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Zambre S, Katarmal P, Pawar S, Dawkhar S, Iyer P, Rajput V, Kadam P, Bhalerao U, Tupekar M, Shah P, Karmodiya K, Dharne M, Roy B, Koraktar S. Wastewater surveillance of severe acute respiratory syndrome coronavirus-2 in open drains of two Indian megacities captures evolutionary lineage transitions: a zonation approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:49670-49681. [PMID: 39078552 DOI: 10.1007/s11356-024-34448-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/18/2024] [Indexed: 07/31/2024]
Abstract
Wastewater-based environmental surveillance (WBES) has been proven as proxy tool for monitoring nucleic acids of pathogens shed by infected population before clinical outcomes. The poor sewershed network of low to middle-income countries (LMICs) leads to most of the wastewater flow through open drains. We studied the effectiveness of WBES using open drain samples to monitor the emergence of the SARS-CoV-2 variants in 2 megacities of India having dense population through zonation approach. Samples from 28 locations spanned into 5 zones of Pune region, Maharashtra, India, were collected on a weekly basis during October 2021 to July 2022. Out of 1115 total processed samples, 303 (~ 27%) tested positive for SARS-CoV-2. The periodical rise and fall in the percentage positivity of the samples was found to be in sync with the abundance of SARS-CoV-2 RNA and the reported COVID-19 active cases for Pune city. Sequencing of the RNA obtained from wastewater samples confirmed the presence of SARS-CoV-2. Of 337 sequences, lineage identification for 242 samples revealed 265 distinct SARS-CoV-2 variants including 10 highly transmissible ones. Importantly, transition from Delta to Omicron variant could be detected in wastewater samples 2 weeks prior to any clinically reported Omicron cases in India. Thus, this study demonstrates the usefulness of open drain samples for real-time monitoring of a viral pathogen's evolutionary dynamics and could be implemented in LMICs.
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Affiliation(s)
- Saee Zambre
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Maharashtra, India
| | - Poonam Katarmal
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Maharashtra, India
| | - Shubhankar Pawar
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Maharashtra, India
| | - Snehal Dawkhar
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Maharashtra, India
| | - Parvati Iyer
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Maharashtra, India
| | - Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
| | - Pradnya Kadam
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Unnati Bhalerao
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Manisha Tupekar
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Priyanki Shah
- Pune Knowledge Cluster (PKC), Savitribai Phule Pune University (SPPU), Pune, Maharashtra, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 41108, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune, Maharashtra, 411008, India
| | - Bishnudeo Roy
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Maharashtra, India
| | - Santosh Koraktar
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Maharashtra, India.
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Hamilton KA, Wade MJ, Barnes KG, Street RA, Paterson S. Wastewater-based epidemiology as a public health resource in low- and middle-income settings. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 351:124045. [PMID: 38677460 DOI: 10.1016/j.envpol.2024.124045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/14/2024] [Accepted: 04/23/2024] [Indexed: 04/29/2024]
Abstract
In the face of emerging and re-emerging diseases, novel and innovative approaches to population scale surveillance are necessary for the early detection and quantification of pathogens. The last decade has seen the rapid development of wastewater and environmental surveillance (WES) to address public health challenges, which has led to establishment of wastewater-based epidemiology (WBE) approaches being deployed to monitor a range of health hazards. WBE exploits the fact that excretions and secretions from urine, and from the gut are discharged in wastewater, particularly sewage, such that sampling sewage systems provides an early warning system for disease outbreaks by providing an early indication of pathogen circulation. While WBE has been mainly used in locations with networked wastewater systems, here we consider its value for less connected populations typical of lower-income settings, and in assess the opportunity afforded by pit latrines to sample communities and localities. We propose that where populations struggle to access health and diagnostic facilities, and despite several additional challenges, sampling unconnected wastewater systems remains an important means to monitor the health of large populations in a relatively cost-effective manner.
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Affiliation(s)
- K A Hamilton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom; International Livestock Research Institute, Nairobi, Kenya, PO Box 30709-00100.
| | - M J Wade
- Data, Analytics & Surveillance Group, UK Health Security Agency, London United Kingdom
| | - K G Barnes
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi; Harvard School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - R A Street
- South African Medical Research Council, Cape Town, Western Cape, South Africa
| | - S Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
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Meghna N, Archana A, Bhushan D, Kumar A, Sarfraz A, Naik BN, Pati BK. Prevalence of SARS-CoV-2 virus in saliva, stool, and urine samples of COVID-19 patients in Bihar, India. Access Microbiol 2024; 6:000693.v4. [PMID: 39045236 PMCID: PMC11261694 DOI: 10.1099/acmi.0.000693.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 04/21/2024] [Indexed: 07/25/2024] Open
Abstract
Introduction. The coronavirus illness caused by SARS-CoV-2 can cause multiple organ involvement, with varying degrees of severity. Besides inhalation as a route for transmission, feco-oral has also been proposed. Its transmission to sewage systems is a growing public health issue. Objective. To detect SARS-CoV-2 RNA in non-respiratory samples (saliva, urine, and stool) collected from COVID-19 cases, in Bihar. Methods. This cross-sectional observational study was conducted from January 2021 to March 2022 on human non-respiratory samples. A total of 345 samples including saliva (116), stool (97), and urine (132) were collected from 143 COVID-19 cases. Samples were analysed for SARS-CoV-2 by multiplex RT-PCR targeted against E, ORF 1ab, and RdRp genes. Results. In this study, out of 143 cases, a total of 107 (74.8 %) were positive for SARS-CoV-2 RNA in at least one of the non-respiratory samples. Conclusion. There is a high prevalence of SARS-CoV-2 virus in non-respiratory samples.
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Affiliation(s)
- Nupur Meghna
- Department of Microbiology, All India Institute of Medical Sciences, Patna, India
| | - Archana Archana
- Department of Microbiology, All India Institute of Medical Sciences, Patna, India
| | - Divendu Bhushan
- Department of General Medicine, All India Institute of Medical Sciences, Patna, India
| | - Abhyuday Kumar
- Department of Anaesthesiology, All India Institute of Medical Sciences, Patna, India
| | - Asim Sarfraz
- Department of Microbiology, All India Institute of Medical Sciences, Patna, India
| | - Bijaya Nanda Naik
- Department of Community and Family Medicine, All India Institute of Medical Sciences, Patna, India
| | - Binod Kumar Pati
- Department of Microbiology, All India Institute of Medical Sciences, Patna, India
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Ruan Y, Huang T, Zhou W, Zhu J, Liang Q, Zhong L, Tang X, Liu L, Chen S, Xie Y. The lead time and geographical variations of Baidu Search Index in the early warning of COVID-19. Sci Rep 2023; 13:14705. [PMID: 37679512 PMCID: PMC10484897 DOI: 10.1038/s41598-023-41939-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 09/04/2023] [Indexed: 09/09/2023] Open
Abstract
Internet search data was a useful tool in the pre-warning of COVID-19. However, the lead time and indicators may change over time and space with the new variants appear and massive nucleic acid testing. Since Omicron appeared in late 2021, we collected the daily number of cases and Baidu Search Index (BSI) of seven search terms from 1 January to 30 April, 2022 in 12 provinces/prefectures to explore the variation in China. Two search peaks of "COVID-19 epidemic", "Novel Coronavirus" and "COVID-19" can be observed. One in January, which showed 3 days lead time in Henan and Tianjin. Another on early March, which occurred 0-28 days ahead of the local epidemic but the lead time had spatial variation. It was 4 weeks in Shanghai, 2 weeks in Henan and 5-8 days in Jilin Province, Jilin and Changchun Prefecture. But it was only 1-3 days in Tianjin, Quanzhou Prefecture, Fujian Province and 0 day in Shenzhen, Shandong Province, Qingdao and Yanbian Prefecture. The BSI was high correlated (rs:0.70-0.93) to the number of cases with consistent epidemiological change trend. The lead time of BSI had spatial and temporal variation and was close related to the strength of nucleic acid testing. The case detection ability should be strengthened when perceiving BSI increase.
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Affiliation(s)
- Yuhua Ruan
- State Key Laboratory of Infectious Disease Prevention and Control (SKLID), National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention (China CDC), Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Tengda Huang
- Department of Epidemiology and Biostatistics, Guangxi Medical University, Nanning, China
| | - Wanwan Zhou
- Department of Epidemiology and Biostatistics, Guangxi Medical University, Nanning, China
| | - Jinhui Zhu
- Guangxi Key Laboratory of Major Infectious Disease Prevention Control and Biosafety Emergency Response, Guangxi Center for Disease Control and Prevention, Nanning, China
| | - Qiuyu Liang
- Department of Health Management, The People's Hospital of Guangxi Zhuang Autonomous Region & Research Center of Health Management, Guangxi Academy of Medical Sciences, Nanning, China
| | - Lixian Zhong
- Department of Epidemiology and Biostatistics, Guangxi Medical University, Nanning, China
| | - Xiaofen Tang
- Department of Epidemiology and Biostatistics, Guangxi Medical University, Nanning, China
| | - Lu Liu
- Department of Epidemiology and Biostatistics, Guangxi Medical University, Nanning, China
| | - Shiwen Chen
- Department of Epidemiology and Biostatistics, Guangxi Medical University, Nanning, China
| | - Yihong Xie
- Department of Epidemiology and Biostatistics, Guangxi Medical University, Nanning, China.
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, Guangxi Medical University, Nanning, China.
