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Calabria de Araujo J, Carvalho APA, Leal CD, Natividade M, Borin M, Guerra A, Carobin N, Sabino A, Almada M, Costa MCM, Saia F, Frutuoso LV, Iani FCM, Adelino T, Fonseca V, Giovanetti M, Alcantara LCJ. Detection of Multiple Human Viruses, including Mpox, Using a Wastewater Surveillance Approach in Brazil. Pathogens 2024; 13:589. [PMID: 39057816 PMCID: PMC11279579 DOI: 10.3390/pathogens13070589] [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: 05/06/2024] [Revised: 07/08/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Sewage surveillance can be used as an effective complementary tool for detecting pathogens in local communities, providing insights into emerging threats and aiding in the monitoring of outbreaks. In this study using qPCR and whole genomic sewage surveillance, we detected the Mpox virus along with other viruses, in municipal and hospital wastewaters in Belo Horizonte, Brazil over a 9-month period (from July 2022 until March 2023). MPXV DNA detection rates varied in our study, with 19.6% (11 out of 56 samples) detected through the hybrid capture method of whole-genome sequencing and 20% (12 out of 60 samples) through qPCR. In hospital wastewaters, the detection rate was higher, at 40% (12 out of 30 samples) compared to 13.3% (4 out of 30 samples) in municipal wastewaters. This variation could be attributed to the relatively low number of MPXV cases reported in the city, which ranged from 106 to 341 cases during the study period, and the dilution effects, given that each of the two wastewater treatment plants (WWTP) investigated serves approximately 1.1 million inhabitants. Additionally, nine other virus families were identified in both hospitals and municipal wastewaters, including Adenoviridade, Astroviridae, Caliciviridae, Picornaviridade, Polyomaviridae, Coronaviridae (which includes SARS-CoV-2), Herspesviridae, Papillomaviridae and Flaviviridae (notably including Dengue). These findings underscore the potential of genomic sewage surveillance as a robust public health tool for monitoring a wide range of viruses circulating in both community and hospitals environments, including MPXV.
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Affiliation(s)
- Juliana Calabria de Araujo
- Department of Sanitary and Environmental Engineering, School of Engineering, Universidade Federal de Minas Gerais—UFMG, Belo Horizonte 31270901, Brazil
| | - Ana Paula Assad Carvalho
- Department of Sanitary and Environmental Engineering, School of Engineering, Universidade Federal de Minas Gerais—UFMG, Belo Horizonte 31270901, Brazil
| | - Cintia D. Leal
- Department of Sanitary and Environmental Engineering, School of Engineering, Universidade Federal de Minas Gerais—UFMG, Belo Horizonte 31270901, Brazil
| | - Manuelle Natividade
- Department of Social Pharmacy, College of Pharmacy, Federal University of Minas Gerais, Belo Horizonte 31270901, Brazil
| | - Marcus Borin
- Department of Social Pharmacy, College of Pharmacy, Federal University of Minas Gerais, Belo Horizonte 31270901, Brazil
| | - Augusto Guerra
- Department of Social Pharmacy, College of Pharmacy, Federal University of Minas Gerais, Belo Horizonte 31270901, Brazil
| | - Natália Carobin
- Clinical and Toxicological Analysis Department, College of Pharmacy, Federal University of Minas Gerais, Belo Horizonte 31270901, Brazil
| | - Adriano Sabino
- Clinical and Toxicological Analysis Department, College of Pharmacy, Federal University of Minas Gerais, Belo Horizonte 31270901, Brazil
| | - Mariana Almada
- Centro Federal de Educação Tecnológica—CEFET-MG, Belo Horizonte 30421169, Brazil
| | | | - Flavia Saia
- Department of Marine Sciences, Marine Institute, Universidade Federal de São Paulo—UNIFESP, Baixada Santista 11070100, Brazil
| | - Livia V. Frutuoso
- General Coordination of Arbovirus Surveillance, Department of Health and Environmental Surveillance, Ministry of Health, Brasília 70304000, Brazil
| | - Felipe C. M. Iani
- Central Public Health Laboratory, Fundação Ezequiel Dias, Belo Horizonte 30510010, Brazil; (F.C.M.I.); (T.A.)
| | - Talita Adelino
- Central Public Health Laboratory, Fundação Ezequiel Dias, Belo Horizonte 30510010, Brazil; (F.C.M.I.); (T.A.)
