Discrimination and surveillance of infectious severe acute respiratory syndrome Coronavirus 2 in wastewater using cell culture and RT-qPCR

Key considerations for pathogen surveillance in wastewater

Wastewater surveillance (WWS) has received significant attention as a rapid, sensitive, and cost-effective tool for monitoring various pathogens in a community. WWS is employed to assess the spatial and temporal trends of diseases and identify their early appearances and reappearances, as well as to detect novel and mutated variants. However, the shedding rates of pathogens vary significantly depending on factors such as disease severity, the physiology of affected individuals, and the characteristics of pathogen. Furthermore, pathogens may exhibit differential fate and decay kinetics in the sewerage system. Variable shedding rates and decay kinetics may affect the detection of pathogens in wastewater. This may influence the interpretation of results and the conclusions of WWS studies. When selecting a pathogen for WWS, it is essential to consider it's specific characteristics. If data are not readily available, factors such as fate, decay, and shedding rates should be assessed before conducting surveillance. Alternatively, these factors can be compared to those of similar pathogens for which such data are available.

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.

Quantitative SARS-CoV-2 exposure assessment for workers in wastewater treatment plants using Monte-Carlo simulation

Several studies on COVID-19 pandemic have shown that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originating from human stool are detected in raw sewage for several days, leading to potential health risks for workers due to the production of bioaerosols and droplets during wastewater treatment process. In this study, data of SARS-CoV-2 concentrations in wastewater were gathered from literatures, and a quantitative microbial risk assessment with Monte Carlo simulation was used to estimate the daily probability of infection risk through exposure to viable infectious viral airborne particles of the workers during four seasons and under six environmental conditions. Inhalation of bioaerosols and direct ingestion of wastewater droplets were selected as exposure pathways. Spearman rank correlation coefficients were used for sensitivity analysis to identify the variables with the greatest influence on the infection risk probability. It was found that the daily probability of infection risk decreased with temperature (T) and relative humidity (RH) increase. The probability of direct droplet ingestion exposure pathway was higher than that of the bioaerosol inhalation pathway. The sensitivity analysis indicated that the most sensitive variable for both exposure pathways was the concentration of SARS-CoV-2 in stool. So, appropriate aeration systems, covering facilities, and effective ventilation are suggested to implement in wastewater treatment plants (WWTPs) to reduce emission concentration. Further to this, the exposure time (t) had a larger variance contribution than T and RH for the bioaerosol inhalation pathway. Implementing measures such as adding more work shifts, mandating personal protective equipment for all workers, and implementing coverage for treatment processes can significantly reduce the risk of infection among workers at WWTPs. These measures are particularly effective during environmental conditions with low temperatures and humidity levels.

Porcine Epidemic Diarrhea Virus, Surrogate for Coronavirus Decay Measurement in French Coastal Waters and Contribution to Coronavirus Risk Evaluation

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in infected patients mainly displays pulmonary and oronasal tropism; however, the presence of the virus has also been demonstrated in the stools of patients and consequently in wastewater treatment plant effluents, raising the question of the potential risk of environmental contamination (such as seawater contamination) through inadequately treated wastewater spillover into surface or coastal waters even if the environmental detection of viral RNA alone does not substantiate risk of infection. Therefore, here, we decided to experimentally evaluate the persistence of the porcine epidemic diarrhea virus (PEDv), considered as a coronavirus representative model, in the coastal environment of France. Coastal seawater was collected, sterile-filtered, and inoculated with PEDv before incubation for 0 to 4 weeks at four temperatures representative of those measured along the French coasts throughout the year (4, 8, 15, and 24°C). The decay rate of PEDv was determined using mathematical modeling and was used to determine the half-life of the virus along the French coast in accordance with temperatures from 2000 to 2021. We experimentally observed an inverse correlation between seawater temperature and the persistence of infectious viruses in seawater and confirm that the risk of transmission of infectious viruses from contaminated stool in wastewater to seawater during recreational practices is very limited. The present work represents a good model to assess the persistence of coronaviruses in coastal environments and contributes to risk evaluation, not only for SARS-CoV-2 persistence, but also for other coronaviruses, specifically enteric coronaviruses from livestock. IMPORTANCE The present work addresses the question of the persistence of coronavirus in marine environments because SARS-CoV-2 is regularly detected in wastewater treatment plants, and the coastal environment, subjected to increasing anthropogenic pressure and the final receiver of surface waters and sometimes insufficiently depurated wastewater, is particularly at risk. The problem also arises in the possibility of soil contamination by CoV from animals, especially livestock, during manure application, where, by soil impregnation and runoff, these viruses can end up in seawater. Our findings are of interest to researchers and authorities seeking to monitor coronaviruses in the environment, either in tourist areas or in regions of the world where centralized systems for wastewater treatment are not implemented, and more broadly, to the scientific community involved in "One Health" approaches.

