SARS-CoV-2 in Wastewater: Methods, Epidemiology and Future Goals

A special issue of Water (ISSN 2073-4441). This special issue belongs to the section "Water and One Health".

Deadline for manuscript submissions: closed (15 May 2023) | Viewed by 22747

Special Issue Editors


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Guest Editor
CSIC - Instituto de Agroquimica y Tecnologia de los Alimentos (IATA), Valencia, Spain
Interests: sewage; food microbiology; fermentation; molecular biology; sanger sequencing; microbial molecular biology
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Instituto Superior Técnico, Lisbon, Portugal
Interests: wastewater-based surveillance; antimicrobial resistance; enteric pathogens; water reuse; vectorborne viruses
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The use of wastewater-based epidemiology (WBE) as a tool for epidemiology tracking has a long history of use in public health, particularly for human enteric viruses. In the midst of the ongoing COVID-19 pandemic, WBE is being implemented globally for the detection of SARS-CoV-2 RNA shed into wastewater, sewers, and sludge. All these studies have been implemented in research contexts; nevertheless, different countries are currently implementing wastewater surveillance into their national or regional COVID-19 monitoring programs for early warning of SARS-CoV-2 community spread, the emergence of SARS-CoV-2 variants, and disease outbreaks. Additionally, WBE has the potential to be applied in high-risk settings such as nursing homes and hospitals or low-resource settings. Moreover, the presence of SARS-CoV-2 in natural and recreational waters has acquired relevance to assessing public health risks. However, analytical methods have not yet been standardized, and it is necessary to develop tools for the analysis and interpretation of all these results.

This special issue arises intending to make a collection of original articles that present new methodologies for the detection of SARS-CoV-2 in wastewater and other environmental waters, improvement of known technologies, techniques for the detection of infectious SARS-CoV-2 particles, methods for the detection of variants in wastewater (RT-qPCR and metagenomics), and new tools for sharing and analyzing all the generated data. In addition, manuscripts investigating the appearance of SARS-CoV-2 and its variants in wastewater and environmental waters are also welcome.

Dr. Alba Pérez-Cataluña
Dr. Silvia Monteiro
Guest Editors

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Keywords

  • wastewater-based epidemiology
  • SARS-CoV-2
  • variants
  • infectivity assessment
  • concentration methods
  • wastewater
  • early-warning system
  • urban water cycle

Published Papers (6 papers)