| | - Vagner Fonseca
- Coordination of Surveillance, Emergency Preparedness and Response (PHE), Pan American Health Organization/World Health Organization (PAHO/WHO), Pan-Americana da Saúde/Organização Mundial da Saúde (OPAS/OMS), Brasilia 70312970, Brazil;
| | - Marta Giovanetti
- Department of Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di, 00128 Roma, Italy;
- René Rachou Institute, Fundação Oswaldo Cruz, Belo Horizonte 30190001, Brazil;
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Zhou X, Liu K, Shi C, Zhang M, Liu S, Hou C, Di B. Estimation of the spatial pattern of gout prevalence across China by wastewater-based epidemiology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171565. [PMID: 38461984 DOI: 10.1016/j.scitotenv.2024.171565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 03/12/2024]
Abstract
Gout is a metabolic arthritis caused by hyperuricemia. In recent years, the prevalence of gout has been increased significantly in China due to the improvement of the living standards, and gout has become another common metabolic disease following diabetes mellitus. Gout severely affects the health status and life quality of human. In order to monitor the near real-time prevalence of gout, a wastewater-based epidemiology (WBE) approach was carried out in 257 Chinese cities using febuxostat as the biomarker. Febuxostat in wastewater was measured by a LC-MS/MS method with satisfactory results of method validation. The average concentration of febuxostat in wastewater was 53.05 ± 31.76 ng/L, with the estimated per capita consumption of 124.40 ± 73.37 mg/day/1000 inhabitant. The calculated prevalence of febuxostat was 0.41 % ± 0.24 %, and the prevalence of gout was finally estimated to be 1.30 % ± 0.77 % (0.60 % to 2.11 %), which was nearly consistent with value of 1.10 % obtained from the Guideline for the diagnosis and management of hyperuricemia and gout in China (2019). The results indicated that the febuxostat-based WBE approach might be reasonable to assess the near real-time gout prevalence in China.
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Affiliation(s)
- Xinxin Zhou
- Department of Pharmacy, China Pharmaceutical University, No.24 Tongjiaxiang Road, Nanjing 210009, PR China
| | - Kexin Liu
- Department of Pharmacy, China Pharmaceutical University, No.24 Tongjiaxiang Road, Nanjing 210009, PR China
| | - Chen Shi
- Department of Pharmacy, China Pharmaceutical University, No.24 Tongjiaxiang Road, Nanjing 210009, PR China
| | - Manlei Zhang
- Department of Pharmacy, China Pharmaceutical University, No.24 Tongjiaxiang Road, Nanjing 210009, PR China
| | - Shucheng Liu
- Department of Pharmacy, China Pharmaceutical University, No.24 Tongjiaxiang Road, Nanjing 210009, PR China
| | - Chenzhi Hou
- Department of Pharmacy, China Pharmaceutical University, No.24 Tongjiaxiang Road, Nanjing 210009, PR China; China National Narcotics Control Commission-China Pharmaceutical University Joint Laboratory on Key Technologies of Narcotics Control, Nanjing 210009, PR China.
| | - Bin Di
- Department of Pharmacy, China Pharmaceutical University, No.24 Tongjiaxiang Road, Nanjing 210009, PR China; China National Narcotics Control Commission-China Pharmaceutical University Joint Laboratory on Key Technologies of Narcotics Control, Nanjing 210009, PR China.
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Combe M, Cherif E, Deremarque T, Rivera-Ingraham G, Seck-Thiam F, Justy F, Doudou JC, Carod JF, Carage T, Procureur A, Gozlan RE. Wastewater sequencing as a powerful tool to reveal SARS-CoV-2 variant introduction and spread in French Guiana, South America. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171645. [PMID: 38479523 DOI: 10.1016/j.scitotenv.2024.171645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/19/2024] [Accepted: 03/09/2024] [Indexed: 03/17/2024]
Abstract
The origin of introduction of a new pathogen in a country, the evolutionary dynamics of an epidemic within a country, and the role of cross-border areas on pathogen dynamics remain complex to disentangle and are often poorly understood. For instance, cross-border areas represent the ideal location for the sharing of viral variants between countries, with international air travel, land travel and waterways playing an important role in the cross-border spread of infectious diseases. Unfortunately, monitoring the point of entry and the evolutionary dynamics of viruses in space and time within local populations remain challenging. Here we tested the efficiency of wastewater-based epidemiology and genotyping in monitoring Covid-19 epidemiology and SARS-CoV-2 variant dynamics in French Guiana, a tropical country located in South America. Our results suggest that wastewater-based epidemiology and genotyping are powerful tools to monitor variant introduction and disease evolution within a tropical country but the inclusion of both clinical and wastewater samples could still improve our understanding of genetic diversity co-circulating. Wastewater sequencing also revealed the cryptic transmission of SARS-CoV-2 variants within the country. Interestingly, we found some amino acid changes specific to the variants co-circulating in French Guiana, suggesting a local evolution of the SARS-CoV-2 variants after their introduction. More importantly, our results showed that the proximity to bordering countries was not the origin of the emergence of the French Guianese B.1.160.25 variant, but rather that this variant emerged from an ancestor B.1.160 variant introduced by European air plane travelers, suggesting thus that air travel remains a significant risk for cross-border spread of infectious diseases. Overall, we suggest that wastewater-based epidemiology and genotyping provides a cost effective and non-invasive approach for pathogen monitoring and an early-warning tool for disease emergence and spread within a tropical country.
