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Takuissu GR, Kenmoe S, Ebogo-Belobo JT, Kengne-Ndé C, Mbaga DS, Bowo-Ngandji A, Ondigui Ndzie JL, Kenfack-Momo R, Tchatchouang S, Kenfack-Zanguim J, Lontuo Fogang R, Zeuko'o Menkem E, Kame-Ngasse GI, Magoudjou-Pekam JN, Suffredini E, Veneri C, Mancini P, Bonanno Ferraro G, Iaconelli M, Verani M, Federigi I, Carducci A, La Rosa G. Exploring adenovirus in water environments: a systematic review and meta-analysis. Int J Environ Health Res 2024; 34:2504-2516. [PMID: 37678554 DOI: 10.1080/09603123.2023.2255559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/01/2023] [Indexed: 09/09/2023]
Abstract
Adenoviruses (AdVs) have a significant impact in both medical and environmental contexts. The objective of this study was to investigate the prevalence of AdV in different water types, such as untreated and treated wastewater, surface water, groundwater, drinking water, and other water matrices. A total of 239 articles were included in this meta-analysis. Adenoviruses were detected in various waters worldwide. The overall prevalence in water was found to be 59.2%, with the highest prevalence in untreated wastewater (83.1%) and treated wastewater (75.3%), followed by "other water matrices" (53.4%), surface water (49.5%) drinking water (22.7%), and groundwater (18.5%). Most of the studies did not assess the viability of the viruses, leading to weak links between water contamination and risk. Both human and animal AdV were found in water environments. The findings suggest that water, including drinking water, could be a significant route of AdV transmission in both developed and developing economies.
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Affiliation(s)
- G R Takuissu
- Centre for Food, Food Security and Nutrition Research, Institute of Medical Research and Medicinal Plants Studies, Yaounde, Cameroon
| | - S Kenmoe
- Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
| | - J T Ebogo-Belobo
- Medical Research Centre, Institute of Medical Research and Medicinal Plants Studies, Yaounde, Cameroon
| | - C Kengne-Ndé
- Epidemiological Surveillance, Evaluation and Research Unit, National AIDS Control Committee, Douala, Cameroon
| | - D S Mbaga
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - A Bowo-Ngandji
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - J L Ondigui Ndzie
- Department of Microbiology, The University of Yaounde I, Yaounde, Cameroon
| | - R Kenfack-Momo
- Department of Biochemistry, The University of Yaounde I, Yaounde, Cameroon
| | - S Tchatchouang
- Scientific Direction, Centre Pasteur du Cameroun, Yaounde, Cameroon
| | - J Kenfack-Zanguim
- Department of Biochemistry, The University of Yaounde I, Yaounde, Cameroon
| | - R Lontuo Fogang
- Department of Animal Biology, University of Dschang, Dschang, Cameroon
| | - E Zeuko'o Menkem
- Department of Biomedical Sciences, University of Buea, Buea, Cameroon
| | - G I Kame-Ngasse
- Medical Research Centre, Institute of Medical Research and Medicinal Plants Studies, Yaounde, Cameroon
| | | | - E Suffredini
- Department of Food Safety, Nutrition and Veterinary public health, Istituto Superiore di Sanità, Rome, Italy
| | - C Veneri
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - P Mancini
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - G Bonanno Ferraro
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - M Verani
- Hygiene and Environmental Virology Laboratory, Department of Biology, University of Pisa, Pisa, Italy
| | - I Federigi
- Hygiene and Environmental Virology Laboratory, Department of Biology, University of Pisa, Pisa, Italy
| | - A Carducci
- Hygiene and Environmental Virology Laboratory, Department of Biology, University of Pisa, Pisa, Italy
| | - G La Rosa
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
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Dlamini M, Msolo L, Ehi Ebomah K, Nontongana N, Ifeanyi Okoh A. A systematic review on the incidence of influenza viruses in wastewater matrices: Implications for public health. PLoS One 2024; 19:e0291900. [PMID: 38662758 PMCID: PMC11045120 DOI: 10.1371/journal.pone.0291900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/05/2024] [Indexed: 04/28/2024] Open
Abstract
Influenza viruses pose a significant public health threat, necessitating comprehensive surveillance strategies to enhance early detection and preventive measures. This systematic review investigates the incidence of influenza viruses in wastewater matrices, aiming to elucidate the potential implications for public health. The study synthesizes existing literature, employing rigorous inclusion criteria to identify relevant studies conducted globally. The essence of the problem lies in the gaps of traditional surveillance methods, which often rely on clinical data and may underestimate the true prevalence of influenza within communities. Wastewater-based epidemiology offers a novel approach to supplementing these conventional methods, providing a broader and more representative assessment of viral circulation. This review systematically examines the methodologies employed in the selected studies, including virus concentration techniques and molecular detection methods, to establish a standardized framework for future research. Our findings reveal a consistent presence of influenza viruses in diverse wastewater matrices across different geographic locations and seasons. Recommendations for future research include the standardization of sampling protocols, improvement of virus concentration methods, and the integration of wastewater surveillance into existing public health frameworks. In conclusion, this systematic review contributes to the understanding of influenza dynamics in wastewater matrices, offering valuable insights for public health practitioners and policymakers. Implementation of wastewater surveillance alongside traditional methods can enhance the resilience of public health systems and better prepare communities for the challenges posed by influenza outbreaks.
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Affiliation(s)
- Mbasa Dlamini
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Department of Biochemistry and Microbiology, Applied and Environmental Microbiology Research Group (AEMREG), University of Fort Hare, Alice, South Africa
| | - Luyanda Msolo
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Department of Biochemistry and Microbiology, Applied and Environmental Microbiology Research Group (AEMREG), University of Fort Hare, Alice, South Africa
| | - Kingsley Ehi Ebomah
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Department of Biochemistry and Microbiology, Applied and Environmental Microbiology Research Group (AEMREG), University of Fort Hare, Alice, South Africa
| | - Nolonwabo Nontongana
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Department of Biochemistry and Microbiology, Applied and Environmental Microbiology Research Group (AEMREG), University of Fort Hare, Alice, South Africa
| | - Anthony Ifeanyi Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Department of Biochemistry and Microbiology, Applied and Environmental Microbiology Research Group (AEMREG), University of Fort Hare, Alice, South Africa
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Wacharapluesadee S, Thippamom N, Hirunpatrawong P, Rattanatumhi K, Sterling SL, Khunnawutmanotham W, Noradechanon K, Maneeorn P, Buathong R, Paitoonpong L, Putcharoen O. Comparative Performance in the Detection of Four Coronavirus Genera from Human, Animal, and Environmental Specimens. Viruses 2024; 16:534. [PMID: 38675878 DOI: 10.3390/v16040534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Emerging coronaviruses (CoVs) are understood to cause critical human and domestic animal diseases; the spillover from wildlife reservoirs can result in mild and severe respiratory illness in humans and domestic animals and can spread more readily in these naïve hosts. A low-cost CoV molecular method that can detect a variety of CoVs from humans, animals, and environmental specimens is an initial step to ensure the early identification of known and new viruses. We examine a collection of 50 human, 46 wastewater, 28 bat, and 17 avian archived specimens using 3 published pan-CoV PCR assays called Q-, W-, and X-CoV PCR, to compare the performance of each assay against four CoV genera. X-CoV PCR can detect all four CoV genera, but Q- and W-CoV PCR failed to detect δ-CoV. In total, 21 (42.0%), 9 (18.0%), and 21 (42.0%) of 50 human specimens and 30 (65.22%), 6 (13.04%), and 27 (58.70%) of 46 wastewater specimens were detected using Q-, W-, and X-CoV PCR assays, respectively. The X-CoV PCR assay has a comparable sensitivity to Q-CoV PCR in bat CoV detection. Combining Q- and X-CoV PCR assays can increase sensitivity and avoid false negative results in the early detection of novel CoVs.
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Affiliation(s)
- Supaporn Wacharapluesadee
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nattakarn Thippamom
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Piyapha Hirunpatrawong
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Khwankamon Rattanatumhi
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Spencer L Sterling
- Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Henry M. Jackson Foundation, Bethesda, MD 20817, USA
| | - Wiparat Khunnawutmanotham
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Kirana Noradechanon
- Department of National Parks, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok 10900, Thailand
| | - Patarapol Maneeorn
- Department of National Parks, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok 10900, Thailand
| | - Rome Buathong
- Department of Disease Control, Ministry of Public Health, Muang, Nonthaburi 11000, Thailand
| | - Leilani Paitoonpong
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Chulalongkorn University, Bangkok 10330, Thailand
| | - Opass Putcharoen
- Thai Red Cross Emerging Infectious Diseases Clinical Center, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Chulalongkorn University, Bangkok 10330, Thailand
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Zhao H, Yang M, Fan X, Gui Q, Yi H, Tong Y, Xiao W. A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants. Viruses 2024; 16:535. [PMID: 38675877 DOI: 10.3390/v16040535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
The concentration of viruses in sewage sludge is significantly higher (10-1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well as their role in the carbon, nitrogen, and phosphorus cycles remain poorly understood. In this study, we employed a shotgun metagenomic approach to investigate the pathogenic bacteria and viral composition and function in two wastewater treatment plants located on a campus. Our analysis revealed the presence of 1334 amplicon sequence variants (ASVs) across six sludge samples, with 242 ASVs (41.22% of total reads) identified as pathogenic bacteria. Arcobacter was found to be the most dominant pathogen accounting for 6.79% of total reads. The virome analysis identified 613 viral genera with Aorunvirus being the most abundant genus at 41.85%. Approximately 0.66% of these viruses were associated with human and animal diseases. More than 60% of the virome consisted of lytic phages. Host prediction analysis revealed that the phages primarily infected Lactobacillus (37.11%), Streptococcus (21.11%), and Staphylococcus (7.11%). Furthermore, our investigation revealed an abundance of auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and phosphorus cycling within the virome. We also detected a total of 113 antibiotic resistance genes (ARGs), covering major classes of antibiotics across all samples analyzed. Additionally, our findings indicated the presence of virulence factors including the clpP gene accounting for approximately 4.78%, along with toxin genes such as the RecT gene representing approximately 73.48% of all detected virulence factors and toxin genes among all samples analyzed. This study expands our understanding regarding both pathogenic bacteria and viruses present within sewage sludge while providing valuable insights into their ecological functions.
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Affiliation(s)
- Haozhe Zhao
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Mingfei Yang
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Xiang Fan
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Qian Gui
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Hao Yi
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Xiao
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China
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5
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Yasui M, Katayama H. Unveiling the viral escape: Quantification of microfloc-bound viruses in precoagulation and membrane filtration. J Water Health 2024; 22:309-320. [PMID: 38421625 PMCID: wh_2024_233 DOI: 10.2166/wh.2024.233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The implementation of precoagulation before the physical removal process is expected to achieve a high virus removal rate. However, viruses may form small flocs and subsequently escape into the effluent during physical removal processes. This study evaluated how viruses in the microflocs could be quantified using conventional virus quantification methods (plaque assay and quantitative polymerase chain reaction (qPCR)) to reveal the risk of underestimating virus concentration. In this study, the microfloc dissolution phenomenon in phosphate buffer solution was employed as a floc dissolution test. Viruses in microflocs formed under the experimental conditions. assuming water treatments, were quantified before and after floc dissolution. The findings revealed that virus concentrations increased by 1.0-3.9 log plaque-forming units/mL according to the plaque assay and by 1.7-4.0 log copies/mL according to the qPCR. This increase occurred after the dissolution of microflocs that were prepared in the humic acid test water. In the case of treated wastewater, virus concentrations increased in all samples according to the plaque assay and in seven of eight samples according to the qPCR. Our results indicate the necessity of careful consideration of virus quantification after precoagulation and physical removal systems.
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Affiliation(s)
- Midori Yasui
- Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Department of Environmental Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8540, Japan E-mail:
| | - Hiroyuki Katayama
- Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Research Center for Water Environment Technology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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6
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Harris E. Wastewater Surveillance Predicts Large-Scale Flu, RSV Trends. JAMA 2023; 330:1422. [PMID: 37755877 DOI: 10.1001/jama.2023.18743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
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7
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Wadi VS, Daou M, Zayed N, AlJabri M, Alsheraifi HH, Aldhaheri SS, Abuoudah M, Alhammadi M, Aldhuhoori M, Lopes A, Alalawi A, Yousef AF, Hasan SW, Alsafar H. Long-term study on wastewater SARS-CoV-2 surveillance across United Arab Emirates. Sci Total Environ 2023; 887:163785. [PMID: 37149161 PMCID: PMC10156646 DOI: 10.1016/j.scitotenv.2023.163785] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/18/2023] [Accepted: 04/23/2023] [Indexed: 05/08/2023]
Abstract
Wastewater-based epidemiology (WBE) demonstrates an efficient tool to monitor and predict SARS-CoV-2 community distribution. Many countries across the world have adopted the technique, however, most of these studies were conducted for a short duration with a limited sampling size. In this study, long-term reliability and quantification of wastewater SARS-CoV-2 surveillance is reported via analyzing 16,858 samples collected from 453 different locations across the United Arab Emirates (UAE) from May 2020 to June 2022. The collected composite samples were first incubated at 60 °C followed by filtration, concentration, and then RNA extraction using commercially available kits. The extracted RNA was then analyzed by one-step RT-qPCR and RT-ddPCR, and the data was compared to the reported clinical cases. The average positivity rate in the wastewater samples was found to be 60.61 % (8.41-96.77 %), however, the positivity rate obtained from the RT-ddPCR was significantly higher than the RT-qPCR suggesting higher sensitivity of RT-ddPCR. Time-lagged correlation analysis indicated an increase in positive cases in the wastewater samples when the clinical positive cases declined suggesting that wastewater data are highly affected by the unreported asymptomatic, pre-symptomatic and recovering individuals. The weekly SARS-CoV-2 viral count in the wastewater samples are positively correlated with the diagnosed new clinical cases throughout the studied period and the studied locations. Viral count in wastewater peaked approximately one to two weeks prior to the peaks appearing in active clinical cases indicating that wastewater viral concentrations are effective in predicting clinical cases. Overall, this study further confirms the long-term sensitivity and robust approach of WBE to detect trends in SARS-CoV-2 spread and helps contribute to pandemic management.
