantified. Spatial and temporal variability of PMMoV was observed throughout the study period. PMMoV concentration was significantly higher during dry weather conditions. Multiple linear regression analysis demonstrates that the number and type of physico-chemical parameters that drive PMMoV variability are site-specific, but overall BOD and alkalinity were the most important predictors. Differences in PMMoV concentration for a single WWTP between two different laboratory methods, along with a weak correlation between pellet mass and TSS using one method may indicate that differences in sample concentration and subjective subsampling bias could alter viral recovery and introduce variability to the data.
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Affiliation(s)
- Eyerusalem Goitom
- Department of Geography & Environmental Studies, Toronto Metropolitan University, Canada
| | - Sarah Ariano
- Department of Geography & Environmental Studies, Toronto Metropolitan University, Canada; Department of Earth and Planetary Sciences, McGill University, Canada
| | - Kim Gilbride
- Department of Chemistry & Biology, Toronto Metropolitan University, Canada
| | - Minqing Ivy Yang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Hui Peng
- Department of Chemistry, University of Toronto, Canada; School of the Environment, University of Toronto, Canada
| | - Nora Dannah
- Department of Chemistry & Biology, Toronto Metropolitan University, Canada
| | - Farnaz Farahbakhsh
- Department of Chemistry & Biology, Toronto Metropolitan University, Canada
| | - Eden Hataley
- Department of Geography & Environmental Studies, Toronto Metropolitan University, Canada
| | - Hooman Sarvi
- Department of Chemistry & Biology, Toronto Metropolitan University, Canada
| | - Jianxian Sun
- Department of Chemistry, University of Toronto, Canada
| | - Hassan Waseem
- Department of Chemistry & Biology, Toronto Metropolitan University, Canada
| | - Claire Oswald
- Department of Geography & Environmental Studies, Toronto Metropolitan University, Canada.
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Combe M, Cherif E, Deremarque T, Rivera-Ingraham G, Seck-Thiam F, Justy F, Doudou JC, Carod JF, Carage T, Procureur A, Gozlan RE. Wastewater sequencing as a powerful tool to reveal SARS-CoV-2 variant introduction and spread in French Guiana, South America. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171645. [PMID: 38479523 DOI: 10.1016/j.scitotenv.2024.171645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/19/2024] [Accepted: 03/09/2024] [Indexed: 03/17/2024]
Abstract
The origin of introduction of a new pathogen in a country, the evolutionary dynamics of an epidemic within a country, and the role of cross-border areas on pathogen dynamics remain complex to disentangle and are often poorly understood. For instance, cross-border areas represent the ideal location for the sharing of viral variants between countries, with international air travel, land travel and waterways playing an important role in the cross-border spread of infectious diseases. Unfortunately, monitoring the point of entry and the evolutionary dynamics of viruses in space and time within local populations remain challenging. Here we tested the efficiency of wastewater-based epidemiology and genotyping in monitoring Covid-19 epidemiology and SARS-CoV-2 variant dynamics in French Guiana, a tropical country located in South America. Our results suggest that wastewater-based epidemiology and genotyping are powerful tools to monitor variant introduction and disease evolution within a tropical country but the inclusion of both clinical and wastewater samples could still improve our understanding of genetic diversity co-circulating. Wastewater sequencing also revealed the cryptic transmission of SARS-CoV-2 variants within the country. Interestingly, we found some amino acid changes specific to the variants co-circulating in French Guiana, suggesting a local evolution of the SARS-CoV-2 variants after their introduction. More importantly, our results showed that the proximity to bordering countries was not the origin of the emergence of the French Guianese B.1.160.25 variant, but rather that this variant emerged from an ancestor B.1.160 variant introduced by European air plane travelers, suggesting thus that air travel remains a significant risk for cross-border spread of infectious diseases. Overall, we suggest that wastewater-based epidemiology and genotyping provides a cost effective and non-invasive approach for pathogen monitoring and an early-warning tool for disease emergence and spread within a tropical country.
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Affiliation(s)
- Marine Combe
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France.
| | - Emira Cherif
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France
| | | | - Georgina Rivera-Ingraham
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France; Centre IRD de Cayenne, Guyane Française, France
| | | | | | | | - Jean-François Carod
- Laboratoire et Pôle Appui aux Fonctions Cliniques, Centre Hospitalier de l'Ouest Guyanais (CHOG), 97320 Saint-Laurent du Maroni, Guyane Française, France
| | - Thierry Carage
- Laboratoire de Biologie Médicale Carage de Kourou, 6 avenue Leopold Heder, 97310 Kourou, Guyane Française, France
| | - Angélique Procureur
- Laboratoire de Biologie Médicale Carage de Kourou, 6 avenue Leopold Heder, 97310 Kourou, Guyane Française, France
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8
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Mullins N, Alashraf AR, McDermott K, Brown RS, Payne SJ. Polyethylenimine mediated recovery of SARS-CoV-2 and total viral RNA: Impact of aqueous conditions on behaviour and recovery. WATER RESEARCH 2024; 253:121207. [PMID: 38401469 DOI: 10.1016/j.watres.2024.121207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/28/2023] [Accepted: 01/26/2024] [Indexed: 02/26/2024]
Abstract
Wastewater-based epidemiology (WBE) is an emerging, practical surveillance tool for monitoring community levels of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, SC2). However, a paucity of data exists regarding SARS-CoV-2 and viral biomarker behaviour in aqueous and wastewater environments. Therefore, there is a pressing need to develop efficient and robust methods that both improve method sensitivity and reduce time and cost. We present a novel method for SARS-CoV-2, Human Coronavirus 229E (229E), and Pepper Mild Mottle Virus (PMMoV) recovery utilizing surface charge-based attraction via the branched cationic polymer, polyethylenimine (PEI). Initially, dose-optimization experiments demonstrated that low concentrations of PEI (0.001% w/v) proved most effective at flocculating suspended viruses and viral material, including additional unbound SC2 viral fragments and/or RNA from raw wastewater. A design-of-experiments (DOE) approach was used to optimize virus and/or viral material aggregation behaviour and recovery across varying aqueous conditions, revealing pH as a major influence on recoverability in this system, combinatorially due to both a reduction in viral material surface charge and increased protonation of PEI-bound amine groups. Overall, this method has shown great promise in significantly improving quantitative viral recovery, providing a straightforward and effective augmentation to standard centrifugation techniques.
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Affiliation(s)
- Nathan Mullins
- Queen's University, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada; McMaster University, Department of Chemical Engineering, Hamilton, Ontario, L8S 4L7, Canada
| | - Abdul Rahman Alashraf
- Queen's University, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada; Queen's University, Beaty Water Research Centre, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada
| | | | - R Stephen Brown
- Queen's University, Department of Chemistry and School of Environmental Studies, Kingston, Ontario, K7L 3N6, Canada; Queen's University, Beaty Water Research Centre, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada.
| | - Sarah Jane Payne
- Queen's University, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada; Queen's University, Beaty Water Research Centre, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada.
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9
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Li Y, Ash K, Alamilla I, Joyner D, Williams DE, McKay PJ, Green B, DeBlander S, North C, Kara-Murdoch F, Swift C, Hazen TC. COVID-19 trends at the University of Tennessee: predictive insights from raw sewage SARS-CoV-2 detection and evaluation and PMMoV as an indicator for human waste. Front Microbiol 2024; 15:1379194. [PMID: 38605711 PMCID: PMC11007199 DOI: 10.3389/fmicb.2024.1379194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Wastewater-based epidemiology (WBE) has become a valuable tool for monitoring the prevalence of SARS-CoV-2 on university campuses. However, concerns about effectiveness of raw sewage as a COVID-19 early warning system still exist, and it's not clear how useful normalization by simultaneous comparison of Pepper Mild Mottle Virus (PMMoV) is in addressing variations resulting from fecal discharge dilution. This study aims to contribute insights into these aspects by conducting an academic-year field trial at the student residences on the University of Tennessee, Knoxville campus, raw sewage. This was done to investigate the correlations between SARS-CoV-2 RNA load, both with and without PMMoV normalization, and various parameters, including active COVID-19 cases, self-isolations, and their combination among all student residents. Significant positive correlations between SARS-CoV-2 RNA load a week prior, during the monitoring week, and the subsequent week with active cases. Despite these correlations, normalization by PMMoV does not enhance these associations. These findings suggest the potential utility of SARS-CoV-2 RNA load as an early warning indicator and provide valuable insights into the application and limitations of WBE for COVID-19 surveillance specifically within the context of raw sewage on university campuses.
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Affiliation(s)
- Ye Li
- Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, United States
| | - Kurt Ash
- Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | - Dominique Joyner
- Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, United States
| | - Daniel Edward Williams
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
| | - Peter J. McKay
- Battelle Memorial Institute, Columbus, OH, United States
| | - Brianna Green
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | - Sydney DeBlander
- College of Natural Science, Michigan State University, East Lansing, MI, United States
| | - Carman North
- Student Health Center, University of Tennessee, Knoxville, TN, United States
| | - Fadime Kara-Murdoch
- Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, United States
- Battelle Memorial Institute, Columbus, OH, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
| | - Cynthia Swift
- Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
| | - Terry C. Hazen
- Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, United States
- Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States
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10
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Aguayo-Acosta A, Oyervides-Muñoz MA, Rodriguez-Aguillón KO, Ovalle-Carcaño A, Romero-Castillo KD, Robles-Zamora A, Johnson M, Parra-Saldívar R, Sosa-Hernández JE. Omicron and Delta variant prevalence detection and identification during the fourth COVID-19 wave in Mexico using wastewater-based epidemiology. IJID REGIONS 2024; 10:44-51. [PMID: 38149263 PMCID: PMC10750064 DOI: 10.1016/j.ijregi.2023.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 12/28/2023]
Abstract
Objectives To identify the SARS-CoV-2 variants Delta and Omicron during the fourth wave of the COVID-19 pandemic in Mexico using samples taken from 19 locations in 18 out of the 32 states. Methods The genetic material concentration was done with PEG/NaCl precipitation, SARS-CoV-2 presence was confirmed by reverse transcriptase-quantitative polymerase chain reaction assay, the variant detection was carried out using a commercial mutation detection panel kit, and variant/mutation confirmation was done by amplicon sequencing of receptor-binding domain target region. The study used 41 samples. Results The Delta variant was confirmed in two samples during August 2021 (Querétaro and CDMX) and in three samples during November 2021 (Aguascalientes, Ciudad Juárez campuses, and Nuevo Leon). In December 2021, another sample with the Delta variant was confirmed in Nuevo Leon. Between January to March 2022 only the presence of Omicron was confirmed, (variant BA.1). Additionally, in this period six samples were identified with the status "Variant Not Determined". Conclusion To our knowledge, this study is one of the first to identify Omicron and Delta variants with polymerase chain reaction in Mexico and Latin America and its distribution across the country with 56% Mexican states making it a viable alternative for variant detection without conducting a large quantity of sequencing of clinical tests.