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Affiliation(s)
- Marine Combe
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France.
| | - Emira Cherif
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France
| | | | - Georgina Rivera-Ingraham
- ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France; Centre IRD de Cayenne, Guyane Française, France
| | | | | | | | - Jean-François Carod
- Laboratoire et Pôle Appui aux Fonctions Cliniques, Centre Hospitalier de l'Ouest Guyanais (CHOG), 97320 Saint-Laurent du Maroni, Guyane Française, France
| | - Thierry Carage
- Laboratoire de Biologie Médicale Carage de Kourou, 6 avenue Leopold Heder, 97310 Kourou, Guyane Française, France
| | - Angélique Procureur
- Laboratoire de Biologie Médicale Carage de Kourou, 6 avenue Leopold Heder, 97310 Kourou, Guyane Française, France
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Abreu MADF, Lopes BC, Assemany PP, Souza ADR, Siniscalchi LAB. COVID-19 cases, vaccination, and SARS-CoV-2 in wastewater: insights from a Brazilian municipality. JOURNAL OF WATER AND HEALTH 2024; 22:268-277. [PMID: 38421621 PMCID: wh_2024_159 DOI: 10.2166/wh.2024.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Vaccines combatting COVID-19 demonstrate the ability to protect against disease and hospitalization, and reduce the likelihood of death caused by SARS-CoV-2. In addition, monitoring viral loads in sewage emerges as another crucial strategy in the epidemiological context, enabling early and collective detection of outbreaks. The study aimed to monitor the viral concentration of SARS-CoV-2 in untreated sewage in a Brazilian municipality. Also, it attempted to correlate these measurements with the number of clinical cases and deaths resulting from COVID-19 between July 2021 and July 2022. SARS-CoV-2 viral RNA was quantified by RT-qPCR. Pearson's correlation was performed to analyze the variables' relationship using the number of cases, deaths, vaccinated individuals, and viral concentration of SARS-CoV-2. The results revealed a significant negative correlation (p < 0.05) between the number of vaccinated individuals and the viral concentration of SARS-CoV-2, suggesting that after vaccination, the RNA viral load concentration was reduced in the sample population by the circulating concentration of wastewater. Consequently, wastewater monitoring, in addition to functioning as an early warning system for the circulation of SARS-CoV-2 and other pathogens, can offer a novel perspective that enhances decision-making, strengthens vaccination campaigns, and contributes to authorities establishing systematic networks for monitoring SARS-CoV-2.