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Affiliation(s)
- Vijay S Wadi
- Center for Membranes and Advanced Water Technology (CMAT), Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Mariane Daou
- Department of Biology, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Noora Zayed
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Maryam AlJabri
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Hamad H Alsheraifi
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Saeed S Aldhaheri
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Miral Abuoudah
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Mohammad Alhammadi
- Emirates Bio-Research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates
| | - Malika Aldhuhoori
- Emirates Bio-Research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates
| | - Alvaro Lopes
- Emirates Bio-Research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates
| | - Abdulrahman Alalawi
- Department of Health, Safety and Environment, Department of Energy, Abu Dhabi, United Arab Emirates
| | - Ahmed F Yousef
- Center for Membranes and Advanced Water Technology (CMAT), Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates; Department of Biology, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Shadi W Hasan
- Center for Membranes and Advanced Water Technology (CMAT), Department of Chemical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates; Emirates Bio-Research Center, Ministry of Interior, Abu Dhabi, United Arab Emirates; Department of Biomedical Engineering, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates.
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Kazenelson J, Jefferson T, Rhodes RG, Cahoon LB, Frampton AR. Detection of SARS-CoV-2 RNA in wastewater from an enclosed college campus serves as an early warning surveillance system. PLoS One 2023; 18:e0288808. [PMID: 37471346 PMCID: PMC10358889 DOI: 10.1371/journal.pone.0288808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 07/05/2023] [Indexed: 07/22/2023] Open
Abstract
SARS-CoV-2, the causative agent of Covid-19, is shed from infected persons in respiratory droplets, feces, and urine. Using quantitative PCR (qPCR), our group hypothesized that we could detect SARS-CoV-2 in wastewater samples collected on a university campus prior to the detection of the virus in individuals on campus. Wastewater samples were collected 3 times a week from 5 locations on the main campus of the University of North Carolina Wilmington (UNCW) from July 24, 2020 to December 21, 2020. Post-collection, total RNA was extracted and SARS-CoV-2 RNA in the samples was detected by qPCR. SARS-CoV-2 signal was detected on campus beginning on August 19 as classes began and the signal increased in both intensity and breadth as the Fall semester progressed. A comparison of two RNA extraction methods from wastewater showed that SARS-CoV-2 was detected more frequently on filter samples versus the direct extracts. Aligning our wastewater data with the reported SARS-CoV-2 cases on the campus Covid-19 dashboard showed the virus signal was routinely detected in the wastewater prior to clusters of individual cases being reported. These data support the testing of wastewater for the presence of SARS-CoV-2 and may be used as part of a surveillance program for detecting the virus in a community prior to an outbreak occurring and could ultimately be incorporated with other SARS-CoV-2 metrics to better inform public health enabling a quick response to contain or mitigating spread of the virus.
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Affiliation(s)
- Jacob Kazenelson
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States of America
| | - Tori Jefferson
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States of America
| | - Ryan G. Rhodes
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States of America
| | - Lawrence B. Cahoon
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States of America
| | - Arthur R. Frampton
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, United States of America
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Koureas M, Mellou K, Vontas A, Kyritsi M, Panagoulias I, Koutsolioutsou A, Mouchtouri VA, Speletas M, Paraskevis D, Hadjichristodoulou C. Wastewater Levels of Respiratory Syncytial Virus Associated with Influenza-like Illness Rates in Children-A Case Study in Larissa, Greece (October 2022-January 2023). Int J Environ Res Public Health 2023; 20:5219. [PMID: 36982128 PMCID: PMC10048987 DOI: 10.3390/ijerph20065219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
The emergence of the COVID-19 pandemic has led to significant progress in the field of wastewater-based surveillance (WBS) of respiratory pathogens and highlighted its potential for a wider application in public health surveillance. This study aimed to evaluate whether monitoring of respiratory syncytial virus (RSV) in wastewater can provide a comprehensive picture of disease transmission at the community level. The study was conducted in Larissa (Central Greece) between October 2022 and January 2023. Forty-six wastewater samples were collected from the inlet of the wastewater treatment plant of Larissa and analyzed with a real-time reverse transcription polymerase chain reaction (RT-PCR) based method. RSV and SARS-CoV-2 wastewater viral loads (genome copies/100,000 inhabitants) were analyzed against sentinel surveillance data on influenza-like illness (ILI) to identify potential associations. Univariate linear regression analysis revealed that RSV wastewater viral load (lagged by one week) and ILI notification rates in children up to 14 years old were strongly associated (std. Beta: 0.73 (95% CI: 0.31-1.14), p = 0.002, R2 = 0.308). A weaker association was found between SARS-CoV-2 viral load and ILI rates in the 15+ age group (std. Beta: 0.56 (95% CI: 0.06-1.05), p = 0.032, R2 = 0.527). The results support the incorporation of RSV monitoring into existing wastewater-based surveillance systems.
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Affiliation(s)
- Michalis Koureas
- Laboratory of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi Str., 41222 Larissa, Greece
| | | | - Alexandros Vontas
- Laboratory of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi Str., 41222 Larissa, Greece
| | - Maria Kyritsi
- Laboratory of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi Str., 41222 Larissa, Greece
| | | | | | - Varvara A. Mouchtouri
- Laboratory of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi Str., 41222 Larissa, Greece
| | - Matthaios Speletas
- Department of Immunology and Histocompatibility, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece
| | | | - Christos Hadjichristodoulou
- Laboratory of Hygiene and Epidemiology, Faculty of Medicine, University of Thessaly, 22 Papakyriazi Str., 41222 Larissa, Greece
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10
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Larkin H. National Academies: Expand US Wastewater Disease Surveillance. JAMA 2023; 329:531. [PMID: 36723984 DOI: 10.1001/jama.2023.0739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Farkas K, Pellett C, Williams R, Alex-Sanders N, Bassano I, Brown MR, Denise H, Grimsley JMS, Kevill JL, Khalifa MS, Pântea I, Story R, Wade MJ, Woodhall N, Jones DL. Rapid Assessment of SARS-CoV-2 Variant-Associated Mutations in Wastewater Using Real-Time RT-PCR. Microbiol Spectr 2023; 11:e0317722. [PMID: 36629447 PMCID: PMC9927140 DOI: 10.1128/spectrum.03177-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/11/2022] [Indexed: 01/12/2023] Open
Abstract
Within months of the COVID-19 pandemic being declared on March 20, 2020, novel, more infectious variants of SARS-CoV-2 began to be detected in geospatially distinct regions of the world. With international travel being a lead cause of spread of the disease, the importance of rapidly identifying variants entering a country is critical. In this study, we utilized wastewater-based epidemiology (WBE) to monitor the presence of variants in wastewater generated in managed COVID-19 quarantine facilities for international air passengers entering the United Kingdom. Specifically, we developed multiplex reverse transcription quantitative PCR (RT-qPCR) assays for the identification of defining mutations associated with Beta (K417N), Gamma (K417T), Delta (156/157DEL), and Kappa (E154K) variants which were globally prevalent at the time of sampling (April to July 2021). The assays sporadically detected mutations associated with the Beta, Gamma, and Kappa variants in 0.7%, 2.3%, and 0.4% of all samples, respectively. The Delta variant was identified in 13.3% of samples, with peak detection rates and concentrations observed in May 2021 (24%), concurrent with its emergence in the United Kingdom. The RT-qPCR results correlated well with those from sequencing, suggesting that PCR-based detection is a good predictor for variant presence; although, inadequate probe binding may lead to false positive or negative results. Our findings suggest that WBE coupled with RT-qPCR may be used as a rapid, initial assessment to identify emerging variants at international borders and mass quarantining facilities. IMPORTANCE With the global spread of COVID-19, it is essential to identify emerging variants which may be more harmful or able to escape vaccines rapidly. To date, the gold standard to assess variants circulating in communities has been the sequencing of the S gene or the whole genome of SARS-CoV-2; however, that approach is time-consuming and expensive. In this study, we developed two duplex RT-qPCR assays to detect and quantify defining mutations associated with the Beta, Gamma, Delta, and Kappa variants. The assays were validated using RNA extracts derived from wastewater samples taken at quarantine facilities. The results showed good correlation with the results of sequencing and demonstrated the emergence of the Delta variant in the United Kingdom in May 2021. The assays developed here enable the assessment of variant-specific mutations within 2 h after the RNA extract was generated which is essential for outbreak rapid response.
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Affiliation(s)
- Kata Farkas
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, United Kingdom
| | - Cameron Pellett
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Rachel Williams
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Natasha Alex-Sanders
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Irene Bassano
- UK Health Security Agency, Environmental Monitoring for Health Protection, London, United Kingdom
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Mathew R. Brown
- UK Health Security Agency, Environmental Monitoring for Health Protection, London, United Kingdom
- School of Engineering, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Hubert Denise
- UK Health Security Agency, Environmental Monitoring for Health Protection, London, United Kingdom
| | - Jasmine M. S. Grimsley
- UK Health Security Agency, Environmental Monitoring for Health Protection, London, United Kingdom
- The London Data Company, London, United Kingdom
| | - Jessica L. Kevill
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Mohammad S. Khalifa
- UK Health Security Agency, Environmental Monitoring for Health Protection, London, United Kingdom
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University, London, United Kingdom
| | - Igor Pântea
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Rich Story
- UK Health Security Agency, Environmental Monitoring for Health Protection, London, United Kingdom
- Servita Professional Services (UK) Ltd., London, United Kingdom
| | - Matthew J. Wade
- UK Health Security Agency, Environmental Monitoring for Health Protection, London, United Kingdom
- School of Engineering, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Nick Woodhall
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
| | - Davey L. Jones
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, United Kingdom
- Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
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12
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Wolfe MK, Yu AT, Duong D, Rane MS, Hughes B, Chan-Herur V, Donnelly M, Chai S, White BJ, Vugia DJ, Boehm AB. Use of Wastewater for Mpox Outbreak Surveillance in California. N Engl J Med 2023; 388:570-572. [PMID: 36652340 DOI: 10.1056/nejmc2213882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | | | | | | | | | | | | | - Shua Chai
- Centers for Disease Control and Prevention, Atlanta, GA
| | | | - Duc J Vugia
- California Department of Public Health, Richmond, CA
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13
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Alahdal HM, Ameen F, AlYahya S, Sonbol H, Khan A, Alsofayan Y, Alahmari A. Municipal wastewater viral pollution in Saudi Arabia: effect of hot climate on COVID-19 disease spreading. Environ Sci Pollut Res Int 2023; 30:25050-25057. [PMID: 34138435 PMCID: PMC8210523 DOI: 10.1007/s11356-021-14809-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/07/2021] [Indexed: 05/02/2023]
Abstract
The viral RNA of SARS-Coronavirus-2 is known to be contaminating municipal wastewater. We aimed to assess if COVID-19 disease is spreading through wastewater. We studied the amount of viral RNA in raw sewage and the efficiency of the sewage treatment to remove the virus. Sewage water was collected before and after the activated sludge process three times during summer 2020 from three different sewage treatment plants. The sewage treatment was efficient in removing SARS-CoV-2 viral RNA. Each sewage treatment plant gathered wastewater from one hospital, of which COVID-19 admissions were used to describe the level of disease occurrence in the area. The presence of SARS-CoV-2 viral RNA-specific target genes (N1, N2, and E) was confirmed using RT-qPCR analysis. However, hospital admission did not correlate significantly with viral RNA. Moreover, viral RNA loads were relatively low, suggesting that sewage might preserve viral RNA in a hot climate only for a short time.