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Ram JL, Shuster W, Gable L, Turner CL, Hartrick J, Vasquez AA, West NW, Bahmani A, David RE. Wastewater Monitoring for Infectious Disease: Intentional Relationships between Academia, the Private Sector, and Local Health Departments for Public Health Preparedness. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:6651. [PMID: 37681792 PMCID: PMC10487196 DOI: 10.3390/ijerph20176651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/29/2023] [Accepted: 07/20/2023] [Indexed: 09/09/2023]
Abstract
The public health emergency caused by the COVID-19 pandemic stimulated stakeholders from diverse disciplines and institutions to establish new collaborations to produce informed public health responses to the disease. Wastewater-based epidemiology for COVID-19 grew quickly during the pandemic and required the rapid implementation of such collaborations. The objective of this article is to describe the challenges and results of new relationships developed in Detroit, MI, USA among a medical school and an engineering college at an academic institution (Wayne State University), the local health department (Detroit Health Department), and an environmental services company (LimnoTech) to utilize markers of the COVID-19 virus, SARS-CoV-2, in wastewater for the goal of managing COVID-19 outbreaks. Our collaborative team resolved questions related to sewershed selection, communication of results, and public health responses and addressed technical challenges that included ground-truthing the sewer maps, overcoming supply chain issues, improving the speed and sensitivity of measurements, and training new personnel to deal with a new disease under pandemic conditions. Recognition of our complementary roles and clear communication among the partners enabled city-wide wastewater data to inform public health responses within a few months of the availability of funding in 2020, and to make improvements in sensitivity and understanding to be made as the pandemic progressed and evolved. As a result, the outbreaks of COVID-19 in Detroit in fall and winter 2021-2022 (corresponding to Delta and Omicron variant outbreaks) were tracked in 20 sewersheds. Data comparing community- and hospital-associated sewersheds indicate a one- to two-week advance warning in the community of subsequent peaks in viral markers in hospital sewersheds. The new institutional relationships impelled by the pandemic provide a good basis for continuing collaborations to utilize wastewater-based human and pathogen data for improving the public health in the future.
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Affiliation(s)
- Jeffrey L. Ram
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (A.A.V.)
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI 48201, USA
| | - William Shuster
- College of Engineering, Wayne State University, Detroit, MI 48202, USA;
| | - Lance Gable
- Law School, Wayne State University, Detroit, MI 48202, USA
| | | | | | - Adrian A. Vasquez
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (A.A.V.)
| | - Nicholas W. West
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (A.A.V.)
| | - Azadeh Bahmani
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (A.A.V.)
| | - Randy E. David
- Detroit Health Department, Detroit, MI 48201, USA
- Department of Family Medicine and Public Health Sciences, School of Medicine, Wayne State University, Detroit, MI 48201, USA
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Zhao L, Geng Q, Corchis-Scott R, McKay RM, Norton J, Xagoraraki I. Targeting a free viral fraction enhances the early alert potential of wastewater surveillance for SARS-CoV-2: a methods comparison spanning the transition between delta and omicron variants in a large urban center. Front Public Health 2023; 11:1140441. [PMID: 37546328 PMCID: PMC10400354 DOI: 10.3389/fpubh.2023.1140441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/30/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction Wastewater surveillance has proven to be a valuable approach to monitoring the spread of SARS-CoV-2, the virus that causes Coronavirus disease 2019 (COVID-19). Recognizing the benefits of wastewater surveillance as a tool to support public health in tracking SARS-CoV-2 and other respiratory pathogens, numerous wastewater virus sampling and concentration methods have been tested for appropriate applications as well as their significance for actionability by public health practices. Methods Here, we present a 34-week long wastewater surveillance study that covers nearly 4 million residents of the Detroit (MI, United States) metropolitan area. Three primary concentration methods were compared with respect to recovery of SARS-CoV-2 from wastewater: Virus Adsorption-Elution (VIRADEL), polyethylene glycol precipitation (PEG), and polysulfone (PES) filtration. Wastewater viral concentrations were normalized using various parameters (flow rate, population, total suspended solids) to account for variations in flow. Three analytical approaches were implemented to compare wastewater viral concentrations across the three primary concentration methods to COVID-19 clinical data for both normalized and non-normalized data: Pearson and Spearman correlations, Dynamic Time Warping (DTW), and Time Lagged Cross Correlation (TLCC) and peak synchrony. Results It was found that VIRADEL, which captures free and suspended virus from supernatant wastewater, was a leading indicator of COVID-19 cases within the region, whereas PEG and PES filtration, which target particle-associated virus, each lagged behind the early alert potential of VIRADEL. PEG and PES methods may potentially capture previously shed and accumulated SARS-CoV-2 resuspended from sediments in the interceptors. Discussion These results indicate that the VIRADEL method can be used to enhance the early-warning potential of wastewater surveillance applications although drawbacks include the need to process large volumes of wastewater to concentrate sufficiently free and suspended virus for detection. While lagging the VIRADEL method for early-alert potential, both PEG and PES filtration can be used for routine COVID-19 wastewater monitoring since they allow a large number of samples to be processed concurrently while being more cost-effective and with rapid turn-around yielding results same day as collection.
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Affiliation(s)
- Liang Zhao
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Robert Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States
| | - John Norton
- Great Lakes Water Authority, Detroit, MI, United States
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
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Nazmul T, Lawal-Ayinde BM, Morita T, Yoshimoto R, Higashiura A, Yamamoto A, Nomura T, Nakano Y, Hirayama M, Kurokawa H, Kitamura Y, Hori K, Sakaguchi T. Capture and neutralization of SARS-CoV-2 and influenza virus by algae-derived lectins with high-mannose and core fucose specificities. Microbiol Immunol 2023. [PMID: 37248051 DOI: 10.1111/1348-0421.13082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 05/02/2023] [Accepted: 05/14/2023] [Indexed: 05/31/2023]
Abstract
We first investigated the interactions between several algae-derived lectins and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). We created lectin columns using high-mannose (HM)-type glycan-specific lectins OAA and KAA-1 or core fucose-specific lectin hypninA-2 and conducted binding experiments with SARS-CoV-2. The results showed that these lectins were capable of binding to the virus. Furthermore, when examining the neutralization ability of nine different lectins, it was found that KAA-1, ESA-2, and hypninA-2 were effective in neutralizing SARS-CoV-2. In competitive inhibition experiments with glycoproteins, neutralization was confirmed to occur through HM-type or core fucose-type glycans. However, neutralization was not observed with other lectins, such as OAA. This trend of KAA-1 and ESA-2 having the neutralizing ability and OAA not having it was also similar to influenza viruses. Electron microscopy observations revealed that KAA-1 and hypninA-2 strongly aggregated SARS-CoV-2 particles, while OAA showed a low degree of aggregation. It is believed that the neutralization of SARS-CoV-2 involves multiple factors, such as glycan attachment sites on the S protein, the size of lectins, and their propensity to aggregate, which cause inhibition of receptor binding or aggregation of virus particles. This study demonstrated that several algae-derived lectins could neutralize SARS-CoV-2 and that lectin columns can effectively recover and concentrate the virus.
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Affiliation(s)
- Tanuza Nazmul
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Basirat M Lawal-Ayinde
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tomoko Morita
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Reiko Yoshimoto
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Akifumi Higashiura
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Akima Yamamoto
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Toshihito Nomura
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - Yukiko Nakano
- Laboratory of Marine Bioresource Chemistry, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Makoto Hirayama
- Laboratory of Marine Bioresource Chemistry, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | | | | | - Kanji Hori
- Laboratory of Marine Bioresource Chemistry, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takemasa Sakaguchi
- Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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8
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Amin N, Haque R, Rahman MZ, Rahman MZ, Mahmud ZH, Hasan R, Islam MT, Sarker P, Sarker S, Adnan SD, Akter N, Johnston D, Rahman M, Liu P, Wang Y, Shirin T, Rahman M, Bhattacharya P. Dependency of sanitation infrastructure on the discharge of faecal coliform and SARS-CoV-2 viral RNA in wastewater from COVID and non-COVID hospitals in Dhaka, Bangladesh. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161424. [PMID: 36623655 PMCID: PMC9822545 DOI: 10.1016/j.scitotenv.2023.161424] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/31/2022] [Accepted: 01/02/2023] [Indexed: 05/25/2023]
Abstract
The detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) RNA in wastewater can be used as an indicator of the presence of SARS-CoV-2 infection in specific catchment areas. We conducted a hospital-based study to explore wastewater management in healthcare facilities and analyzed SARS-CoV-2 RNA in the hospital wastewater in Dhaka city during the Coronavirus disease (COVID-19) outbreak between September 2020-January 2021. We selected three COVID-hospitals, two non-COVID-hospitals, and one non-COVID-hospital with COVID wards, conducted spot-checks of the sanitation systems (i.e., toilets, drainage, and septic-tank), and collected 90 untreated wastewater effluent samples (68 from COVID and 22 from non-COVID hospitals). E. coli was detected using a membrane filtration technique and reported as colony forming unit (CFU). SARS-CoV-2 RNA was detected using the iTaq Universal Probes One-Step kit for RT-qPCR amplification of the SARS-CoV-2 ORF1ab and N gene targets and quantified for SARS-CoV-2 genome equivalent copies (GEC) per mL of sample. None of the six hospitals had a primary wastewater treatment facility; two COVID hospitals had functional septic tanks, and the rest of the hospitals had either broken onsite systems or no containment of wastewater. Overall, 100 % of wastewater samples were positive with a high concentration of E. coli (mean = 7.0 log10 CFU/100 mL). Overall, 67 % (60/90) samples were positive for SARS-CoV-2. The highest SARS-CoV-2 concentrations (median: 141 GEC/mL; range: 13-18,214) were detected in wastewater from COVID-hospitals, and in non-COVID-hospitals, the median SARS-CoV-2 concentration was 108 GEC/mL (range: 30-1829). Our results indicate that high concentrations of E. coli and SARS-CoV-2 were discharged through the hospital wastewater (both COVID and non-COVID) without treatment into the ambient water bodies. Although there is no evidence for transmission of SARS-CoV-2 via wastewater, this study highlights the significant risk posed by wastewater from health care facilities in Dhaka for the many other diseases that are spread via faecal oral route. Hospitals in low-income settings could function as sentinel sites to monitor outbreaks through wastewater-based epidemiological surveillance systems. Hospitals should aim to adopt the appropriate wastewater treatment technologies to reduce the discharge of pathogens into the environment and mitigate environmental exposures.
