Prevalence of SARS-CoV-2 genes in water reclamation facilities: From influent to anaerobic digester

Protocol for detection of pathogenic enteric RNA viruses by regular monitoring of environmental samples from wastewater treatment plants using droplet digital PCR

BACKGROUND

The present comprehensive protocol is focused on the detection of pathogenic enteric RNA viruses, explicitly focusing on norovirus genogroup Ⅱ (GⅡ), astrovirus, rotavirus, Aichi virus, sapovirus, hepatitis A and E viruses in wastewater treatment plants through droplet digital PCR (ddPCR). Enteric viruses are of significant public health concern, as they are the leading cause of diseases like gastroenteritis. Regular monitoring of environmental samples, particularly from wastewater treatment plants, is crucial for early detection and control of these viruses. This research aims to improve the understanding of the prevalence and dynamics of enteric viruses in urban India and will serve as a model for similar studies in other regions. Our protocol's objective is to establish a novel ddPCR-based methodology for the detection and molecular characterization of enteric viruses present in wastewater samples sourced from Bhopal, India. Our assay is capable of accurately quantifying virus concentrations without standard curves, minimizing extensive optimization, and enhancing sensitivity and precision, especially for low-abundance targets.

METHODS

The study involves fortnightly collecting and analyzing samples from nine wastewater treatment plants over two years, ensuring comprehensive coverage and consistent data. Our study innovatively applies ddPCR to simultaneously detect and quantify enteric viruses in wastewater, a more advanced technique. Additionally, we will employ next-generation sequencing for detailed viral genome identification in samples tested positive for pathogenic viruses.

CONCLUSION

This study will aid in understanding these viruses' genetic diversity and mutation rates, which is crucial for developing tailored intervention strategies. The findings will be instrumental in shaping public health responses and improving epidemiological surveillance, especially in localities heaving sewage networks.

A scoping review of global SARS-CoV-2 wastewater-based epidemiology in light of COVID-19 pandemic

Recently, wastewater-based epidemiology (WBE) research has experienced a strong impetus during the Coronavirus disease 2019 (COVID-19) pandemic. However, a few technical issues related to surveillance strategies, such as standardized procedures ranging from sampling to testing protocols, need to be resolved in preparation for future infectious disease outbreaks. This review highlights the study characteristics, potential use of WBE and overview of methods, as well as methods utilized to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) including its variant in wastewater. A literature search was performed electronically in PubMed and Scopus according to PRISMA guidelines for relevant peer-reviewed articles published between January 2020 and March 2022. The search identified 588 articles, out of which 221 fulfilled the necessary criteria and are discussed in this review. Most global WBE studies were conducted in North America (n = 75, 34 %), followed by Europe (n = 68, 30.8 %), and Asia (n = 43, 19.5 %). The review also showed that most of the application of WBE observed were to correlate SARS-CoV-2 ribonucleic acid (RNA) trends in sewage with epidemiological data (n = 90, 40.7 %). The techniques that were often used globally for sample collection, concentration, preferred matrix recovery control and various sample types were also discussed. Overall, this review provided a framework for researchers specializing in WBE to apply strategic approaches to their research questions in achieving better functional insights. In addition, areas that needed more in-depth analysis, data collection, and ideas for new initiatives were identified.

A mass balance approach for quantifying the role of natural decay and fate mechanisms on SARS-CoV-2 genetic marker removal during water reclamation

The recent SARS-CoV-2 outbreak yielded substantial data regarding virus fate and prevalence at water reclamation facilities (WRFs), identifying influential factors as natural decay, adsorption, light, pH, salinity, and antagonistic microorganisms. However, no studies have quantified the impact of these factors in full scale WRFs. Utilizing a mass balance approach, we assessed the impact of natural decay and other fate mechanisms on genetic marker removal during water reclamation, through the use of sludge and wastewater genetic marker loading estimates. Results indicated negligible removal of genetic markers during P/PT (primary effluent (PE) p value: 0.267; preliminary and primary treatment (P/PT) accumulation p value: 0.904; and thickened primary sludge (TPS) p value: 0.076) indicating no contribution of natural decay and other fate mechanisms toward removal in P/PT. Comparably, adsorption and decomposition was found to be the dominant pathway for genetic marker removal (thickened waste activated sludge (TWAS) log loading 9.75 log10 GC/day); however, no estimation of log genetic marker accumulation could be carried out due to high detections in TWAS. PRACTITIONER POINTS: The mass balance approach suggested that the contribution of natural decay and other fate mechanisms to virus removal during wastewater treatment are negligible compared with adsorption and decomposition in P/PT (p value: 0.904). During (P/PT), a higher viral load remained in the (PE) (14.16 log10 GC/day) compared with TPS (13.83 log10 GC/day); however, no statistical difference was observed (p value: 0.280) indicting that adsorption/decomposition most probably did not occur. In secondary treatment (ST), viral genetic markers in TWAS were consistently detected (13.41 log10 GC/day) compared with secondary effluent (SE), indicating that longer HRT and the potential presence of extracellular polymeric substance-containing enriched biomass enabled adsorption/decomposition. Estimations of total solids and volatile solids for TPS and TWAS indicated that adsorption affinity was different between solids sampling locations (p value: <0.0001).