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Affiliation(s)
- Mariana Aparecida de Freitas Abreu
- Department of Environmental Engineering (DAM), Federal University of Lavras (UFLA), Lavras, Brazil; Applied Microbiology Laboratory at the Environmental Engineering Department of UFLA, Federal University of Lavras (UFLA), Lavras, Brazil E-mail:
| | - Bruna Coelho Lopes
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Paula Peixoto Assemany
- Department of Environmental Engineering (DAM), Federal University of Lavras (UFLA), Lavras, Brazil; Applied Microbiology Laboratory at the Environmental Engineering Department of UFLA, Federal University of Lavras (UFLA), Lavras, Brazil
| | - Aline Dos Reis Souza
- Department of Environmental Engineering (DAM), Federal University of Lavras (UFLA), Lavras, Brazil
| | - Luciene Alves Batista Siniscalchi
- Department of Environmental Engineering (DAM), Federal University of Lavras (UFLA), Lavras, Brazil; Applied Microbiology Laboratory at the Environmental Engineering Department of UFLA, Federal University of Lavras (UFLA), Lavras, Brazil
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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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Kumar M, Joshi M, Prajapati B, Sirikanchana K, Mongkolsuk S, Kumar R, Gallage TP, Joshi C. Early warning of statewide COVID-19 Omicron wave by sentineled urbanized sewer network monitoring using digital PCR in a province capital city, of Gujarat, India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167060. [PMID: 37709091 DOI: 10.1016/j.scitotenv.2023.167060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/15/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Wastewater-based epidemiology (WBE) has been implemented globally. However, there remains confusion about the number and frequency of samples to be collected, as well as which types of treatment systems can provide reliable specific details about the virus prevalence in specific areas or communities, enabling prompt management and intervention measures. More research is necessary to fully comprehend the possibility of deploying sentinel locations in sewer networks in larger geographic areas. The present study introduces the first report on wastewater-based surveillance in Gandhinagar City using digital PCR (d-PCR) as a SARS-Cov-2 quantification tool, which describes the viral load from five pumping stations in Gandhinagar from October 2021 to March 2022. Raw wastewater samples (n = 119) were received and analyzed weekly to detect SARS-CoV-2 RNA, 109 of which were positive for N1 or N2 genes. The monthly variation analysis in viral genome copies depicted the highest concentrations in January 2022 and February 2022 (p < 0.05; Wilcoxon signed rank test) coincided with the Omicron wave, which contributed mainly from Vavol and Jaspur pumping stations. Cross-correlation analysis indicated that WBE from five stations in Gandhinagar, i.e., capital city sewer networks, provided two-week lead times to the citywide and statewide active cases (time-series cross-correlation function [CCF]; 0.666 and 0.648, respectively), mainly from individual contributions of the urbanized Kudasan and Vavol stations (CCF; 0.729 and 0.647, respectively). These findings suggest that sewer pumping stations in urbanized neighborhoods can be used as sentinel sites for statewide clinical surveillance and that WBE surveillance using digital PCR can be an efficient monitoring and management tool.
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Affiliation(s)
- Manish Kumar
- Sustainability Cluster, School of Engineering, University of Petroleum & Energy Studies, Dehradun, Uttarakhand 248007, India; Escuela de Ingeniería y Ciencias, Technologico de Monterrey, Campus Monterey, Monterrey 64849, Nuevo Leon, Mexico.
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Bhumika Prajapati
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Rakesh Kumar
- School of Ecology and Environment Studies, Nalanda University, Rajgir 803116, India; Department of Biosystems Engineering, Auburn University, Auburn, AL 36849, USA
| | - Tharindu Pollwatta Gallage
- Program in Environmental Toxicology, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
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Zhong Y, Hou C, Gao X, Wang M, Yao Y, Chen M, Di B, Su M. Application of wastewater-based epidemiology to estimate the usage of beta-agonists in 31 cities in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 894:164956. [PMID: 37343858 DOI: 10.1016/j.scitotenv.2023.164956] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/23/2023]
Abstract
The illegal use of beta-agonists could cause severe problems to human health. In this study, the usage of beta-agonists in 31 cities across China was estimated using wastewater-based epidemiology (WBE). The proposed method is based on solid-phase extraction (SPE) and LC-MS/MS and was developed and validated to determine the concentration of seven beta-agonists in wastewater. A population model based on cotinine (COT), NH4-N and the flow volume was constructed to estimate the population equivalents for different wastewater treatment plants (WWTPs). Clenbuterol and ractopamine are banned in China for both animal husbandry and medical use, but were nevertheless detected in some wastewater samples at rates of 6.2 % and 4.7 %, respectively (n = 339). The WBE-based consumption of clenbuterol and ractopamine were compared with the acceptable daily intake (ADI) and the health risks were assessed by their hazard quotients (0.26-6.62 for clenbuterol and 9.27 × 10-4-0.05 for ractopamine). Salbutamol, clorprenaline and terbutaline were observed in practically all wastewater samples at concentrations of up to several ng/L, whereas the formoterol and bambuterol concentrations were below the detection limit in all samples. Salbutamol consumption (7.35 ± 4.14 mg/1000 inh/day) was highest among the examined beta-agonists and varied regionally. Beta-agonist consumption based on WBE was higher in some cities than that based on medical survey data, indicating potential illegal use. These results show that WBE can be a straightforward and supplementary method for monitoring beta-agonist usage at the population level and spatially.