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Affiliation(s)
- Hadil M Alahdal
- Department of Biology, Faculty of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fuad Ameen
- Department of Botany & Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
| | - Sami AlYahya
- National Center for Biotechnology, King Abdulaziz City for Science & Technology, Riyadh, Saudi Arabia
| | - Hana Sonbol
- Department of Biology, Faculty of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Anas Khan
- Department of Emergency Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Global Center for Mass Gatherings Medicine, Ministry of Health, P.O. Box 11461, Riyadh, Saudi Arabia
| | - Yousef Alsofayan
- Global Center for Mass Gatherings Medicine, Ministry of Health, P.O. Box 11461, Riyadh, Saudi Arabia
| | - Ahmed Alahmari
- Global Center for Mass Gatherings Medicine, Ministry of Health, P.O. Box 11461, Riyadh, Saudi Arabia
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14
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15
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Abstract
Wastewater contains information on pathogen spread, evolution, and outbreak risk.
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Affiliation(s)
- Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
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16
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Rothman JA, Whiteson KL. Sequencing and Variant Detection of Eight Abundant Plant-Infecting Tobamoviruses across Southern California Wastewater. Microbiol Spectr 2022; 10:e0305022. [PMID: 36374107 PMCID: PMC9769696 DOI: 10.1128/spectrum.03050-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
Tobamoviruses are agriculturally relevant viruses that cause crop losses and have infected plants in many regions of the world. These viruses are frequently found in municipal wastewater, likely coming from human diet and industrial waste across wastewater catchment areas. As part of a large wastewater-based epidemiology study across Southern California, we analyzed RNA sequence data from 275 influent wastewater samples obtained from eight wastewater treatment plants with a catchment area of approximately 16 million people from July 2020 to August 2021. We assembled 1,083 high-quality genomes, enumerated viral sequencing reads, and detected thousands of single nucleotide variants from eight common tobamoviruses: bell pepper mottle virus, cucumber green mottle mosaic virus, pepper mild mottle virus, tobacco mild green mosaic virus, tomato brown rugose fruit virus, tomato mosaic virus, tomato mottle mosaic virus, and tropical soda apple mosaic virus. We show that single nucleotide variants had amino acid-altering consequences along with synonymous mutations, which represents potential evolution with functional consequences in genomes of these viruses. Our study shows the importance of wastewater sequencing to monitor the genomic diversity of these plant-infecting viruses, and we suggest that our data could be used to continue tracking the genomic variability of such pathogens. IMPORTANCE Diseases caused by viruses in the genus Tobamovirus cause crop losses around the world. As with other viruses, mutation occurring in the virus's genomes can have functional consequences and may alter viral infectivity. Many of these plant-infecting viruses have been found in wastewater, likely coming from human consumption of infected plants and produce. By sequencing RNA extracted from influent wastewater obtained from eight wastewater treatment plants in Southern California, we assembled high-quality viral genomes and detected thousands of single nucleotide variants from eight tobamoviruses. Our study shows that Tobamovirus genomes vary at many positions, which may have important consequences when designing assays for the detection of these viruses by agricultural or environmental scientists.
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Affiliation(s)
- Jason A. Rothman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Katrine L. Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
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17
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Mabasa VV, van Zyl WB, Ismail A, Allam M, Taylor MB, Mans J. Multiple Novel Human Norovirus Recombinants Identified in Wastewater in Pretoria, South Africa by Next-Generation Sequencing. Viruses 2022; 14:v14122732. [PMID: 36560736 PMCID: PMC9788511 DOI: 10.3390/v14122732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The genogroup II genotype 4 (GII.4) noroviruses are a major cause of viral gastroenteritis. Since the emergence of the Sydney_2012 variant, no novel norovirus GII.4 variants have been reported. The high diversity of noroviruses and periodic emergence of novel strains necessitates continuous global surveillance. The aim of this study was to assess the diversity of noroviruses in selected wastewater samples from Pretoria, South Africa (SA) using amplicon-based next-generation sequencing (NGS). Between June 2018 and August 2020, 200 raw sewage and final effluent samples were collected fortnightly from two wastewater treatment plants in Pretoria. Viruses were recovered using skimmed milk flocculation and glass wool adsorption-elution virus recovery methods and screened for noroviruses using a one-step real-time reverse-transcription PCR (RT-PCR). The norovirus BC genotyping region (570-579 bp) was amplified from detected norovirus strains and subjected to Illumina MiSeq NGS. Noroviruses were detected in 81% (162/200) of samples. The majority (89%, 89/100) of raw sewage samples were positive for at least one norovirus, compared with 73% (73/100) of final effluent samples. Overall, a total of 89 different GI and GII RdRp-capsid combinations were identified, including 51 putative novel recombinants, 34 previously reported RdRp-capsid combinations, one emerging novel recombinant and three Sanger-sequencing confirmed novel recombinants.
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Affiliation(s)
- Victor Vusi Mabasa
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | - Walda Brenda van Zyl
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- National Health Laboratory Service, Tshwane Academic Division, Pretoria 0002, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Maureen Beatrice Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | - Janet Mans
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- Correspondence: ; Tel.: +27-12-319-2660
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18
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Tang X, Fan C, Zeng G, Zhong L, Li C, Ren X, Song B, Liu X. Phage-host interactions: The neglected part of biological wastewater treatment. Water Res 2022; 226:119183. [PMID: 36244146 DOI: 10.1016/j.watres.2022.119183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/29/2022] [Accepted: 09/29/2022] [Indexed: 05/25/2023]
Abstract
In wastewater treatment plants (WWTPs), the stable operation of biological wastewater treatment is strongly dependent on the stability of associated microbiota. Bacteriophages (phages), viruses that specifically infect bacteria and archaea, are highly abundant and diverse in WWTPs. Although phages do not have known metabolic functions for themselves, they can shape functional microbiota via various phage-host interactions to impact biological wastewater treatment. However, the developments of phage-host interaction in WWTPs and their impact on biological wastewater treatment are overlooked. Here, we review the current knowledge regarding the phage-host interactions in biological wastewater treatment, mainly focusing on the characteristics of different phage populations, the phage-driven changes in functional microbiota, and the potential driving factors of phage-host interactions. We also discuss the efforts required further to understand and manipulate the phage-host interactions in biological wastewater treatment. Overall, this review advocates more attention to the phage dynamics in WWTPs.
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Affiliation(s)
- Xiang Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Changzheng Fan
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China.
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Linrui Zhong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Chao Li
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China; Nova Skantek (Hunan) Environ Energy Co., Ltd., Changsha 410100, P.R. China
| | - Xiaoya Ren
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Biao Song
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Xigui Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
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19
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Cao H, Mao K, Ran F, Xu P, Zhao Y, Zhang X, Zhou H, Yang Z, Zhang H, Jiang G. Paper Device Combining CRISPR/Cas12a and Reverse-Transcription Loop-Mediated Isothermal Amplification for SARS-CoV-2 Detection in Wastewater. Environ Sci Technol 2022; 56:13245-13253. [PMID: 36040863 PMCID: PMC9454323 DOI: 10.1021/acs.est.2c04727] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 05/04/2023]
Abstract
Wastewater-based surveillance of the COVID-19 pandemic holds great promise; however, a point-of-use detection method for SARS-CoV-2 in wastewater is lacking. Here, a portable paper device based on CRISPR/Cas12a and reverse-transcription loop-mediated isothermal amplification (RT-LAMP) with excellent sensitivity and specificity was developed for SARS-CoV-2 detection in wastewater. Three primer sets of RT-LAMP and guide RNAs (gRNAs) that could lead Cas12a to recognize target genes via base pairing were used to perform the high-fidelity RT-LAMP to detect the N, E, and S genes of SARS-CoV-2. Due to the trans-cleavage activity of CRISPR/Cas12a after high-fidelity amplicon recognition, carboxyfluorescein-ssDNA-Black Hole Quencher-1 and carboxyfluorescein-ssDNA-biotin probes were adopted to realize different visualization pathways via a fluorescence or lateral flow analysis, respectively. The reactions were integrated into a paper device for simultaneously detecting the N, E, and S genes with limits of detection (LODs) of 25, 310, and 10 copies/mL, respectively. The device achieved a semiquantitative analysis from 0 to 310 copies/mL due to the different LODs of the three genes. Blind experiments demonstrated that the device was suitable for wastewater analysis with 97.7% sensitivity and 82% semiquantitative accuracy. This is the first semiquantitative endpoint detection of SARS-CoV-2 in wastewater via different LODs, demonstrating a promising point-of-use method for wastewater-based surveillance.
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Affiliation(s)
- Haorui Cao
- State Key Laboratory of Environmental Geochemistry,
Institute of Geochemistry, Chinese Academy of Sciences,
Guiyang550081, China
- University of Chinese Academy of
Sciences, Beijing100049, China
| | - Kang Mao
- State Key Laboratory of Environmental Geochemistry,
Institute of Geochemistry, Chinese Academy of Sciences,
Guiyang550081, China
| | - Fang Ran
- State Key Laboratory of Environmental Geochemistry,
Institute of Geochemistry, Chinese Academy of Sciences,
Guiyang550081, China
| | - Pengqi Xu
- Precision Medicine Center, The Seventh
Affiliated Hospital, Sun Yat-sen University, Shenzhen518107,
China
| | - Yirong Zhao
- State Key Laboratory of Environmental Geochemistry,
Institute of Geochemistry, Chinese Academy of Sciences,
Guiyang550081, China
- University of Chinese Academy of
Sciences, Beijing100049, China
| | - Xiangyan Zhang
- Guizhou Provincial People’s
Hospital, Guiyang550002, China
| | - Hourong Zhou
- Guizhou Provincial People’s
Hospital, Guiyang550002, China
- Jiangjunshan Hospital of Guizhou
Province, Guiyang550001, China
| | - Zhugen Yang
- School of Water, Energy, and Environment,
Cranfield University, CranfieldMK43 0AL,
UK
| | - Hua Zhang
- State Key Laboratory of Environmental Geochemistry,
Institute of Geochemistry, Chinese Academy of Sciences,
Guiyang550081, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and
Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing100085, China
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20
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Solis-Moreira J. Study: New Wastewater Surveillance Method Detected SARS-CoV-2 Variants of Concern Up to 2 Weeks Before Clinical Tests. JAMA 2022; 328:914-915. [PMID: 36001330 DOI: 10.1001/jama.2022.12563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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21
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de Sousa ARV, do Carmo Silva L, de Curcio JS, da Silva HD, Eduardo Anunciação C, Maria Salem Izacc S, Neto FOS, de Paula Silveira Lacerda E. "pySewage": a hybrid approach to predict the number of SARS-CoV-2-infected people from wastewater in Brazil. Environ Sci Pollut Res Int 2022; 29:67260-67269. [PMID: 35524091 PMCID: PMC9075719 DOI: 10.1007/s11356-022-20609-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/30/2022] [Indexed: 05/21/2023]
Abstract
It is well known that the new coronavirus pandemic has global environmental, public health, and economic implications. In this sense, this study aims to monitor SARS-CoV-2 in the largest wastewater treatment plant of Goiânia, which processes wastewater from more than 700,000 inhabitants, and to correlate the molecular and clinical data collected. Influent and effluent samples were collected at Dr. Helio de Seixo Britto's wastewater treatment plant from January to August 2021. Viral concentration was performed with polyethylene glycol before viral RNA extraction. Real-time qPCR (N1 and N2 gene assays) was performed to detect and quantify the viral RNA present in the samples. The results showed that 43.63% of the samples were positive. There is no significant difference between the detection of primers N1 (mean 3.23 log10 genome copies/L, std 0.23) and N2 (mean 2.95 log10 genome copies/L, std 0.29); also, there is no significant difference between the detection of influent and effluent samples. Our molecular data revealed a positive correlation with clinical data, and infection prevalence was higher than clinical data. In addition, we developed a user-friendly web application to predict the number of infected people based on the detection of viral load present in wastewater samples and may be applied as a public policy strategy for monitoring ongoing outbreaks.
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Affiliation(s)
| | - Lívia do Carmo Silva
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Juliana Santana de Curcio
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Hugo Delleon da Silva
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
- Universitary Center of Goiás (UNIGOIÁS), Goiânia, Goiás, Brazil
| | - Carlos Eduardo Anunciação
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Silvia Maria Salem Izacc
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
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22
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Thongpradit S, Prasongtanakij S, Srisala S, Chanprasertyothin S, Pasomsub E, Ongphiphadhanakul B. The Detection of SARS-CoV2 Antigen in Wastewater Using an Automated Chemiluminescence Enzyme Immunoassay. IJERPH 2022; 19:ijerph19137783. [PMID: 35805441 PMCID: PMC9265940 DOI: 10.3390/ijerph19137783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 02/01/2023]
Abstract
The SARS-CoV-2 virus, which is driving the current COVID-19 epidemic, has been detected in wastewater and is being utilized as a surveillance tool to establish an early warning system to aid in the management and prevention of future pandemics. qPCR is the method usually used to detect SARS-CoV-2 in wastewater. There has been no study using an immunoassay that is less laboratory-intensive than qPCR with a shorter turnaround time. Therefore, we aimed to evaluate the performance of an automated chemiluminescence enzyme immunoassay (CLEIA) for SARS-CoV-2 antigen in wastewater. The CLEIA assay achieved 100% sensitivity and 66.7% specificity in a field-captured wastewater sample compared to the gold standard RT-qPCR. Our early findings suggest that the SARS-CoV-2 antigen can be identified in wastewater samples using an automated CLEIA, reducing the turnaround time and improving the performance of SARS-CoV-2 wastewater monitoring during the pandemic.
