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Acheampong E, Husain AA, Dudani H, Nayak AR, Nag A, Meena E, Shrivastava SK, McClure P, Tarr AW, Crooks C, Lade R, Gomes RL, Singer A, Kumar S, Bhatnagar T, Arora S, Kashyap RS, Monaghan TM. Population infection estimation from wastewater surveillance for SARS-CoV-2 in Nagpur, India during the second pandemic wave. PLoS One 2024; 19:e0303529. [PMID: 38809825 PMCID: PMC11135679 DOI: 10.1371/journal.pone.0303529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
Wastewater-based epidemiology (WBE) has emerged as an effective environmental surveillance tool for predicting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease outbreaks in high-income countries (HICs) with centralized sewage infrastructure. However, few studies have applied WBE alongside epidemic disease modelling to estimate the prevalence of SARS-CoV-2 in low-resource settings. This study aimed to explore the feasibility of collecting untreated wastewater samples from rural and urban catchment areas of Nagpur district, to detect and quantify SARS-CoV-2 using real-time qPCR, to compare geographic differences in viral loads, and to integrate the wastewater data into a modified Susceptible-Exposed-Infectious-Confirmed Positives-Recovered (SEIPR) model. Of the 983 wastewater samples analyzed for SARS-CoV-2 RNA, we detected significantly higher sample positivity rates, 43.7% (95% confidence interval (CI) 40.1, 47.4) and 30.4% (95% CI 24.66, 36.66), and higher viral loads for the urban compared with rural samples, respectively. The Basic reproductive number, R0, positively correlated with population density and negatively correlated with humidity, a proxy for rainfall and dilution of waste in the sewers. The SEIPR model estimated the rate of unreported coronavirus disease 2019 (COVID-19) cases at the start of the wave as 13.97 [95% CI (10.17, 17.0)] times that of confirmed cases, representing a material difference in cases and healthcare resource burden. Wastewater surveillance might prove to be a more reliable way to prepare for surges in COVID-19 cases during future waves for authorities.
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Affiliation(s)
- Edward Acheampong
- Department of Statistics and Actuarial Science, University of Ghana, Legon, Accra, Ghana
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Aliabbas A. Husain
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Hemanshi Dudani
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Amit R. Nayak
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Aditi Nag
- Dr B.Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Ekta Meena
- Dr B.Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Sandeep K. Shrivastava
- Dr B.Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Patrick McClure
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Alexander W. Tarr
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Colin Crooks
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | | | - Rachel L. Gomes
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Andrew Singer
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Saravana Kumar
- ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Tarun Bhatnagar
- ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Sudipti Arora
- Dr B.Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Rajpal Singh Kashyap
- Dr B.Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Tanya M. Monaghan
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
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Perry WB, Chrispim MC, Barbosa MRF, de Souza Lauretto M, Razzolini MTP, Nardocci AC, Jones O, Jones DL, Weightman A, Sato MIZ, Montagner C, Durance I. Cross-continental comparative experiences of wastewater surveillance and a vision for the 21st century. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170842. [PMID: 38340868 DOI: 10.1016/j.scitotenv.2024.170842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
The COVID-19 pandemic has brought the epidemiological value of monitoring wastewater into sharp focus. The challenges of implementing and optimising wastewater monitoring vary significantly from one region to another, often due to the array of different wastewater systems around the globe, as well as the availability of resources to undertake the required analyses (e.g. laboratory infrastructure and expertise). Here we reflect on the local and shared challenges of implementing a SARS-CoV-2 monitoring programme in two geographically and socio-economically distinct regions, São Paulo state (Brazil) and Wales (UK), focusing on design, laboratory methods and data analysis, and identifying potential guiding principles for wastewater surveillance fit for the 21st century. Our results highlight the historical nature of region-specific challenges to the implementation of wastewater surveillance, including previous experience of using wastewater surveillance, stakeholders involved, and nature of wastewater infrastructure. Building on those challenges, we then highlight what an ideal programme would look like if restrictions such as resource were not a constraint. Finally, we demonstrate the value of bringing multidisciplinary skills and international networks together for effective wastewater surveillance.