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Research

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13 pages, 1166 KiB  
Communication
Comparison of Two Methods for SARS-CoV-2 Detection in Wastewater: A Case Study from Sofia, Bulgaria
by Mihaela Belouhova, Slavil Peykov, Vesela Stefanova and Yana Topalova
Water 2023, 15(4), 658; https://doi.org/10.3390/w15040658 - 8 Feb 2023
Cited by 3 | Viewed by 2947
Abstract
Wastewater surveillance for monitoring the spread of SARS-CoV-2 remains important even in the current endemic stage of the COVID-19 outbreak. This approach has already demonstrated its value by providing early warnings of coronavirus spread in different communities. The aim of the present publication [...] Read more.
Wastewater surveillance for monitoring the spread of SARS-CoV-2 remains important even in the current endemic stage of the COVID-19 outbreak. This approach has already demonstrated its value by providing early warnings of coronavirus spread in different communities. The aim of the present publication is to share relevant experience from the Center of Competence “Clean&Circle”, obtained in the development of an effective strategy for SARS-CoV-2 detection in the wastewater of Sofia, Bulgaria. Using four different RNA concentration/extraction methods, we revealed that the key hindering factor for successful viral detection was the presence of PCR inhibitors in the wastewater. The most efficient way to overcome their presence turned out to be the application of a specialized polymerase in the RT-PCR detection setup. Our data showed that using such an enzyme increases the detection efficiency from 1.9% to 70.5% in samples with a spiked control virus. We also evaluated the recovery rates of viral particles by using silica columns (71%), PEG precipitation (23%), ultrafiltration (15%), and MCE filtration (10%). These results support the international effort to unify and standardize the various techniques used for SARS-CoV-2 monitoring in wastewater. Full article
(This article belongs to the Special Issue SARS-CoV-2 in Wastewater: Methods, Epidemiology and Future Goals)
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20 pages, 1561 KiB  
Article
Critical Evaluation of Different Passive Sampler Materials and Approaches for the Recovery of SARS-CoV-2, Faecal-Indicator Viruses and Bacteria from Wastewater
by Davey L. Jones, Jasmine M. S. Grimsley, Jessica L. Kevill, Rachel Williams, Cameron Pellett, Kathryn Lambert-Slosarska, Andrew C. Singer, Gwion B. Williams, Rafael Bargiela, Robert W. Brown, Matthew J. Wade and Kata Farkas
Water 2022, 14(21), 3568; https://doi.org/10.3390/w14213568 - 6 Nov 2022
Cited by 7 | Viewed by 3561
Abstract
During the COVID-19 pandemic, wastewater-based epidemiology (WBE) has proven to be an effective tool for monitoring the prevalence of SARS-CoV-2 in urban communities. However, low-cost, simple, and reliable wastewater sampling techniques are still needed to promote the widespread adoption of WBE in many [...] Read more.
During the COVID-19 pandemic, wastewater-based epidemiology (WBE) has proven to be an effective tool for monitoring the prevalence of SARS-CoV-2 in urban communities. However, low-cost, simple, and reliable wastewater sampling techniques are still needed to promote the widespread adoption of WBE in many countries. Since their first use for public health surveillance in the 1950s, many types of passive samplers have been proposed, however, there have been few systematic studies comparing their ability to co-capture enveloped viruses and bacteria. Here, we evaluated the laboratory and field performance of 8 passive sampler materials (NanoCeram, ZetaPlus, nylon and ion exchange membranes, cellulose acetate filters, glass wool, cotton-based Moore swabs and tampons) to capture viruses and bacteria from wastewater. Viral capture focused on SARS-CoV-2, the bacteriophage Phi6 and the faecal marker virus, crAssphage. We showed that the best performing passive sampler in terms of cost, ease of deployment and viral capture were the electronegative cotton-based swabs and tampons. We speculate that viral capture is a combination of trapping of particulate matter to which viruses are attached, as well as electrostatic attraction of viral particles from solution. When deployed at wastewater treatment plants, the passive samplers worked best up to 6 h, after which they became saturated or exhibited a loss of virus, probably due to night-time wash-out. The patterns of viral capture across the different sampling materials were similar providing evidence that they can be used to monitor multiple public health targets. The types of bacteria trapped by the passive samplers were material-specific, but possessed a different 16S rRNA gene profile to the wastewater, suggesting preferential retention of specific bacteria. We conclude that the choice of passive sampler and deployment time greatly influences the pattern and amount of viral and bacterial capture. Full article
(This article belongs to the Special Issue SARS-CoV-2 in Wastewater: Methods, Epidemiology and Future Goals)
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15 pages, 3014 KiB  
Article
Effect of Time and Temperature on SARS-CoV-2 in Municipal Wastewater Conveyance Systems
by Melissa K. Schussman and Sandra L. McLellan
Water 2022, 14(9), 1373; https://doi.org/10.3390/w14091373 - 23 Apr 2022
Cited by 11 | Viewed by 2349
Abstract
Wastewater surveillance for SARS-CoV-2 is becoming a widespread public health metric, but little is known about pre-analytical influences on these measurements. We examined SARS-CoV-2 loads from two sewer service areas with different travel times that were within the same metropolitan area. Throughout the [...] Read more.
Wastewater surveillance for SARS-CoV-2 is becoming a widespread public health metric, but little is known about pre-analytical influences on these measurements. We examined SARS-CoV-2 loads from two sewer service areas with different travel times that were within the same metropolitan area. Throughout the one-year study, case rates were nearly identical between the two service areas allowing us to compare differences in empirical concentrations relative to conveyance system characteristics and wastewater treatment plant parameters. We found time did not have a significant effect on degradation of SARS-CoV-2 when using average transit times (22 vs. 7.5 h) (p = 0.08), or under low flow conditions when transit times are greater (p = 0.14). Flow increased rather than decreased SARS-CoV-2 case-adjusted concentrations, but this increase was only significant in one service area. Warmer temperatures (16.8–19.8 °C) compared with colder (8.4–12.3 °C) reduced SARS-CoV-2 case-adjusted loads by ~50% in both plants (p < 0.05). Decreased concentrations in warmer temperatures may be an important factor to consider when comparing seasonal dynamics. Oxygen demand and suspended solids had no significant effect on SARS-CoV-2 case-adjusted loads overall. Understanding wastewater conveyance system influences prior to sample collection will improve comparisons of regional or national data for SARS-CoV-2 community infections. Full article
(This article belongs to the Special Issue SARS-CoV-2 in Wastewater: Methods, Epidemiology and Future Goals)
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14 pages, 4226 KiB  
Article
Genome Sequencing of SARS-CoV-2 Allows Monitoring of Variants of Concern through Wastewater
by Malte Herold, Aymeric Fouquier d'Hérouël, Patrick May, Francesco Delogu, Anke Wienecke-Baldacchino, Jessica Tapp, Cécile Walczak, Paul Wilmes, Henry-Michel Cauchie, Guillaume Fournier and Leslie Ogorzaly
Water 2021, 13(21), 3018; https://doi.org/10.3390/w13213018 - 27 Oct 2021
Cited by 18 | Viewed by 4464
Abstract
Monitoring SARS-CoV-2 in wastewater has shown to be an effective tool for epidemiological surveillance. More specifically, RNA levels determined with RT-qPCR have been shown to track with the infection dynamics within the population. However, the surveillance of individual lineages circulating in the population [...] Read more.
Monitoring SARS-CoV-2 in wastewater has shown to be an effective tool for epidemiological surveillance. More specifically, RNA levels determined with RT-qPCR have been shown to track with the infection dynamics within the population. However, the surveillance of individual lineages circulating in the population based on genomic sequencing of wastewater samples is challenging, as the genetic material constitutes a mixture of different viral haplotypes. Here, we identify specific signature mutations from individual SARS-CoV-2 lineages in wastewater samples to estimate lineages circulating in Luxembourg. We compare circulating lineages and mutations to those detected in clinical samples amongst infected individuals. We show that especially for dominant lineages, the allele frequencies of signature mutations correspond to the occurrence of particular lineages in the population. In addition, we provide evidence that regional clusters can also be discerned. We focused on the time period between November 2020 and March 2021 in which several variants of concern emerged and specifically traced the lineage B.1.1.7, which became dominant in Luxembourg during that time. During the subsequent time points, we were able to reconstruct short haplotypes, highlighting the co-occurrence of several signature mutations. Our results highlight the potential of genomic surveillance in wastewater samples based on amplicon short-read data. By extension, our work provides the basis for the early detection of novel SARS-CoV-2 variants. Full article
(This article belongs to the Special Issue SARS-CoV-2 in Wastewater: Methods, Epidemiology and Future Goals)
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13 pages, 578 KiB  
Article
Key SARS-CoV-2 Mutations of Alpha, Gamma, and Eta Variants Detected in Urban Wastewaters in Italy by Long-Read Amplicon Sequencing Based on Nanopore Technology
by Giuseppina La Rosa, David Brandtner, Pamela Mancini, Carolina Veneri, Giusy Bonanno Ferraro, Lucia Bonadonna, Luca Lucentini and Elisabetta Suffredini
Water 2021, 13(18), 2503; https://doi.org/10.3390/w13182503 - 13 Sep 2021
Cited by 27 | Viewed by 5099
Abstract
The emergence of SARS-CoV-2 variants of concern (VOCs) and variants of interest (VOIs) poses an increased risk to global public health and underlines the need to prioritise monitoring and research to better respond to the COVID-19 pandemic. Wastewater monitoring can be used to [...] Read more.
The emergence of SARS-CoV-2 variants of concern (VOCs) and variants of interest (VOIs) poses an increased risk to global public health and underlines the need to prioritise monitoring and research to better respond to the COVID-19 pandemic. Wastewater monitoring can be used to monitor SARS-CoV-2 spread and to track SARS-CoV-2 variants. A long read amplicon sequencing approach based on the Oxford Nanopore technology, targeting the spike protein, was applied to detect SARS-CoV-2 variants in sewage samples collected in central Italy on April 2021. Next-generation sequencing was performed on three pooled samples. For variant identification, two approaches–clustering (unsupervised) and classification (supervised)–were implemented, resulting in the detection of two VOCs and one VOI. Key mutations of the Alpha variant (B.1.1.7) were detected in all of the pools, accounting for the vast majority of NGS reads. In two different pools, mutations of the Gamma (P.1) and Eta (B.1.525) variants were also detected, accounting for 22.4%, and 1.3% of total NGS reads of the sample, respectively. Results were in agreement with data on variant circulation in Italy at the time of wastewater sample collection. For each variant, in addition to the signature key spike mutations, other less common mutations were detected, including the amino acid substitutions S98F and E484K in the Alpha cluster (alone and combined), and S151I in the Eta cluster. Results of the present study show that the long-read sequencing nanopore technology can be successfully used to explore SARS-CoV-2 diversity in sewage samples, where multiple variants can be present, and that the approach is sensitive enough to detect variants present at low abundance in wastewater samples. In conclusion, wastewater monitoring can help one discover the spread of variants in a community and early detect the emerging of clinically relevant mutations or variants. Full article
(This article belongs to the Special Issue SARS-CoV-2 in Wastewater: Methods, Epidemiology and Future Goals)
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Review