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Affiliation(s)
- Supranee Thongpradit
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.T.); (S.S.); (S.C.); (B.O.)
| | - Somsak Prasongtanakij
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.T.); (S.S.); (S.C.); (B.O.)
- Correspondence:
| | - Supanart Srisala
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.T.); (S.S.); (S.C.); (B.O.)
| | - Suwannee Chanprasertyothin
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.T.); (S.S.); (S.C.); (B.O.)
| | - Ekawat Pasomsub
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Boonsong Ongphiphadhanakul
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (S.T.); (S.S.); (S.C.); (B.O.)
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
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23
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Kumblathan T, Piroddi N, Hrudey SE, Li XF. Wastewater Based Surveillance of SARS-CoV-2: Challenges and Perspective from a Canadian Inter-laboratory Study. J Environ Sci (China) 2022; 116:229-232. [PMID: 35219421 PMCID: PMC8789553 DOI: 10.1016/j.jes.2022.01.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada
| | - Nicholas Piroddi
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada
| | - Steve E Hrudey
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Albert T6G 2G3a, Canada.
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24
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Nattino G, Castiglioni S, Cereda D, Della Valle PG, Pellegrinelli L, Bertolini G, Pariani E. Association Between SARS-CoV-2 Viral Load in Wastewater and Reported Cases, Hospitalizations, and Vaccinations in Milan, March 2020 to November 2021. JAMA 2022; 327:1922-1924. [PMID: 35363259 PMCID: PMC9115613 DOI: 10.1001/jama.2022.4908] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This study evaluates the association between SARS-CoV-2 load in urban wastewater and surveillance indicators of infection prevalence and severity in Milan, Italy.
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Affiliation(s)
- Giovanni Nattino
- Department of Public Health, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Ranica, Italy
| | - Sara Castiglioni
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
| | - Danilo Cereda
- Directorate General for Health, Lombardy Region, Milan, Italy
| | - Petra Giulia Della Valle
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, Milano, Italy
| | - Guido Bertolini
- Department of Public Health, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Ranica, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milano, Italy
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25
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Abstract
Monitoring the progression of SARS-CoV-2 outbreaks requires accurate estimation of the unobservable fraction of the population infected over time in addition to the observed numbers of COVID-19 cases, as the latter present a distorted view of the pandemic due to changes in test frequency and coverage over time. The objective of this report is to describe and illustrate an approach that produces representative estimates of the unobservable cumulative incidence of infection by scaling the daily concentrations of SARS-CoV-2 RNA in wastewater from the consistent population contribution of fecal material to the sewage collection system.
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Affiliation(s)
- Edward H Kaplan
- Yale School of Management, Yale University, New Haven, CT, 06520, USA.
- Yale School of Public Health, Yale University, New Haven, CT, 06520, USA.
- Department of Chemical and Environmental Engineering, School of Engineering and Applied Science, Yale University, New Haven, CT, 06520, USA.
| | - Alessandro Zulli
- Department of Chemical and Environmental Engineering, School of Engineering and Applied Science, Yale University, New Haven, CT, 06520, USA
| | - Marcela Sanchez
- Department of Chemical and Environmental Engineering, School of Engineering and Applied Science, Yale University, New Haven, CT, 06520, USA
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, School of Engineering and Applied Science, Yale University, New Haven, CT, 06520, USA
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26
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Peterson SW, Lidder R, Daigle J, Wonitowy Q, Dueck C, Nagasawa A, Mulvey MR, Mangat CS. RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples. Sci Total Environ 2022. [PMID: 34756912 DOI: 10.1101/2021.05.20.21257536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
SARS-CoV-2 variants of concern (VoC) have been increasingly detected in clinical surveillance in Canada and internationally. These VoC are associated with higher transmissibility rates and in some cases, increased mortality. In this work we present a national wastewater survey of the distribution of three SARS-CoV-2 mutations found in the B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma) VoC, namely the S-gene 69-70 deletion, N501Y mutation, and N-gene D3L. RT-qPCR allelic discrimination assays were sufficiently sensitive and specific for detection and relative quantitation of SARS-CoV-2 variants in wastewater to allow for rapid population-level screening and surveillance. We tested 261 samples collected from 5 Canadian cities (Vancouver, Edmonton, Toronto, Montreal, and Halifax) and 6 communities in the Northwest Territories from February 16th to March 28th, 2021. VoC were not detected in the Territorial communities, suggesting the absence of VoC SARS-CoV-2 cases in those communities. Percentage of variant remained low throughout the study period in the majority of the sites tested, however the Toronto sites showed a marked increase from ~25% to ~75% over the study period. The results of this study highlight the utility of population level molecular surveillance of SARS-CoV-2 VoC using wastewater. Wastewater monitoring for VoC can be a powerful tool in informing public health responses, including monitoring trends independent of clinical surveillance and providing early warning to communities.
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Affiliation(s)
- Shelley W Peterson
- Wastewater Surveillance, One-Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Ravinder Lidder
- Wastewater Surveillance, One-Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jade Daigle
- Wastewater Surveillance, One-Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Quinn Wonitowy
- Wastewater Surveillance, One-Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Codey Dueck
- Wastewater Surveillance, One-Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Audra Nagasawa
- Centre for Population Health Data, Statistics Canada, Ottawa, Ontario, Canada
| | - Michael R Mulvey
- Wastewater Surveillance, One-Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba. 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
| | - Chand S Mangat
- Wastewater Surveillance, One-Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba. 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.
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27
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Peterson SW, Lidder R, Daigle J, Wonitowy Q, Dueck C, Nagasawa A, Mulvey MR, Mangat CS. RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples. Sci Total Environ 2022; 810:151283. [PMID: 34756912 PMCID: PMC8552806 DOI: 10.1016/j.scitotenv.2021.151283] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 05/02/2023]
Abstract
SARS-CoV-2 variants of concern (VoC) have been increasingly detected in clinical surveillance in Canada and internationally. These VoC are associated with higher transmissibility rates and in some cases, increased mortality. In this work we present a national wastewater survey of the distribution of three SARS-CoV-2 mutations found in the B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma) VoC, namely the S-gene 69-70 deletion, N501Y mutation, and N-gene D3L. RT-qPCR allelic discrimination assays were sufficiently sensitive and specific for detection and relative quantitation of SARS-CoV-2 variants in wastewater to allow for rapid population-level screening and surveillance. We tested 261 samples collected from 5 Canadian cities (Vancouver, Edmonton, Toronto, Montreal, and Halifax) and 6 communities in the Northwest Territories from February 16th to March 28th, 2021. VoC were not detected in the Territorial communities, suggesting the absence of VoC SARS-CoV-2 cases in those communities. Percentage of variant remained low throughout the study period in the majority of the sites tested, however the Toronto sites showed a marked increase from ~25% to ~75% over the study period. The results of this study highlight the utility of population level molecular surveillance of SARS-CoV-2 VoC using wastewater. Wastewater monitoring for VoC can be a powerful tool in informing public health responses, including monitoring trends independent of clinical surveillance and providing early warning to communities.
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Affiliation(s)
- Shelley W Peterson
- Wastewater Surveillance, One-Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Ravinder Lidder
- Wastewater Surveillance, One-Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jade Daigle
- Wastewater Surveillance, One-Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Quinn Wonitowy
- Wastewater Surveillance, One-Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Codey Dueck
- Wastewater Surveillance, One-Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Audra Nagasawa
- Centre for Population Health Data, Statistics Canada, Ottawa, Ontario, Canada
| | - Michael R Mulvey
- Wastewater Surveillance, One-Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba. 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
| | - Chand S Mangat
- Wastewater Surveillance, One-Health Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba. 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.
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28
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Smyth DS, Trujillo M, Gregory DA, Cheung K, Gao A, Graham M, Guan Y, Guldenpfennig C, Hoxie I, Kannoly S, Kubota N, Lyddon TD, Markman M, Rushford C, San KM, Sompanya G, Spagnolo F, Suarez R, Teixeiro E, Daniels M, Johnson MC, Dennehy JJ. Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. Nat Commun 2022; 13:635. [PMID: 35115523 PMCID: PMC8813986 DOI: 10.1038/s41467-022-28246-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/10/2022] [Indexed: 11/21/2022] Open
Abstract
Tracking SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant to naturally acquired or vaccine-induced immunity. To monitor New York City (NYC) for the presence of novel variants, we deep sequence most of the receptor binding domain coding sequence of the S protein of SARS-CoV-2 isolated from the New York City wastewater. Here we report detecting increasing frequencies of novel cryptic SARS-CoV-2 lineages not recognized in GISAID's EpiCoV database. These lineages contain mutations that had been rarely observed in clinical samples, including Q493K, Q498Y, E484A, and T572N and share many mutations with the Omicron variant of concern. Some of these mutations expand the tropism of SARS-CoV-2 pseudoviruses by allowing infection of cells expressing the human, mouse, or rat ACE2 receptor. Finally, pseudoviruses containing the spike amino acid sequence of these lineages were resistant to different classes of receptor binding domain neutralizing monoclonal antibodies. We offer several hypotheses for the anomalous presence of these lineages, including the possibility that these lineages are derived from unsampled human COVID-19 infections or that they indicate the presence of a non-human animal reservoir.
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Affiliation(s)
- Davida S Smyth
- Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, TX, 78224, USA
| | - Monica Trujillo
- Department of Biological Sciences and Geology, Queensborough Community College of The City University of New York, Queens, NY, 11364, USA
| | - Devon A Gregory
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Kristen Cheung
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Anna Gao
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Maddie Graham
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Yue Guan
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Caitlyn Guldenpfennig
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Irene Hoxie
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Sherin Kannoly
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Nanami Kubota
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Terri D Lyddon
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Michelle Markman
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Clayton Rushford
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Kaung Myat San
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Geena Sompanya
- Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, TX, 78224, USA
| | - Fabrizio Spagnolo
- Department of Biological & Environmental Sciences, Long Island University-Post, Greenvale, New York, 11548, USA
| | - Reinier Suarez
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Emma Teixeiro
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Mark Daniels
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA.
| | - John J Dennehy
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA.
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29
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Kirby AE, Welsh RM, Marsh ZA, Yu AT, Vugia DJ, Boehm AB, Wolfe MK, White BJ, Matzinger SR, Wheeler A, Bankers L, Andresen K, Salatas C, Gregory DA, Johnson MC, Trujillo M, Kannoly S, Smyth DS, Dennehy JJ, Sapoval N, Ensor K, Treangen T, Stadler LB, Hopkins L. Notes from the Field: Early Evidence of the SARS-CoV-2 B.1.1.529 (Omicron) Variant in Community Wastewater - United States, November-December 2021. MMWR Morb Mortal Wkly Rep 2022; 71:103-105. [PMID: 35051130 PMCID: PMC8774157 DOI: 10.15585/mmwr.mm7103a5] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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30
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Abstract
Since the start of the coronavirus disease-2019 (COVID-19) pandemic, there has been interest in using wastewater monitoring as an approach for disease surveillance. A significant uncertainty that would improve the interpretation of wastewater monitoring data is the intensity and timing with which individuals shed RNA from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into wastewater. By combining wastewater and case surveillance data sets from a university campus during a period of heightened surveillance, we inferred that individual shedding of RNA into wastewater peaks on average 6 days (50% uncertainty interval (UI): 6-7; 95% UI: 4-8) following infection, and that wastewater measurements are highly overdispersed [negative binomial dispersion parameter, k = 0.39 (95% credible interval: 0.32-0.48)]. This limits the utility of wastewater surveillance as a leading indicator of secular trends in SARS-CoV-2 transmission during an epidemic, and implies that it could be most useful as an early warning of rising transmission in areas where transmission is low or clinical testing is delayed or of limited capacity.
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Affiliation(s)
- Sean Cavany
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
| | - Aaron Bivins
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, USA
| | - Zhenyu Wu
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, USA
| | - Devin North
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, USA
| | - T Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
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31
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Cavany S, Bivins A, Wu Z, North D, Bibby K, Perkins TA. Inferring SARS-CoV-2 RNA shedding into wastewater relative to the time of infection. Epidemiol Infect 2022; 150:e21. [PMID: 35068403 PMCID: PMC8795777 DOI: 10.1017/s0950268821002752] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/18/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
Since the start of the coronavirus disease-2019 (COVID-19) pandemic, there has been interest in using wastewater monitoring as an approach for disease surveillance. A significant uncertainty that would improve the interpretation of wastewater monitoring data is the intensity and timing with which individuals shed RNA from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into wastewater. By combining wastewater and case surveillance data sets from a university campus during a period of heightened surveillance, we inferred that individual shedding of RNA into wastewater peaks on average 6 days (50% uncertainty interval (UI): 6-7; 95% UI: 4-8) following infection, and that wastewater measurements are highly overdispersed [negative binomial dispersion parameter, k = 0.39 (95% credible interval: 0.32-0.48)]. This limits the utility of wastewater surveillance as a leading indicator of secular trends in SARS-CoV-2 transmission during an epidemic, and implies that it could be most useful as an early warning of rising transmission in areas where transmission is low or clinical testing is delayed or of limited capacity.