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Affiliation(s)
- Yuling Zhong
- School of Pharmacy, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing, 210009, China; China National Narcotics Control Commission, China Pharmaceutical University Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing, 210009, China
| | - Chenzhi Hou
- School of Pharmacy, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing, 210009, China; China National Narcotics Control Commission, China Pharmaceutical University Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing, 210009, China
| | - Xinyi Gao
- School of Pharmacy, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing, 210009, China
| | - Mingyu Wang
- School of Pharmacy, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing, 210009, China
| | - Yan Yao
- School of Pharmacy, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing, 210009, China; China National Narcotics Control Commission, China Pharmaceutical University Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing, 210009, China
| | - Mengyi Chen
- School of Pharmacy, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing, 210009, China; China National Narcotics Control Commission, China Pharmaceutical University Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing, 210009, China
| | - Bin Di
- School of Pharmacy, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing, 210009, China; China National Narcotics Control Commission, China Pharmaceutical University Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing, 210009, China; Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, No. 639 Longmian Avenue, Nanjing, 211100, China.
| | - Mengxiang Su
- School of Pharmacy, China Pharmaceutical University, No. 24 Tongjiaxiang Road, Nanjing, 210009, China; China National Narcotics Control Commission, China Pharmaceutical University Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing, 210009, China; Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, No. 639 Longmian Avenue, Nanjing, 211100, China.
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Schill R, Nelson KL, Harris-Lovett S, Kantor RS. The dynamic relationship between COVID-19 cases and SARS-CoV-2 wastewater concentrations across time and space: Considerations for model training data sets. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162069. [PMID: 36754324 PMCID: PMC9902279 DOI: 10.1016/j.scitotenv.2023.162069] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
During the COVID-19 pandemic, wastewater-based surveillance has been used alongside diagnostic testing to monitor infection rates. With the decline in cases reported to public health departments due to at-home testing, wastewater data may serve as the primary input for epidemiological models, but training these models is not straightforward. We explored factors affecting noise and bias in the ratio between wastewater and case data collected in 26 sewersheds in California from October 2020 to March 2022. The strength of the relationship between wastewater and case data appeared dependent on sampling frequency and population size, but was not increased by wastewater normalization to flow rate or case count normalization to testing rates. Additionally, the lead and lag times between wastewater and case data varied over time and space, and the ratio of log-transformed individual cases to wastewater concentrations changed over time. This ratio decreased between the Epsilon/Alpha and Delta variant surges of COVID-19 and increased during the Omicron BA.1 variant surge, and was also related to the diagnostic testing rate. Based on this analysis, we present a framework of scenarios describing the dynamics of the case to wastewater ratio to aid in data handling decisions for ongoing modeling efforts.
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Affiliation(s)
- Rebecca Schill
- TUM School of Engineering and Design, Technical University of Munich, Germany
| | - Kara L Nelson
- Civil and Environmental Engineering, University of California, Berkeley, CA, USA
| | | | - Rose S Kantor
- Civil and Environmental Engineering, University of California, Berkeley, CA, USA.
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Sangsanont J, Rattanakul S, Makkaew P, Precha N, Rukthanapitak P, Sresung M, Siri Y, Kitajima M, Takeda T, Haramoto E, Puenpa J, Wanlapakorn N, Poovorawan Y, Mongkolsuk S, Sirikanchana K. Wastewater monitoring in tourist cities as potential sentinel sites for near real-time dynamics of imported SARS-CoV-2 variants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160317. [PMID: 36436629 PMCID: PMC9691270 DOI: 10.1016/j.scitotenv.2022.160317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/29/2022] [Accepted: 11/16/2022] [Indexed: 05/05/2023]
Abstract
Wastewater-based epidemiology (WBE) complements the clinical surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants' distribution in populations. Many developed nations have established national and regional WBE systems; however, governance and budget constraints could be obstacles for low- and middle-income countries. An urgent need thus exists to identify hotspots to serve as sentinel sites for WBE. We hypothesized that representative wastewater treatment plants (WWTPs) in two international gateway cities, Bangkok and Phuket, Thailand, could be sentineled for SARS-CoV-2 and its variants to reflect the clinical distribution patterns at city level and serve as early indicators of new variants entering the country. Municipal wastewater samples (n = 132) were collected from eight representative municipal WWTPs in Bangkok and Phuket during 19 sampling events from October 2021 to March 2022, which were tested by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) using the US CDC N1 and N2 multiplex and variant (Alpha, Delta, and Omicron BA.1 and BA.2) singleplex assays. The variant detection ratios from Bangkok and Phuket followed similar trends to the national clinical testing data, and each variant's viral loads agreed with the daily new cases (3-d moving average). Omicron BA.1 was detected in Phuket wastewater prior to Bangkok, possibly due to Phuket's WWTPs serving tourist communities. We found that the Omicron BA.1 and BA.2 viral loads predominantly drove the SARS-CoV-2 resurgence. We also noted a shifting pattern in the Bangkok WBE from a 22-d early warning in early 2021 to a near real-time pattern in late 2021. The potential application of tourist hotspots for WBE to indicate the arrival of new variants and re-emerging or unprecedented infectious agents could support tourism-dependent economies by complementing the reduced clinical regulations while maintaining public health protection via wastewater surveillance.