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Affiliation(s)
| | - Mariana Cardoso Chrispim
- Environmental and Biosciences Department, School of Business, Innovation and Sustainability, Halmstad University, Kristian IV:s väg 3, 30118 Halmstad, Sweden
| | - Mikaela Renata Funada Barbosa
- Environmental Analysis Department, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo CEP 05459-900, Brazil; NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Marcelo de Souza Lauretto
- NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil; School of Arts, Sciences and Humanities, University of Sao Paulo, Rua Arlindo Bettio, 1000, São Paulo CEP 03828-000, Brazil
| | - Maria Tereza Pepe Razzolini
- NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil; School of Public Health, University of Sao Paulo, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Adelaide Cassia Nardocci
- NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil; School of Public Health, University of Sao Paulo, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Owen Jones
- School of Mathematics, Cardiff University, Cardiff CF24 4AG, UK
| | - Davey L Jones
- Environment Centre Wales, Bangor University, Bangor LL57 2UW, UK; Food Futures Institute, Murdoch University, Murdoch WA 6105, Australia
| | | | - Maria Inês Zanoli Sato
- Environmental Analysis Department, Environmental Company of the São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo CEP 05459-900, Brazil; NARA - Center for Research in Environmental Risk Assessment, School of Public Health, Environmental Health Department, Av. Dr Arnaldo, 715, 01246-904 São Paulo, Brazil
| | - Cassiana Montagner
- Environmental Chemistry Laboratory, Institute of Chemistry, University of Campinas, Campinas, São Paulo 13083970, Brazil
| | - Isabelle Durance
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.
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Cheng K, Lv Y, Li C, Cheng S, Xu S, Gao X, Xu H. Meta-analysis of the SARS-CoV-2 positivity rate in municipal wastewater. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:119. [PMID: 38483628 DOI: 10.1007/s10653-024-01895-7] [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: 12/20/2023] [Accepted: 01/29/2024] [Indexed: 03/19/2024]
Abstract
The aim of this study is to conduct a systematic analysis of the SARS-CoV-2 levels in urban sewage and evaluate the associated positivity rates, thereby developing comprehensive insights into the epidemic situation and providing valuable inputs for the development of effective disease prevention and control strategies. The PubMed, Scopus, Embase, China National Knowledge Infrastructure, Wanfang Database, and VIP databases were systematically searched based on the predefined retrieval strategy. The literature published up to February 2023 was meticulously screened according to the predetermined inclusion and exclusion criteria, and the relevant data were extracted for subsequent integration. The quality assessment of the included studies adhered to the rigorous Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement guidelines. The meta-analysis was conducted using Stata 17.0 software. The meta-analysis included a total of 34 studies, encompassing 8429 municipal wastewater samples. A random effects model was employed for the analysis, revealing an overall SARS-CoV-2 positivity rate of 53.7% in the municipal wastewater samples. The subgroup analyses demonstrated significant regional variations in the SARS-CoV-2 positivity rate in municipal wastewater, with Africa exhibiting the highest rate at 62.5% (95% confidence interval [CI] 47.4 ~ 76.0%) and Oceania displaying the lowest at 33.3% (95% CI 22.0 ~ 46.3%). However, the subgroup analyses based on the sampling site, strain prevalence period, and laboratory testing method did not yield any statistically significant differences. The SARS-CoV-2 positivity rate in wastewater is relatively high globally, although it exhibits regional disparities. Regions with larger populations and lower economic levels demonstrate higher viral detection rates in sewage. Different types of wastewater sampling sites can be employed to monitor distinct aspects of the COVID-19 pandemic. Continuous surveillance of SARS-CoV-2 in wastewater plays a pivotal role in complementing clinical data, helping to track outbreak progression across diverse regions.
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Affiliation(s)
- Keyi Cheng
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, Zhejiang, China
| | - Ye Lv
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, Zhejiang, China
| | - Chaokang Li
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, Zhejiang, China
| | - Shi Cheng
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, Zhejiang, China
| | - Shanshan Xu
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, Zhejiang, China
| | - Xin Gao
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, Zhejiang, China
| | - Hong Xu
- Hangzhou Center for Disease Control and Prevention, Hangzhou, 310021, Zhejiang, China.