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Affiliation(s)
- Alberto Aguayo-Acosta
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Mariel Araceli Oyervides-Muñoz
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Kassandra O. Rodriguez-Aguillón
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Antonio Ovalle-Carcaño
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | | | | | - Marc Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, USA
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey, Mexico
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
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11
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Sharma V, Takamura H, Biyani M, Honda R. Real-Time On-Site Monitoring of Viruses in Wastewater Using Nanotrap ® Particles and RICCA Technologies. BIOSENSORS 2024; 14:115. [PMID: 38534222 DOI: 10.3390/bios14030115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/10/2024] [Accepted: 02/17/2024] [Indexed: 03/28/2024]
Abstract
Wastewater-based epidemiology (WBE) is an effective and efficient tool for the early detection of infectious disease outbreaks in a community. However, currently available methods are laborious, costly, and time-consuming due to the low concentration of viruses and the presence of matrix chemicals in wastewater that may interfere with molecular analyses. In the present study, we designed a highly sensitive "Quick Poop (wastewater with fecal waste) Sensor" (termed, QPsor) using a joint approach of Nanotrap microbiome particles and RICCA (RNA Isothermal Co-Assisted and Coupled Amplification). Using QPsor, the WBE study showed a strong correlation with standard PEG concentrations and the qPCR technique. Using a closed format for a paper-based lateral flow assay, we were able to demonstrate the potential of our assay as a real-time, point-of-care test by detecting the heat-inactivated SARS-CoV-2 virus in wastewater at concentrations of 100 copies/mL and within one hour. As a proof-of-concept demonstration, we analyzed the presence of viral RNA of the SARS-CoV-2 virus and PMMoV in raw wastewater samples from wastewater treatment plants on-site and within 60 min. The results show that the QPsor method can be an effective tool for disease outbreak detection by combining an AI-enabled case detection model with real-time on-site viral RNA extraction and amplification, especially in the absence of intensive clinical laboratory facilities. The lab-free, lab-quality test capabilities of QPsor for viral prevalence and transmission in the community can contribute to the efficient management of pandemic situations.
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Affiliation(s)
- Vishnu Sharma
- BioSeeds Corporation, Ishikawa Create Labo-202, Asahidai 2-13, Nomi 923-1211, Ishikawa, Japan
| | - Hitomi Takamura
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa 920-1164, Ishikawa, Japan
| | - Manish Biyani
- BioSeeds Corporation, Ishikawa Create Labo-202, Asahidai 2-13, Nomi 923-1211, Ishikawa, Japan
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa 920-1164, Ishikawa, Japan
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12
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Téblick L, Lipovac M, Burdier FR, De Smet A, Bell M, van den Borst E, Matheeussen V, Vorsters A. Concentration strategies for spiked and naturally present biomarkers in non-invasively collected first-void urine. Eur J Med Res 2024; 29:131. [PMID: 38368382 PMCID: PMC10873940 DOI: 10.1186/s40001-024-01719-5] [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: 01/03/2024] [Accepted: 02/08/2024] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND First-void urine (FVU) provides a non-invasive method for collecting a wide range of biomarkers found in genital tract secretions. To optimize biomarker collection in FVU, this study investigated the impact of naturally present and supplemented precipitating agents: uromodulin (UMOD) and polyethylene glycol (PEG), on the concentration of human papillomavirus (HPV) pseudovirions (PsV), cell-free DNA (cfDNA), and cellular genomic DNA (gDNA) through centrifugation. METHODS FVU samples from ten healthy female volunteers, along with a control sample, were spiked with seal herpesvirus 1 (PhHV-1) DNA, HPV16 plasmid DNA, and HPV16 PsV with an enhanced green fluorescent protein (EGFP) reporter. The samples were subjected to various concentration protocols involving PEG precipitation, low-speed centrifugation (5 min at 1000×g), and medium-speed centrifugation (1 h at 3000×g). Subsequently, quantitative PCR (qPCR) was used to assess cellular and cell-free glyceraldehyde-3-phosphate dehydrogenase (GAPDH) DNA, cell-free PhHV-1 and HPV16 DNA, and PsV (EGFP) DNA. In addition, UMOD levels were measured. RESULTS The findings revealed that PEG significantly increased the concentration of cfDNA and gDNA in the pellet after centrifugation, with the most pronounced effect observed for cfDNA. Moreover, low-speed centrifugation without PEG effectively depleted cellular gDNA while preserving cfDNA in the supernatants. Pseudovirions were consistently pelleted, even with low-speed centrifugation, and a positive but not significant effect of PEG on PsV (EGFP) DNA yield in the pellet was observed. Additionally, a significant correlation was observed between UMOD and GAPDH, HPV16, and PsV (EGFP) DNA quantities in the pellet. Furthermore, large variations among the FVU samples were observed. CONCLUSIONS With this study, we provide novel insights into how various biomarker precipitation protocols, including both the properties of FVU and the use of PEG as a precipitating agent, influence the concentration of cfDNA, cellular gDNA, and pseudovirions.
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Affiliation(s)
- Laura Téblick
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, 2610, Wilrijk-Antwerp, Belgium.
| | - Marijana Lipovac
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, 2610, Wilrijk-Antwerp, Belgium
| | - F Ricardo Burdier
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, 2610, Wilrijk-Antwerp, Belgium
| | - Annemie De Smet
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, 2610, Wilrijk-Antwerp, Belgium
| | - Margo Bell
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, 2610, Wilrijk-Antwerp, Belgium
| | - Eef van den Borst
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, 2610, Wilrijk-Antwerp, Belgium
- Centre of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, 2650, Edegem, Belgium
| | - Veerle Matheeussen
- Department of Microbiology, Antwerp University Hospital (UZA), 2650, Edegem-Antwerp, Belgium
- Department of Medical Microbiology (LMM), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, 2610, Wilrijk-Antwerp, Belgium
- Department of Medical Biochemistry, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610, Wilrijk-Antwerp, Belgium
| | - Alex Vorsters
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, 2610, Wilrijk-Antwerp, Belgium
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13
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Akter J, Smith WJ, Liu Y, Kim I, Simpson SL, Thai P, Korajkic A, Ahmed W. Comparison of adsorption-extraction (AE) workflows for improved measurements of viral and bacterial nucleic acid in untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:167966. [PMID: 38476760 PMCID: PMC10927021 DOI: 10.1016/j.scitotenv.2023.167966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The lack of standardized methods and large differences in virus concentration and extraction workflows have hampered Severe Acute Respiratory Syndrome (SARS-CoV-2) wastewater surveillance and data reporting practices. Numerous studies have shown that adsorption-extraction (AE) method holds promise, yet several uncertainties remain regarding the optimal AE workflow. Several procedural components may influence the recovered concentrations of target nucleic acid, including membrane types, homogenization instruments, speed and duration, and lysis buffer. In this study, 42 different AE workflows that varied these components were compared to determine the optimal workflow by quantifying endogenous SARS-CoV-2, human adenovirus 40/41 (HAdV 40/41), and a bacterial marker gene of fecal contamination (Bacteroides HF183). Our findings suggest that the workflow chosen had a significant impact on SARS-CoV-2 concentrations, whereas it had minimal impact on HF183 and no effect on HAdV 40/41 concentrations. When comparing individual components in a workflow, such as membrane type (MF-Millipore™ 0.45 μm MCE vs. Isopore™ 0.40 μm), we found that they had no impact on SARS-CoV-2, HAdV 40/41, and HF183 concentrations. This suggests that at least some consumables and equipment are interchangeable. Buffer PM1 + TRIzol-based workflows yielded higher concentrations of SARS-CoV-2 than other workflows. HF183 concentrations were higher in workflows without chloroform. Similarly, higher homogenization speeds (5000-10,000 rpm) led to increased concentrations of SARS-CoV-2 and HF183 but had no effect on HAdV 40/41. Our findings indicate that minor enhancements to the AE workflow can improve the recovery of viruses and bacteria from the wastewater, leading to improved outcomes from wastewater surveillance efforts.
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Affiliation(s)
- Jesmin Akter
- Department of Civil and Environmental Engineering, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Gyeonggi-do 10223, Republic of Korea
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J.M. Smith
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Yawen Liu
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
- State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Ilho Kim
- Department of Civil and Environmental Engineering, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Department of Environmental Research, Korea Institute of Civil Engineering and Building Technology (KICT), Gyeonggi-do 10223, Republic of Korea
| | | | - Phong Thai
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 4102 Brisbane, Australia
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
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14
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Brighton K, Fisch S, Wu H, Vigil K, Aw TG. Targeted community wastewater surveillance for SARS-CoV-2 and Mpox virus during a festival mass-gathering event. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167443. [PMID: 37793442 DOI: 10.1016/j.scitotenv.2023.167443] [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: 06/11/2023] [Revised: 08/24/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023]
Abstract
Wastewater surveillance has emerged recently as a powerful approach to understanding infectious disease dynamics in densely populated zones. Wastewater surveillance, while promising as a public health tool, is often hampered by slow turn-around times, complex analytical protocols, and resource-intensive techniques. In this study, we evaluated an affinity capture method and microfluidic digital PCR as a rapid approach to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), mpox (formerly known as monkeypox) virus, and fecal indicator, pepper mild mottle virus (PMMoV) in wastewater during a mass-gathering event. Wastewater samples (n = 131) were collected from residential and commercial manholes, pump stations, and a city's wastewater treatment plant. The use of Nanotrap® Microbiome Particles and microfluidic digital PCR produced comparable results to other established methodologies, with reduced process complexity and analytical times, providing same day results for public health preparedness and response. Using indigenous SARS-CoV-2 and PMMoV in wastewater, the average viral recovery efficiency was estimated at 10.1 %. Both SARS-CoV-2 N1 and N2 genes were consistently detected throughout the sampling period, with increased RNA concentrations mainly in wastewater samples collected from commercial area after festival mass gatherings. The mpox virus was sporadically detected in wastewater samples during the surveillance period, without distinct temporal trends. SARS-CoV-2 RNA concentrations in the city's wastewater mirrored the city's COVID-19 cases, confirming the predictive properties of wastewater surveillance. Wastewater surveillance continues to be beneficial for tracking diseases that display gastrointestinal symptoms, including SARS-CoV-2, and can be a powerful tool for sentinel surveillance. However, careful site selection and a thorough understanding of community dynamics are necessary when performing targeted surveillance during temporary mass-gathering events as potential confirmation bias may occur.