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Affiliation(s)
- Nuhu Amin
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh; Institute for Sustainable Futures, University of Technology Sydney, 235 Jones St, Ultimo, NSW, 2007, Australia.
| | - Rehnuma Haque
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh; School of Medicine, Stanford University, Stanford, CA, USA
| | - Md Ziaur Rahman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammed Ziaur Rahman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Zahid Hayat Mahmud
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Rezaul Hasan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Md Tahmidul Islam
- COVID-19 Research@KTH, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, SE 114 28 Stockholm, Sweden; WaterAid, Bangladesh
| | - Protim Sarker
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Supriya Sarker
- Directorate General of Health Services (DGHS), Bangladesh
| | | | - Nargis Akter
- Water, Sanitation & Hygiene (WASH) section, UNICEF, Bangladesh
| | - Dara Johnston
- Water, Sanitation & Hygiene (WASH) section, UNICEF, Bangladesh
| | - Mahbubur Rahman
- Institute of Epidemiology, Disease Control and Research (IEDCR), Bangladesh
| | - Pengbo Liu
- Center for Global Safe Water, Sanitation, and Hygiene, Emory University, Atlanta, GA, USA
| | - Yuke Wang
- Center for Global Safe Water, Sanitation, and Hygiene, Emory University, Atlanta, GA, USA
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Bangladesh
| | - Mahbubur Rahman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Prosun Bhattacharya
- COVID-19 Research@KTH, Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, SE 114 28 Stockholm, Sweden
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Levican J, Ampuero M, Rabello C, Venegas I, Quarleri J, Gaggero A. Changing molecular epidemiology of Hepatitis A virus in Santiago, Chile from 2010 to 2021. INFECTION, GENETICS AND EVOLUTION 2023; 111:105428. [PMID: 36990306 DOI: 10.1016/j.meegid.2023.105428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
OBJECTIVES Hepatitis A (HAV) virus causes asymptomatic to life-treating fulminant hepatitis. During infection, patients show large viral excretion in their stools. Resistance of HAV to environmental conditions, allows us to recover viral nucleotide sequences from wastewater and trace its evolutionary history. METHODS We characterize twelve years of HAV circulation in wastewater from Santiago, Chile, and conducted phylogenetic analyses to decipher the dynamics of circulating lineages. RESULTS We observed the exclusive circulation of the HAV IA genotype. The molecular epidemiologic analyses showed a steady circulation of a dominant lineage with low genetic diversity (d = 0,007) between 2010 and 2017. An outbreak of Hepatitis A associated with men who have sex with men, in 2017 was associated with the irruption of a new lineage. Remarkably, a dramatic change in the dynamic of HAV circulation was observed in the period post-outbreak; between 2017 and 2021 when 4 different lineages were transiently detected. Exhaustive phylogenetic analyses indicate that these lineages were introduced and possibly derived from isolates from other Latin American countries. CONCLUSION The HAV circulation in recent years in Chile is rapidly changing and suggests that this phenomenon could be a consequence of massive population migrations in Latin America caused by political instability and natural disasters.
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Affiliation(s)
- Jorge Levican
- Laboratorio de Virología Ambiental, Programa de Virología, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Manuel Ampuero
- Laboratorio de Virología Ambiental, Programa de Virología, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Camila Rabello
- Laboratorio de Virología Ambiental, Programa de Virología, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Ignacio Venegas
- Laboratorio de Virología Ambiental, Programa de Virología, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Jorge Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Facultad de Medicina, Consejo de Investigaciones Científicas y Técnicas (CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aldo Gaggero
- Laboratorio de Virología Ambiental, Programa de Virología, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago, Chile.
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10
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Daza-Torres ML, Montesinos-López JC, Kim M, Olson R, Bess CW, Rueda L, Susa M, Tucker L, García YE, Schmidt AJ, Naughton CC, Pollock BH, Shapiro K, Nuño M, Bischel HN. Model training periods impact estimation of COVID-19 incidence from wastewater viral loads. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159680. [PMID: 36306854 PMCID: PMC9597566 DOI: 10.1016/j.scitotenv.2022.159680] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 05/13/2023]
Abstract
Wastewater-based epidemiology (WBE) has been deployed broadly as an early warning tool for emerging COVID-19 outbreaks. WBE can inform targeted interventions and identify communities with high transmission, enabling quick and effective responses. As the wastewater (WW) becomes an increasingly important indicator for COVID-19 transmission, more robust methods and metrics are needed to guide public health decision-making. This research aimed to develop and implement a mathematical framework to infer incident cases of COVID-19 from SARS-CoV-2 levels measured in WW. We propose a classification scheme to assess the adequacy of model training periods based on clinical testing rates and assess the sensitivity of model predictions to training periods. A testing period is classified as adequate when the rate of change in testing is greater than the rate of change in cases. We present a Bayesian deconvolution and linear regression model to estimate COVID-19 cases from WW data. The effective reproductive number is estimated from reconstructed cases using WW. The proposed modeling framework was applied to three Northern California communities served by distinct WW treatment plants. The results showed that training periods with adequate testing are essential to provide accurate projections of COVID-19 incidence.
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Affiliation(s)
- Maria L Daza-Torres
- Department of Public Health Sciences, University of California Davis, Davis, CA 95616, United States.
| | | | - Minji Kim
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
| | - Rachel Olson
- Department of Civil and Environmental Engineering, University of California Davis, Davis, CA 95616, United States
| | - C Winston Bess
- Department of Civil and Environmental Engineering, University of California Davis, Davis, CA 95616, United States
| | - Lezlie Rueda
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
| | - Mirjana Susa
- Department of Public Health Sciences, University of California Davis, Davis, CA 95616, United States
| | - Linnea Tucker
- Department of Civil and Environmental Engineering, University of California Davis, Davis, CA 95616, United States
| | - Yury E García
- Department of Public Health Sciences, University of California Davis, Davis, CA 95616, United States
| | - Alec J Schmidt
- Department of Public Health Sciences, University of California Davis, Davis, CA 95616, United States
| | - Colleen C Naughton
- Department of Civil and Environmental Engineering, University of California Merced, Merced, CA 95343, United States
| | - Brad H Pollock
- Department of Public Health Sciences, University of California Davis, Davis, CA 95616, United States
| | - Karen Shapiro
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, United States
| | - Miriam Nuño
- Department of Public Health Sciences, University of California Davis, Davis, CA 95616, United States
| | - Heather N Bischel
- Department of Civil and Environmental Engineering, University of California Davis, Davis, CA 95616, United States.
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11
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Sabzchi-Dehkharghani H, Samadi Kafil H, Majnooni-Heris A, Akbarzadeh A, Naderi-Ahranjani R, Fakherifard A, Mosaferi M, Gilani N, Noury M, Eydi P, Sayyari Sis S, Toghyanian N, Yegani R. Investigation of SARS-CoV-2 RNA contamination in water supply resources of Tabriz metropolitan during a peak of COVID-19 pandemic. SUSTAINABLE WATER RESOURCES MANAGEMENT 2022; 9:21. [PMID: 36570697 PMCID: PMC9759279 DOI: 10.1007/s40899-022-00809-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
It is crucial to have access to clean water resources during the COVID-19 pandemic for hygiene, since virus infection through wastewater leaks in metropolitan areas can be a threat. Accurate monitoring of urban water resources during the pandemic seems to be the only way to confirm safe and infected resources. Here, in this study, the amount of Severe Acute Respiratory Syndrome Coronavirus 2's Ribonucleic Acid (SARS-CoV-2 RNA) in the Tabriz urban water network located in the northwest of Iran was investigated by an extensive sampling of the city's water sources at a severe peak of the COVID-19 pandemic. The sampling process comprised a range of water sources, including wells, qanats, water treatment facilities, dams, and reservoirs. For each sample, a combination of polyethylene glycol (PEG) and sodium chloride (NaCl) was used for concentration and a laboratory RNA-based method was conducted for quantification. Before applying the extraction and quantification procedure to real samples, the proposed concentration method was verified with synthetic serum samples for the first time. After the concentration, RNA extraction was done by the BehPrep extraction column method, and Reverse Transcription Polymerase Chain Reaction (RT-PCR) detection of the virus was done by Covitech COVID-19 RT-PCR kit. In none of the water supply resources, SARS-COV-2 RNA has been detected except in a sample grabbed from a well adjacent to an urban wastewater discharge point downstream. The results of molecular analysis for the positive sample showed that the CT value and concentration of the virus genome were equal to 32.57 and 5720 copies/L, respectively. Quantitative analysis of real samples shows that the city's water network was safe at the time of the study. However, given that the positive sample was exposed to wastewater leakage, periodic sampling from wells and qanats is suggested during the pandemic until it can be proven that the leakage to these water sources is impossible.