SARS-CoV-2 in the environment: Contamination routes, detection methods, persistence and removal in wastewater treatment plants

The present study reviewed the occurrence of SARS-CoV-2 RNA and the evaluation of virus infectivity in feces and environmental matrices. The detection of SARS-CoV-2 RNA in feces and wastewater samples, reported in several studies, has generated interest and concern regarding the possible fecal-oral route of SARS-CoV-2 transmission. To date, the presence of viable SARS-CoV-2 in feces of COVID-19 infected people is not clearly confirmed although its isolation from feces of six different patients. Further, there is no documented evidence on the infectivity of SARS-CoV-2 in wastewater, sludge and environmental water samples, although the viral genome has been detected in these matrices. Decay data revealed that SARS-CoV-2 RNA persisted longer than infectious particle in all aquatic environment, indicating that genome quantification of SARS-CoV-2 does not imply the presence of infective viral particles. In addition, this review also outlined the fate of SARS-CoV-2 RNA during the different steps in the wastewater treatment plant and focusing on the virus elimination along the sludge treatment line. Studies showed complete removal of SARS-CoV-2 during the tertiary treatment. Moreover, thermophilic sludge treatments present high efficiency in SARS-CoV-2 inactivation. Further studies are required to provide more evidence with respect to the inactivation behavior of infectious SARS-CoV-2 in different environmental matrices and to examine factors affecting SARS-CoV-2 persistence.

SARS-CoV-2 in outdoor air following the third wave lockdown release, Portugal, 2021

Aiming to contribute with more data on the presence of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in outdoor environments, we performed air sampling in outdoor terraces from restaurants in three major cities of Portugal in April 2021, following the third wave lockdown release in the country. Air samples (n=19) were collected in 19 restaurant terraces during lunch time. Each air sample was collected using a Coriolis Compact air sampler, followed by RNA extraction and real-time quantitative PCR for the detection of viral RNA. Viral viability was also assessed through RNAse pre-treatment of samples. Only one of the 19 air samples was positive for SARS-CoV-2 RNA, with 7337 gene copies m-3 for the genomic region N2, with no viable virus in this sample. The low number of positive samples found in this study is not surprising, as sampling took place in outdoor settings where air circulation is optimal, and aerosols are rapidly dispersed by the air currents. These results are consistent with previous reports stating that transmission of SARS-CoV-2 in outdoor spaces is low, although current evidence shows an association of exposures in settings where drinking and eating is possible on-site with an increased risk in acquiring SARS-CoV-2 infection. Moreover, the minimal infectious dose for SARS-CoV-2 still needs to be determined so that the real risk of infection in different environments can be accurately established.