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Affiliation(s)
- Keegan Brighton
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Samuel Fisch
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Huiyun Wu
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Katie Vigil
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA.
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15
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Zhang H, Long Y, Peng Y, Chen Y, Hu C, Chen J, Chen X, Guo A. Soluble expression and purification of recombinant bovine ferritin H-chain. Protein Expr Purif 2023; 211:106340. [PMID: 37481118 DOI: 10.1016/j.pep.2023.106340] [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: 05/15/2023] [Revised: 07/03/2023] [Accepted: 07/19/2023] [Indexed: 07/24/2023]
Abstract
Ferritin is a potential medicine delivery vehicle and vaccine platform, and its efficient expression is a prerequisite for widespread application. This study introduces a soluble expression strategy for recombinant bovine ferritin heavy chain (rFTH) in a prokaryotic system and an improved protein purification method. The amplified rFTH gene was ligated into the prokaryotic expression vector pET30a. The recombinant vectors with the N-terminal His-tag(N-His) or C-terminal His-tag(C-His) were translated and expressed separately. The results showed that the solubility of rFTH with C-His was significantly higher than that with N-His. The expression of rFTH with C-His was attempted at 37 °C and 16 °C, respectively. The results showed that the proportion of soluble protein expressed at 37 °C was more than 90%, higher than that expressed at 16 °C. Then rFTH with C-His was purified successfully using anion exchange chromatography, modified PEG precipitation, and dialysis. The rFTH protein was characterized using SDS-PAGE, Native-PAGE, Western blot, transmission electron microscopy, and dynamic light scattering. The results demonstrated that the purified rFTH protein self-assembled into ferritin nanoparticles with a regular shape and uniform size. This study sheds new light on the soluble expression of ferritin and provides a foundation for the construction of bovine ferritin nanoparticle production platforms.
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Affiliation(s)
- Haoyun Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yiting Long
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongchong Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yingyu Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Changmin Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianguo Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xi Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Aizhen Guo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China; Hubei Hongshan Laboratory, Wuhan, 430070, China; Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Wuhan, 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, China.
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16
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Rusková M, Bučková M, Puškárová A, Cíchová M, Janská V, Achs A, Šubr Z, Kuchta T, Pangallo D. Comparison of ordinary reverse transcription real-time polymerase chain reaction (qRT-PCR) with a newly developed one-step single-tube nested real-time RT-PCR (OSN-qRT-PCR) for sensitive detection of SARS-CoV-2 in wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:95579-95589. [PMID: 37553492 PMCID: PMC10482794 DOI: 10.1007/s11356-023-29123-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 07/29/2023] [Indexed: 08/10/2023]
Abstract
Wastewater monitoring has proven to be an important approach to detecting and controlling the development of the SARS-CoV-2 pandemic. Various tests based on reverse transcription real-time PCR (qRT-PCR) have been developed and used for the detection of SARS-CoV-2 in wastewater samples. In this study, we attempted to increase the sensitivity of qRT-PCR by developing a one-step single-tube nested qRT-PCR assay (OSN-qRT-PCR). Two variants were developed, oriented to nucleocapsid phosphoprotein gene (N) and to spike protein gene (S), respectively. The performance of conventional qRT-PCR assays oriented to these genes with two novel OSN-qRT-PCR assays were firstly optimized using wastewater artificially contaminated with two encapsidated RNA mimic systems harboring a portion either N or S gene (ENRM and ESRM, respectively). The assays were coupled to a polyethylene glycol-based RNA precipitation/extraction method and applied to detect SARS-CoV-2 in wastewater samples from four cities in Slovakia. Both novel OSN-qRT-PCR assays demonstrated higher detection rates than the ordinary qRT-PCR counterparts. The virus levels in the analyzed wastewater samples had a high or very high relation with the numbers of clinical cases in the monitored regions. In fact, correlation with a 3-, 4-, or 5-day temporal offset was revealed. The OSN-qRT-PCR assays demonstrated robustness, mainly in samples with low viral loads.
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Affiliation(s)
- Magdaléna Rusková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Mária Bučková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Andrea Puškárová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Marianna Cíchová
- Water Research Institute, Nábrežie Arm. Gen. L. Svobodu 5, 812 49, Bratislava, Slovakia
| | - Veronika Janská
- Water Research Institute, Nábrežie Arm. Gen. L. Svobodu 5, 812 49, Bratislava, Slovakia
| | - Adam Achs
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská Cesta 9, 845 05, Bratislava, Slovakia
| | - Zdeno Šubr
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology, Dúbravská Cesta 9, 845 05, Bratislava, Slovakia
| | - Tomáš Kuchta
- Department of Microbiology, Molecular Biology and Biotechnology, Food Research Institute, National Agricultural and Food Centre, Priemyselná 4, 824 75, Bratislava, Slovakia
| | - Domenico Pangallo
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia.
- Caravella, s.r.o., Tupolevova 2, 851 01, Bratislava, Slovakia.
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17
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Zhao L, Geng Q, Corchis-Scott R, McKay RM, Norton J, Xagoraraki I. Targeting a free viral fraction enhances the early alert potential of wastewater surveillance for SARS-CoV-2: a methods comparison spanning the transition between delta and omicron variants in a large urban center. Front Public Health 2023; 11:1140441. [PMID: 37546328 PMCID: PMC10400354 DOI: 10.3389/fpubh.2023.1140441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/30/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction Wastewater surveillance has proven to be a valuable approach to monitoring the spread of SARS-CoV-2, the virus that causes Coronavirus disease 2019 (COVID-19). Recognizing the benefits of wastewater surveillance as a tool to support public health in tracking SARS-CoV-2 and other respiratory pathogens, numerous wastewater virus sampling and concentration methods have been tested for appropriate applications as well as their significance for actionability by public health practices. Methods Here, we present a 34-week long wastewater surveillance study that covers nearly 4 million residents of the Detroit (MI, United States) metropolitan area. Three primary concentration methods were compared with respect to recovery of SARS-CoV-2 from wastewater: Virus Adsorption-Elution (VIRADEL), polyethylene glycol precipitation (PEG), and polysulfone (PES) filtration. Wastewater viral concentrations were normalized using various parameters (flow rate, population, total suspended solids) to account for variations in flow. Three analytical approaches were implemented to compare wastewater viral concentrations across the three primary concentration methods to COVID-19 clinical data for both normalized and non-normalized data: Pearson and Spearman correlations, Dynamic Time Warping (DTW), and Time Lagged Cross Correlation (TLCC) and peak synchrony. Results It was found that VIRADEL, which captures free and suspended virus from supernatant wastewater, was a leading indicator of COVID-19 cases within the region, whereas PEG and PES filtration, which target particle-associated virus, each lagged behind the early alert potential of VIRADEL. PEG and PES methods may potentially capture previously shed and accumulated SARS-CoV-2 resuspended from sediments in the interceptors. Discussion These results indicate that the VIRADEL method can be used to enhance the early-warning potential of wastewater surveillance applications although drawbacks include the need to process large volumes of wastewater to concentrate sufficiently free and suspended virus for detection. While lagging the VIRADEL method for early-alert potential, both PEG and PES filtration can be used for routine COVID-19 wastewater monitoring since they allow a large number of samples to be processed concurrently while being more cost-effective and with rapid turn-around yielding results same day as collection.
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Affiliation(s)
- Liang Zhao
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Robert Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States
| | - John Norton
- Great Lakes Water Authority, Detroit, MI, United States
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
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Ciannella S, González-Fernández C, Gomez-Pastora J. Recent progress on wastewater-based epidemiology for COVID-19 surveillance: A systematic review of analytical procedures and epidemiological modeling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:162953. [PMID: 36948304 PMCID: PMC10028212 DOI: 10.1016/j.scitotenv.2023.162953] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 05/13/2023]
Abstract
On March 11, 2020, the World Health Organization declared the coronavirus disease 2019 (COVID-19), whose causative agent is the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), a pandemic. This virus is predominantly transmitted via respiratory droplets and shed via sputum, saliva, urine, and stool. Wastewater-based epidemiology (WBE) has been able to monitor the circulation of viral pathogens in the population. This tool demands both in-lab and computational work to be meaningful for, among other purposes, the prediction of outbreaks. In this context, we present a systematic review that organizes and discusses laboratory procedures for SARS-CoV-2 RNA quantification from a wastewater matrix, along with modeling techniques applied to the development of WBE for COVID-19 surveillance. The goal of this review is to present the current panorama of WBE operational aspects as well as to identify current challenges related to it. Our review was conducted in a reproducible manner by following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for systematic reviews. We identified a lack of standardization in wastewater analytical procedures. Regardless, the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) approach was the most reported technique employed to detect and quantify viral RNA in wastewater samples. As a more convenient sample matrix, we suggest the solid portion of wastewater to be considered in future investigations due to its higher viral load compared to the liquid fraction. Regarding the epidemiological modeling, the data-driven approach was consistently used for the prediction of variables associated with outbreaks. Future efforts should also be directed toward the development of rapid, more economical, portable, and accurate detection devices.
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Affiliation(s)
- Stefano Ciannella
- Department of Chemical Engineering, Texas Tech University, Lubbock 79409, TX, USA.
| | - Cristina González-Fernández
- Department of Chemical Engineering, Texas Tech University, Lubbock 79409, TX, USA; Departamento de Ingenierías Química y Biomolecular, Universidad de Cantabria, Avda. Los Castros, s/n, 39005 Santander, Spain.