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Affiliation(s)
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Rana Naderi-Ahranjani
- Membrane Technology Research Center, Faculty of Chemical Engineering, Sahand University of Technology, PO. BOX 51335/1996, Tabriz, Iran
| | - Ahmad Fakherifard
- Department of Water Engineering, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Mohammad Mosaferi
- Health and Environment Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Neda Gilani
- Department of Statistics and Epidemiology, Faculty of Health, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mojtaba Noury
- Iranian Water Resources Management Company, Tehran, Iran
| | - Parisa Eydi
- Membrane Technology Research Center, Faculty of Chemical Engineering, Sahand University of Technology, PO. BOX 51335/1996, Tabriz, Iran
| | - Sajjad Sayyari Sis
- Membrane Technology Research Center, Faculty of Chemical Engineering, Sahand University of Technology, PO. BOX 51335/1996, Tabriz, Iran
| | | | - Reza Yegani
- Membrane Technology Research Center, Faculty of Chemical Engineering, Sahand University of Technology, PO. BOX 51335/1996, Tabriz, Iran
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12
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West NW, Vasquez AA, Bahmani A, Khan MF, Hartrick J, Turner CL, Shuster W, Ram JL. Sensitive detection of SARS-CoV-2 molecular markers in urban community sewersheds using automated viral RNA purification and digital droplet PCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157547. [PMID: 35872187 PMCID: PMC9303066 DOI: 10.1016/j.scitotenv.2022.157547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
Wastewater based epidemiology (WBE) has emerged as a strategy to identify, locate, and manage outbreaks of COVID-19, and thereby possibly prevent surges in cases, which overwhelm local to global health care networks. The WBE process is based on assaying municipal wastewater for molecular markers of the SARS-CoV-2 virus. Standard processes for purifying viral RNA from municipal wastewater are often time-consuming and require the handling of large quantities of wastewater, negatively affecting throughput, timely reporting, and safety. We demonstrate here an automated, faster system to purify viral RNA from smaller volumes of wastewater but with increased sensitivity for detection of SARS-CoV-2 markers. We document the effectiveness of this new approach by way of comparison to the PEG/NaCl/Qiagen method prescribed by the State of Michigan for SARS-CoV-2 wastewater monitoring and show its application to several Detroit sewersheds. Specifically, compared to the PEG/NaCl/Qiagen method, viral RNA purification using the PerkinElmer Chemagic™ 360 lowered handling time, decreased the amount of wastewater required by ten-fold, increased the amount of RNA isolated per μl of final elution product by approximately five-fold, and effectively removed ddPCR inhibitors from most sewershed samples. For detection of markers on the borderline of viral detectability, we found that use of the Chemagic™ 360 enabled the measurement of viral markers in a significant number of samples for which the result with the PEG/NaCl/Qiagen method was below the level of detectability. The improvement in detectability of the viral markers might be particularly important for early warning to public health authorities at the beginning of an outbreak. Applied to sewersheds in Detroit, the technique enabled more sensitive detection of SARS-CoV-2 markers with good correlation between wastewater signals and COVID-19 cases in the sewersheds. We also discuss advantages and disadvantages of several automated RNA purification systems, made by Promega, PerkinElmer, and ThermoFisher.
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Affiliation(s)
- Nicholas W West
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Adrian A Vasquez
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Azadeh Bahmani
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Mohammed F Khan
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | | | | | - William Shuster
- Department of Civil and Environmental Engineering, Wayne State University, Detroit, MI 48202, USA
| | - Jeffrey L Ram
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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13
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Soni V, Paital S, Raizada P, Ahamad T, Khan AAP, Thakur S, Singh P, Hussain CM, Sharma S, Nadda AK. Surveillance of omicron variants through wastewater epidemiology: Latest developments in environmental monitoring of pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:156724. [PMID: 35716753 PMCID: PMC9197784 DOI: 10.1016/j.scitotenv.2022.156724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/09/2022] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
WBE has been a monitoring system that can give purposeful and inclusive real-time assessments of civic society as well as environmental health. This concept review introduces WBE as a surveillance scheme and initial warning outbreaks of contagious diseases caused by harmful SARS-CoV-2 with pandemic potential. Examining biomarkers of contagious diseases as evidence in polluted water taken from wastewater treatment plants suggests that these systems can be examined to get epidemiological data for checking the transmission of infectious B.1.1.529 to different areas. Thereafter, various benefits of surveillance are provided to analyse health information and pinpoint different problems that may be occurring in the workstation. Surveillance is followed by intervention steps that improved the work environment and prevent further progression of the disease. This information will help to improve early detection strategies, designing a prevention strategy to reduce their spread, infection control and therapies, thus, strengthening our global preparedness to fight future epidemics. In the end, a comprehensive discussion on the remaining challenges and opportunities for epidemiology has been given for future research perspectives.
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Affiliation(s)
- Vatika Soni
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173212, India
| | - Shilpa Paital
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173212, India
| | - Pankaj Raizada
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173212, India
| | - Tansir Ahamad
- Department of Chemistry, College of Science, King Saud University, Saudi Arabia.
| | - Aftab Aslam Parwaz Khan
- Center of Excellence for Advanced Materials Research, King Abdulaziz University, P. O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Sourbh Thakur
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland.
| | - Pardeep Singh
- School of Advanced Chemical Sciences, Shoolini University, Solan, Himachal Pradesh 173212, India.
| | - Chaudhery Mustansar Hussain
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA.
| | - Swati Sharma
- University Institute of Biotechnology, Chandigarh University, Chandigarh-Ludhiana Highway, Mohali, Punjab, India
| | - Ashok Kumar Nadda
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan 173234, Himachal Pradesh, India
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14
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Murni IK, Oktaria V, Handley A, McCarthy DT, Donato CM, Nuryastuti T, Supriyati E, Putri DAD, Sari HM, Laksono IS, Thobari JA, Bines JE. The feasibility of SARS-CoV-2 surveillance using wastewater and environmental sampling in Indonesia. PLoS One 2022; 17:e0274793. [PMID: 36240187 PMCID: PMC9565423 DOI: 10.1371/journal.pone.0274793] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/05/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Wastewater-based epidemiology (WBE) surveillance as an early warning system (EWS) for monitoring community transmission of SARS-CoV-2 in low- and middle-income country (LMIC) settings, where diagnostic testing capacity is limited, needs further exploration. We explored the feasibility to conduct a WBE surveillance in Indonesia, one of the global epicenters of the COVID-19 pandemic in the middle of 2021, with the fourth largest population in the world where sewer and non-sewered sewage systems are implemented. The feasibility and resource capacity to collect samples on a weekly or fortnightly basis with grab and/or passive sampling methods, as well as to conduct qualitative and quantitative identification of SARS-CoV-2 ribonucleic acid (RNA) using real-time RT-PCR (RT-qPCR) testing of environmental samples were explored. MATERIALS AND METHODS We initiated a routine surveillance of wastewater and environmental sampling at three predetermined districts in Special Region of Yogyakarta Province. Water samples were collected from central and community wastewater treatment plants (WWTPs), including manholes flowing to the central WWTP, and additional soil samples were collected for the near source tracking (NST) locations (i.e., public spaces where people congregate). RESULTS We began collecting samples in the Delta wave of the COVID-19 pandemic in Indonesia in July 2021. From a 10-week period, 54% (296/544) of wastewater and environmental samples were positive for SARS-CoV-2 RNA. The sample positivity rate decreased in proportion with the reported incidence of COVID-19 clinical cases in the community. The highest positivity rate of 77% in week 1, was obtained for samples collected in July 2021 and decreased to 25% in week 10 by the end of September 2021. CONCLUSION A WBE surveillance system for SARS-CoV-2 in Indonesia is feasible to monitor the community burden of infections. Future studies testing the potential of WBE and EWS for signaling early outbreaks of SARS-CoV-2 transmissions in this setting are required.
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Affiliation(s)
- Indah K. Murni
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Faculty of Medicine, Child Health Department, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- * E-mail: (IKM); (VO)
| | - Vicka Oktaria
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Faculty of Medicine, Department of Biostatistics, Epidemiology and Population Health, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- * E-mail: (IKM); (VO)
| | - Amanda Handley
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Medicines Development for Global Health, Southbank, Victoria, Australia
| | - David T. McCarthy
- Department of Civil Engineering, Environmental and Public Health Microbiology Lab (EPHM Lab), Monash University, Clayton, Victoria, Australia
| | - Celeste M. Donato
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Titik Nuryastuti
- Faculty of Medicine, Department of Microbiology, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Faculty of Medicine, Center for Tropical Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi Astuti Dharma Putri
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hendri Marinda Sari
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ida Safitri Laksono
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Faculty of Medicine, Child Health Department, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Jarir At Thobari
- Faculty of Medicine, Center for Child Health–Pediatric Research Office, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Julie E. Bines
- Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Department of Gastroenterology and Clinical Nutrition, Royal Children’s Hospital Melbourne, Parkville, Victoria, Australia
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15
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Tamáš M, Potocarova A, Konecna B, Klucar Ľ, Mackulak T. Wastewater Sequencing-An Innovative Method for Variant Monitoring of SARS-CoV-2 in Populations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:9749. [PMID: 35955106 PMCID: PMC9367975 DOI: 10.3390/ijerph19159749] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 05/14/2023]
Abstract
The SARS-CoV-2 outbreak has already affected more than 555 million people, and 6.3 million people have died. Due to its high infectivity, it is crucial to track SARS-CoV-2 outbreaks early to prevent the spread of infection. Wastewater monitoring appears to be a powerful and effective tool for managing epidemiological situations. Due to emerging mutations of SARS-CoV-2, there is a need to monitor mutations in order to control the pandemic. Since the sequencing of randomly chosen individuals is time-consuming and expensive, sequencing of wastewater plays an important role in revealing the dynamics of infection in a population. The sampling method used is a crucial factor and significantly impacts the results. Wastewater can be collected as a grab sample or as a 24 h composite sample. Another essential factor is the sample volume, as is the method of transport used. This review discusses different pretreatment procedures and RNA extraction, which may be performed using various methods, such as column-based extraction, TRIzol, or magnetic extraction. Each of the methods has its advantages and disadvantages, which are described accordingly. RT-qPCR is a procedure that confirms the presence of SARS-CoV-2 genes before sequencing. This review provides an overview of currently used methods for preparing wastewater samples, from sampling to sequencing.