Adapted methods for monitoring influenza virus and respiratory syncytial virus in sludge and wastewater

Wastewater-based surveillance constitutes a valuable methodology for the continuous monitoring of viral circulation, with the capacity to function as an early warning system. It holds particular significance in scenarios where respiratory viruses exhibit overlapping clinical presentations, as occurs with SARS-CoV-2, influenza virus (IV), and respiratory syncytial virus (RSV), and allows seasonal virus outbreaks to be distinguished from COVID-19 peaks. Furthermore, sewage sludge, given it harbors concentrated human waste from a large population, serves as a substantial reservoir for pathogen detection. To effectively integrate wastewater-based epidemiology into infectious disease surveillance, the detection methods employed in wastewater samples must be adapted to the distinct characteristics of sludge matrices. In this study, we adapted and applied protocols for the detection of IV and RSV in sewage sludge, comparing their performance with the results obtained in wastewater. To assess the efficiency of these protocols, sludge and wastewater samples were spiked with IV and RSV RNA, either free or incorporated in lentiviral particles. Samples were concentrated using the aluminum hydroxide adsorption-precipitation method before viral RNA extraction. Absolute virus quantification was carried out by RT-qPCR, including an internal control to monitor potential inhibitory factors. Recovery efficiencies for both free IV and RSV RNA were 60 % in sludge, and 75 % and 71 % respectively in wastewater, whereas the values for IV and RSV RNA in lentiviral particles were 16 % and 10 % in sludge and 21 % and 17 % in wastewater respectively. Additionally, the protocol enabled the quantification of naturally occurring IV and RSV in wastewater and sludge samples collected from two wastewater treatment plants during the winter months, thus affirming the efficacy of the employed methodologies.

Evaluation of wastewater-based epidemiology of COVID-19 approaches in Singapore's 'closed-system' scenario: A long-term country-wide assessment

With the COVID-19 pandemic the use of WBE to track diseases spread has rapidly evolved into a widely applied strategy worldwide. However, many of the current studies lack the necessary systematic approach and supporting quality of epidemiological data to fully evaluate the effectiveness and usefulness of such methods. Use of WBE in a very low disease prevalence setting and for long-term monitoring has yet to be validated and it is critical for its intended use as an early warning system. In this study we seek to evaluate the sensitivity of WBE approaches under low prevalence of disease and ability to provide early warning. Two monitoring scenarios were used: (i) city wide monitoring (population 5,700,000) and (ii) community/localized monitoring (population 24,000 to 240,000). Prediction of active cases by WBE using multiple linear regression shows that a multiplexed qPCR approach with three gene targets has a significant advantage over single-gene monitoring approaches, with R2 = 0.832 (RMSE 0.053) for an analysis using N, ORF1ab and S genes (R2 = 0.677 to 0.793 for single gene strategies). A predicted disease prevalence of 0.001% (1 in 100,000) for a city-wide monitoring was estimated by the multiplexed RT-qPCR approach and was corroborated by epidemiological data evidence in three 'waves'. Localized monitoring setting shows an estimated detectable disease prevalence of ∼0.002% (1 in 56,000) and is supported by the geospatial distribution of active cases and local population dynamics data. Data analysis also shows that this approach has a limitation in sensitivity, or hit rate, of 62.5 % and an associated high miss rate (false negative rate) of 37.5 % when compared to available epidemiological data. Nevertheless, our study shows that, with enough sampling resolution, WBE at a community level can achieve high precision and accuracies for case detection (96 % and 95 %, respectively) with low false omission rate (4.5 %) even at low disease prevalence levels.

Detecting SARS-CoV-2 in sludge samples: A systematic review

AIMS

This paper aims to review the main sludge concentration methods used for SARS-CoV-2 detection in sewage sludge samples, discussing the main methods and sample volume related to increased viral load. In addition, we aim to evaluate the countries associated with increased positivity rates for SARS-CoV-2 in sludge samples.