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19
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Tang L, Wu J, Liu R, Feng Z, Zhang Y, Zhao Y, Li Y, Yang K. Exploration on wastewater-based epidemiology of SARS-CoV-2: Mimic relative quantification with endogenous biomarkers as internal reference. Heliyon 2023; 9:e15705. [PMID: 37124340 PMCID: PMC10122556 DOI: 10.1016/j.heliyon.2023.e15705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/02/2023] Open
Abstract
Wastewater-based epidemiology has become a powerful surveillance tool for monitoring the pandemic of COVID-19. Although it is promising to quantitatively correlate the SARS-CoV-2 RNA concentration in wastewater with the incidence of community infection, there is still no consensus on whether the viral nucleic acid concentration in sewage should be normalized against the abundance of endogenous biomarkers and which biomarker should be used as a reference for the normalization. Here, several candidate endogenous reference biomarkers for normalization of SARS-CoV-2 signal in municipal sewage were evaluated. The human fecal indicator virus (crAssphage) is a promising candidate of endogenous reference biomarker for data normalization of both DNA and RNA viruses for its intrinsic viral nature and high and stable content in sewage. Without constructing standard curves, the relative quantification of sewage viral nucleic acid against the abundance of the reference biomarker can be used to correlate with community COVID-19 incidence, which was proved via mimic experiments by spiking pseudovirus of different concentrations in sewage samples. Dilution of pseudovirus-seeded wastewater did not affect the relative abundance of viral nucleic acid, demonstrating that relative quantification can overcome the sewage dilution effects caused by the greywater input, precipitation and/or groundwater infiltration. The process of concentration, recovery and detection of the endogenous biomarker was consistent with that of SARS-CoV-2 RNA. Thus, it is necessary to co-quantify the endogenous biomarker because it can be not only an internal reference for data normalization, but also a process control.
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Affiliation(s)
- Langjun Tang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Jinyong Wu
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Rui Liu
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Zhongxi Feng
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Yanan Zhang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Yingzhe Zhao
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Yonghong Li
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Kun Yang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, China
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20
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Lamba S, Ganesan S, Daroch N, Paul K, Joshi SG, Sreenivas D, Nataraj A, Srikantaiah V, Mishra R, Ramakrishnan U, Ishtiaq F. SARS-CoV-2 infection dynamics and genomic surveillance to detect variants in wastewater - a longitudinal study in Bengaluru, India. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2023; 11:100151. [PMID: 36688230 PMCID: PMC9847225 DOI: 10.1016/j.lansea.2023.100151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/01/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023]
Abstract
Background Environmental surveillance (ES) of a pathogen is crucial for understanding the community load of disease. As an early warning system, ES for SARS-CoV-2 has complemented routine diagnostic surveillance by capturing near real-time virus circulation at a population level. Methods In this longitudinal study conducted between January 2022 and June 2022 in 28 sewershed sites in Bengaluru city (∼11 million inhabitants), we quantified weekly SARS-CoV-2 RNA concentrations to track infection dynamics and provide evidence of change in the relative abundance of emerging variants. Findings We describe an early warning system using the exponentially weighted moving average control chart and demonstrate how SARS-CoV-2 RNA concentrations in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 8-14 days earlier in wastewater than in clinical data. This was further corroborated by showing that the estimated number of infections is strongly correlated with SARS-CoV-2 RNA copies detected in the wastewater. Using a deconvolution matrix, we detected emerging variants of concern up to two months earlier in wastewater samples. In addition, we found a huge diversity in variants detected in wastewater compared to clinical samples. The findings from this study have been discussed regularly with local authorities to inform policy-making decisions. Interpretation Our study highlights that quantifying viral titre, correlating it with a known number of cases in the area, and combined with genomic surveillance helps in tracking variants of concern (VOC) over time and space, enabling timely and making informed policy decisions. Funding This work has been supported by funding from the Rockefeller Foundation grant to National Centre for Biological Sciences, TIFR) and the Indian Council of Medical Research grant to (FI) Tata Institute for Genetics and Society and Tata Trusts.
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Affiliation(s)
- Sanjay Lamba
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Sutharsan Ganesan
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Namrta Daroch
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Kiran Paul
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Soumya Gopal Joshi
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Darshan Sreenivas
- National Centre for Biological Sciences, TIFR, Bellary Road, Bengaluru, 560065, India
| | - Annamalai Nataraj
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | | | - Rakesh Mishra
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, Bellary Road, Bengaluru, 560065, India
| | - Farah Ishtiaq
- Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India,Corresponding author. Tata Institute for Genetics and Society, GKVK Post, Bellary Road, Bengaluru, 560065, India
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21
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Saingam P, Li B, Nguyen Quoc B, Jain T, Bryan A, Winkler MKH. Wastewater surveillance of SARS-CoV-2 at intra-city level demonstrated high resolution in tracking COVID-19 and calibration using chemical indicators. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 866:161467. [PMID: 36626989 PMCID: PMC9825140 DOI: 10.1016/j.scitotenv.2023.161467] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 12/17/2022] [Accepted: 01/04/2023] [Indexed: 05/12/2023]
Abstract
Wastewater-based epidemiology has proven to be a supportive tool to better comprehend the dynamics of the COVID-19 pandemic. As the disease moves into endemic stage, the surveillance at wastewater sub-catchments such as pump station and manholes is providing a novel mechanism to examine the reemergence and to take measures that can prevent the spread. However, there is still a lack of understanding when it comes to wastewater-based epidemiology implementation at the smaller intra-city level for better granularity in data, and dilution effect of rain precipitation at pump stations. For this study, grab samples were collected from six areas of Seattle between March-October 2021. These sampling sites comprised five manholes and one pump station with population ranging from 2580 to 39,502 per manhole/pump station. The wastewater samples were analyzed for SARS-CoV-2 RNA concentrations, and we also obtained the daily COVID-19 cases (from individual clinical testing) for each corresponding sewershed, which ranged from 1 to 12 and the daily incidence varied between 3 and 64 per 100,000 of population. Rain precipitation lowered viral RNA levels and sensitivity of viral detection but wastewater total ammonia (NH4+-N) and phosphate (PO43--P) were shown as potential chemical indicators to calibrate/level out the dilution effect. These chemicals showed the potential in improving the wastewater surveillance capacity of COVID-19.
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Affiliation(s)
- Prakit Saingam
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA.
| | - Bo Li
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Bao Nguyen Quoc
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Tanisha Jain
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Andrew Bryan
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Mari K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA.
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22
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Lucansky V, Samec M, Burjanivova T, Lukacova E, Kolkova Z, Holubekova V, Turyova E, Hornakova A, Zaborsky T, Podlesniy P, Reizigova L, Dankova Z, Novakova E, Pecova R, Calkovska A, Halasova E. Comparison of the methods for isolation and detection of SARS-CoV-2 RNA in municipal wastewater. Front Public Health 2023; 11:1116636. [PMID: 36960362 PMCID: PMC10028190 DOI: 10.3389/fpubh.2023.1116636] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/17/2023] [Indexed: 03/09/2023] Open
Abstract
Introduction Coronavirus SARS-CoV-2 is a causative agent responsible for the current global pandemic situation known as COVID-19. Clinical manifestations of COVID-19 include a wide range of symptoms from mild (i.e., cough, fever, dyspnea) to severe pneumonia-like respiratory symptoms. SARS-CoV-2 has been demonstrated to be detectable in the stool of COVID-19 patients. Waste-based epidemiology (WBE) has been shown as a promising approach for early detection and monitoring of SARS-CoV-2 in the local population performed via collection, isolation, and detection of viral pathogens from environmental sources. Methods In order to select the optimal protocol for monitoring the COVID-19 epidemiological situation in region Turiec, Slovakia, we (1) compared methods for SARS-CoV-2 separation and isolation, including virus precipitation by polyethylene glycol (PEG), virus purification via ultrafiltration (Vivaspin®) and subsequent isolation by NucleoSpin RNA Virus kit (Macherey-Nagel), and direct isolation from wastewater (Zymo Environ Water RNA Kit); (2) evaluated the impact of water freezing on SARS- CoV-2 separation, isolation, and detection; (3) evaluated the role of wastewater filtration on virus stability; and (4) determined appropriate methods including reverse transcription-droplet digital PCR (RT-ddPCR) and real-time quantitative polymerase chain reaction (RT-qPCR) (targeting the same genes, i.e., RdRp and gene E) for quantitative detection of SARS-CoV-2 in wastewater samples. Results (1) Usage of Zymo Environ Water RNA Kit provided superior quality of isolated RNA in comparison with both ultracentrifugation and PEG precipitation. (2) Freezing of wastewater samples significantly reduces the RNA yield. (3) Filtering is counterproductive when Zymo Environ Water RNA Kit is used. (4) According to the specificity and sensitivity, the RT-ddPCR outperforms RT-qPCR. Discussion The results of our study suggest that WBE is a valuable early warning alert and represents a non-invasive approach to monitor viral pathogens, thus protects public health on a regional and national level. In addition, we have shown that the sensitivity of testing the samples with a nearer detection limit can be improved by selecting the appropriate combination of enrichment, isolation, and detection methods.