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Affiliation(s)
- Sean Cavany
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
| | - Aaron Bivins
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, USA
| | - Zhenyu Wu
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, USA
| | - Devin North
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, USA
| | - T. Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
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32
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Abstract
Since the start of the coronavirus disease-2019 (COVID-19) pandemic, there has been interest in using wastewater monitoring as an approach for disease surveillance. A significant uncertainty that would improve the interpretation of wastewater monitoring data is the intensity and timing with which individuals shed RNA from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into wastewater. By combining wastewater and case surveillance data sets from a university campus during a period of heightened surveillance, we inferred that individual shedding of RNA into wastewater peaks on average 6 days (50% uncertainty interval (UI): 6-7; 95% UI: 4-8) following infection, and that wastewater measurements are highly overdispersed [negative binomial dispersion parameter, k = 0.39 (95% credible interval: 0.32-0.48)]. This limits the utility of wastewater surveillance as a leading indicator of secular trends in SARS-CoV-2 transmission during an epidemic, and implies that it could be most useful as an early warning of rising transmission in areas where transmission is low or clinical testing is delayed or of limited capacity.
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Affiliation(s)
- Sean Cavany
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
| | - Aaron Bivins
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, USA
| | - Zhenyu Wu
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, USA
| | - Devin North
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, USA
| | - T Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
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Vilibic-Cavlek T, Stevanovic V, Brlek-Gorski D, Ferencak I, Ferenc T, Ujevic-Bosnjak M, Tabain I, Janev-Holcer N, Perkovic I, Anticevic M, Bekavac B, Kaic B, Mrzljak A, Ganjto M, Zmak L, Mauric Maljkovic M, Jelicic P, Bucic L, Barbic L. Emerging Trends in the Epidemiology of COVID-19: The Croatian 'One Health' Perspective. Viruses 2021; 13:2354. [PMID: 34960623 PMCID: PMC8707935 DOI: 10.3390/v13122354] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 02/07/2023] Open
Abstract
During the four pandemic waves, a total of 560,504 cases and 10,178 deaths due to COVID-19 were reported in Croatia. The Alpha variant, dominant from March 2021 (>50% of positive samples), was rapidly replaced by Delta variants (>90%) by August 2021. Several seroprevalence studies were conducted in different populations (general population, children/adolescents, professional athletes, healthcare workers, veterinarians) and in immunocompromised patients (hemodialysis patients, liver/kidney transplant recipients). After the first pandemic wave, seroprevalence rates of neutralizing (NT) antibodies were reported to be 0.2-5.5%. Significantly higher seropositivity was detected during/after the second wave, 2.6-18.7%. Two studies conducted in pet animals (February-June 2020/July-December 2020) reported SARS-CoV-2 NT antibodies in 0.76% of cats and 0.31-14.69% of dogs, respectively. SARS-CoV-2 NT antibodies were not detected in wildlife. Environmental samples taken in the households of COVID-19 patients showed high-touch personal objects as most frequently contaminated (17.3%), followed by surfaces in patients' rooms (14.6%), kitchens (13.3%) and bathrooms (8.3%). SARS-CoV-2 RNA was also detected in 96.8% affluent water samples, while all effluent water samples tested negative. Detection of SARS-CoV-2 in humans, animals and the environment suggests that the 'One Health' approach is critical to controlling COVID-19 and future pandemics.
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Affiliation(s)
- Tatjana Vilibic-Cavlek
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (I.F.); (I.T.)
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Vladimir Stevanovic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine University of Zagreb, 10000 Zagreb, Croatia;
| | - Diana Brlek-Gorski
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
| | - Ivana Ferencak
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (I.F.); (I.T.)
| | - Thomas Ferenc
- Clinical Department of Diagnostic and Interventional Radiology, Merkur University Hospital, 10000 Zagreb, Croatia;
| | - Magdalena Ujevic-Bosnjak
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
| | - Irena Tabain
- Department of Virology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (I.F.); (I.T.)
| | - Natasa Janev-Holcer
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
- Department of Social Medicine and Epidemiology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Ivana Perkovic
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
| | - Mario Anticevic
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
| | - Barbara Bekavac
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
| | - Bernard Kaic
- Department of Epidemiology, Croatian Institute of Public Health, 10000 Zagreb, Croatia;
| | - Anna Mrzljak
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
- Department of Gastroenterology and Hepatology, University Hospital Center Zagreb, 10000 Zagreb, Croatia
| | - Marin Ganjto
- Zagreb Wastewater-Management and Operation Ltd., 10000 Zagreb, Croatia;
| | - Ljiljana Zmak
- Department for Tuberculosis, Croatian Institute of Public Health, 10000 Zagreb, Croatia;
| | - Maja Mauric Maljkovic
- Department for Animal Breeding and Livestock Production, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Pavle Jelicic
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
| | - Lovro Bucic
- Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; (D.B.-G.); (M.U.-B.); (N.J.-H.); (I.P.); (M.A.); (B.B.); (P.J.); (L.B.)
| | - Ljubo Barbic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine University of Zagreb, 10000 Zagreb, Croatia;
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Stahl EC, Gopez AR, Tsuchida CA, Fan VB, Moehle EA, Witkowsky LB, Hamilton JR, Lin-Shiao E, McElroy M, McDevitt SL, Ciling A, Tsui CK, Pestal K, Gildea HK, Keller A, Sylvain IA, Williams C, Hirsh A, Ehrenberg AJ, Kantor R, Metzger M, Nelson KL, Urnov FD, Ringeisen BR, Giannikopoulos P, Doudna JA. LuNER: Multiplexed SARS-CoV-2 detection in clinical swab and wastewater samples. PLoS One 2021; 16:e0258263. [PMID: 34758033 PMCID: PMC8580221 DOI: 10.1371/journal.pone.0258263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/22/2021] [Indexed: 01/03/2023] Open
Abstract
Clinical and surveillance testing for the SARS-CoV-2 virus relies overwhelmingly on RT-qPCR-based diagnostics, yet several popular assays require 2-3 separate reactions or rely on detection of a single viral target, which adds significant time, cost, and risk of false-negative results. Furthermore, multiplexed RT-qPCR tests that detect at least two SARS-CoV-2 genes in a single reaction are typically not affordable for large scale clinical surveillance or adaptable to multiple PCR machines and plate layouts. We developed a RT-qPCR assay using the Luna Probe Universal One-Step RT-qPCR master mix with publicly available primers and probes to detect SARS-CoV-2 N gene, E gene, and human RNase P (LuNER) to address these shortcomings and meet the testing demands of a university campus and the local community. This cost-effective test is compatible with BioRad or Applied Biosystems qPCR machines, in 96 and 384-well formats, with or without sample pooling, and has a detection sensitivity suitable for both clinical reporting and wastewater surveillance efforts.
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Affiliation(s)
- Elizabeth C. Stahl
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Allan R. Gopez
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Connor A. Tsuchida
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Vinson B. Fan
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Erica A. Moehle
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Lea B. Witkowsky
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Jennifer R. Hamilton
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Enrique Lin-Shiao
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Matthew McElroy
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Shana L. McDevitt
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Alison Ciling
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - C. Kimberly Tsui
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Kathleen Pestal
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Holly K. Gildea
- University of California, Berkeley, Berkeley, CA, United States of America
| | - Amanda Keller
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Iman A. Sylvain
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Clara Williams
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Ariana Hirsh
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | | | - Rose Kantor
- University of California, Berkeley, Berkeley, CA, United States of America
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, United States of America
| | - Matthew Metzger
- University of California, Berkeley, Berkeley, CA, United States of America
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, United States of America
| | - Kara L. Nelson
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, United States of America
| | - Fyodor D. Urnov
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Bradley R. Ringeisen
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Petros Giannikopoulos
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
| | - Jennifer A. Doudna
- University of California, Berkeley, Berkeley, CA, United States of America
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, CA, United States of America
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Rothman JA, Loveless TB, Kapcia J, Adams ED, Steele JA, Zimmer-Faust AG, Langlois K, Wanless D, Griffith M, Mao L, Chokry J, Griffith JF, Whiteson KL. RNA Viromics of Southern California Wastewater and Detection of SARS-CoV-2 Single-Nucleotide Variants. Appl Environ Microbiol 2021; 87:e0144821. [PMID: 34550753 PMCID: PMC8579973 DOI: 10.1128/aem.01448-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/14/2021] [Indexed: 11/20/2022] Open
Abstract
Municipal wastewater provides an integrated sample of a diversity of human-associated microbes across a sewershed, including viruses. Wastewater-based epidemiology (WBE) is a promising strategy to detect pathogens and may serve as an early warning system for disease outbreaks. Notably, WBE has garnered substantial interest during the coronavirus disease 2019 (COVID-19) pandemic to track disease burden through analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Throughout the COVID-19 outbreak, tracking SARS-CoV-2 in wastewater has been an important tool for understanding the spread of the virus. Unlike traditional sequencing of SARS-CoV-2 isolated from clinical samples, which adds testing burden to the health care system, in this study, metatranscriptomics was used to sequence virus directly from wastewater. Here, we present a study in which we explored RNA viral diversity through sequencing 94 wastewater influent samples across seven wastewater treatment plants (WTPs), collected from August 2020 to January 2021, representing approximately 16 million people in Southern California. Enriched viral libraries identified a wide diversity of RNA viruses that differed between WTPs and over time, with detected viruses including coronaviruses, influenza A, and noroviruses. Furthermore, single-nucleotide variants (SNVs) of SARS-CoV-2 were identified in wastewater, and we measured proportions of overall virus and SNVs across several months. We detected several SNVs that are markers for clinically important SARS-CoV-2 variants along with SNVs of unknown function, prevalence, or epidemiological consequence. Our study shows the potential of WBE to detect viruses in wastewater and to track the diversity and spread of viral variants in urban and suburban locations, which may aid public health efforts to monitor disease outbreaks. IMPORTANCE Wastewater-based epidemiology (WBE) can detect pathogens across sewersheds, which represents the collective waste of human populations. As there is a wide diversity of RNA viruses in wastewater, monitoring the presence of these viruses is useful for public health, industry, and ecological studies. Specific to public health, WBE has proven valuable during the coronavirus disease 2019 (COVID-19) pandemic to track the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) without adding burden to health care systems. In this study, we used metatranscriptomics and reverse transcription-droplet digital PCR (RT-ddPCR) to assay RNA viruses across Southern California wastewater from August 2020 to January 2021, representing approximately 16 million people from Los Angeles, Orange, and San Diego counties. We found that SARS-CoV-2 quantification in wastewater correlates well with county-wide COVID-19 case data, and that we can detect SARS-CoV-2 single-nucleotide variants through sequencing. Likewise, wastewater treatment plants (WTPs) harbored different viromes, and we detected other human pathogens, such as noroviruses and adenoviruses, furthering our understanding of wastewater viral ecology.
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Affiliation(s)
- Jason A. Rothman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Theresa B. Loveless
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, USA
| | - Joseph Kapcia
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Eric D. Adams
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
| | - Joshua A. Steele
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | | | - Kylie Langlois
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - David Wanless
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Madison Griffith
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Lucy Mao
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Jeffrey Chokry
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - John F. Griffith
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Katrine L. Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California, USA
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Melvin RG, Hendrickson EN, Chaudhry N, Georgewill O, Freese R, Schacker TW, Simmons GE. A novel wastewater-based epidemiology indexing method predicts SARS-CoV-2 disease prevalence across treatment facilities in metropolitan and regional populations. Sci Rep 2021; 11:21368. [PMID: 34725394 PMCID: PMC8560786 DOI: 10.1038/s41598-021-00853-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/19/2021] [Indexed: 12/14/2022] Open
Abstract
There is a need for wastewater based epidemiological (WBE) methods that integrate multiple, variously sized surveillance sites across geographic areas. We developed a novel indexing method, Melvin's Index, that provides a normalized and standardized metric of wastewater pathogen load for qPCR assays that is resilient to surveillance site variation. To demonstrate the utility of Melvin's Index, we used qRT-PCR to measure SARS-CoV-2 genomic RNA levels in influent wastewater from 19 municipal wastewater treatment facilities (WWTF's) of varying sizes and served populations across the state of Minnesota during the Summer of 2020. SARS-CoV-2 RNA was detected at each WWTF during the 20-week sampling period at a mean concentration of 8.5 × 104 genome copies/L (range 3.2 × 102-1.2 × 109 genome copies/L). Lag analysis of trends in Melvin's Index values and clinical COVID-19 cases showed that increases in indexed wastewater SARS-CoV-2 levels precede new clinical cases by 15-17 days at the statewide level and by up to 25 days at the regional/county level. Melvin's Index is a reliable WBE method and can be applied to both WWTFs that serve a wide range of population sizes and to large regions that are served by multiple WWTFs.