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Affiliation(s)
- Jatuwat Sangsanont
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Water Science and Technology for Sustainable Environmental Research Group, Chulalongkorn University, Bangkok 10330, Thailand
| | - Surapong Rattanakul
- Department of Environmental Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Prasert Makkaew
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Nopadol Precha
- Department of Environmental Health and Technology, School of Public Health, Walailak University, Nakhon Si Thammarat 80160, Thailand; One Health Research Center, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Pratchaya Rukthanapitak
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Montakarn Sresung
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Yadpiroon Siri
- Environmental, Safety Technology and Health Program, School of Public Health, Walailak University, Thaiburi, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, Hokkaido 060-8628, Japan
| | - Tomoko Takeda
- Department of Earth and Planetary Science, The University of Tokyo, 113-0033, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi 400-8511, Japan
| | - Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Skorn Mongkolsuk
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok 10400, Thailand.
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10
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de Araújo JC, Madeira CL, Bressani T, Leal C, Leroy D, Machado EC, Fernandes LA, Espinosa MF, Freitas GTO, Leão T, Mota VT, Pereira AD, Perdigão C, Tröger F, Ayrimoraes S, de Melo MC, Laguardia F, Reis MTP, Mota C, Chernicharo CAL. Quantification of SARS-CoV-2 in wastewater samples from hospitals treating COVID-19 patients during the first wave of the pandemic in Brazil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160498. [PMID: 36436622 PMCID: PMC9691275 DOI: 10.1016/j.scitotenv.2022.160498] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 06/04/2023]
Abstract
The COVID-19 pandemic has caused a global health crisis, and wastewater-based epidemiology (WBE) has emerged as an important tool to assist public health decision-making. Recent studies have shown that the SARS-CoV-2 RNA concentration in wastewater samples is a reliable indicator of the severity of the pandemic for large populations. However, few studies have established a strong correlation between the number of infected people and the viral concentration in wastewater due to variations in viral shedding over time, viral decay, infiltration, and inflow. Herein we present the relationship between the number of COVID-19-positive patients and the viral concentration in wastewater samples from three different hospitals (A, B, and C) in the city of Belo Horizonte, Minas Gerais, Brazil. A positive and strong correlation between wastewater SARS-CoV-2 concentration and the number of confirmed cases was observed for Hospital B for both regions of the N gene (R = 0.89 and 0.77 for N1 and N2, respectively), while samples from Hospitals A and C showed low and moderate correlations, respectively. Even though the effects of viral decay and infiltration were minimized in our study, the variability of viral shedding throughout the infection period and feces dilution due to water usage for different activities in the hospitals could have affected the viral concentrations. These effects were prominent in Hospital A, which had the smallest sewershed population size, and where no correlation between the number of defecations from COVID-19 patients and viral concentration in wastewater was observed. Although we could not determine trends in the number of infected patients through SARS-CoV-2 concentrations in hospitals' wastewater samples, our results suggest that wastewater monitoring can be efficient for the detection of infected individuals at a local level, complementing clinical data.