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Long A, Loethen K, Behzadnezhad A, Zhang W. A snapshot of SARS-CoV-2 viral RNA throughout wastewater treatment plants in Arkansas. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2024; 96:e10992. [PMID: 38291790 DOI: 10.1002/wer.10992] [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: 08/03/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can spread the viral RNA in wastewater by the feces of those experience COVID-19 symptoms. While wastewater monitoring of SARS-CoV-2 in the raw sewage has been confirmed as an effective tool to predict COVID-19 infection, the goal of this study is to assess the presence of SARS-CoV-2 viral RNA throughout various wastewater treatment processes. Wastewater samples were collected from wastewater treatment plants (WWTPs) in the state of Arkansas from August 2020 to June 2021 and measured for the relative concentration of SARS-CoV-2 viral RNA using RT-qPCR. The gene concentrations in the raw wastewater measured in this study were similar to other published studies, targeting the N1 and N2 genes of the virus. The viral RNA concentration was measured after each wastewater treatment step within WWTPs, including primary sedimentation, activated sludge, filtration and disinfection. Results show the most viral RNA removal occurred in the secondary treatment (activated sludge). The viral RNA was only occasionally detected after disinfection (chlorination or UV disinfection). Overall, WWTPs can remove the SARS-CoV-2 viral RNA at an average of 98.7%, while complete removal was achieved on 82% of the sampling days. Further investigation is required to ensure complete viral RNA removal from wastewater such as improving existing treatment process or supplementing with additional treatment steps. PRACTITIONER POINTS: The viral RNA of SARS-CoV-2 was detected in Arkansas wastewater treatment plants. SARS-CoV-2 was rarely detected in treated effluent from wastewater treatment plants. Activated sludge was effective removing SARS-CoV-2 viral RNA from wastewater. This study was limited by the direct RNA extraction from wastewater, which lowered the sensitivity of detection.
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Affiliation(s)
- Aaron Long
- Department of Civil Engineering, University of Arkansas, Fayetteville, Arkansas, USA
| | - Katie Loethen
- Department of Biological Engineering, University of Arkansas, Fayetteville, Arkansas, USA
| | - Asal Behzadnezhad
- Department of Civil Engineering, University of Arkansas, Fayetteville, Arkansas, USA
| | - Wen Zhang
- Department of Civil Engineering, University of Arkansas, Fayetteville, Arkansas, USA
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Kanchan S, Ogden E, Kesheri M, Skinner A, Miliken E, Lyman D, Armstrong J, Sciglitano L, Hampikian G. COVID-19 hospitalizations and deaths predicted by SARS-CoV-2 levels in Boise, Idaho wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167742. [PMID: 37852488 DOI: 10.1016/j.scitotenv.2023.167742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/22/2023] [Accepted: 10/09/2023] [Indexed: 10/20/2023]
Abstract
The viral load of COVID-19 in untreated wastewater from Idaho's capital city Boise, ID (Ada County) has been used to predict changes in hospital admissions (statewide in Idaho) and deaths (Ada County) using distributed fixed lag modeling and artificial neural networks (ANN). The wastewater viral counts were used to determine the lag time between peaks in wastewater viral counts and COVID-19 hospitalizations as well as deaths (14 and 23 days, respectively). Quantitative measurement of SARS-CoV-2 viral RNA counts in the untreated wastewater was determined three times a week using RT-qPCR over a span of 13 months. To mitigate the effects of PCR inhibitors in wastewater, a series of dilution tests were conducted, and the 1/4 dilution was used to generate the most successful model. Wastewater SARS-CoV-2 viral RNA counts and hospitalization from June 7, 2021 to December 29, 2021 were used as training data to predict hospitalizations; and wastewater SARS-CoV-2 viral RNA counts and deaths from June 7, 2021 to December 20, 2021 were used as training data to predict deaths. These training data were used to make predictive ANN models for future hospitalizations and deaths. To the best of our knowledge, this is the first report of prediction of deaths from COVID-19 based on wastewater SARS-CoV-2 viral RNA counts using machine learning-based multilayered ANN. The applied modeling demonstrates that wastewater surveillance data can be combined with hospitalizations and death data to generate machine learning-based ANN models that predict future COVID-19 hospital admissions and deaths, providing an early warning for medical response teams and healthcare policymakers.
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Affiliation(s)
- Swarna Kanchan
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America; Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, 25701, United States of America
| | - Ernie Ogden
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Minu Kesheri
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America; Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, 25701, United States of America
| | - Alexis Skinner
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Erin Miliken
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Devyn Lyman
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Jacob Armstrong
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Lawrence Sciglitano
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America
| | - Greg Hampikian
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, United States of America.
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Baz Lomba JA, Pires J, Myrmel M, Arnø JK, Madslien EH, Langlete P, Amato E, Hyllestad S. Effectiveness of environmental surveillance of SARS-CoV-2 as an early-warning system: Update of a systematic review during the second year of the pandemic. JOURNAL OF WATER AND HEALTH 2024; 22:197-234. [PMID: 38295081 PMCID: wh_2023_279 DOI: 10.2166/wh.2023.279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
The aim of this updated systematic review was to offer an overview of the effectiveness of environmental surveillance (ES) of SARS-CoV-2 as a potential early-warning system (EWS) for COVID-19 and new variants of concerns (VOCs) during the second year of the pandemic. An updated literature search was conducted to evaluate the added value of ES of SARS-CoV-2 for public health decisions. The search for studies published between June 2021 and July 2022 resulted in 1,588 publications, identifying 331 articles for full-text screening. A total of 151 publications met our inclusion criteria for the assessment of the effectiveness of ES as an EWS and early detection of SARS-CoV-2 variants. We identified a further 30 publications among the grey literature. ES confirms its usefulness as an EWS for detecting new waves of SARS-CoV-2 infection with an average lead time of 1-2 weeks for most of the publication. ES could function as an EWS for new VOCs in areas with no registered cases or limited clinical capacity. Challenges in data harmonization and variant detection require standardized approaches and innovations for improved public health decision-making. ES confirms its potential to support public health decision-making and resource allocation in future outbreaks.