METHODS

This systematic methodology was registered in PROSPERO and followed the PRISMA guidelines. The search was carried out in the SciELO, PubMed/MEDLINE, Lilacs, and Google Scholar databases in January-March 2022. Quantitative studies with conclusive results were included in this review. Concentration methods (polyethylene glycol (PEG), PEG + NaCl, gravity thickening, skimmed milk flocculation, ultrafiltration, filtration using charged filters, primary sedimentation, and anaerobic digestion), as well as detection methods (RTqPCR and reverse transcription droplet digital PCR assay) were evaluated in this review. The SPSS v23 software program was used for statistical analysis.

RESULTS

PEG (with or without NaCl addition) and gravity thickening were the most used sludge concentration methods to detect SARS-CoV-2. The main method associated with increased viral load (>2,02 × 10^4 copies/mL) was PEG + NaCl (p < 0.05, Mann-Whitney test). The average positivity rate for SARS-CoV-2 in sludge samples was 61 %, and a correlation was found between the sludge volume and the viral load (ro 0.559, p = 0.03, Spearman correlation).

CONCLUSION

The sludge volume may influence the SARS-CoV-2 load since the virus can adhere to solid particles in these samples. Other factors may be associated with SARS-CoV-2 load, including the methods used; especially PEG + NaCl may result in a high viral load detected in sludge, and may provide a suitable pH for SARS-CoV-2 recovery.

A safe haven of SARS-CoV-2 in the environment: Prevalence and potential transmission risks in the effluent, sludge, and biosolids

The novel coronavirus, SARS-CoV-2, which has caused millions of death globally is recognized to be unstable and recalcitrant in the environment, especially in the way it has been evolving to form new and highly transmissible variants. Of particular concerns are human-environment interactions and the handling and reusing the environmental materials, such as effluents, sludge, or biosolids laden with the SARS-CoV-2 without adequate treatments, thereby suggesting potential transmission and health risks. This study assesses the prevalence of SARS-CoV-2 RNA in effluents, sludge, and biosolids. Further, we evaluate the environmental, ecological, and health risks of reusing these environmental materials by wastewater/sludge workers and farmers. A systematic review of literature from the Scopus database resulted in a total of 21 articles (11 for effluents, 8 for sludge, and 2 for biosolids) that met the criteria for meta-analysis, which are then subdivided into 30 meta-analyzed studies. The prevalence of SAR-CoV-2 RNA in effluent and sludge based on random-effect models are 27.51 and 1012.25, respectively, with a 95% CI between 6.14 and 48.89 for the effluent, and 104.78 and 1019.71 for the sludge. However, the prevalence of SARS-CoV-2 RNA in the biosolids based on the fixed-effect model is 30.59, with a 95% CI between 10.10 and 51.08. The prevalence of SARS-CoV-2 RNA in environmental materials indicates the inefficiency in some of the treatment systems currently deployed to inactivate and remove the novel virus, which could be a potential health risk concern to vulnerable wastewater workers in particular, and the environmental and ecological issues for the population at large. This timely review portends the associated risks in handling and reusing environmental materials without proper and adequate treatments.

An opinion on Wastewater-Based Epidemiological Monitoring (WBEM) with Clinical Diagnostic Test (CDT) for detecting high-prevalence areas of community COVID-19 Infections

Wastewater-Based Epidemiological Monitoring (WBEM) is an efficient surveillance tool during the COVID-19 pandemic as it meets all requirements of a complete monitoring system including early warning, tracking the current trend, prevalence of the disease, detection of genetic diversity as well asthe up-surging SARS-CoV-2 new variants with mutations from the wastewater samples. Subsequently, Clinical Diagnostic Test is widely acknowledged as the global gold standard method for disease monitoring, despite several drawbacks such as high diagnosis cost, reporting bias, and the difficulty of tracking asymptomatic patients (silent spreaders of the COVID-19 infection who manifest nosymptoms of the disease). In this current reviewand opinion-based study, we first propose a combined approach) for detecting COVID-19 infection in communities using wastewater and clinical sample testing, which may be feasible and effective as an emerging public health tool for the long-term nationwide surveillance system. The viral concentrations in wastewater samples can be used as indicatorsto monitor ongoing SARS-CoV-2 trends, predict asymptomatic carriers, and detect COVID-19 hotspot areas, while clinical sampleshelp in detecting mostlysymptomaticindividuals for isolating positive cases in communities and validate WBEM protocol for mass vaccination including booster doses for COVID-19.