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Affiliation(s)
- Michal Tamáš
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radinského 9, 81237 Bratislava, Slovakia
- Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, 81372 Bratislava, Slovakia
| | - Alena Potocarova
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 81108 Bratislava, Slovakia
| | - Barbora Konecna
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 81108 Bratislava, Slovakia
| | - Ľubos Klucar
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 84551 Bratislava, Slovakia
| | - Tomas Mackulak
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radinského 9, 81237 Bratislava, Slovakia
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16
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Hyllestad S, Myrmel M, Lomba JAB, Jordhøy F, Schipper SK, Amato E. Effectiveness of environmental surveillance of SARS-CoV-2 as an early warning system during the first year of the COVID-19 pandemic: a systematic review. JOURNAL OF WATER AND HEALTH 2022; 20:1223-1242. [PMID: 36044191 DOI: 10.2166/wh.2022.115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Since infected persons shed SARS-CoV-2 in faeces before symptoms appear, environmental surveillance (ES) may serve as an early warning system (EWS) for COVID-19 and new variants of concern. The ES of SARS-CoV-2 has been widely reviewed; however, its effectiveness as an EWS for SARS-CoV-2 in terms of timeliness, sensitivity and specificity has not been systematically assessed. We conducted a systematic review to identify and synthesise evidence on the ES of SARS-CoV-2 as an EWS to evaluate the added value for public health. Of 1,014 studies identified, we considered 29 for a qualitative synthesis of the timeliness of ES as an EWS for COVID-19, while six studies were assessed for the ability to detect new variants and two for both aims. The synthesis indicates ES may serve as an EWS of 1-2 weeks. ES could complement clinical surveillance for SARS-CoV-2; however, its cost-benefit value for public health decisions needs to be assessed based on the stage of the pandemic and resources available. Studies focusing methodological knowledge gaps as well as how to use and interpret ES signals for public health actions are needed, as is the sharing of knowledge within countries/areas with long experience of such surveillance.
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Affiliation(s)
- Susanne Hyllestad
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
| | - Mette Myrmel
- Faculty of Veterinary Medicine, Virology Unit, Norwegian University of Life Science (NMBU), Oslo, Norway
| | - Jose Antonio Baz Lomba
- Department of Environmental Chemistry and Technology, Norwegian Institute for Water Research (NIVA), Oslo, Norway
| | - Fredrik Jordhøy
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
| | - Svanhild Kjørsvik Schipper
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
| | - Ettore Amato
- Department for Infection Control and Preparedness, Norwegian Institute of Public Health (NIPH), Oslo, Norway E-mail:
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17
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Aga DS, Halwatura LM. Wastewater Surveillance of Pharmaceuticals and Genes: Challenges and Opportunities. LCGC NORTH AMERICA 2022. [DOI: 10.56530/lcgc.na.vk9190q2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Wastewater-based epidemiology (WBE) using viral nucleic acids to predict community viral outbreaks has many challenges, including interferences from the wastewater matrix. Liquid chromatography with tandem mass spectrometry (LC–MS/MS) monitoring of pharmaceutically active compounds, such as antivirals and over-the-counter drugs commonly used to relieve the symptoms of infection, could complement information provided by molecular techniques. For instance, residues of drugs associated with managing Covid-19 symptoms, including azithromycin, chloroquine, hydroxychloroquine, and lopinavir, have been detected in influent wastewater. A significant correlation can be observed between the total of Covid-19–related drugs detected and the 5-day rolling averages of reported cases. Spikes in acetaminophen concentrations can also be observed a couple of weeks before a spike in SARS-CoV-2 RNA copies in wastewater, suggesting that over-the-counter analgesic concentrations in raw sewage may be used to complement viral RNA data as an early-warning system for effective management of viral outbreaks at the community level. Sample preparation and analysis of pharmaceuticals in wastewater present unique challenges and are discussed in this article.
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18
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Designing for COVID-2x: Reflecting on Future-Proofing Human Habitation for the Inevitable Next Pandemic. BUILDINGS 2022. [DOI: 10.3390/buildings12070976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The COVID-19 pandemic of 2020–2022 has revealed the vulnerability of modern society to a highly contagious airborne virus. Many spaces in the urban and built environment designed during the late twentieth and early twenty-first century are ill-suited to maintain the level of social distancing required to reduce the probability of virus transmission. Enclosed spaces—in particular, communal circulation spaces such as corridors, elevators and lobbies—have proven loci of transmission, together with circulating reticulated air and lack of proper ventilation. While urban planning needs to incorporate the lessons learnt during COVID-19 in order to future-proof our communities through the provision of well-designed greenspaces, the main burden will fall on architects, who will play an instrumental role in designing buildings that are fit-for purpose. This conceptual paper reviews the status quo and discusses a number of strategies to future-proof human habitation for the inevitable next pandemic.
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Extensive Wastewater-Based Epidemiology as a Resourceful Tool for SARS-CoV-2 Surveillance in a Low-to-Middle-Income Country through a Successful Collaborative Quest: WBE, Mobility, and Clinical Tests. WATER 2022. [DOI: 10.3390/w14121842] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The COVID-19 pandemic has challenged healthcare systems worldwide. Efforts in low-to-middle-income countries (LMICs) cannot keep stride with infection rates, especially during peaks. A strong international collaboration between Arizona State University (ASU), Tec de Monterrey (TEC), and Servicios de Agua y Drenaje de Monterrey (Local Water Utilities) is acting to integrate wastewater-based epidemiology (WBE) of SARS-CoV-2 in the region as a complementary approach to aid the healthcare system. Wastewater was collected from four sewer catchments in the Monterrey Metropolitan area in Mexico (pop. 4,643,232) from mid-April 2020 to February 2021 (44 weeks, n = 644). Raw wastewater was filtered and filter-concentrated, the RNA was extracted using columns, and the Charité/Berlin protocol was used for the RT-qPCR. The viral loads obtained between the first (June 2020) and second waves (February 2021) of the pandemic were similar; in contrast, the clinical cases were fewer during the first wave, indicating poor coverage. During the second wave of the pandemic, the SARS-CoV-2 quantification in wastewater increased 14 days earlier than the COVID-19 clinical cases reported. This is the first long-term WBE study in Mexico and demonstrates its value in pandemic management.
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20
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Zamhuri SA, Soon CF, Nordin AN, Ab Rahim R, Sultana N, Khan MA, Lim GP, Tee KS. A review on the contamination of SARS-CoV-2 in water bodies: Transmission route, virus recovery and recent biosensor detection techniques. SENSING AND BIO-SENSING RESEARCH 2022; 36:100482. [PMID: 35251937 PMCID: PMC8889793 DOI: 10.1016/j.sbsr.2022.100482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 12/11/2022] Open
Abstract
The discovery of SARS-CoV-2 virus in the water bodies has been reported, and the risk of virus transmission to human via the water route due to poor wastewater management cannot be disregarded. The main source of the virus in water bodies is the sewage network systems which connects to the surface water. Wastewater-based epidemiology has been applied as an early surveillance tool to sense SARS-CoV-2 virus in the sewage network. This review discussed possible transmission routes of the SARS-CoV-2 virus and the challenges of the existing method in detecting the virus in wastewater. One significant challenge for the detection of the virus is that the high virus loading is diluted by the sheer volume of the wastewater. Hence, virus preconcentration from water samples prior to the application of virus assay is essential to accurately detect traceable virus loading. The preparation time, materials and conditions, virus type, recovery percentage, and various virus recovery techniques are comprehensively discussed in this review. The practicability of molecular methods such as Polymer-Chain-Reaction (PCR) for the detection of SARS-CoV-2 in wastewater will be revealed. The conventional virus detection techniques have several shortcomings and the potential of biosensors as an alternative is also considered. Biosensing techniques have also been proposed as an alternative to PCR and have reported detection limits of 10 pg/μl. This review serves to guide the reader on the future designs and development of highly sensitive, robust and, cost effective SARS-CoV-2 lab-on-a-chip biosensors for use in complex wastewater.
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Affiliation(s)
- Siti Adibah Zamhuri
- Microelectronics and Nanotechnology-Shamsuddin Research Centre, Universiti Tun Hussein Onn Malaysia, 86400, Parit Raja, Batu Pahat, Johor, Malaysia
| | - Chin Fhong Soon
- Microelectronics and Nanotechnology-Shamsuddin Research Centre, Universiti Tun Hussein Onn Malaysia, 86400, Parit Raja, Batu Pahat, Johor, Malaysia
- Faculty of Electrical and Electronic Engineering, Universiti Tun Hussein Onn Malaysia, 86400, Parit Raja, Batu Pahat, Johor, Malaysia
| | - Anis Nurashikin Nordin
- Department of Electrical and Computer Engineering, Kulliyah of Engineering, International University of Islam Malaysia, 53100, Jalan Gombak, Kuala Lumpur, Malaysia
| | - Rosminazuin Ab Rahim
- Department of Electrical and Computer Engineering, Kulliyah of Engineering, International University of Islam Malaysia, 53100, Jalan Gombak, Kuala Lumpur, Malaysia
| | | | - Muhammad Arif Khan
- Microelectronics and Nanotechnology-Shamsuddin Research Centre, Universiti Tun Hussein Onn Malaysia, 86400, Parit Raja, Batu Pahat, Johor, Malaysia
| | - Gim Pao Lim
- Microelectronics and Nanotechnology-Shamsuddin Research Centre, Universiti Tun Hussein Onn Malaysia, 86400, Parit Raja, Batu Pahat, Johor, Malaysia
| | - Kian Sek Tee
- Faculty of Electrical and Electronic Engineering, Universiti Tun Hussein Onn Malaysia, 86400, Parit Raja, Batu Pahat, Johor, Malaysia
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21
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Wang X, Wu T, Oliveira LFS, Zhang D. Sheet, Surveillance, Strategy, Salvage and Shield in global biodefense system to protect the public health and tackle the incoming pandemics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153469. [PMID: 35093353 PMCID: PMC8799268 DOI: 10.1016/j.scitotenv.2022.153469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/23/2022] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
The pandemic of COVID-19 challenges the global health system and raises our concerns on the next waves of other emerging infectious diseases. Considering the lessons from the failure of world's pandemic warning system against COVID-19, many scientists and politicians have mentioned different strategies to improve global biodefense system, among which Sheet, Surveillance, Strategy, Salvage and Shield (5S) are frequently discussed. Nevertheless, the current focus is mainly on the optimization and management of individual strategy, and there are limited attempts to combine the five strategies as an integral global biodefense system. Sheet represents the biosafety datasheet for biohazards in natural environment and human society, which helps our deeper understanding on the geographical pattern, transmission routes and infection mechanism of pathogens. Online surveillance and prognostication network is an environmental Surveillance tool for monitoring the outbreak of pandemic diseases and alarming the risks to take emergency actions, targeting aerosols, waters, soils and animals. Strategy is policies and legislations for social distancing, lockdown and personal protective equipment to block the spread of infectious diseases in communities. Clinical measures are Salvage on patients by innovating appropriate medicines and therapies. The ultimate defensive Shield is vaccine development to protect healthy crowds from infection. Fighting against COVID-19 and other emerging infectious diseases is a long rocky journey, requiring the common endeavors of scientists and politicians from all countries around the world. 5S in global biodefense system bring a ray of light to the current darkest and future road from environmental and geographical perspectives.