Validation of the efficacy of air purifiers using molecular techniques

The importance of air purifiers has increased in recent years, especially with the "coronavirus disease 2019" pandemic. The efficacy of air purifiers is usually determined under laboratory conditions before widespread application. The standard procedure for testing depends on virus cultivation and titration on cell culture. This, however, requires several days to deliver results. The aim of this study was to establish a rapid molecular assay which can differentiate between intact infectious and distorted non-infectious virus particles. Feline Coronavirus was selected as model for screening. First the samples were pretreated with enzymes (universal nuclease and RNase cocktail enzyme mixture) or viability dye (propidium monoazide) to eliminate any free nucleic acids. The ribonucleic acid (RNA) from intact virus was released via magnetic beads-based extraction, then the amount of the RNA was determined using real-time reverse transcription polymerase chain reaction (RT-PCR) or reverse transcription recombinase-aided amplification (RT-RAA). All results were compared to the infectivity assay based on the calculation of the 50% tissue culture infectious dose (TCID50). The nuclease has eliminated 100% of the free Feline Coronavirus RNA, while propidium monoazide underperformed (2.3-fold decrease in free RNA). Both RT-RAA and real-time RT-PCR produced similar results to the infectivity assay on cell culture with limit of detection of 102 TCID50/mL. Two UV-C air purifiers with prosperities of 100% inactivation of the viruses were used to validate the established procedure. Both real-time RT-PCR and RT-RAA were able to differentiate between intact virus particles and free RNA. To conclude, this study revealed a promising rapid method to validate the efficacy of air purifiers by combining enzymatic pretreatment and molecular assays.

Advances in virus detection methods for wastewater-based epidemiological applications

Wastewater-based epidemiology (WBE) is a powerful tool that has the potential to reveal the extent of an ongoing disease outbreak or to predict an emerging one. Recent studies have shown that SARS-CoV-2 concentration in wastewater may be correlated with the number of COVID-19 cases in the corresponding population. Most of the recent studies and applications of wastewater-based surveillance of SARS-CoV-2 applied the "gold standard" real-time quantitative reverse transcription-polymerase chain reaction (RT-qPCR) detection method. However, this method also has its limitations. The paper aimed to present recent improvements and applications of the PCR-based methods for SARS-CoV-2 monitoring in wastewater. Furthermore, it aimed to review alternative methods utilized and/or proposed for the detection of the virus in wastewater matrices. From the review, it was found that several studies have investigated the use of reverse-transcription digital polymerase reaction (RT-dPCR), which was generally shown to have a lower limit of detection (LOD) over the RT-qPCR. Aside from this, non-PCR-based and non-RNA based methods have also been explored for the detection of SARS-CoV-2 in wastewater, with detailed attention given to the detection of SARS-CoV-2 proteins. The potential methods for protein detection include mass spectrometry, the use of immunosensors, and nanotechnological applications. In addition, the review of recent studies also revealed two types of emerging methods related to the detection of SARS-CoV-2 in wastewater: i) capsid-integrity assays to infer about the infectivity of SARS-CoV-2 present in wastewater, and ii) alternative methods for detection of SARS-CoV-2 variants of concern (VOCs) in wastewater. The recent studies on proposed methods of SARS-CoV-2 detection in wastewater have considered improving this approach in one or more of the following aspects: rapidity, simplicity, cost, sensitivity, and specificity. However, further studies are needed in order to realize the full application of these methods for WBE in the field.

"pySewage": a hybrid approach to predict the number of SARS-CoV-2-infected people from wastewater in Brazil

It is well known that the new coronavirus pandemic has global environmental, public health, and economic implications. In this sense, this study aims to monitor SARS-CoV-2 in the largest wastewater treatment plant of Goiânia, which processes wastewater from more than 700,000 inhabitants, and to correlate the molecular and clinical data collected. Influent and effluent samples were collected at Dr. Helio de Seixo Britto's wastewater treatment plant from January to August 2021. Viral concentration was performed with polyethylene glycol before viral RNA extraction. Real-time qPCR (N1 and N2 gene assays) was performed to detect and quantify the viral RNA present in the samples. The results showed that 43.63% of the samples were positive. There is no significant difference between the detection of primers N1 (mean 3.23 log10 genome copies/L, std 0.23) and N2 (mean 2.95 log10 genome copies/L, std 0.29); also, there is no significant difference between the detection of influent and effluent samples. Our molecular data revealed a positive correlation with clinical data, and infection prevalence was higher than clinical data. In addition, we developed a user-friendly web application to predict the number of infected people based on the detection of viral load present in wastewater samples and may be applied as a public policy strategy for monitoring ongoing outbreaks.