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Affiliation(s)
- Richard G Melvin
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, USA
| | - Emily N Hendrickson
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, USA
| | - Nabiha Chaudhry
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, USA
| | - Onimitein Georgewill
- National Summer Undergraduate Research Program, University of Maryland, College Park, MD, USA
| | - Rebecca Freese
- Biostatistical Design and Analysis Center, Clinical and Translational Science Institute, University of Minnesota, Minneapolis, MN, USA
| | - Timothy W Schacker
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Glenn E Simmons
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, USA.
- Carcinogenesis and Chemoprevention Program, Masonic Cancer Center, Minneapolis, MN, USA.
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37
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Corchis-Scott R, Geng Q, Seth R, Ray R, Beg M, Biswas N, Charron L, Drouillard KD, D'Souza R, Heath DD, Houser C, Lawal F, McGinlay J, Menard SL, Porter LA, Rawlings D, Scholl ML, Siu KWM, Tong Y, Weisener CG, Wilhelm SW, McKay RML. Averting an Outbreak of SARS-CoV-2 in a University Residence Hall through Wastewater Surveillance. Microbiol Spectr 2021; 9:e0079221. [PMID: 34612693 DOI: 10.1101/2021.06.23.21259176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
A wastewater surveillance program targeting a university residence hall was implemented during the spring semester 2021 as a proactive measure to avoid an outbreak of COVID-19 on campus. Over a period of 7 weeks from early February through late March 2021, wastewater originating from the residence hall was collected as grab samples 3 times per week. During this time, there was no detection of SARS-CoV-2 by reverse transcriptase quantitative PCR (RT-qPCR) in the residence hall wastewater stream. Aiming to obtain a sample more representative of the residence hall community, a decision was made to use passive samplers beginning in late March onwards. Adopting a Moore swab approach, SARS-CoV-2 was detected in wastewater samples just 2 days after passive samplers were deployed. These samples also tested positive for the B.1.1.7 (Alpha) variant of concern (VOC) using RT-qPCR. The positive result triggered a public health case-finding response, including a mobile testing unit deployed to the residence hall the following day, with testing of nearly 200 students and staff, which identified two laboratory-confirmed cases of Alpha variant COVID-19. These individuals were relocated to a separate quarantine facility, averting an outbreak on campus. Aggregating wastewater and clinical data, the campus wastewater surveillance program has yielded the first estimates of fecal shedding rates of the Alpha VOC of SARS-CoV-2 in individuals from a nonclinical setting. IMPORTANCE Among early adopters of wastewater monitoring for SARS-CoV-2 have been colleges and universities throughout North America, many of whom are using this approach to monitor congregate living facilities for early evidence of COVID-19 infection as an integral component of campus screening programs. Yet, while there have been numerous examples where wastewater monitoring on a university campus has detected evidence for infection among community members, there are few examples where this monitoring triggered a public health response that may have averted an actual outbreak. This report details a wastewater-testing program targeting a residence hall on a university campus during spring 2021, when there was mounting concern globally over the emergence of SARS-CoV-2 variants of concern, reported to be more transmissible than the wild-type Wuhan strain. In this communication, we present a clear example of how wastewater monitoring resulted in actionable responses by university administration and public health, which averted an outbreak of COVID-19 on a university campus.
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Affiliation(s)
- Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Rajesh Seth
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
- Civil and Environmental Engineering, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Rajan Ray
- Civil and Environmental Engineering, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Mohsan Beg
- Student Counselling Centre, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Nihar Biswas
- Civil and Environmental Engineering, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Lynn Charron
- Residence Services, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Kenneth D Drouillard
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
- School of the Environment, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Ramsey D'Souza
- Windsor-Essex County Health Unit, Windsor, Ontario, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
- Department of Integrative Biology, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Chris Houser
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
- School of the Environment, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Felicia Lawal
- Windsor-Essex County Health Unit, Windsor, Ontario, Canada
| | - James McGinlay
- Residence Services, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Sherri Lynne Menard
- Environmental Health and Safety, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Lisa A Porter
- Department of Biomedical Sciences, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Diane Rawlings
- Residence Services, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Matthew L Scholl
- Student Health Services, University of Windsorgrid.267455.7University of Windsor, grid.267455.7, Windsor, Ontario, Canada
| | - K W Michael Siu
- Department of Chemistry and Biochemistry, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Christopher G Weisener
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
- School of the Environment, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Tennessee, USA
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
| | - R Michael L McKay
- Great Lakes Institute for Environmental Research, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
- School of the Environment, University of Windsorgrid.267455.7, Windsor, Ontario, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
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38
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Corchis-Scott R, Geng Q, Seth R, Ray R, Beg M, Biswas N, Charron L, Drouillard KD, D’Souza R, Heath DD, Houser C, Lawal F, McGinlay J, Menard SL, Porter LA, Rawlings D, Scholl ML, Siu KWM, Tong Y, Weisener CG, Wilhelm SW, McKay RML. Averting an Outbreak of SARS-CoV-2 in a University Residence Hall through Wastewater Surveillance. Microbiol Spectr 2021; 9:e0079221. [PMID: 34612693 PMCID: PMC8510253 DOI: 10.1128/spectrum.00792-21] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/06/2021] [Indexed: 12/23/2022] Open
Abstract
A wastewater surveillance program targeting a university residence hall was implemented during the spring semester 2021 as a proactive measure to avoid an outbreak of COVID-19 on campus. Over a period of 7 weeks from early February through late March 2021, wastewater originating from the residence hall was collected as grab samples 3 times per week. During this time, there was no detection of SARS-CoV-2 by reverse transcriptase quantitative PCR (RT-qPCR) in the residence hall wastewater stream. Aiming to obtain a sample more representative of the residence hall community, a decision was made to use passive samplers beginning in late March onwards. Adopting a Moore swab approach, SARS-CoV-2 was detected in wastewater samples just 2 days after passive samplers were deployed. These samples also tested positive for the B.1.1.7 (Alpha) variant of concern (VOC) using RT-qPCR. The positive result triggered a public health case-finding response, including a mobile testing unit deployed to the residence hall the following day, with testing of nearly 200 students and staff, which identified two laboratory-confirmed cases of Alpha variant COVID-19. These individuals were relocated to a separate quarantine facility, averting an outbreak on campus. Aggregating wastewater and clinical data, the campus wastewater surveillance program has yielded the first estimates of fecal shedding rates of the Alpha VOC of SARS-CoV-2 in individuals from a nonclinical setting. IMPORTANCE Among early adopters of wastewater monitoring for SARS-CoV-2 have been colleges and universities throughout North America, many of whom are using this approach to monitor congregate living facilities for early evidence of COVID-19 infection as an integral component of campus screening programs. Yet, while there have been numerous examples where wastewater monitoring on a university campus has detected evidence for infection among community members, there are few examples where this monitoring triggered a public health response that may have averted an actual outbreak. This report details a wastewater-testing program targeting a residence hall on a university campus during spring 2021, when there was mounting concern globally over the emergence of SARS-CoV-2 variants of concern, reported to be more transmissible than the wild-type Wuhan strain. In this communication, we present a clear example of how wastewater monitoring resulted in actionable responses by university administration and public health, which averted an outbreak of COVID-19 on a university campus.
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Affiliation(s)
- Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - Rajesh Seth
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- Civil and Environmental Engineering, University of Windsor, Windsor, Ontario, Canada
| | - Rajan Ray
- Civil and Environmental Engineering, University of Windsor, Windsor, Ontario, Canada
| | - Mohsan Beg
- Student Counselling Centre, University of Windsor, Windsor, Ontario, Canada
| | - Nihar Biswas
- Civil and Environmental Engineering, University of Windsor, Windsor, Ontario, Canada
| | - Lynn Charron
- Residence Services, University of Windsor, Windsor, Ontario, Canada
| | - Kenneth D. Drouillard
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- School of the Environment, University of Windsor, Windsor, Ontario, Canada
| | - Ramsey D’Souza
- Windsor-Essex County Health Unit, Windsor, Ontario, Canada
| | - Daniel D. Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- Department of Integrative Biology, University of Windsor, Windsor, Ontario, Canada
| | - Chris Houser
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- School of the Environment, University of Windsor, Windsor, Ontario, Canada
| | - Felicia Lawal
- Windsor-Essex County Health Unit, Windsor, Ontario, Canada
| | - James McGinlay
- Residence Services, University of Windsor, Windsor, Ontario, Canada
| | - Sherri Lynne Menard
- Environmental Health and Safety, University of Windsor, Windsor, Ontario, Canada
| | - Lisa A. Porter
- Department of Biomedical Sciences, University of Windsor, Windsor, Ontario, Canada
| | - Diane Rawlings
- Residence Services, University of Windsor, Windsor, Ontario, Canada
| | - Matthew L. Scholl
- Student Health Services, University of Windsor, Windsor, Ontario, Canada
| | - K. W. Michael Siu
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Christopher G. Weisener
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- School of the Environment, University of Windsor, Windsor, Ontario, Canada
| | - Steven W. Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Tennessee, USA
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
| | - R. Michael L. McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- School of the Environment, University of Windsor, Windsor, Ontario, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
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Krivoňáková N, Šoltýsová A, Tamáš M, Takáč Z, Krahulec J, Ficek A, Gál M, Gall M, Fehér M, Krivjanská A, Horáková I, Belišová N, Bímová P, Škulcová AB, Mackuľak T. Mathematical modeling based on RT-qPCR analysis of SARS-CoV-2 in wastewater as a tool for epidemiology. Sci Rep 2021; 11:19456. [PMID: 34593871 PMCID: PMC8484274 DOI: 10.1038/s41598-021-98653-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/09/2021] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerges to scientific research and monitoring of wastewaters to predict the spread of the virus in the community. Our study investigated the COVID-19 disease in Bratislava, based on wastewater monitoring from September 2020 until March 2021. Samples were analyzed from two wastewater treatment plants of the city with reaching 0.6 million monitored inhabitants. Obtained results from the wastewater analysis suggest significant statistical dependence. High correlations between the number of viral particles in wastewater and the number of reported positive nasopharyngeal RT-qPCR tests of infected individuals with a time lag of 2 weeks/12 days (R2 = 83.78%/R2 = 52.65%) as well as with a reported number of death cases with a time lag of 4 weeks/27 days (R2 = 83.21%/R2 = 61.89%) was observed. The obtained results and subsequent mathematical modeling will serve in the future as an early warning system for the occurrence of a local site of infection and, at the same time, predict the load on the health system up to two weeks in advance.
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Affiliation(s)
- Naďa Krivoňáková
- Institute of Information Engineering, Automation, and Mathematics, Department of Mathematics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovakia
| | - Andrea Šoltýsová
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
- Institute for Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Dúbravska Cesta 9, 84505, Bratislava, Slovakia
| | - Michal Tamáš
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic.
| | - Zdenko Takáč
- Institute of Information Engineering, Automation, and Mathematics, Department of Mathematics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovakia
| | - Ján Krahulec
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Andrej Ficek
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Miroslav Gál
- Department of Inorganic Technology, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovakia
| | - Marián Gall
- Institute of Information Engineering, Automation, and Mathematics, Department of Mathematics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovakia
| | - Miroslav Fehér
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic
| | - Anna Krivjanská
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic
| | - Ivana Horáková
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic
| | - Noemi Belišová
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic
| | - Paula Bímová
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic
| | - Andrea Butor Škulcová
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic
| | - Tomáš Mackuľak
- Department of Environmental Engineering, Faculty of Chemistry and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37, Bratislava, Slovak Republic
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Godini H, Hoseinzadeh E, Hossini H. Water and wastewater as potential sources of SARS-CoV-2 transmission: a systematic review. Rev Environ Health 2021; 36:309-317. [PMID: 33594845 DOI: 10.1515/reveh-2020-0148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 01/20/2021] [Indexed: 05/17/2023]
Abstract
An important group of viruses are Coronaviruses that affect the health of people worldwide, in particular the acute respiratory syndrome. The present work has addressed the updated literature on the topic of coronaviruses transmission through water and wastewater as well as identified gaps in research to inform future studies. In total, 198 articles were selected, then after screening, 48 eligible studies were fully reviewed. Accordingly, the studies showed that the coronavirus has been isolated and identified from water as well as wastewater. The results of researches show that the presence of SARS-Co-2 virus in municipal wastewater is possible due to the excretion of the virus in human feces. In addition, the SARS-Co-2 virus was isolated from contaminated water and rivers, but there is insufficient evidence for virus transmission by water and wastewater. Water and wastewater treatment methods are able to reduce the pollution load caused by this virus in water sources. Water disinfection has an effective role in removing it from water and wastewater sources. Due to the short period of time in the global pandemic and the small number of studies in this field, further studies are needed to make a definite statement about the transferability of virus in water and wastewater.