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Affiliation(s)
- Xinzi Wang
- School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Tianyun Wu
- Research Institute for Environmental Innovation (Tsinghua-Suzhou), Suzhou 215163, PR China
| | - Luis F S Oliveira
- Departamento de Ingeniería Civil y Arquitectura, Universidad de Lima, Avenida Javier Prado Este 4600, Santiago de Surco 1503, Peru; Department of Civil and Environmental, Universidad de la Costa, Calle 58 #55-66, 080002 Barranquilla, Atlántico, Colombia
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, PR China.
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22
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Oh C, Kim K, Araud E, Wang L, Shisler JL, Nguyen TH. A novel approach to concentrate human and animal viruses from wastewater using receptors-conjugated magnetic beads. WATER RESEARCH 2022; 212:118112. [PMID: 35091223 DOI: 10.1016/j.watres.2022.118112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/07/2023]
Abstract
Viruses are present at low concentrations in wastewater; therefore, an effective method for concentrating virus particles is necessary for accurate wastewater-based epidemiology (WBE). We designed a novel approach to concentrate human and animal viruses from wastewater using porcine gastric mucin-conjugated magnetic beads (PGM-MBs). We systematically evaluated the performances of the PGM-MBs method (sensitivity, specificity, and robustness to environmental inhibitors) with six viral species, including Tulane virus (a surrogate for human norovirus), rotavirus, adenovirus, porcine coronavirus (transmissible gastroenteritis virus or TGEV), and two human coronaviruses (NL63 and SARS-CoV-2) in influent wastewater and raw sewage samples. We determined the multiplication factor (the ratio of genome concentration of the final solution to that of the initial solution) for the PGM-MBs method, which ranged from 1.3 to 64.0 depending on the viral species. Because the recovery efficiency was significantly higher when calculated with virus titers than it was with genome concentration, the PGM-MBs method could be an appropriate tool for assessing the risk to humans who are inadvertently exposed to wastewater contaminated with infectious viruses. Furthermore, PCR inhibitors were not concentrated by PGM-MBs, suggesting that this tool will be successful for use with environmental samples. In addition, the PGM-MBs method is cost-effective (0.5 USD/sample) and has a fast turnaround time (3 h from virus concentration to genome quantification). Thus, this method can be implemented in high throughput facilities. Because of its strong performance, intrinsic characteristics of targeting the infectious virus, robustness to wastewater, and adaptability to high throughput systems, the PGM-MBs method can be successfully applied to WBE and ultimately provides valuable public health information.
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Affiliation(s)
- Chamteut Oh
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, United States.
| | - Kyukyoung Kim
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, United States
| | - Elbashir Araud
- Holonyak Micro & Nanotechnology Lab, University of Illinois at Urbana-Champaign
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, United States
| | - Joanna L Shisler
- Department of Microbiology, University of Illinois at Urbana-Champaign, United States
| | - Thanh H Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, United States; Institute of Genomic Biology, University of Illinois at Urbana-Champaign, United States
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23
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Solo-Gabriele HM, Kumar S, Abelson S, Penso J, Contreras J, Babler KM, Sharkey ME, Mantero AMA, Lamar WE, Tallon JJ, Kobetz E, Solle NS, Shukla BS, Kenney RJ, Mason CE, Schürer SC, Vidovic D, Williams SL, Grills GS, Jayaweera DT, Mirsaeidi M, Kumar N. COVID-19 Prediction using Genomic Footprint of SARS-CoV-2 in Air, Surface Swab and Wastewater Samples. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.03.14.22272314. [PMID: 35313580 PMCID: PMC8936103 DOI: 10.1101/2022.03.14.22272314] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Importance Genomic footprints of pathogens shed by infected individuals can be traced in environmental samples. Analysis of these samples can be employed for noninvasive surveillance of infectious diseases. Objective To evaluate the efficacy of environmental surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for predicting COVID-19 cases in a college dormitory. Design Using a prospective experimental design, air, surface swabs, and wastewater samples were collected from a college dormitory from March to May 2021. Students were randomly screened for COVID-19 during the study period. SARS-CoV-2 in environmental samples was concentrated with electronegative filtration and quantified using Volcano 2 nd Generation-qPCR. Descriptive analyses were conducted to examine the associations between time-lagged SARS-CoV-2 in environmental samples and clinically diagnosed COVID-19 cases. Setting This study was conducted in a residential dormitory at the University of Miami, Coral Gables campus, FL, USA. The dormitory housed about 500 students. Participants Students from the dormitory were randomly screened, for COVID-19 for 2-3 days / week while entering or exiting the dormitory. Main Outcome Clinically diagnosed COVID-19 cases were of our main interest. We hypothesized that SARS-CoV-2 detection in environmental samples was an indicator of the presence of local COVID-19 cases in the dormitory, and SARS-CoV-2 can be detected in the environmental samples several days prior to the clinical diagnosis of COVID-19 cases. Results SARS-CoV-2 genomic footprints were detected in air, surface swab and wastewater samples on 52 (63.4%), 40 (50.0%) and 57 (68.6%) days, respectively, during the study period. On 19 (24%) of 78 days SARS-CoV-2 was detected in all three sample types. Clinically diagnosed COVID-19 cases were reported on 11 days during the study period and SARS-CoV-2 was also detected two days before the case diagnosis on all 11 (100%), 9 (81.8%) and 8 (72.7%) days in air, surface swab and wastewater samples, respectively. Conclusion Proactive environmental surveillance of SARS-CoV-2 or other pathogens in a community/public setting has potential to guide targeted measures to contain and/or mitigate infectious disease outbreaks. Key Points Question: How effective is environmental surveillance of SARS-CoV-2 in public places for early detection of COVID-19 cases in a community?Findings: All clinically confirmed COVID-19 cases were predicted with the aid of 2 day lagged SARS-CoV-2 in environmental samples in a college dormitory. However, the prediction efficiency varied by sample type: best prediction by air samples, followed by wastewater and surface swab samples. SARS-CoV-2 was also detected in these samples even on days without any reported cases of COVID-19, suggesting underreporting of COVID-19 cases.Meaning: SARS-CoV-2 can be detected in environmental samples several days prior to clinical reporting of COVID-19 cases. Thus, proactive environmental surveillance of microbiome in public places can serve as a mean for early detection of location-time specific outbreaks of infectious diseases. It can also be used for underreporting of infectious diseases.
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Affiliation(s)
- Helena M. Solo-Gabriele
- Department of Chemical, Environmental, and Materials Engineering, College of Engineering, University of Miami; Coral Gables FL
| | - Shelja Kumar
- Department of Public Health Sciences, Miller School of Medicine, University of Miami; Miami FL 33136
| | - Samantha Abelson
- Department of Public Health Sciences, Miller School of Medicine, University of Miami; Miami FL 33136
| | - Johnathon Penso
- Department of Public Health Sciences, Miller School of Medicine, University of Miami; Miami FL 33136
| | - Julio Contreras
- Department of Public Health Sciences, Miller School of Medicine, University of Miami; Miami FL 33136
| | - Kristina M. Babler
- Department of Chemical, Environmental, and Materials Engineering, College of Engineering, University of Miami; Coral Gables FL
| | - Mark E. Sharkey
- Department of Medicine, Miller School of Medicine, University of Miami; Miami FL
| | - Alejandro M. A. Mantero
- Department of Public Health Sciences, Miller School of Medicine, University of Miami; Miami FL 33136
| | - Walter E. Lamar
- Facilities Safety & Compliance, Miller School of Medicine, University of Miami; Miami FL
| | - John J. Tallon
- Facilities and Operations, University of Miami; Coral Gables FL
| | - Erin Kobetz
- Department of Medicine, Miller School of Medicine, University of Miami; Miami FL
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami; Miami FL
| | - Natasha Schaefer Solle
- Department of Medicine, Miller School of Medicine, University of Miami; Miami FL
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami; Miami FL
| | - Bhavarth S. Shukla
- Department of Medicine, Miller School of Medicine, University of Miami; Miami FL
| | - Richard J. Kenney
- Department of Housing & Residential Life, University of Miami; Coral Gables FL
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College; New York City NY
| | - Stephan C. Schürer
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami; Miami FL
- Institute for Data Science & Computing, University of Miami; Coral Gables FL
- Department of Molecular & Cellular Pharmacology, Miller School of Medicine, University of Miami; Miami FL
| | - Dusica Vidovic
- Department of Molecular & Cellular Pharmacology, Miller School of Medicine, University of Miami; Miami FL
| | - Sion L. Williams
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami; Miami FL
| | - George S. Grills
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami; Miami FL
| | | | - Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville University of Florida, Jacksonville FL
| | - Naresh Kumar
- Department of Public Health Sciences, Miller School of Medicine, University of Miami; Miami FL 33136
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24
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Tharak A, Kopperi H, Hemalatha M, Kiran U, C. G. G, Moharir S, Mishra RK, Mohan SV. Longitudinal and Long-Term Wastewater Surveillance for COVID-19: Infection Dynamics and Zoning of Urban Community. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19052697. [PMID: 35270390 PMCID: PMC8910010 DOI: 10.3390/ijerph19052697] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023]
Abstract
Wastewater-based epidemiology (WBE) is emerging as a potential approach to study the infection dynamics of SARS-CoV-2 at a community level. Periodic sewage surveillance can act as an indicative tool to predict the early surge of pandemic within the community and understand the dynamics of infection and, thereby, facilitates for proper healthcare management. In this study, we performed a long-term epidemiological surveillance to assess the SARS-CoV-2 spread in domestic sewage over one year (July 2020 to August 2021) by adopting longitudinal sampling to represent a selected community (~2.5 lakhs population). Results indicated temporal dynamics in the viral load. A consistent amount of viral load was observed during the months from July 2020 to November 2020, suggesting a higher spread of the viral infection among the community, followed by a decrease in the subsequent two months (December 2020 and January 2021). A marginal increase was observed during February 2021, hinting at the onset of the second wave (from March 2021) that reached it speak in April 2021. Dynamics of the community infection rates were calculated based on the viral gene copies to assess the severity of COVID-19 spread. With the ability to predict the infection spread, longitudinal WBE studies also offer the prospect of zoning specific areas based on the infection rates. Zoning of the selected community based on the infection rates assists health management to plan and manage the infection in an effective way. WBE promotes clinical inspection with simultaneous disease detection and management, in addition to an advance warning signal to anticipate outbreaks, with respect to the slated community/zones, to tackle, prepare for and manage the pandemic.