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Affiliation(s)
- Vincent Lucansky
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin (JFMED CU), Comenius University in Bratislava, Martin, Slovakia
| | - Marek Samec
- Department of Pathophysiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Tatiana Burjanivova
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Eva Lukacova
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Zuzana Kolkova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin (JFMED CU), Comenius University in Bratislava, Martin, Slovakia
| | - Veronika Holubekova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin (JFMED CU), Comenius University in Bratislava, Martin, Slovakia
| | - Eva Turyova
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Hornakova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin (JFMED CU), Comenius University in Bratislava, Martin, Slovakia
| | - Tibor Zaborsky
- RÚVZ (Regional Office of Public Health), Martin, Slovakia
| | - Petar Podlesniy
- Centro Investigacion Biomedica en Red Enfermedades Neurodegenerativas (CiberNed), Madrid, Spain
| | - Lenka Reizigova
- Center for Microbiology and Infection Prevention, Department of Laboratory Medicine, Faculty of Health Care and Social Work, Trnava University, Trnava, Slovakia
| | - Zuzana Dankova
- Biobank for Cancer and Rare Diseases, Jessenius Faculty of Medicine in Martin (JFMED CU), Comenius University in Bratislava, Martin, Slovakia
| | - Elena Novakova
- Department of Microbiology and Immunology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Renata Pecova
- Department of Pathophysiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Calkovska
- Department of Physiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Erika Halasova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin (JFMED CU), Comenius University in Bratislava, Martin, Slovakia
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23
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Ahmed W, Bivins A, Korajkic A, Metcalfe S, Smith WJM, Simpson SL. Comparative analysis of Adsorption-Extraction (AE) and Nanotrap® Magnetic Virus Particles (NMVP) workflows for the recovery of endogenous enveloped and non-enveloped viruses in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160072. [PMID: 36356768 PMCID: PMC10823496 DOI: 10.1016/j.scitotenv.2022.160072] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
In this study, two virus concentration methods, namely Adsorption-Extraction (AE) and Nanotrap® Magnetic Virus Particles (NMVP) along with commercially available extraction kits were used to quantify endogenous pepper mild mottle virus (PMMoV) and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in nucleic acid extracted from 48 wastewater samples collected over six events from eight wastewater treatment plants (WWTPs). The main aim was to determine which workflow (i.e., concentration and extraction methods) produces greater concentrations of endogenous PMMoV and SARS-CoV-2 gene copies (GC) in comparison with each other. Turbidity and total suspended solids (TSS) of wastewater samples within and among the eight WWTPs were highly variable (41-385 NTU and 77-668 mg/L TSS). In 58 % of individual wastewater samples, the log10 GC concentrations of PMMoV were greater by NMVP workflow compared to AE workflow. Paired measurements of PMMoV GC/10 mL from AE and NMVP across all 48 wastewater samples were weakly correlated (r = 0.455, p = 0.001) and demonstrated a poor linear relationship (r2 = 0.207). The log10 GC concentrations of SARS-CoV-2 in 69 % of individual samples were greater by AE workflow compared to NMVP workflow. In contrast to PMMoV, the AE and NMVP derived SARS-CoV-2 GC counts were strongly correlated (r = 0.859, p < 0.001) and demonstrated a strong linear relationship (r2 = 0.738). In general, the PMMoV GC achieved by the NMVP workflow decreased with increasing turbidity, but the PMMoV GC by the AE workflow did not appear to be as sensitive to either turbidity or TSS levels. These findings suggest that wastewater sample turbidity or suspended solids concentration, and the intended target for analysis should be considered when validating an optimal workflow for wastewater surveillance of viruses.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Aaron Bivins
- Department of Civil and Environmental Engineering, Louisiana State University, 3255 Patrick F. Taylor Hall, Baton Rouge, LA 70803, USA
| | - Asja Korajkic
- United States Environmental Protection Agency, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J M Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
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24
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Maal-Bared R, Qiu Y, Li Q, Gao T, Hrudey SE, Bhavanam S, Ruecker NJ, Ellehoj E, Lee BE, Pang X. Does normalization of SARS-CoV-2 concentrations by Pepper Mild Mottle Virus improve correlations and lead time between wastewater surveillance and clinical data in Alberta (Canada): comparing twelve SARS-CoV-2 normalization approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158964. [PMID: 36167131 PMCID: PMC9508694 DOI: 10.1016/j.scitotenv.2022.158964] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 05/02/2023]
Abstract
Wastewater-based surveillance (WBS) data normalization is an analyte measurement correction that addresses variations resulting from dilution of fecal discharge by non-sanitary sewage, stormwater or groundwater infiltration. No consensus exists on what WBS normalization parameters result in the strongest correlations and lead time between SARS-CoV-2 WBS data and COVID-19 cases. This study compared flow, population size and biomarker normalization impacts on the correlations and lead times for ten communities in twelve sewersheds in Alberta (Canada) between September 2020 and October 2021 (n = 1024) to determine if normalization by Pepper Mild Mottle Virus (PMMoV) provides any advantages compared to other normalization parameters (e.g., flow, reported and dynamic population sizes, BOD, TSS, NH3, TP). PMMoV concentrations (GC/mL) corresponded with plant influent flows and were highest in the urban centres. SARS-CoV-2 target genes E, N1 and N2 were all negatively associated with wastewater influent pH, while PMMoV was positively associated with temperature. Pooled data analysis showed that normalization increased ρ-values by almost 0.1 and was highest for ammonia, TKN and TP followed by PMMoV. Normalization by other parameters weakened associations. None of the differences were statistically significant. Site-specific correlations showed that normalization of SARS-CoV-2 data by PMMoV only improved correlations significantly in two of the twelve systems; neither were large sewersheds or combined sewer systems. In five systems, normalization by traditional wastewater strength parameters and dynamic population estimates improved correlations. Lead time ranged between 1 and 4 days in both pooled and site-specific comparisons. We recommend that WBS researchers and health departments: a) Investigate WWTP influent properties (e.g., pH) in the WBS planning phase and use at least two parallel approaches for normalization only if shown to provide value; b) Explore normalization by wastewater strength parameters and dynamic population size estimates further; and c) Evaluate purchasing an influent flow meter in small communities to support long-term WBS efforts and WWTP management.
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Affiliation(s)
- Rasha Maal-Bared
- Quality Assurance and Environment, EPCOR Water, Edmonton, Alberta, Canada.
| | - Yuanyuan Qiu
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Qiaozhi Li
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Tiejun Gao
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Steve E Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Sudha Bhavanam
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Norma J Ruecker
- Water Quality Services, City of Calgary, Calgary, Alberta, Canada
| | - Erik Ellehoj
- Ellehoj Redmond Consulting, Edmonton, Alberta, Canada
| | - Bonita E Lee
- Department of Paediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Xiaoli Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada; Public Health Laboratories (ProvLab), Alberta Precision Laboratories (APL), Edmonton, Alberta, Canada
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25
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Wang R, Alamin M, Tsuji S, Hara-Yamamura H, Hata A, Zhao B, Ihara M, Honda R. Removal performance of SARS-CoV-2 in wastewater treatment by membrane bioreactor, anaerobic-anoxic-oxic, and conventional activated sludge processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158310. [PMID: 36030862 PMCID: PMC9411102 DOI: 10.1016/j.scitotenv.2022.158310] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/10/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
The potential risk of SARS-CoV-2 in treated effluent from a wastewater treatment plant (WWTP) is concerned since SARS-CoV-2 is contained in wastewater during the COVID-19 outbreak. However, the removal of SARS-CoV-2 in WWTP has not been well investigated. The objectives of this study were (i) to clarify the removal performance of SARS-CoV-2 during wastewater treatment, (ii) to compare the removal performance of different secondary treatment processes, and (iii) to evaluate applicability of pepper mild mottle of virus (PMMoV) as a performance indicator for the reduction of SARS-CoV-2 RNA in wastewater treatment. Influent wastewater, secondary-treatment effluent (before chlorination), and final effluent (after chlorination) samples were collected from a WWTP from May 28 to September 24, 2020, during the COVID-19 outbreak in Japan. The target WWTP had three parallel treatment systems employing conventional activated sludge (CAS), anaerobic-anoxic -oxic (A2O), and membrane bioreactor (MBR) processes. SARS-CoV-2 in both the liquid and solid fractions of the influent wastewater was concentrated and quantified using RT-qPCR. SARS-CoV-2 in treated effluent was concentrated from 10 L samples to achieve a detection limit as low as 10 copies/L. The log reduction value (LRV) of SARS-CoV-2 was 2.7 ± 0.86 log10 in CAS, 1.6 ± 0.50 log10 in A2O, and 3.6 ± 0.62 log10 in MBR. The lowest LRV observed during the sampling period was 2.8 log10 in MBR, 1.2 log10 in CAS, and 1.0 log10 in A2O process, indicating that the MBR had the most stable reduction performance. PMMoV was found to be a good indicator virus to evaluate reduction performance of SARS-CoV-2 independent of the process configuration because the LRV of PMMoV was significantly lower than that of SARS-CoV-2 in the CAS, A2O and MBR processes.
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Affiliation(s)
- Rongxuan Wang
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
| | - Md Alamin
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
| | - Shohei Tsuji
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Japan
| | - Hiroe Hara-Yamamura
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Japan
| | - Akihiko Hata
- Department of Environmental and Civil Engineering, Toyama Prefectural University, Imizu, Japan
| | - Bo Zhao
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, PR China; Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, Otsu, Japan
| | - Masaru Ihara
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, Otsu, Japan; Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Japan
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Japan; Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, Otsu, Japan.
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26
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Fonseca MS, Machado BAS, Rolo CDA, Hodel KVS, Almeida EDS, de Andrade JB. Evaluation of SARS-CoV-2 concentrations in wastewater and river water samples. CASE STUDIES IN CHEMICAL AND ENVIRONMENTAL ENGINEERING 2022; 6:100214. [PMID: 37520921 PMCID: PMC9055419 DOI: 10.1016/j.cscee.2022.100214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 05/02/2023]
Abstract
There are only a few established methods to determine the concentration of encapsulated viruses, such as SARS-CoV-2, in water matrices, limiting the application of wastewater-based epidemiology (WBE)-an important tool for public health research. The present study compared four methods that are commonly used to concentrate non-encapsulated enteric viruses for determining SARS-CoV-2 concentration in wastewater and wastewater-enriched river water samples. The four methods tested were electronegative membrane with Mg+2 addition, aluminum hydroxide-based precipitation, polyethylene glycol (PEG) 8000 precipitation, and ultrafiltration (with porosity of 10 and 50 kDa). Prior to the concentration step, filtration or centrifugation was performed to remove suspended particles from the samples (pretreatment). To evaluate the recovery efficiency (%), samples of SARS-CoV-2 from nasopharyngeal swabs obtained from RT-qPCR-positive patients were used as spiked samples. The second part of the analysis involved the quantification of the SARS-CoV-2 copy number in analytes without SARS-CoV-2-spiked samples. Among the tested methods, pretreatment via centrifugation followed by ultrafiltration with a 50-kDa cut-off was found the most efficient method for wastewater samples with spiked samples (54.3 or 113.01% efficiency). For the wastewater-enriched river samples with spiked samples, pretreatment via centrifugation followed by filtration using an electronegative membrane was the most efficient method (110.8% and 95.9% for N1 and N2 markers, respectively). However, ultrafiltration of the raw river water samples using 10 or 50 kDa cut-off filters and PEG 8000 precipitation showed the best concentration efficiency based on copy number, regardless of the pretreatment approach or sample type (values ranging from 3 × 105 to 6.7 × 103). The effectiveness of the concentration method can vary depending on the type of sample and concentration method. We consider that this study will contribute to more widespread use of WBE for the environmental surveillance of SARS-CoV-2.