Reduction and liquid-solid partitioning of SARS-CoV-2 and adenovirus throughout the different stages of a pilot-scale wastewater treatment plant

Investigating waterborne viruses is of great importance to minimizing risks to public health. Viruses tend to adsorb to sludge particles from wastewater processes by electrostatic and hydrophobic interactions between virus, aquatic matrix, and particle surface. Sludge is often re-used in agriculture; therefore, its evaluation is also of great interest to public health. In the present study, a pilot scale system treating real domestic wastewater from a large city in Brazil was used to evaluate the removal, the overall reduction, and liquid-solid partitioning of human adenovirus (HAdV), the novel coronavirus (SARS-CoV-2) and fecal indicators (F-specific coliphages and E. coli). The system consists of a high-rate algal pond (HRAP) post-treating the effluent of an upflow anaerobic sludge blanket (UASB) reactor. Samples were collected from the influent and effluent of each unit, as well as from the sludge of the UASB and from the microalgae biomass in the HRAP. Pathogens and indicators were quantified by quantitative polymerase chain reaction (qPCR) (for HAdV), qPCR with reverse transcription (RTqPCR) (for SARS-CoV-2), the double agar plaque assay (for coliphages), and the most probable number (MPN) method (for E. coli). The removal and overall reduction of HAdV and SARS-CoV-2 was greater than 1-log10. Almost 60% of remaining SARS-CoV-2 RNA and more than 70% of remaining HAdV DNA left the system in the sludge, demonstrating that both viruses may have affinity for solids. Coliphages showed a much lower affinity to solids, with only 3.7% leaving the system in the sludge. The system performed well in terms of the removal of organic matter and ammoniacal nitrogen, however tertiary treatment would be necessary to provide further pathogen reduction, if the effluent is to be reused in agriculture. To our knowledge, this is the first study that evaluated the reduction and partitioning of SARS-CoV-2 and HAdV through the complete cycle of a wastewater treatment system consisting of a UASB reactor followed by HRAPs.

Interactions between virus surrogates and sewage sludge vary by viral analyte: Recovery, persistence, and sorption

Sewage sludge, as a reservoir of viruses, may pose threats to human health. Understanding how virus particles interact with sludge is the key to controlling virus exposure and transmission. In this study, we investigated the recovery, survivability, and sorption of four typical virus surrogates with different structures (Phi6, MS2, T4, and Phix174) in sewage sludge. The most effective elution method varies by viral analyte, while the ultrafiltration method could significantly reduce the recovery loss for all four viruses. Compared with nonenveloped viruses, the poor recoveries of Phi6 during elution (<15%) limited its efficient detection. The inactivation kinetics of four viruses in solid-containing sludge were significantly faster than those in solid-removed samples at 25 °C, indicating that the solid fraction of sludge played an important role in virus inactivation. Although enveloped Phi6 was more vulnerable in both solid-removed and solid-containing sludge samples, it could remain viable for several hours at 25 °C and several days at 4 °C, which may pose an infection risk during sludge collection, transportation, and treatment process. The adsorption and desorption behavior of viruses in sludge could be affected by virus envelope structure, capsid proteins, and virus particle size. Phi6 adsorption to sludge was great with log K_F of 6.51 ± 0.53, followed by Phix174, MS2, and T4. Additionally, more than 95% of Phi6, MS2, and T4 adsorbed to sludge were strongly bound, and a considerable fraction of strongly-bound virus was confirmed to retain viability. These results shed light on the environmental behavior of viruses in sewage sludge and provide a theoretical basis for the risk assessment for sludge treatment and disposal.

Wastewater surveillance to infer COVID-19 transmission: A systematic review

Successful detection of SARS-COV-2 in wastewater suggests the potential utility of wastewater-based epidemiology (WBE) for COVID-19 community surveillance. This systematic review aims to assess the performance of wastewater surveillance as early warning system of COVID-19 community transmission. A systematic search was conducted in PubMed, Medline, Embase and the WBE Consortium Registry according to PRISMA guidelines for relevant articles published until 31st July 2021. Relevant data were extracted and summarized. Quality of each paper was assessed using an assessment tool adapted from Bilotta et al.'s tool for environmental science. Of 763 studies identified, 92 studies distributed across 34 countries were shortlisted for qualitative synthesis. A total of 26,197 samples were collected between January 2020 and May 2021 from various locations serving population ranging from 321 to 11,400,000 inhabitants. Overall sample positivity was moderate at 29.2% in all examined settings with the spike (S) gene having maximum rate of positive detections and nucleocapsid (N) gene being the most targeted. Wastewater signals preceded confirmed cases by up to 63 days, with 13 studies reporting sample positivity before the first cases were detected in the community. At least 50 studies reported an association of viral load with community cases. While wastewater surveillance cannot replace large-scale diagnostic testing, it can complement clinical surveillance by providing early signs of potential transmission for more active public health responses. However, more studies using standardized and validated methods are required along with risk analysis and modelling to understand the dynamics of viral outbreaks.