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Affiliation(s)
- Juliana Calábria de Araújo
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil.
| | - Camila L Madeira
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Thiago Bressani
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Cíntia Leal
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Deborah Leroy
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Elayne C Machado
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Luyara A Fernandes
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Maria Fernanda Espinosa
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Gabriel Tadeu O Freitas
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Thiago Leão
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Vera Tainá Mota
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Alyne Duarte Pereira
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | | | - Flávio Tröger
- National Agency for Water and Sanitation (ANA), Brazil
| | | | | | | | | | - César Mota
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
| | - Carlos A L Chernicharo
- Department of Sanitary and Environmental Engineering (DESA), Federal University of Minas Gerais (UFMG), Brazil
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11
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Acosta N, Bautista MA, Waddell BJ, Du K, McCalder J, Pradhan P, Sedaghat N, Papparis C, Beaudet AB, Chen J, Van Doorn J, Xiang K, Chan L, Vivas L, Low K, Lu X, Lee J, Westlund P, Chekouo T, Dai X, Cabaj J, Bhatnagar S, Ruecker N, Achari G, Clark RG, Pearce C, Harrison JJ, Meddings J, Leal J, Ellison J, Missaghi B, Kanji JN, Larios O, Rennert‐May E, Kim J, Hrudey SE, Lee BE, Pang X, Frankowski K, Conly J, Hubert CRJ, Parkins MD. Surveillance for SARS-CoV-2 and its variants in wastewater of tertiary care hospitals correlates with increasing case burden and outbreaks. J Med Virol 2023; 95:e28442. [PMID: 36579780 PMCID: PMC9880705 DOI: 10.1002/jmv.28442] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022]
Abstract
Wastewater-based SARS-CoV-2 surveillance enables unbiased and comprehensive monitoring of defined sewersheds. We performed real-time monitoring of hospital wastewater that differentiated Delta and Omicron variants within total SARS-CoV-2-RNA, enabling correlation to COVID-19 cases from three tertiary-care facilities with >2100 inpatient beds in Calgary, Canada. RNA was extracted from hospital wastewater between August/2021 and January/2022, and SARS-CoV-2 quantified using RT-qPCR. Assays targeting R203M and R203K/G204R established the proportional abundance of Delta and Omicron, respectively. Total and variant-specific SARS-CoV-2 in wastewater was compared to data for variant specific COVID-19 hospitalizations, hospital-acquired infections, and outbreaks. Ninety-six percent (188/196) of wastewater samples were SARS-CoV-2 positive. Total SARS-CoV-2 RNA levels in wastewater increased in tandem with total prevalent cases (Delta plus Omicron). Variant-specific assessments showed this increase to be mainly driven by Omicron. Hospital-acquired cases of COVID-19 were associated with large spikes in wastewater SARS-CoV-2 and levels were significantly increased during outbreaks relative to nonoutbreak periods for total SARS-CoV2, Delta and Omicron. SARS-CoV-2 in hospital wastewater was significantly higher during the Omicron-wave irrespective of outbreaks. Wastewater-based monitoring of SARS-CoV-2 and its variants represents a novel tool for passive COVID-19 infection surveillance, case identification, containment, and potentially to mitigate viral spread in hospitals.
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Affiliation(s)
- Nicole Acosta
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | | | - Barbara J. Waddell
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | - Kristine Du
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | - Janine McCalder
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Puja Pradhan
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Navid Sedaghat
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Chloe Papparis
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | | | - Jianwei Chen
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | | | - Kevin Xiang
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Leslie Chan
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Laura Vivas
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Kashtin Low
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | - Xuewen Lu
- Department of Mathematics and StatisticsUniversity of CalgaryCalgaryCanada
| | - Jangwoo Lee
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada
| | | | - Thierry Chekouo
- Department of Mathematics and StatisticsUniversity of CalgaryCalgaryCanada,Division of Biostatistics, School of Public HealthUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Xiaotian Dai
- Department of Mathematics and StatisticsUniversity of CalgaryCalgaryCanada
| | - Jason Cabaj
- Department of Community Health SciencesUniversity of CalgaryCalgaryCanada,Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Provincial Population & Public HealthAlberta Health ServicesCalgaryCanada,O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada
| | - Srijak Bhatnagar
- Faculty of Science and TechnologyAthabasca UniversityAthabascaAlbertaCanada
| | | | - Gopal Achari
- Department of Civil EngineeringUniversity of CalgaryCalgaryCanada
| | - Rhonda G. Clark
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada
| | - Craig Pearce
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Joe J. Harrison
- Department of Biological SciencesUniversity of CalgaryCalgaryCanada,Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Jon Meddings