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Affiliation(s)
- Maísa Santos Fonseca
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Bruna Aparecida Souza Machado
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
- SENAI CIMATEC, Manufacturing and Technology Integrated Campus, University Center SENAI CIMATEC, Salvador, Bahia, Brazil
| | - Carolina de Araújo Rolo
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Katharine Valéria Saraiva Hodel
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
| | - Edna Dos Santos Almeida
- SENAI CIMATEC, Manufacturing and Technology Integrated Campus, University Center SENAI CIMATEC, Salvador, Bahia, Brazil
| | - Jailson Bittencourt de Andrade
- SENAI CIMATEC, SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, Salvador, 41650-010, Brazil
- SENAI CIMATEC, Manufacturing and Technology Integrated Campus, University Center SENAI CIMATEC, Salvador, Bahia, Brazil
- Instituto Nacional de Ciência e Tecnologia em Energia e Ambiente - INCT E&A, Federal University of Bahia, Salvador, 40170-115, Brazil
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Suddhapas K, Choi MH, Shortreed MR, Timperman A. Evaluation of Variant-Specific Peptides for Detection of SARS-CoV-2 Variants of Concern. J Proteome Res 2022; 21:2443-2452. [PMID: 36108102 PMCID: PMC10318299 DOI: 10.1021/acs.jproteome.2c00325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The SARS-CoV-2 omicron variant presented significant challenges to the global effort to counter the pandemic. SARS-CoV-2 is predicted to remain prevalent for the foreseeable future, making the ability to identify SARS-CoV-2 variants imperative in understanding and controlling the pandemic. The predominant variant discovery method, genome sequencing, is time-consuming, insensitive, and expensive. Ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) offers an exciting alternative detection modality provided that variant-containing peptide markers are sufficiently detectable from their tandem mass spectra (MS/MS). We have synthesized model tryptic peptides of SARS-CoV-2 variants alpha, beta, gamma, delta, and omicron and evaluated their signal intensity, HCD spectra, and reverse phase retention time. Detection limits of 781, 781, 65, and 65 amol are obtained for the molecular ions of the proteotypic peptides, beta (QIAPGQTGNIADYNYK), gamma (TQLPSAYTNSFTR), delta (VGGNYNYR), and omicron (TLVKQLSSK), from neat solutions. These detection limits are on par with the detection limits of a previously reported proteotypic peptide from the SARS-CoV-2 spike protein, HTPINLVR. This study demonstrates the potential to differentiate SARS-CoV-2 variants through their proteotypic peptides with an approach that is broadly applicable across a wide range of pathogens.
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Affiliation(s)
- Kantaphon Suddhapas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - M Hannah Choi
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - AaronT Timperman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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28
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Li X, Ahmed W, Wu Z, Xia Y. Developing a novel Bifidobacterium phage quantitative polymerase chain reaction-based assay for tracking untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155815. [PMID: 35550888 DOI: 10.1016/j.scitotenv.2022.155815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Microbial source tracking (MST) tools provide insights on fecal pollution levels in aquatic environments using predominantly quantitative PCR (qPCR) assays that target host-associated molecular marker genes. Existing wastewater-associated marker genes have shown limited or significant cross-reactions with non-human fecal samples. In this study, we mined the current Gut Phage Database (GPD) and designed a novel untreated wastewater-specific Bifidobacterium phage qPCR assay (i.e., Bifi assay). The sensitivity and specificity of the Bifi marker genes were assessed by collectively analyzing untreated (n = 33) and treated (n = 15) wastewater and non-human fecal samples (i.e., Rabbit, mouse, cow, horse, pig, chicken, sheep, dog, deer, kangaroos; n = 113) in Shenzhen, Guangdong Province, China and Brisbane, Australia. Bifi assay revealed 100% host-specificity against non-human fecal samples collected from Shenzhen and Brisbane. Furthermore, this marker gene was also detected in all untreated and treated wastewater samples, whose concentrations ranged from 5.54 to 6.83 log10 GC/L. In Shenzhen, the concentrations of Bifi marker gene were approximately two orders of magnitude lower than Bacteroides (HF183/BacR287 assay) and CrAssphage (CPQ_56 assay). The concentration of Bifi marker gene in untreated wastewater from Brisbane was 1.35 log10 greater than those in Shenzhen. Our results suggest that Bifi marker gene has the potential to detect and quantify the levels of human fecal pollution in Shenzhen and Brisbane. If additional detection sensitivity is required for environmental studies, Bifi marker gene should be paired with either CrAssphage or HF183/BacR287 marker genes.
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Affiliation(s)
- Xiang Li
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Ziqi Wu
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yu Xia
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
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Hasan AEZ, Julistiono H, Bermawie N, Riyanti EI, Arifni FR. Soursop leaves (Annona muricata L.) endophytic fungi anticancer activity against HeLa cells. Saudi J Biol Sci 2022; 29:103354. [PMID: 35813114 PMCID: PMC9256652 DOI: 10.1016/j.sjbs.2022.103354] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 05/11/2022] [Accepted: 06/15/2022] [Indexed: 12/24/2022] Open
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30
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Fahrenfeld NL, Morales Medina WR, D'Elia S, Deshpande AS, Ehasz G. Year-long wastewater monitoring for SARS-CoV-2 signals in combined and separate sanitary sewers. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2022; 94:e10768. [PMID: 35918060 DOI: 10.1021/acsestwater.1c00345] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/07/2022] [Accepted: 07/01/2022] [Indexed: 05/27/2023]
Abstract
COVID-19 wastewater-based epidemiology has been performed in catchments of various sizes and sewer types with many short-term studies available and multi-seasonal studies emerging. The objective of this study was to compare weekly observations of SARS-CoV-2 genes in municipal wastewater across multiple seasons for different systems as a factor of sewer type (combined, separate sanitary) and system size. Sampling occurred following the first wave of SARS-CoV-2 cases in the study region (June 2020) and continued through the third wave (May 2021), the period during which clinical testing was widely available and different variants dominated clinical cases. The strongest correlations were observed between wastewater N1 concentrations and the cumulative clinical cases reported in the 2 weeks prior to wastewater sampling, followed by the week prior, new cases, and the week after wastewater sampling. Sewer type and size did not necessarily explain the strength of the correlations, indicating that other non-sewer factors may be impacting the observations. In-system sampling results for the largest system sampled are presented for 1 month. Removing wet weather days from the data sets improved even the flow-normalized correlations for the systems, potentially indicating that interpreting results during wet weather events may be more complicated than simply accounting for dilution. PRACTITIONER POINTS: SARS-CoV-2 in wastewater correlated best with total clinical cases reported in 2 weeks before wastewater sampling at the utility level. Study performed when clinical testing was widespread during the year after the first COVID-19 wave in the region. Sewer type and size did not necessarily explain correlation strength between clinical cases and wastewater-based epidemiology results. Removing wet weather days improved correlations for 3/4 utilities studied, including both separate sanitary and combined sewers.
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Affiliation(s)
- Nicole L Fahrenfeld
- Department of Civil and Environmental Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - William R Morales Medina
- Department of Microbiology and Molecular Genetics, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Stephanie D'Elia
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Aishwarya S Deshpande
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Genevieve Ehasz
- Department of Civil and Environmental Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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31
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Rusková M, Bučková M, Achs A, Puškárová A, Wu JH, Kuchta T, Šubr Z, Pangallo D. Useful molecular tools for facing next pandemic events: Effective sample preparation and improved RT-PCR for highly sensitive detection of SARS-CoV-2 in wastewater environment. Int J Hyg Environ Health 2022; 245:114017. [PMID: 35939897 PMCID: PMC9346026 DOI: 10.1016/j.ijheh.2022.114017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/22/2022] [Accepted: 07/27/2022] [Indexed: 10/28/2022]
Abstract
Viral pandemics can be inevitable in the next future. Considering SARS-CoV-2 pandemics as an example, there seems to be a need to develop a surveillance system able to monitor the presence of potential pathogenic agents. The sewage and wastewater environments demonstrated to be suitable targets for such kind of analysis. In addition, it is important to have reliable molecular diagnostic tools and also to develop a robust detection strategy. In this study, an effective sample preparation procedure was selected from four options and combined with a newly developed improved RT-PCR. First, a model viral system was constructed, containing a fragment of the SARS-CoV-2 gene encoding for the Spike protein. The encapsidated S RNA mimic (ESRM) was based on the plum pox virus (PPV) genome with the inserted targeted gene fragment. ESRM was used for seeding wastewater samples in order to evaluate the viral recovery of four different viral RNA concentration/extraction methods. The efficiency of individual approaches was assessed by the use of a quantitative reverse transcription PCR (qRT-PCR) and by a one-step single-tube nested quantitative reverse transcription PCR (OSN-qRT-PCR). For the detection of viruses in wastewater samples with low viral loads, OSN-qRT-PCR assay produced the most satisfactory results and the highest sensitivity.
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Affiliation(s)
- Magdaléna Rusková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia
| | - Mária Bučková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia
| | - Adam Achs
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology. Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Andrea Puškárová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia
| | - Jer-Horng Wu
- National Cheng Kung University, Department of Environmental Engineering. University Road 1, East District, 701 01, Tainan City, Taiwan
| | - Tomáš Kuchta
- Department of Microbiology, Molecular Biology and Biotechnology, Food Research Institute, National Agricultural and Food Centre, Priemyselná 4, 824 75, Bratislava, Slovakia
| | - Zdeno Šubr
- Biomedical Research Center, Slovak Academy of Sciences, Institute of Virology. Dúbravská cesta 9, 845 05, Bratislava, Slovakia
| | - Domenico Pangallo
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia.