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13 pages, 645 KiB  
Review
The Detection of SARS-CoV-2 in the Environment: Lessons from Wastewater
by Tasha Marie Santiago-Rodriguez
Water 2022, 14(4), 599; https://doi.org/10.3390/w14040599 - 16 Feb 2022
Cited by 2 | Viewed by 2332
Abstract
Wastewater has historically been an important source of enteric pathogens, as well as a source of unconventational or unexpected pathogens, including those present in the respiratory tract, saliva, urine, and blood. This is the case with SARS-CoV-2, the causative agent of the most [...] Read more.
Wastewater has historically been an important source of enteric pathogens, as well as a source of unconventational or unexpected pathogens, including those present in the respiratory tract, saliva, urine, and blood. This is the case with SARS-CoV-2, the causative agent of the most recent pandemic. SARS-CoV-2 has been identified in wastewater across various geographical regions prior to, and during, the report of cases. The detection of SARS-CoV-2 in wastewater is usually performed using molecular techniques targeting specific genomic regions. High-throughput sequencing techniques, both untargeted and targeted or amplicon-based, are also being applied in combination with molecular techniques for the detection of SARS-CoV-2 variants to determine the genetic diversity and phylogenetic relatedness. The identification of SARS-CoV-2 in wastewater has a number of epidemiological, biological, and ecological applications, which can be incorporated into future outbreaks, epidemics, or pandemics. Full article
(This article belongs to the Special Issue SARS-CoV-2 in Wastewater: Methods, Epidemiology and Future Goals)
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