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Affiliation(s)
- Hatam Godini
- Department of Environmental Health Engineering, School of Health, Alborz University of Medical Sciences, Karaj, Iran
- Research Center for Health, Safety, and Environment, Alborz University of Medical Science, Karaj, Iran
| | - Edris Hoseinzadeh
- Student Research Committee, Saveh University of Medical Sciences, Saveh, Iran
| | - Hooshyar Hossini
- Department of Environmental Health Engineering, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Trujillo M, Cheung K, Gao A, Hoxie I, Kannoly S, Kubota N, San KM, Smyth DS, Dennehy JJ. Protocol for safe, affordable, and reproducible isolation and quantitation of SARS-CoV-2 RNA from wastewater. PLoS One 2021; 16:e0257454. [PMID: 34555079 PMCID: PMC8459947 DOI: 10.1371/journal.pone.0257454] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 09/01/2021] [Indexed: 12/15/2022] Open
Abstract
The following protocol describes our workflow for processing wastewater with the goal of detecting the genetic signal of SARS-CoV-2. The steps include pasteurization, virus concentration, RNA extraction, and quantification by RT-qPCR. We include auxiliary steps that provide new users with tools and strategies that will help troubleshoot key steps in the process. This protocol is one of the safest, cheapest, and most reproducible approaches for the detection of SARS-CoV-2 RNA in wastewater. Owing to a pasteurization step, it is safe for use in a BSL2 facility. In addition to making the protocol safe for the personnel involved, pasteurization had the added benefit of increasing the SARS-CoV-2 genetic signal. Furthermore, the RNA obtained using this protocol can be sequenced using both Sanger and Illumina sequencing technologies. The protocol was adopted by the New York City Department of Environmental Protection in August 2020 to monitor SARS-CoV-2 prevalence in wastewater in all five boroughs of the city. In the future, this protocol could be used to detect a variety of other clinically relevant viruses in wastewater and serve as a foundation of a wastewater surveillance strategy for monitoring community spread of known and emerging viral pathogens.
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Affiliation(s)
- Monica Trujillo
- Department of Biology, Queensborough Community College, The City University of New York, New York City, New York, United States of America
| | - Kristen Cheung
- Biology Department, Queens College, The City University of New York, New York City, New York, United States of America
| | - Anna Gao
- Biology Department, Queens College, The City University of New York, New York City, New York, United States of America
| | - Irene Hoxie
- Biology Department, Queens College, The City University of New York, New York City, New York, United States of America
- Biology Doctoral Program, The Graduate Center, The City University of New York, New York City, New York, United States of America
| | - Sherin Kannoly
- Biology Department, Queens College, The City University of New York, New York City, New York, United States of America
| | - Nanami Kubota
- Biology Department, Queens College, The City University of New York, New York City, New York, United States of America
| | - Kaung Myat San
- Biology Department, Queens College, The City University of New York, New York City, New York, United States of America
| | - Davida S. Smyth
- Department of Natural Sciences and Mathematics, Eugene Lang College of Liberal Arts at The New School, New York City, New York, United States of America
| | - John J. Dennehy
- Biology Department, Queens College, The City University of New York, New York City, New York, United States of America
- Biology Doctoral Program, The Graduate Center, The City University of New York, New York City, New York, United States of America
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Abstract
Plateaus and rebounds of various epidemiological indicators are widely reported in Covid-19 pandemics studies but have not been explained so far. Here, we address this problem and explain the appearance of these patterns. We start with an empirical study of an original dataset obtained from highly precise measurements of SARS-CoV-2 concentration in wastewater over nine months in several treatment plants around the Thau lagoon in France. Among various features, we observe that the concentration displays plateaus at different dates in various locations but at the same level. In order to understand these facts, we introduce a new mathematical model that takes into account the heterogeneity and the natural variability of individual behaviours. Our model shows that the distribution of risky behaviours appears as the key ingredient for understanding the observed temporal patterns of epidemics.
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Affiliation(s)
- Henri Berestycki
- École des Hautes Études en Sciences Sociales and CNRS, CAMS, Paris, France.
- Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
| | - Benoît Desjardins
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli, Gif-sur-Yvette, France
- Geobiomics, 75 Av. des Champs-Elysées, 75008, Paris, France
| | - Bruno Heintz
- Geobiomics, 75 Av. des Champs-Elysées, 75008, Paris, France
| | - Jean-Marc Oury
- Geobiomics, 75 Av. des Champs-Elysées, 75008, Paris, France
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Kirby AE, Walters MS, Jennings WC, Fugitt R, LaCross N, Mattioli M, Marsh ZA, Roberts VA, Mercante JW, Yoder J, Hill VR. Using Wastewater Surveillance Data to Support the COVID-19 Response - United States, 2020-2021. MMWR Morb Mortal Wkly Rep 2021; 70:1242-1244. [PMID: 34499630 PMCID: PMC8437053 DOI: 10.15585/mmwr.mm7036a2] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Wastewater surveillance, the measurement of pathogen levels in wastewater, is used to evaluate community-level infection trends, augment traditional surveillance that leverages clinical tests and services (e.g., case reporting), and monitor public health interventions (1). Approximately 40% of persons infected with SARS-CoV-2, the virus that causes COVID-19, shed virus RNA in their stool (2); therefore, community-level trends in SARS-CoV-2 infections, both symptomatic and asymptomatic (2) can be tracked through wastewater testing (3-6). CDC launched the National Wastewater Surveillance System (NWSS) in September 2020 to coordinate wastewater surveillance programs implemented by state, tribal, local, and territorial health departments to support the COVID-19 pandemic response. In the United States, wastewater surveillance was not previously implemented at the national level. As of August 2021, NWSS includes 37 states, four cities, and two territories. This report summarizes NWSS activities and describes innovative applications of wastewater surveillance data by two states, which have included generating alerts to local jurisdictions, allocating mobile testing resources, evaluating irregularities in traditional surveillance, refining health messaging, and forecasting clinical resource needs. NWSS complements traditional surveillance and enables health departments to intervene earlier with focused support in communities experiencing increasing concentrations of SARS-CoV-2 in wastewater. The ability to conduct wastewater surveillance is not affected by access to health care or the clinical testing capacity in the community. Robust, sustainable implementation of wastewater surveillance requires public health capacity for wastewater testing, analysis, and interpretation. Partnerships between wastewater utilities and public health departments are needed to leverage wastewater surveillance data for the COVID-19 response for rapid assessment of emerging threats and preparedness for future pandemics.
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44
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Crowe J, Schnaubelt AT, SchmidtBonne S, Angell K, Bai J, Eske T, Nicklin M, Pratt C, White B, Crotts-Hannibal B, Staffend N, Herrera V, Cobb J, Conner J, Carstens J, Tempero J, Bouda L, Ray M, Lawler JV, Campbell WS, Lowe JM, Santarpia J, Bartelt-Hunt S, Wiley M, Brett-Major D, Logan C, Broadhurst MJ. Assessment of a Program for SARS-CoV-2 Screening and Environmental Monitoring in an Urban Public School District. JAMA Netw Open 2021. [PMID: 34550382 DOI: 10.1101/2021.04.14.21255036v1%0a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
IMPORTANCE Scalable programs for school-based SARS-CoV-2 testing and surveillance are needed to guide in-person learning practices and inform risk assessments in kindergarten through 12th grade settings. OBJECTIVES To characterize SARS-CoV-2 infections in staff and students in an urban public school setting and evaluate test-based strategies to support ongoing risk assessment and mitigation for kindergarten through 12th grade in-person learning. DESIGN, SETTING, AND PARTICIPANTS This pilot quality improvement program engaged 3 schools in Omaha, Nebraska, for weekly saliva polymerase chain reaction testing of staff and students participating in in-person learning over a 5-week period from November 9 to December 11, 2020. Wastewater, air, and surface samples were collected weekly and tested for SARS-CoV-2 RNA to evaluate surrogacy for case detection and interrogate transmission risk of in-building activities. MAIN OUTCOMES AND MEASURES SARS-CoV-2 detection in saliva and environmental samples and risk factors for SARS-CoV-2 infection. RESULTS A total of 2885 supervised, self-collected saliva samples were tested from 458 asymptomatic staff members (mean [SD] age, 42.9 [12.4] years; 303 women [66.2%]; 25 Black or African American [5.5%], 83 Hispanic [18.1%], 312 White [68.1%], and 35 other or not provided [7.6%]) and 315 students (mean age, 14.2 [0.7] years; 151 female students [48%]; 20 Black or African American [6.3%], 201 Hispanic [63.8%], 75 White [23.8%], and 19 other race or not provided [6.0%]). A total of 46 cases of SARS-CoV-2 (22 students and 24 staff members) were detected, representing an increase in cumulative case detection rates from 1.2% (12 of 1000) to 7.0% (70 of 1000) among students and from 2.1% (21 of 1000) to 5.3% (53 of 1000) among staff compared with conventional reporting mechanisms during the pilot period. SARS-CoV-2 RNA was detected in wastewater samples from all pilot schools as well as in air samples collected from 2 choir rooms. Sequencing of 21 viral genomes in saliva specimens demonstrated minimal clustering associated with 1 school. Geographical analysis of SARS-CoV-2 cases reported district-wide demonstrated higher community risk in zip codes proximal to the pilot schools. CONCLUSIONS AND RELEVANCE In this study of staff and students in 3 urban public schools in Omaha, Nebraska, weekly screening of asymptomatic staff and students by saliva polymerase chain reaction testing was associated with increased SARS-CoV-2 case detection, exceeding infection rates reported at the county level. Experiences differed among schools, and virus sequencing and geographical analyses suggested a dynamic interplay of school-based and community-derived transmission risk. Collectively, these findings provide insight into the performance and community value of test-based SARS-CoV-2 screening and surveillance strategies in the kindergarten through 12th grade educational setting.
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Affiliation(s)
- John Crowe
- Omaha Public School District, Omaha, Nebraska
| | - Andy T Schnaubelt
- Department of Neurosurgery, University of Nebraska Medical Center, Omaha
| | | | - Kathleen Angell
- Department of Epidemiology, University of Nebraska Medical Center, Omaha
| | - Julia Bai
- Department of Epidemiology, University of Nebraska Medical Center, Omaha
| | - Teresa Eske
- Omaha Public School District, Omaha, Nebraska
| | | | - Catherine Pratt
- Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha
| | - Bailey White
- Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha
| | | | - Nicholas Staffend
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - Vicki Herrera
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | | | - Jennifer Conner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - Julie Carstens
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - Jonell Tempero
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - Lori Bouda
- Omaha Public School District, Omaha, Nebraska
| | - Matthew Ray
- Omaha Public School District, Omaha, Nebraska
| | - James V Lawler
- Department of Medicine, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
| | - W Scott Campbell
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - John-Martin Lowe
- Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
| | - Joshua Santarpia
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
| | | | - Michael Wiley
- Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
| | - David Brett-Major
- Department of Epidemiology, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
| | | | - M Jana Broadhurst
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
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45
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Crowe J, Schnaubelt AT, SchmidtBonne S, Angell K, Bai J, Eske T, Nicklin M, Pratt C, White B, Crotts-Hannibal B, Staffend N, Herrera V, Cobb J, Conner J, Carstens J, Tempero J, Bouda L, Ray M, Lawler JV, Campbell WS, Lowe JM, Santarpia J, Bartelt-Hunt S, Wiley M, Brett-Major D, Logan C, Broadhurst MJ. Assessment of a Program for SARS-CoV-2 Screening and Environmental Monitoring in an Urban Public School District. JAMA Netw Open 2021; 4:e2126447. [PMID: 34550382 PMCID: PMC8459193 DOI: 10.1001/jamanetworkopen.2021.26447] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/27/2021] [Indexed: 02/01/2023] Open
Abstract
Importance Scalable programs for school-based SARS-CoV-2 testing and surveillance are needed to guide in-person learning practices and inform risk assessments in kindergarten through 12th grade settings. Objectives To characterize SARS-CoV-2 infections in staff and students in an urban public school setting and evaluate test-based strategies to support ongoing risk assessment and mitigation for kindergarten through 12th grade in-person learning. Design, Setting, and Participants This pilot quality improvement program engaged 3 schools in Omaha, Nebraska, for weekly saliva polymerase chain reaction testing of staff and students participating in in-person learning over a 5-week period from November 9 to December 11, 2020. Wastewater, air, and surface samples were collected weekly and tested for SARS-CoV-2 RNA to evaluate surrogacy for case detection and interrogate transmission risk of in-building activities. Main Outcomes and Measures SARS-CoV-2 detection in saliva and environmental samples and risk factors for SARS-CoV-2 infection. Results A total of 2885 supervised, self-collected saliva samples were tested from 458 asymptomatic staff members (mean [SD] age, 42.9 [12.4] years; 303 women [66.2%]; 25 Black or African American [5.5%], 83 Hispanic [18.1%], 312 White [68.1%], and 35 other or not provided [7.6%]) and 315 students (mean age, 14.2 [0.7] years; 151 female students [48%]; 20 Black or African American [6.3%], 201 Hispanic [63.8%], 75 White [23.8%], and 19 other race or not provided [6.0%]). A total of 46 cases of SARS-CoV-2 (22 students and 24 staff members) were detected, representing an increase in cumulative case detection rates from 1.2% (12 of 1000) to 7.0% (70 of 1000) among students and from 2.1% (21 of 1000) to 5.3% (53 of 1000) among staff compared with conventional reporting mechanisms during the pilot period. SARS-CoV-2 RNA was detected in wastewater samples from all pilot schools as well as in air samples collected from 2 choir rooms. Sequencing of 21 viral genomes in saliva specimens demonstrated minimal clustering associated with 1 school. Geographical analysis of SARS-CoV-2 cases reported district-wide demonstrated higher community risk in zip codes proximal to the pilot schools. Conclusions and Relevance In this study of staff and students in 3 urban public schools in Omaha, Nebraska, weekly screening of asymptomatic staff and students by saliva polymerase chain reaction testing was associated with increased SARS-CoV-2 case detection, exceeding infection rates reported at the county level. Experiences differed among schools, and virus sequencing and geographical analyses suggested a dynamic interplay of school-based and community-derived transmission risk. Collectively, these findings provide insight into the performance and community value of test-based SARS-CoV-2 screening and surveillance strategies in the kindergarten through 12th grade educational setting.