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32
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Ahmed W, Bivins A, Metcalfe S, Smith WJM, Verbyla ME, Symonds EM, Simpson SL. Evaluation of process limit of detection and quantification variation of SARS-CoV-2 RT-qPCR and RT-dPCR assays for wastewater surveillance. WATER RESEARCH 2022; 213:118132. [PMID: 35152136 PMCID: PMC8812148 DOI: 10.1016/j.watres.2022.118132] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/21/2022] [Accepted: 01/29/2022] [Indexed: 05/21/2023]
Abstract
Effective wastewater surveillance of SARS-CoV-2 RNA requires the rigorous characterization of the limit of detection resulting from the entire sampling process - the process limit of detection (PLOD). Yet to date, no studies have gone beyond quantifying the assay limit of detection (ALOD) for RT-qPCR or RT-dPCR assays. While the ALOD is the lowest number of gene copies (GC) associated with a 95% probability of detection in a single PCR reaction, the PLOD represents the sensitivity of the method after considering the efficiency of all processing steps (e.g., sample handling, concentration, nucleic acid extraction, and PCR assays) to determine the number of GC in the wastewater sample matrix with a specific probability of detection. The primary objective of this study was to estimate the PLOD resulting from the combination of primary concentration and extraction with six SARS-CoV-2 assays: five RT-qPCR assays (US CDC N1 and N2, China CDC N and ORF1ab (CCDC N and CCDC ORF1ab), and E_Sarbeco RT-qPCR, and one RT-dPCR assay (US CDC N1 RT-dPCR) using two models (exponential survival and cumulative Gaussian). An adsorption extraction (AE) concentration method (i.e., virus adsorption on membrane and the RNA extraction from the membrane) was used to concentrate gamma-irradiated SARS-CoV-2 seeded into 36 wastewater samples. Overall, the US CDC N1 RT-dPCR and RT-qPCR assays had the lowest ALODs (< 10 GC/reaction) and PLODs (<3,954 GC/50 mL; 95% probability of detection) regardless of the seeding level and model used. Nevertheless, consistent amplification and detection rates decreased when seeding levels were < 2.32 × 103 GC/50 mL even for US CDC N1 RT-qPCR and RT-dPCR assays. Consequently, when SARS-CoV-2 RNA concentrations are expected to be low, it may be necessary to improve the positive detection rates of wastewater surveillance by analyzing additional field and RT-PCR replicates. To the best of our knowledge, this is the first study to assess the SARS-CoV-2 PLOD for wastewater and provides important insights on the analytical limitations for trace detection of SARS-CoV-2 RNA in wastewater.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN, 46556, USA
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J M Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Matthew E Verbyla
- Department of Civil, Construction and Environmental Engineering, San Diego State University, San Diego, CA, USA
| | - Erin M Symonds
- Department of Anthropology, Southern Methodist University, Dallas, Texas, USA
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Torii S, Oishi W, Zhu Y, Thakali O, Malla B, Yu Z, Zhao B, Arakawa C, Kitajima M, Hata A, Ihara M, Kyuwa S, Sano D, Haramoto E, Katayama H. Comparison of five polyethylene glycol precipitation procedures for the RT-qPCR based recovery of murine hepatitis virus, bacteriophage phi6, and pepper mild mottle virus as a surrogate for SARS-CoV-2 from wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150722. [PMID: 34610400 PMCID: PMC8487407 DOI: 10.1016/j.scitotenv.2021.150722] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 05/04/2023]
Abstract
Polyethylene glycol (PEG) precipitation is one of the conventional methods for virus concentration. This technique has been used to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. The procedures and seeded surrogate viruses were different among implementers; thus, the reported whole process recovery efficiencies considerably varied among studies. The present study compared five PEG precipitation procedures, with different operational parameters, for the RT-qPCR-based whole process recovery efficiency of murine hepatitis virus (MHV), bacteriophage phi6, and pepper mild mottle virus (PMMoV), and molecular process recovery efficiency of murine norovirus using 34 raw wastewater samples collected in Japan. The five procedures yielded significantly different whole process recovery efficiency of MHV (0.070%-2.6%) and phi6 (0.071%-0.51%). The observed concentration of indigenous PMMoV ranged from 8.9 to 9.7 log (8.2 × 108 to 5.6 × 109) copies/L. Interestingly, PEG precipitation with 2-h incubation outperformed that with overnight incubation partially due to the difference in molecular process recovery efficiency. The recovery load of MHV exhibited a positive correlation (r = 0.70) with that of PMMoV, suggesting that PMMoV is the potential indicator of the recovery efficiency of SARS-CoV-2. In addition, we reviewed 13 published studies and found considerable variability between different studies in the whole process recovery efficiency of enveloped viruses by PEG precipitation. This was due to the differences in operational parameters and surrogate viruses as well as the differences in wastewater quality and bias in the measurement of the seeded load of surrogate viruses, resulting from the use of different analytes and RNA extraction methods. Overall, the operational parameters (e.g., incubation time and pretreatment) should be optimized for PEG precipitation. Co-quantification of PMMoV may allow for the normalization of SARS-CoV-2 RNA concentration by correcting for the differences in whole process recovery efficiency and fecal load among samples.
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Affiliation(s)
- Shotaro Torii
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Wakana Oishi
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yifan Zhu
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Ocean Thakali
- Department of Engineering, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Zaizhi Yu
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Bo Zhao
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan
| | - Chisato Arakawa
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Akihiko Hata
- Faculty of Engineering, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
| | - Masaru Ihara
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga 520-0811, Japan; Faculty of Agriculture and Marine Science, Kochi University, Monobe-Otsu 200, Nankoku, Kochi 783-8502 Japan
| | - Shigeru Kyuwa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - 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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Calderón-Franco D, Orschler L, Lackner S, Agrawal S, Weissbrodt DG. Monitoring SARS-CoV-2 in sewage: Toward sentinels with analytical accuracy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150244. [PMID: 34798752 PMCID: PMC8428994 DOI: 10.1016/j.scitotenv.2021.150244] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/21/2021] [Accepted: 09/05/2021] [Indexed: 05/07/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemia has been one of the most difficult challenges humankind has recently faced. Wastewater-based epidemiology has emerged as a tool for surveillance and mitigation of potential viral outbreaks, circumventing biases introduced by clinical patient testing. Due to the situation urgency, protocols followed for isolating viral RNA from sewage were not adapted for such sample matrices. In parallel to their implementation for fast collection of data to sustain surveillance and mitigation decisions, molecular protocols need to be harmonized to deliver accurate, reproducible, and comparable analytical outputs. Here we studied analytical variabilities linked to viral RNA isolation methods from sewage. Three different influent wastewater volumes were used to assess the effects of filtered volumes (50, 100 or 500 mL) for capturing viral particles. Three different concentration strategies were tested: electronegative membranes, polyethersulfone membranes, and anion-exchange diethylaminoethyl cellulose columns. To compare the number of viral particles, different RNA isolation methods (column-based vs. magnetic beads) were compared. The effect of extra RNA purification steps and different RT-qPCR strategies (one step vs. two-step) were also evaluated. Results showed that the combination of 500 mL filtration volume through electronegative membranes and without multiple RNA purification steps (using column-based RNA purification) using two-step RT-qPCR avoided false negatives when basal viral load in sewage are present and yielded more consistent results during the surveillance done during the second-wave in Delft (The Hague area, The Netherlands). By paving the way for standardization of methods for the sampling, concentration and molecular detection of SARS-CoV-2 viruses from sewage, these findings can help water and health surveillance authorities to use and trust results coming from wastewater based epidemiology studies in order to anticipate SARS-CoV-2 outbreaks.
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Affiliation(s)
- David Calderón-Franco
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Laura Orschler
- Technische Universität Darmstadt, Institute IWAR, 8 Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
| | - Susanne Lackner
- Technische Universität Darmstadt, Institute IWAR, 8 Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
| | - Shelesh Agrawal
- Technische Universität Darmstadt, Institute IWAR, 8 Franziska-Braun-Straße 7, 64287 Darmstadt, Germany
| | - David G Weissbrodt
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
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35
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Ahmed W, Bivins A, Simpson SL, Smith WJM, Metcalfe S, McMinn B, Symonds EM, Korajkic A. Comparative analysis of rapid concentration methods for the recovery of SARS-CoV-2 and quantification of human enteric viruses and a sewage-associated marker gene in untreated wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149386. [PMID: 34388890 PMCID: PMC8325557 DOI: 10.1016/j.scitotenv.2021.149386] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 05/18/2023]
Abstract
To support public-health-related disease surveillance and monitoring, it is crucial to concentrate both enveloped and non-enveloped viruses from domestic wastewater. To date, most concentration methods were developed for non-enveloped viruses, and limited studies have directly compared the recovery efficiency of both types of viruses. In this study, the effectiveness of two different concentration methods (Concentrating pipette (CP) method and an adsorption-extraction (AE) method amended with MgCl2) were evaluated for untreated wastewater matrices using three different viruses (SARS-CoV-2 (seeded), human adenovirus 40/41 (HAdV 40/41), and enterovirus (EV)) and a wastewater-associated bacterial marker gene targeting Lachnospiraceae (Lachno3). For SARS-CoV-2, the estimated mean recovery efficiencies were significantly greater by as much as 5.46 times, using the CP method than the AE method amended with MgCl2. SARS-CoV-2 RNA recovery was greater for samples with higher titer seeds regardless of the method, and the estimated mean recovery efficiencies using the CP method were 25.1 ± 11% across ten WWTPs when wastewater samples were seeded with 5 × 104 gene copies (GC) of SARS-CoV-2. Meanwhile, the AE method yielded significantly greater concentrations of indigenous HAdV 40/41 and Lachno3 from wastewater compared to the CP method. Finally, no significant differences in indigenous EV concentrations were identified in comparing the AE and CP methods. These data indicate that the most effective concentration method varies by microbial analyte and that the priorities of the surveillance or monitoring program should be considered when choosing the concentration method.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | | | - Wendy J M Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Brian McMinn
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Erin M Symonds
- College of Marine Science, University of South Florida, 140 7th Ave South, St. Petersburg, FL 33701, USA
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
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Wang Q, Liu L. On the Critical Role of Human Feces and Public Toilets in the Transmission of COVID-19: Evidence from China. SUSTAINABLE CITIES AND SOCIETY 2021; 75:103350. [PMID: 34540563 PMCID: PMC8433098 DOI: 10.1016/j.scs.2021.103350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 05/05/2023]
Abstract
The surprising spread speed of the COVID-19 pandemic creates an urgent need for investigating the transmission chain or transmission pattern of COVID-19 beyond the traditional respiratory channels. This study therefore examines whether human feces and public toilets play a critical role in the transmission of COVID-19. First, it develops a theoretical model that simulates the transmission chain of COVID-19 through public restrooms. Second, it uses stabilized epidemic data from China to empirically examine this theory, conducting an empirical estimation using a two-stage least squares (2SLS) model with appropriate instrumental variables (IVs). This study confirms that the wastewater directly promotes the transmission of COVID-19 within a city. However, the role of garbage in this transmission chain is more indirect in the sense that garbage has a complex relationship with public toilets, and it promotes the transmission of COVID-19 within a city through interaction with public toilets and, hence, human feces. These findings have very strong policy implications in the sense that if we can somehow use the ratio of public toilets as a policy instrument, then we can find a way to minimize the total number of infections in a region. As shown in this study, pushing the ratio of public toilets (against open defecation) to the local population in a city to its optimal level would help to reduce the total infection in a region.