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Affiliation(s)
- Jose Antonio Baz Lomba
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway E-mail:
| | - João Pires
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway; ECDC fellowship Programme, Public Health Microbiology path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Mette Myrmel
- Faculty of Veterinary Medicine, Virology Unit, Norwegian University of Life Science (NMBU), Oslo, Norway
| | - Jorunn Karterud Arnø
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Elisabeth Henie Madslien
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Petter Langlete
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Ettore Amato
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Susanne Hyllestad
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
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7
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Stockdale SR, Blanchard AM, Nayak A, Husain A, Nashine R, Dudani H, McClure CP, Tarr AW, Nag A, Meena E, Sinha V, Shrivastava SK, Hill C, Singer AC, Gomes RL, Acheampong E, Chidambaram SB, Bhatnagar T, Vetrivel U, Arora S, Kashyap RS, Monaghan TM. RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2023; 14:100205. [PMID: 37193348 PMCID: PMC10150210 DOI: 10.1016/j.lansea.2023.100205] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 04/10/2023] [Accepted: 04/24/2023] [Indexed: 05/18/2023]
Abstract
Background The COVID-19 pandemic showcased the power of genomic sequencing to tackle the emergence and spread of infectious diseases. However, metagenomic sequencing of total microbial RNAs in wastewater has the potential to assess multiple infectious diseases simultaneously and has yet to be explored. Methods A retrospective RNA-Seq epidemiological survey of 140 untreated composite wastewater samples was performed across urban (n = 112) and rural (n = 28) areas of Nagpur, Central India. Composite wastewater samples were prepared by pooling 422 individual grab samples collected prospectively from sewer lines of urban municipality zones and open drains of rural areas from 3rd February to 3rd April 2021, during the second COVID-19 wave in India. Samples were pre-processed and total RNA was extracted prior to genomic sequencing. Findings This is the first study that has utilised culture and/or probe-independent unbiased RNA-Seq to examine Indian wastewater samples. Our findings reveal the detection of zoonotic viruses including chikungunya, Jingmen tick and rabies viruses, which have not previously been reported in wastewater. SARS-CoV-2 was detectable in 83 locations (59%), with stark abundance variations observed between sampling sites. Hepatitis C virus was the most frequently detected infectious virus, identified in 113 locations and co-occurring 77 times with SARS-CoV-2; and both were more abundantly detected in rural areas than urban zones. Concurrent identification of segmented virus genomic fragments of influenza A virus, norovirus, and rotavirus was observed. Geographical differences were also observed for astrovirus, saffold virus, husavirus, and aichi virus that were more prevalent in urban samples, while the zoonotic viruses chikungunya and rabies, were more abundant in rural environments. Interpretation RNA-Seq can effectively detect multiple infectious diseases simultaneously, facilitating geographical and epidemiological surveys of endemic viruses that could help direct healthcare interventions against emergent and pre-existent infectious diseases as well as cost-effectively and qualitatively characterising the health status of the population over time. Funding UK Research and Innovation (UKRI) Global Challenges Research Fund (GCRF) grant number H54810, as supported by Research England.