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Jenine Leal
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Community Health SciencesUniversity of CalgaryCalgaryCanada,O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada,Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Jennifer Ellison
- Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Bayan Missaghi
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Jamil N. Kanji
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonAlbertaCanada,Alberta Precision Laboratories, Public Health LaboratoryAlberta Health ServicesEdmontonAlbertaCanada,Department of Pathology and Laboratory MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Oscar Larios
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Infection Prevention and ControlAlberta Health ServicesCalgaryCanada,Alberta Precision Laboratories, Public Health LaboratoryAlberta Health ServicesEdmontonAlbertaCanada
| | - Elissa Rennert‐May
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of Community Health SciencesUniversity of CalgaryCalgaryCanada,Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada,Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | - Joseph Kim
- Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Infection Prevention and ControlAlberta Health ServicesCalgaryCanada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonAlbertaCanada,Department of Analytical and Environmental ToxicologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Bonita E. Lee
- Department of PediatricsUniversity of AlbertaEdmontonAlbertaCanada,Women & Children's Health Research InstituteEdmontonAlbertaCanada,Li Ka Shing Institute of VirologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Xiaoli Pang
- Department of Laboratory Medicine and PathologyUniversity of AlbertaEdmontonAlbertaCanada,Alberta Precision Laboratories, Public Health LaboratoryAlberta Health ServicesEdmontonAlbertaCanada,Li Ka Shing Institute of VirologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Kevin Frankowski
- Advancing Canadian Water AssetsUniversity of CalgaryCalgaryCanada
| | - John Conly
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,O'Brien Institute for Public HealthUniversity of CalgaryCalgaryCanada,Infection Prevention and ControlAlberta Health ServicesCalgaryCanada,Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Department of Pathology and Laboratory MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada
| | | | - Michael D. Parkins
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryCanada,Department of MedicineUniversity of Calgary and Alberta Health ServicesCalgaryCanada,Snyder Institute for Chronic DiseasesUniversity of Calgary and Alberta Health ServicesCalgaryCanada
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12
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Malla B, Thakali O, Shrestha S, Segawa T, Kitajima M, Haramoto E. Application of a high-throughput quantitative PCR system for simultaneous monitoring of SARS-CoV-2 variants and other pathogenic viruses in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158659. [PMID: 36096223 PMCID: PMC9461275 DOI: 10.1016/j.scitotenv.2022.158659] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 05/11/2023]
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are continuously emerging, highlighting the importance of regular surveillance of SARS-CoV-2 and other epidemiologically significant pathogenic viruses in the current context. Reverse transcription-quantitative PCR (RT-qPCR) is expensive, time-consuming, labor-intensive, requires a large reagent volume, and only tests a few targets in a single run. High-throughput qPCR (HT-qPCR) utilizing the Biomark HD system (Fluidigm) can be used as an alternative. This study applied an HT-qPCR to simultaneously detect SARS-CoV-2, SARS-CoV-2 nucleotide substituted RNA, and other pathogenic viruses in wastewater. Wastewater samples were collected from the coronavirus disease 2019 (COVID-19) quarantine facility between October 2020 and February 2021 (n = 4) and from the combined and separated sewer lines of a wastewater treatment plant (WWTP) in Yokkaichi, Mie Prefecture, Japan, between March and August 2021 (n = 23 each). The samples were analyzed by HT-qPCR using five SARS-CoV-2, nine SARS-CoV-2 spike gene nucleotide substitution-specific, five pathogenic viruses, and three process control assays. All samples from the quarantine facility tested positive for SARS-CoV-2 and the nucleotide substitutions N501Y and S69-70 del (Alpha variant) were detected in the December 2020 sample, coinciding with the first clinical case in Japan. Only three WWTP samples were positive when tested with a single SARS-CoV-2 assay, whereas more than eight samples were positive when tested with all assays, indicating that using multiple assays increases the likelihood of detection. The nucleotide substitution L452R (Delta variant) was detected in the WWTP samples of Mie Prefecture in April 2021, but the detection of Delta variant from patients had not been reported until May 2021. Aichi virus 1 and norovirus GII were prevalent in WWTP samples. This study demonstrated that HT-qPCR may be the most time- and cost-efficient method for tracking COVID-19 and broadly monitoring community health.
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Affiliation(s)
- Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Ocean Thakali
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan; Institute for the Advanced Study of Sustainability, United Nations University, 5-53-70 Jingumae, Shibuya-ku, Tokyo 150-8925, Japan
| | - Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan
| | - Masaaki Kitajima
- Division of Environmental 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.
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