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Affiliation(s)
- Athmakuri Tharak
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India; (A.T.); (H.K.); (M.H.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India;
| | - Harishankar Kopperi
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India; (A.T.); (H.K.); (M.H.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India;
| | - Manupati Hemalatha
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India; (A.T.); (H.K.); (M.H.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India;
| | - Uday Kiran
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India;
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad 500007, India; (G.C.G.); (S.M.)
| | - Gokulan C. G.
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad 500007, India; (G.C.G.); (S.M.)
| | - Shivranjani Moharir
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad 500007, India; (G.C.G.); (S.M.)
| | - Rakesh K. Mishra
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India;
- CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad 500007, India; (G.C.G.); (S.M.)
- Correspondence: (R.K.M.); (S.V.M.)
| | - S. Venkata Mohan
- Bioengineering and Environmental Sciences Lab, Department of Energy and Environmental Engineering (DEEE), CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India; (A.T.); (H.K.); (M.H.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India;
- Correspondence: (R.K.M.); (S.V.M.)
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25
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Shah S, Gwee SXW, Ng JQX, Lau N, Koh J, Pang J. Wastewater surveillance to infer COVID-19 transmission: A systematic review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 804:150060. [PMID: 34798721 PMCID: PMC8423771 DOI: 10.1016/j.scitotenv.2021.150060] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 05/18/2023]
Abstract
Successful detection of SARS-COV-2 in wastewater suggests the potential utility of wastewater-based epidemiology (WBE) for COVID-19 community surveillance. This systematic review aims to assess the performance of wastewater surveillance as early warning system of COVID-19 community transmission. A systematic search was conducted in PubMed, Medline, Embase and the WBE Consortium Registry according to PRISMA guidelines for relevant articles published until 31st July 2021. Relevant data were extracted and summarized. Quality of each paper was assessed using an assessment tool adapted from Bilotta et al.'s tool for environmental science. Of 763 studies identified, 92 studies distributed across 34 countries were shortlisted for qualitative synthesis. A total of 26,197 samples were collected between January 2020 and May 2021 from various locations serving population ranging from 321 to 11,400,000 inhabitants. Overall sample positivity was moderate at 29.2% in all examined settings with the spike (S) gene having maximum rate of positive detections and nucleocapsid (N) gene being the most targeted. Wastewater signals preceded confirmed cases by up to 63 days, with 13 studies reporting sample positivity before the first cases were detected in the community. At least 50 studies reported an association of viral load with community cases. While wastewater surveillance cannot replace large-scale diagnostic testing, it can complement clinical surveillance by providing early signs of potential transmission for more active public health responses. However, more studies using standardized and validated methods are required along with risk analysis and modelling to understand the dynamics of viral outbreaks.
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Affiliation(s)
- Shimoni Shah
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore.
| | - Sylvia Xiao Wei Gwee
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore.
| | - Jamie Qiao Xin Ng
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore.
| | - Nicholas Lau
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore.
| | - Jiayun Koh
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore.
| | - Junxiong Pang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Centre for Infectious Disease Epidemiology and Research, National University of Singapore, Singapore 117549, Singapore.
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26
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Sobsey MD. Absence of virological and epidemiological evidence that SARS-CoV-2 poses COVID-19 risks from environmental fecal waste, wastewater and water exposures. JOURNAL OF WATER AND HEALTH 2022; 20:126-138. [PMID: 35100160 DOI: 10.2166/wh.2021.182] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This review considers evidence for infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presence and COVID-19 infection and illness resulting from exposure to environmental fecal wastes and waters. There is no documented evidence that (1) infectious, replication-capable SARS-CoV-2 is present in environmental fecal wastes, wastewater or water, and (2) well-documented epidemiological evidence of COVID-19 infection, illness or death has never been reported for these exposure media. COVID-19 is transmitted mainly by direct personal contact and respiratory secretions as airborne droplets and aerosols, and less so by respiratory-secreted fomites via contact (touch) exposures. While SARS-CoV-2 often infects the gastrointestinal tract of infected people, its presence as infectious, replication-capable virus in environmental fecal wastes and waters has never been documented. There is only rare and unquantified evidence of infectious, replication-capable SARS-CoV-2 in recently shed feces of COVID-19 hospital patients. The human infectivity dose-response relationship of SARS-CoV-2 is unknown, thereby making it impossible to estimate evidence-based quantitative health effects assessments by quantitative microbial risk assessment methods requiring both known exposure assessment and health effects assessment data. The World Health Organization, Water Environment Federation, US Centers for Disease Control and Prevention and others do not consider environmental fecal wastes and waters as sources of exposure to infectious SARS-CoV-2 causing COVID-19 infection and illness.
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Affiliation(s)
- Mark D Sobsey
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, USA E-mail:
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27
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Barrios ME, Díaz SM, Torres C, Costamagna DM, Blanco Fernández MD, Mbayed VA. Dynamics of SARS-CoV-2 in wastewater in three districts of the Buenos Aires metropolitan region, Argentina, throughout nine months of surveillance: A pilot study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149578. [PMID: 34426365 PMCID: PMC8359566 DOI: 10.1016/j.scitotenv.2021.149578] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 05/17/2023]
Abstract
In the current pandemic of COVID-19, sewage surveillance of SARS-CoV-2 genome has been used to complement viral epidemiology in different countries. The aim of this work was to introduce and evaluate this wastewater-based tool in the metropolitan region of Buenos Aires, Argentina. As a pilot study, surveillance of SARS-CoV-2 in wastewater from three districts of this area was performed for more than nine months from June 2020 to April 2021. Viruses present in the samples were concentrated using polyethylene glycol precipitation and quantified using RT-qPCR CDC N1 assay. Virus recovery for SARS-CoV-2 and a potential surrogate, bovine coronavirus Mebus strain, that shares the Betacoronavirus genus and structural characteristics with SARS-CoV-2, were evaluated after concentration and detection procedures. Recovery of both viruses did not differ significantly, with a median for SARS-CoV-2 and BCoV of 0.085 (95% CI: 0.021-0.179) and 0.262 (95% CI: 1.18 × 10-5-0.564) respectively. The concentration of SARS-CoV-2 genome in wastewater ranged from 10 -1 to 10 3 cg/ml, depending on the wastewater treatment plant, type of collection site, viral recovery of the concentration method and the epidemiological situation of the outbreaks. Significant correlations were observed between SARS-CoV-2 concentration in wastewater and reported clinical cases, reinforcing the utility of this approach to monitor the epidemiological status of populations.
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Affiliation(s)
- Melina Elizabeth Barrios
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Junín 954 (C1113AAD), Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 (C1425FQB), Ciudad Autónoma de Buenos Aires, Argentina.
| | - Sofía Micaela Díaz
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBAVIM), Junín 954 (C1113AAD), Ciudad Autónoma de Buenos Aires, Argentina; Ministerio de Ciencia, Tecnología e Innovación, Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), Godoy Cruz 2370 (C1425FQD), Ciudad Autónoma de Buenos Aires, Argentina.
| | - Carolina Torres
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 (C1425FQB), Ciudad Autónoma de Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBAVIM), Junín 954 (C1113AAD), Ciudad Autónoma de Buenos Aires, Argentina.
| | | | - María Dolores Blanco Fernández
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 (C1425FQB), Ciudad Autónoma de Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBAVIM), Junín 954 (C1113AAD), Ciudad Autónoma de Buenos Aires, Argentina.
| | - Viviana Andrea Mbayed
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290 (C1425FQB), Ciudad Autónoma de Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBAVIM), Junín 954 (C1113AAD), Ciudad Autónoma de Buenos Aires, Argentina.