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Affiliation(s)
| | - Adam M. Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Amit Nayak
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Aliabbas Husain
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Rupam Nashine
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Hemanshi Dudani
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - C. Patrick McClure
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Alexander W. Tarr
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, United Kingdom
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Aditi Nag
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Ekta Meena
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Vikky Sinha
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Sandeep K. Shrivastava
- Centre for Innovation, Research & Development, Dr. B. Lal Clinical Laboratory Pvt. Ltd., Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Andrew C. Singer
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Rachel L. Gomes
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, United Kingdom
| | - Edward Acheampong
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, United Kingdom
- Department of Statistics and Actuarial Science, University of Ghana, P.O. Box, LG 115, Legon, Ghana
| | - Saravana B. Chidambaram
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru, 570015, KA, India
| | - Tarun Bhatnagar
- ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Umashankar Vetrivel
- National Institute of Traditional Medicine, Indian Council of Medical Research, Belagavi, 590010, India
- Virology and Biotechnology Division, ICMR-National Institute for Research in Tuberculosis, Chennai, 600031, India
| | - Sudipti Arora
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Rajpal Singh Kashyap
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Tanya M. Monaghan
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
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8
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Jiang G, Liu Y, Tang S, Kitajima M, Haramoto E, Arora S, Choi PM, Jackson G, D'Aoust PM, Delatolla R, Zhang S, Guo Y, Wu J, Chen Y, Sharma E, Prosun TA, Zhao J, Kumar M, Honda R, Ahmed W, Meiman J. Moving forward with COVID-19: Future research prospects of wastewater-based epidemiology methodologies and applications. CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH 2023; 33:100458. [PMID: 37034453 PMCID: PMC10065412 DOI: 10.1016/j.coesh.2023.100458] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Wastewater-based epidemiology (WBE) has been demonstrated for its great potential in tracking of coronavirus disease 2019 (COVID-19) transmission among populations despite some inherent methodological limitations. These include non-optimized sampling approaches and analytical methods; stability of viruses in sewer systems; partitioning/retention in biofilms; and the singular and inaccurate back-calculation step to predict the number of infected individuals in the community. Future research is expected to (1) standardize best practices in wastewater sampling, analysis and data reporting protocols for the sensitive and reproducible detection of viruses in wastewater; (2) understand the in-sewer viral stability and partitioning under the impacts of dynamic wastewater flow, properties, chemicals, biofilms and sediments; and (3) achieve smart wastewater surveillance with artificial intelligence and big data models. Further specific research is essential in the monitoring of other viral pathogens with pandemic potential and subcatchment applications to maximize the benefits of WBE beyond COVID-19.
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Affiliation(s)
- Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Yanchen Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Song Tang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health (NIEH), Chinese Center for Disease Control and Prevention (China CDC), Chaoyang District, Beijing 100021, China
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sudipti Arora
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, 302017, India
| | - Phil M Choi
- Water Unit, Health Protection Branch, Queensland Public Health and Scientific Services, Queensland Health, Australia
| | - Greg Jackson
- Water Unit, Health Protection Branch, Queensland Public Health and Scientific Services, Queensland Health, Australia
| | - Patrick M D'Aoust
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Robert Delatolla
- Department of Civil Engineering, University of Ottawa, Ottawa, Ontario, Canada
| | - Shuxin Zhang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Ying Guo
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Jiangping Wu
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Yan Chen
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Elipsha Sharma
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Tanjila Alam Prosun
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Jiawei Zhao
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Manish Kumar
- Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Campus Monterey, Monterrey, 64849, Nuevo Leon, Mexico
| | - Ryo Honda
- Faculty of Geosciences and Civil Engineering, Kanazawa University, Kanazawa, Japan
| | - Warish Ahmed
- CSIRO Environment, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Jon Meiman
- Wisconsin Department of Health Services, Madison, WI 53701, USA
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9
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Maryam S, Ul Haq I, Yahya G, Ul Haq M, Algammal AM, Saber S, Cavalu S. COVID-19 surveillance in wastewater: An epidemiological tool for the monitoring of SARS-CoV-2. Front Cell Infect Microbiol 2023; 12:978643. [PMID: 36683701 PMCID: PMC9854263 DOI: 10.3389/fcimb.2022.978643] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/03/2022] [Indexed: 01/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has prompted a lot of questions globally regarding the range of information about the virus's possible routes of transmission, diagnostics, and therapeutic tools. Worldwide studies have pointed out the importance of monitoring and early surveillance techniques based on the identification of viral RNA in wastewater. These studies indicated the presence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in human feces, which is shed via excreta including mucus, feces, saliva, and sputum. Subsequently, they get dumped into wastewater, and their presence in wastewater provides a possibility of using it as a tool to help prevent and eradicate the virus. Its monitoring is still done in many regions worldwide and serves as an early "warning signal"; however, a lot of limitations of wastewater surveillance have also been identified.
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Affiliation(s)
- Sajida Maryam
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Ihtisham Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
- Department of Physical Chemistry and Polymers Technology, Silesian University of Technology, Gliwice, Poland
- Joint Doctoral School, Silesian University of Technology, Gliwice, Poland
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Mehboob Ul Haq
- Department of Biosciences, The Commission on Science and Technology for Sustainable Development in the South (COMSATS) University Islamabad (CUI), Islamabad, Pakistan
| | - Abdelazeem M Algammal
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Sameh Saber
- Department of Pharmacology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, Egypt
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
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