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Affiliation(s)
- Qiuyun Wang
- School of Economics, Southwestern University of Finance and Economics, P.R China
| | - Lu Liu
- School of Economics, Southwestern University of Finance and Economics, P.R China
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Wolfe MK, Topol A, Knudson A, Simpson A, White B, Vugia DJ, Yu AT, Li L, Balliet M, Stoddard P, Han GS, Wigginton KR, Boehm AB. High-Frequency, High-Throughput Quantification of SARS-CoV-2 RNA in Wastewater Settled Solids at Eight Publicly Owned Treatment Works in Northern California Shows Strong Association with COVID-19 Incidence. mSystems 2021; 6:e0082921. [PMID: 34519528 PMCID: PMC8547422 DOI: 10.1128/msystems.00829-21] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/30/2021] [Indexed: 01/19/2023] Open
Abstract
A number of recent retrospective studies have demonstrated that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater are associated with coronavirus disease 2019 (COVID-19) cases in the corresponding sewersheds. Implementing high-resolution, prospective efforts across multiple plants depends on sensitive measurements that are representative of COVID-19 cases, scalable for high-throughput analysis, and comparable across laboratories. We conducted a prospective study across eight publicly owned treatment works (POTWs). A focus on SARS-CoV-2 RNA in solids enabled us to scale up our measurements with a commercial lab partner. Samples were collected daily, and results were posted to a website within 24 h. SARS-CoV-2 RNA in daily samples correlated with the incidence of COVID-19 cases in the sewersheds; a 1 log10 increase in SARS-CoV-2 RNA in settled solids corresponds to a 0.58 log10 (4×) increase in sewershed incidence rate. SARS-CoV-2 RNA signals measured with the commercial laboratory partner were comparable across plants and comparable to measurements conducted in a university laboratory when normalized by pepper mild mottle virus (PMMoV) RNA. Results suggest that SARS-CoV-2 RNA should be detectable in settled solids for COVID-19 incidence rates of >1/100,000 (range, 0.8 to 2.3 cases per 100,000). These sensitive, representative, scalable, and comparable methods will be valuable for future efforts to scale up wastewater-based epidemiology. IMPORTANCE Access to reliable, rapid monitoring data is critical to guide response to an infectious disease outbreak. For pathogens that are shed in feces or urine, monitoring wastewater can provide a cost-effective snapshot of transmission in an entire community via a single sample. In order for a method to be useful for ongoing COVID-19 monitoring, it should be sensitive for detection of low concentrations of SARS-CoV-2, representative of incidence rates in the community, scalable to generate data quickly, and comparable across laboratories. This paper presents a method utilizing wastewater solids to meet these goals, producing measurements of SARS-CoV-2 RNA strongly associated with COVID-19 cases in the sewershed of a publicly owned treatment work. Results, provided within 24 h, can be used to detect incidence rates as low as approximately 1/100,000 cases and can be normalized for comparison across locations generating data using different methods.
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Affiliation(s)
- Marlene K. Wolfe
- Department of Civil & Environmental Engineering, Stanford University, Stanford, California, USA
| | - Aaron Topol
- Verily Life Sciences, South San Francisco, California, USA
| | - Alisha Knudson
- Verily Life Sciences, South San Francisco, California, USA
| | - Adrian Simpson
- Verily Life Sciences, South San Francisco, California, USA
| | - Bradley White
- Verily Life Sciences, South San Francisco, California, USA
| | - Duc J. Vugia
- California Department of Public Health, Infectious Diseases Branch, Richmond, California, USA
| | - Alexander T. Yu
- California Department of Public Health, Infectious Diseases Branch, Richmond, California, USA
| | - Linlin Li
- County of Santa Clara Public Health Department, San Jose, California, USA
| | - Michael Balliet
- County of Santa Clara Department of Environmental Health, San Jose, California, USA
| | - Pamela Stoddard
- County of Santa Clara Public Health Department, San Jose, California, USA
| | - George S. Han
- County of Santa Clara Public Health Department, San Jose, California, USA
| | - Krista R. Wigginton
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexandria B. Boehm
- Department of Civil & Environmental Engineering, Stanford University, Stanford, California, USA
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38
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Wolfe MK, Topol A, Knudson A, Simpson A, White B, Vugia DJ, Yu AT, Li L, Balliet M, Stoddard P, Han GS, Wigginton KR, Boehm AB. High-Frequency, High-Throughput Quantification of SARS-CoV-2 RNA in Wastewater Settled Solids at Eight Publicly Owned Treatment Works in Northern California Shows Strong Association with COVID-19 Incidence. mSystems 2021; 6:e0082921. [PMID: 34519528 DOI: 10.1101/2021.07.16.21260627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
A number of recent retrospective studies have demonstrated that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater are associated with coronavirus disease 2019 (COVID-19) cases in the corresponding sewersheds. Implementing high-resolution, prospective efforts across multiple plants depends on sensitive measurements that are representative of COVID-19 cases, scalable for high-throughput analysis, and comparable across laboratories. We conducted a prospective study across eight publicly owned treatment works (POTWs). A focus on SARS-CoV-2 RNA in solids enabled us to scale up our measurements with a commercial lab partner. Samples were collected daily, and results were posted to a website within 24 h. SARS-CoV-2 RNA in daily samples correlated with the incidence of COVID-19 cases in the sewersheds; a 1 log10 increase in SARS-CoV-2 RNA in settled solids corresponds to a 0.58 log10 (4×) increase in sewershed incidence rate. SARS-CoV-2 RNA signals measured with the commercial laboratory partner were comparable across plants and comparable to measurements conducted in a university laboratory when normalized by pepper mild mottle virus (PMMoV) RNA. Results suggest that SARS-CoV-2 RNA should be detectable in settled solids for COVID-19 incidence rates of >1/100,000 (range, 0.8 to 2.3 cases per 100,000). These sensitive, representative, scalable, and comparable methods will be valuable for future efforts to scale up wastewater-based epidemiology. IMPORTANCE Access to reliable, rapid monitoring data is critical to guide response to an infectious disease outbreak. For pathogens that are shed in feces or urine, monitoring wastewater can provide a cost-effective snapshot of transmission in an entire community via a single sample. In order for a method to be useful for ongoing COVID-19 monitoring, it should be sensitive for detection of low concentrations of SARS-CoV-2, representative of incidence rates in the community, scalable to generate data quickly, and comparable across laboratories. This paper presents a method utilizing wastewater solids to meet these goals, producing measurements of SARS-CoV-2 RNA strongly associated with COVID-19 cases in the sewershed of a publicly owned treatment work. Results, provided within 24 h, can be used to detect incidence rates as low as approximately 1/100,000 cases and can be normalized for comparison across locations generating data using different methods.
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Affiliation(s)
- Marlene K Wolfe
- Department of Civil & Environmental Engineering, Stanford Universitygrid.168010.e, Stanford, California, USA
| | - Aaron Topol
- Verily Life Sciences, South San Francisco, California, USA
| | - Alisha Knudson
- Verily Life Sciences, South San Francisco, California, USA
| | - Adrian Simpson
- Verily Life Sciences, South San Francisco, California, USA
| | - Bradley White
- Verily Life Sciences, South San Francisco, California, USA
| | - Duc J Vugia
- California Department of Public Health, Infectious Diseases Branch, Richmond, California, USA
| | - Alexander T Yu
- California Department of Public Health, Infectious Diseases Branch, Richmond, California, USA
| | - Linlin Li
- County of Santa Clara Public Health Department, San Jose, California, USA
| | - Michael Balliet
- County of Santa Clara Department of Environmental Health, San Jose, California, USA
| | - Pamela Stoddard
- County of Santa Clara Public Health Department, San Jose, California, USA
| | - George S Han
- County of Santa Clara Public Health Department, San Jose, California, USA
| | - Krista R Wigginton
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexandria B Boehm
- Department of Civil & Environmental Engineering, Stanford Universitygrid.168010.e, Stanford, California, USA
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39
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González-Reyes JR, Hernández-Flores MDLL, Paredes-Zarco JE, Téllez-Jurado A, Fayad-Meneses O, Carranza-Ramírez L. Detection of SARS-CoV-2 in Wastewater Northeast of Mexico City: Strategy for Monitoring and Prevalence of COVID-19. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:8547. [PMID: 34444296 PMCID: PMC8393920 DOI: 10.3390/ijerph18168547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/06/2021] [Accepted: 08/08/2021] [Indexed: 12/15/2022]
Abstract
A month-long wastewater sampling project was conducted along the northeast periphery of Mexico City, specifically in the state of Hidalgo, to assess the presence of SARS-CoV-2. To determine the prevalence of infection and obtain a range of COVID-19 cases in the main metropolitan zones. Viral RNA residues (0-197,655 copies/L) were measured in wastewater from the five central municipalities in the state. By recording the number of RNA viral copies per liter, micro-basins delimitation, demographic and physiological data, an interval of infected people and virus prevalence was estimated using a Monte Carlo model (with 90% confidence) in the micro-basin of five municipalities with metropolitan influence or industrial activity. Our procedure determined that the percentage of the infected population ranges from 1.4% to 41.7%, while the official data reports 0.1-0.3%. This model is proposed as a helpful method of regional epidemiological monitoring through the analysis of viral prevalence.
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Affiliation(s)
- José Roberto González-Reyes
- Investigación Aplicada para el Bienestar Social y Ambiental Asociación Civil (INABISA A.C.), Pachuca 42088, Mexico; (J.R.G.-R.); (J.E.P.-Z.)
| | | | - Jesús Eduardo Paredes-Zarco
- Investigación Aplicada para el Bienestar Social y Ambiental Asociación Civil (INABISA A.C.), Pachuca 42088, Mexico; (J.R.G.-R.); (J.E.P.-Z.)
| | - Alejandro Téllez-Jurado
- Laboratorio de Agrobiotecnología, Universidad Politécnica de Pachuca, Carretera Pachuca-Cd. Sahagún km 20, Zempoala 43830, Mexico;
| | - Omar Fayad-Meneses
- Consejo Ejecutivo del Complejo Científico y Tecnológico Sincrotrón, San Agustín Tlaxiaca 42163, Mexico; (O.F.-M.); (L.C.-R.)
| | - Lamán Carranza-Ramírez
- Consejo Ejecutivo del Complejo Científico y Tecnológico Sincrotrón, San Agustín Tlaxiaca 42163, Mexico; (O.F.-M.); (L.C.-R.)
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