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Alhama J, Maestre JP, Martín MÁ, Michán C. Monitoring COVID-19 through SARS-CoV-2 quantification in wastewater: progress, challenges and prospects. Microb Biotechnol 2021; 15:1719-1728. [PMID: 34905659 PMCID: PMC9151337 DOI: 10.1111/1751-7915.13989] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/13/2022] Open
Abstract
Wastewater‐Based Epidemiology (WBE) is widely used to monitor the progression of the current SARS‐CoV‐2 pandemic at local levels. In this review, we address the different approaches to the steps needed for this surveillance: sampling wastewaters (WWs), concentrating the virus from the samples and quantifying them by qPCR, focusing on the main limitations of the methodologies used. Factors that can influence SARS‐CoV‐2 monitoring in WWs include: (i) physical parameters as temperature that can hamper the detection in warm seasons and tropical regions, (ii) sampling methodologies and timetables, being composite samples and Moore swabs the less variable and more sensitive approaches, (iii) virus concentration methodologies that need to be feasible and practicable in simpler laboratories and (iv) detection methodologies that should tend to use faster and cost‐effective procedures. The efficiency of WW treatments and the use of WWs for SARS‐CoV‐2 variants detection are also addressed. Furthermore, we discuss the need for the development of common standardized protocols, although these must be versatile enough to comprise variations among target communities. WBE screening of risk populations will allow for the prediction of future outbreaks, thus alerting authorities to implement early action measurements.
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Affiliation(s)
- José Alhama
- Department of Biochemistry and Molecular Biology, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, Córdoba, 14071, Spain
| | - Juan P Maestre
- Department of Civil, Architectural, and Environmental Engineering, The University of Texas at Austin, 301 E. Dean Keeton St., Stop C1786, Austin, TX, 78712, USA
| | - M Ángeles Martín
- Department of Inorganic Chemistry and Chemical Engineering, Area of Chemical Engineering, Universidad de Córdoba, Institute of Fine Chemistry and Nanochemistry (IUNAN), Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Marie Curie, Córdoba, 14071, Spain
| | - Carmen Michán
- Department of Biochemistry and Molecular Biology, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario CeiA3, Edificio Severo Ochoa, Córdoba, 14071, Spain
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Sangkham S. A review on detection of SARS-CoV-2 RNA in wastewater in light of the current knowledge of treatment process for removal of viral fragments. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 299:113563. [PMID: 34488114 PMCID: PMC8373619 DOI: 10.1016/j.jenvman.2021.113563] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/02/2021] [Accepted: 08/17/2021] [Indexed: 05/05/2023]
Abstract
The entire globe is affected by the novel disease of coronavirus 2019 (COVID-19 or 2019-nCoV), which is formally recognised as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The World Health Organisation (WHO) announced this disease as a global pandemic. The presence of SARS-CoV-2 RNA in unprocessed wastewater has become a cause of worry due to these emerging pathogens in the process of wastewater treatment, as reported in the present study. This analysis intends to interpret the fate, environmental factors and route of transmission of SARS-CoV-2, along with its eradication by treating the wastewater for controlling and preventing its further spread. Different recovery estimations of the virus have been depicted by the detection of SARS-CoV-2 RNA in wastewater through the viral concentration techniques. Most frequently used viral concentration techniques include polyethylene glycol (PEG) precipitation, ultrafiltration, electronegative membrane, and ultracentrifugation, after which the detection and quantification of SARS-CoV-2 RNA are done in wastewater samples through quantitative reverse transcription-polymerase chain reaction (RT-qPCR). The wastewater treatment plant (WWTP) holds the key responsibility of eliminating pathogens prior to the discharge of wastewater into surface water bodies. The removal of SARS-CoV-2 RNA at the treatment stage is dependent on the operations of wastewater treatment systems during the outbreak of the virus; particularly, in the urban and extensively populated regions. Efficient primary, secondary and tertiary methods of wastewater treatment and disinfection can reduce or inactivate SARS-CoV-2 RNA before being drained out. Nonetheless, further studies regarding COVID-19-related disinfectants, environment conditions and viral concentrations in each treatment procedure, implications on the environment and regular monitoring of transmission need to be done urgently. Hence, monitoring the SARS-CoV-2 RNA in samples of wastewater under the procedure of wastewater-based epidemiology (WBE) supplement the real-time data pertaining to the investigation of the COVID-19 pandemic in the community, regional and national levels.
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Affiliation(s)
- Sarawut Sangkham
- Department of Environmental Health, School of Public Health, University of Phayao, Muang District, Phayao, 56000, Thailand.
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30
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Wang Q, Liu L. On the Critical Role of Human Feces and Public Toilets in the Transmission of COVID-19: Evidence from China. SUSTAINABLE CITIES AND SOCIETY 2021; 75:103350. [PMID: 34540563 PMCID: PMC8433098 DOI: 10.1016/j.scs.2021.103350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 05/05/2023]
Abstract
The surprising spread speed of the COVID-19 pandemic creates an urgent need for investigating the transmission chain or transmission pattern of COVID-19 beyond the traditional respiratory channels. This study therefore examines whether human feces and public toilets play a critical role in the transmission of COVID-19. First, it develops a theoretical model that simulates the transmission chain of COVID-19 through public restrooms. Second, it uses stabilized epidemic data from China to empirically examine this theory, conducting an empirical estimation using a two-stage least squares (2SLS) model with appropriate instrumental variables (IVs). This study confirms that the wastewater directly promotes the transmission of COVID-19 within a city. However, the role of garbage in this transmission chain is more indirect in the sense that garbage has a complex relationship with public toilets, and it promotes the transmission of COVID-19 within a city through interaction with public toilets and, hence, human feces. These findings have very strong policy implications in the sense that if we can somehow use the ratio of public toilets as a policy instrument, then we can find a way to minimize the total number of infections in a region. As shown in this study, pushing the ratio of public toilets (against open defecation) to the local population in a city to its optimal level would help to reduce the total infection in a region.
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Affiliation(s)
- Qiuyun Wang
- School of Economics, Southwestern University of Finance and Economics, P.R China
| | - Lu Liu
- School of Economics, Southwestern University of Finance and Economics, P.R China
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31
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Van Poelvoorde LAE, Delcourt T, Coucke W, Herman P, De Keersmaecker SCJ, Saelens X, Roosens NHC, Vanneste K. Strategy and Performance Evaluation of Low-Frequency Variant Calling for SARS-CoV-2 Using Targeted Deep Illumina Sequencing. Front Microbiol 2021; 12:747458. [PMID: 34721349 PMCID: PMC8548777 DOI: 10.3389/fmicb.2021.747458] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/21/2021] [Indexed: 12/24/2022] Open
Abstract
The ongoing COVID-19 pandemic, caused by SARS-CoV-2, constitutes a tremendous global health issue. Continuous monitoring of the virus has become a cornerstone to make rational decisions on implementing societal and sanitary measures to curtail the virus spread. Additionally, emerging SARS-CoV-2 variants have increased the need for genomic surveillance to detect particular strains because of their potentially increased transmissibility, pathogenicity and immune escape. Targeted SARS-CoV-2 sequencing of diagnostic and wastewater samples has been explored as an epidemiological surveillance method for the competent authorities. Currently, only the consensus genome sequence of the most abundant strain is taken into consideration for analysis, but multiple variant strains are now circulating in the population. Consequently, in diagnostic samples, potential co-infection(s) by several different variants can occur or quasispecies can develop during an infection in an individual. In wastewater samples, multiple variant strains will often be simultaneously present. Currently, quality criteria are mainly available for constructing the consensus genome sequence, and some guidelines exist for the detection of co-infections and quasispecies in diagnostic samples. The performance of detection and quantification of low-frequency variants using whole genome sequencing (WGS) of SARS-CoV-2 remains largely unknown. Here, we evaluated the detection and quantification of mutations present at low abundances using the mutations defining the SARS-CoV-2 lineage B.1.1.7 (alpha variant) as a case study. Real sequencing data were in silico modified by introducing mutations of interest into raw wild-type sequencing data, or by mixing wild-type and mutant raw sequencing data, to construct mixed samples subjected to WGS using a tiling amplicon-based targeted metagenomics approach and Illumina sequencing. As anticipated, higher variation and lower sensitivity were observed at lower coverages and allelic frequencies. We found that detection of all low-frequency variants at an abundance of 10, 5, 3, and 1%, requires at least a sequencing coverage of 250, 500, 1500, and 10,000×, respectively. Although increasing variability of estimated allelic frequencies at decreasing coverages and lower allelic frequencies was observed, its impact on reliable quantification was limited. This study provides a highly sensitive low-frequency variant detection approach, which is publicly available at https://galaxy.sciensano.be, and specific recommendations for minimum sequencing coverages to detect clade-defining mutations at certain allelic frequencies. This approach will be useful to detect and quantify low-frequency variants in both diagnostic (e.g., co-infections and quasispecies) and wastewater [e.g., multiple variants of concern (VOCs)] samples.
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Affiliation(s)
- Laura A. E. Van Poelvoorde
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Thomas Delcourt
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Wim Coucke
- Quality of Laboratories, Sciensano, Brussels, Belgium
| | - Philippe Herman
- Expertise and Service Provision, Sciensano, Brussels, Belgium
| | | | - Xavier Saelens
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | | | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
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32
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Preparing for COVID-2x: Urban Planning Needs to Regard Urological Wastewater as an Invaluable Communal Public Health Asset and Not as a Burden. URBAN SCIENCE 2021. [DOI: 10.3390/urbansci5040075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Prior to the COVID-19 pandemic, the analysis of urological wastewater had been a matter of academic curiosity and community-wide big-picture studies looking at drug use or the presence of select viruses such as Hepatitis. The COVID-19 pandemic saw systematic testing of urological wastewater emerge as a significant early detection tool for the presence of SARS-CoV-2 in a community. Even though the pandemic still rages in all continents, it is time to consider the post-pandemic world. This paper posits that urban planners should treat urological wastewater as a communal public health asset and that future sewer design should allow for stratified multi-order sampling.
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