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Affiliation(s)
- John Crowe
- Omaha Public School District, Omaha, Nebraska
| | - Andy T. Schnaubelt
- Department of Neurosurgery, University of Nebraska Medical Center, Omaha
| | | | - Kathleen Angell
- Department of Epidemiology, University of Nebraska Medical Center, Omaha
| | - Julia Bai
- Department of Epidemiology, University of Nebraska Medical Center, Omaha
| | - Teresa Eske
- Omaha Public School District, Omaha, Nebraska
| | | | - Catherine Pratt
- Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha
| | - Bailey White
- Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha
| | | | - Nicholas Staffend
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - Vicki Herrera
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | | | - Jennifer Conner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - Julie Carstens
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - Jonell Tempero
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - Lori Bouda
- Omaha Public School District, Omaha, Nebraska
| | - Matthew Ray
- Omaha Public School District, Omaha, Nebraska
| | - James V. Lawler
- Department of Medicine, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
| | - W. Scott Campbell
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - John-Martin Lowe
- Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
| | - Joshua Santarpia
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
| | | | - Michael Wiley
- Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
| | - David Brett-Major
- Department of Epidemiology, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
| | | | - M. Jana Broadhurst
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
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Guo W, Cao Y, Kong X, Kong S, Xu T. Potential threat of SARS-CoV-2 in coastal waters. Ecotoxicol Environ Saf 2021; 220:112409. [PMID: 34116332 PMCID: PMC8185187 DOI: 10.1016/j.ecoenv.2021.112409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 05/14/2023]
Abstract
A novel coronavirus (SARS-CoV-2) has caused more than 150 million confirmed infections worldwide, while it is not clear whether it affects the coastal waters. This paper proposed a biophysical model based on 16 scenarios with different virus half-life parameters to assess potential viral contamination from 25 municipal sewage outfalls into the Bohai Sea. Viral concentration maps showing spatial and temporal changes are provided based on a biophysical model under multiple scenarios. Results demonstrate that adjacent sea areas can become exposed to SARS-CoV-2 via water-borne transport from outfalls, with a higher risk in winter, because SARS-CoV-2 can be highly stable at low temperature. As coastal waters are the ultimate sink for wastewater and the epidemic will last for long time, this work is of great importance to raise awareness, identify vulnerable areas for marine mammals, and avoid the risk of exposure of tourists at bathing beach.
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Affiliation(s)
- Weijun Guo
- College of Environmental Sciences and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yimeng Cao
- College of Environmental Sciences and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Xiangpeng Kong
- College of Environmental Sciences and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Shujun Kong
- College of Environmental Sciences and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Tiaojian Xu
- The State Key Laboratory of Coastal and Offshore Engineering, Dalian University of Technology, Dalian 116024, China.
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Flood MT, D'Souza N, Rose JB, Aw TG. Methods Evaluation for Rapid Concentration and Quantification of SARS-CoV-2 in Raw Wastewater Using Droplet Digital and Quantitative RT-PCR. Food Environ Virol 2021; 13:303-315. [PMID: 34296387 PMCID: PMC8297606 DOI: 10.1007/s12560-021-09488-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 07/13/2021] [Indexed: 05/20/2023]
Abstract
Wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging public health tool to understand the spread of Coronavirus Disease 2019 (COVID-19) in communities. The performance of different virus concentration methods and PCR methods needs to be evaluated to ascertain their suitability for use in the detection of SARS-CoV-2 in wastewater. We evaluated ultrafiltration and polyethylene glycol (PEG) precipitation methods to concentrate SARS-CoV-2 from sewage in wastewater treatment plants and upstream in the wastewater network (e.g., manholes, lift stations). Recovery of viruses by different concentration methods was determined using Phi6 bacteriophage as a surrogate for enveloped viruses. Additionally, the presence of SARS-CoV-2 in all wastewater samples was determined using reverse transcription quantitative PCR (RT-qPCR) and reverse transcription droplet digital PCR (RT-ddPCR), targeting three genetic markers (N1, N2 and E). Using spiked samples, the Phi6 recoveries were estimated at 2.6-11.6% using ultrafiltration-based methods and 22.2-51.5% using PEG precipitation. There was no significant difference in recovery efficiencies (p < 0.05) between the PEG procedure with and without a 16 h overnight incubation, demonstrating the feasibility of obtaining same day results. The SARS-CoV-2 genetic markers were more often detected by RT-ddPCR than RT-qPCR with higher sensitivity and precision. While all three SARS-CoV-2 genetic markers were detected using RT-ddPCR, the levels of E gene were almost below the limit of detection using RT-qPCR. Collectively, our study suggested PEG precipitation is an effective low-cost procedure which allows a large number of samples to be processed simultaneously in a routine wastewater monitoring for SARS-CoV-2. RT-ddPCR can be implemented for the absolute quantification of SARS-CoV-2 genetic markers in different wastewater matrices.
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Affiliation(s)
- Matthew T Flood
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal Street, Suite 2100, New Orleans, LA, 70112, USA.
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48
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Crowe J, Schnaubelt AT, SchmidtBonne S, Angell K, Bai J, Eske T, Nicklin M, Pratt C, White B, Crotts-Hannibal B, Staffend N, Herrera V, Cobb J, Conner J, Carstens J, Tempero J, Bouda L, Ray M, Lawler JV, Campbell WS, Lowe JM, Santarpia J, Bartelt-Hunt S, Wiley M, Brett-Major D, Logan C, Broadhurst MJ. Assessment of a Program for SARS-CoV-2 Screening and Environmental Monitoring in an Urban Public School District. JAMA Netw Open 2021; 4:e2126447. [PMID: 34550382 DOI: 10.1101/2021.04.14.21255036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
IMPORTANCE Scalable programs for school-based SARS-CoV-2 testing and surveillance are needed to guide in-person learning practices and inform risk assessments in kindergarten through 12th grade settings. OBJECTIVES To characterize SARS-CoV-2 infections in staff and students in an urban public school setting and evaluate test-based strategies to support ongoing risk assessment and mitigation for kindergarten through 12th grade in-person learning. DESIGN, SETTING, AND PARTICIPANTS This pilot quality improvement program engaged 3 schools in Omaha, Nebraska, for weekly saliva polymerase chain reaction testing of staff and students participating in in-person learning over a 5-week period from November 9 to December 11, 2020. Wastewater, air, and surface samples were collected weekly and tested for SARS-CoV-2 RNA to evaluate surrogacy for case detection and interrogate transmission risk of in-building activities. MAIN OUTCOMES AND MEASURES SARS-CoV-2 detection in saliva and environmental samples and risk factors for SARS-CoV-2 infection. RESULTS A total of 2885 supervised, self-collected saliva samples were tested from 458 asymptomatic staff members (mean [SD] age, 42.9 [12.4] years; 303 women [66.2%]; 25 Black or African American [5.5%], 83 Hispanic [18.1%], 312 White [68.1%], and 35 other or not provided [7.6%]) and 315 students (mean age, 14.2 [0.7] years; 151 female students [48%]; 20 Black or African American [6.3%], 201 Hispanic [63.8%], 75 White [23.8%], and 19 other race or not provided [6.0%]). A total of 46 cases of SARS-CoV-2 (22 students and 24 staff members) were detected, representing an increase in cumulative case detection rates from 1.2% (12 of 1000) to 7.0% (70 of 1000) among students and from 2.1% (21 of 1000) to 5.3% (53 of 1000) among staff compared with conventional reporting mechanisms during the pilot period. SARS-CoV-2 RNA was detected in wastewater samples from all pilot schools as well as in air samples collected from 2 choir rooms. Sequencing of 21 viral genomes in saliva specimens demonstrated minimal clustering associated with 1 school. Geographical analysis of SARS-CoV-2 cases reported district-wide demonstrated higher community risk in zip codes proximal to the pilot schools. CONCLUSIONS AND RELEVANCE In this study of staff and students in 3 urban public schools in Omaha, Nebraska, weekly screening of asymptomatic staff and students by saliva polymerase chain reaction testing was associated with increased SARS-CoV-2 case detection, exceeding infection rates reported at the county level. Experiences differed among schools, and virus sequencing and geographical analyses suggested a dynamic interplay of school-based and community-derived transmission risk. Collectively, these findings provide insight into the performance and community value of test-based SARS-CoV-2 screening and surveillance strategies in the kindergarten through 12th grade educational setting.
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Affiliation(s)
- John Crowe
- Omaha Public School District, Omaha, Nebraska
| | - Andy T Schnaubelt
- Department of Neurosurgery, University of Nebraska Medical Center, Omaha
| | | | - Kathleen Angell
- Department of Epidemiology, University of Nebraska Medical Center, Omaha
| | - Julia Bai
- Department of Epidemiology, University of Nebraska Medical Center, Omaha
| | - Teresa Eske
- Omaha Public School District, Omaha, Nebraska
| | | | - Catherine Pratt
- Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha
| | - Bailey White
- Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha
| | | | - Nicholas Staffend
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - Vicki Herrera
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | | | - Jennifer Conner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - Julie Carstens
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - Jonell Tempero
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - Lori Bouda
- Omaha Public School District, Omaha, Nebraska
| | - Matthew Ray
- Omaha Public School District, Omaha, Nebraska
| | - James V Lawler
- Department of Medicine, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
| | - W Scott Campbell
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
| | - John-Martin Lowe
- Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
| | - Joshua Santarpia
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
| | | | - Michael Wiley
- Department of Environmental, Agricultural, and Occupational Health, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
| | - David Brett-Major
- Department of Epidemiology, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
| | | | - M Jana Broadhurst
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha
- Global Center for Health Security, University of Nebraska Medical Center, Omaha
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49
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Abstract
Sequencing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from wastewater has become a useful tool in monitoring the spread of viral variants. Approaches to this task have been varied, relying on differing sequencing methods and computational analyses. We used a novel computation workflow based on amplicon sequencing of SARS-CoV-2 spike domains in order to track viral populations in wastewater. As part of this workflow, we developed a program, SAM Refiner, that has a variety of outputs, including novel variant reporting as well as functions designed to remove polymerase chain reaction (PCR) generated chimeric sequences. With these methods, we were able to track viral population dynamics over time. We report here on the emergence of two variants of concern, B.1.1.7 (Alpha) and P.1 (Gamma), and their displacement of the D614G B.1 variant in a Missouri sewershed.
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Affiliation(s)
- Devon A Gregory
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65201, USA
| | - Chris G Wieberg
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65102, USA
| | - Jeff Wenzel
- Bureau of Environmental Epidemiology, Missouri Department of Health and Senior Services, Division of Community and Public Health, Jefferson City, MO 65102, USA
| | - Chung-Ho Lin
- Center for Agroforestry, School of Natural Resources, University of Missouri, Columbia, MO 65201, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65201, USA
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50
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Gregory DA, Wieberg CG, Wenzel J, Lin CH, Johnson MC. Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. Viruses 2021; 13:1647. [PMID: 34452511 PMCID: PMC8402658 DOI: 10.3390/v13081647] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/11/2021] [Accepted: 08/17/2021] [Indexed: 12/18/2022] Open
Abstract
Sequencing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from wastewater has become a useful tool in monitoring the spread of viral variants. Approaches to this task have been varied, relying on differing sequencing methods and computational analyses. We used a novel computation workflow based on amplicon sequencing of SARS-CoV-2 spike domains in order to track viral populations in wastewater. As part of this workflow, we developed a program, SAM Refiner, that has a variety of outputs, including novel variant reporting as well as functions designed to remove polymerase chain reaction (PCR) generated chimeric sequences. With these methods, we were able to track viral population dynamics over time. We report here on the emergence of two variants of concern, B.1.1.7 (Alpha) and P.1 (Gamma), and their displacement of the D614G B.1 variant in a Missouri sewershed.
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Affiliation(s)
- Devon A. Gregory
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65201, USA;
| | - Chris G. Wieberg
- Water Protection Program, Missouri Department of Natural Resources, Jefferson City, MO 65102, USA;
| | - Jeff Wenzel
- Bureau of Environmental Epidemiology, Missouri Department of Health and Senior Services, Division of Community and Public Health, Jefferson City, MO 65102, USA;
| | - Chung-Ho Lin
- Center for Agroforestry, School of Natural Resources, University of Missouri, Columbia, MO 65201, USA;
| | - Marc C. Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65201, USA;
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