The first detection of SARS-CoV-2 RNA in urban wastewater in Giza, Egypt

The new coronavirus (SARS-CoV-2) is a respiratory virus causing coronavirus disease (COVID-19). Individuals with COVID-19 can shed the viral genome in their feces, even if they do not have symptoms, and the virus can be detected in wastewater. The current study provides the first surveillance of SARS-CoV-2 RNA genome in the wastewater in Egypt. To study this aim, untreated influent (n = 48) and treated effluent (n = 48) samples were collected between January and December 2021 from the wastewater treatment plant in Giza. The viral RNA genome was determined by reverse transcription-polymerase chain reaction (RT-PCR) (S, E, and N target regions) and real-time quantitative reverse transcription-PCR (RT-qPCR) (N1 and N2 target regions). The RT-PCR assay failed to detect SARS-CoV-2 RNA in all samples analyzed, whereas RT-qPCR succeeded in the detection of N gene of SARS-CoV-2 in 62.5% of untreated influent samples. The RT-qPCR Ct values of those samples tested positive ranged from 19.9 to 30.1 with a mean of 23. The treated effluent samples were negative for viral RNA detected by both RT-PCR and RT-qPCR, indicating the efficiency of the sewage treatment plant in degrading SARS-CoV-2. Our preliminary findings provide evidence for the value of wastewater epidemiology approach for the surveillance of SARS-CoV-2 in the population to assist in the responses of public health to COVID-19 outbreak.

Non-Coding RNAs in Tuberculosis Epidemiology: Platforms and Approaches for Investigating the Genome's Dark Matter

A growing amount of information about the different types, functions, and roles played by non-coding RNAs (ncRNAs) is becoming available, as more and more research is done. ncRNAs have been identified as potential therapeutic targets in the treatment of tuberculosis (TB), because they may be essential regulators of the gene network. ncRNA profiling and sequencing has recently revealed significant dysregulation in tuberculosis, primarily due to aberrant processes of ncRNA synthesis, including amplification, deletion, improper epigenetic regulation, or abnormal transcription. Despite the fact that ncRNAs may have a role in TB characteristics, the detailed mechanisms behind these occurrences are still unknown. The dark matter of the genome can only be explored through the development of cutting-edge bioinformatics and molecular technologies. In this review, ncRNAs' synthesis and functions are discussed in detail, with an emphasis on the potential role of ncRNAs in tuberculosis. We also focus on current platforms, experimental strategies, and computational analyses to explore ncRNAs in TB. Finally, a viewpoint is presented on the key challenges and novel techniques for the future and for a wide-ranging therapeutic application of ncRNAs.

Photoinactivation of Phage Phi6 as a SARS-CoV-2 Model in Wastewater: Evidence of Efficacy and Safety

The last two years have been marked by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. This virus is found in the intestinal tract; it reaches wastewater systems and, consequently, the natural receiving water bodies. As such, inefficiently treated wastewater (WW) can be a means of contamination. The currently used methods for the disinfection of WW can lead to the formation of toxic compounds and can be expensive or inefficient. As such, new and alternative approaches must be considered, namely, photodynamic inactivation (PDI). In this work, the bacteriophage φ6 (or, simply, phage φ6), which has been used as a suitable model for enveloped RNA viruses, such as coronaviruses (CoVs), was used as a model of SARS-CoV-2. Firstly, to understand the virus's survival in the environment, phage φ6 was subjected to different laboratory-controlled environmental conditions (temperature, pH, salinity, and solar and UV-B irradiation), and its persistence over time was assessed. Second, to assess the efficiency of PDI towards the virus, assays were performed in both phosphate-buffered saline (PBS), a commonly used aqueous matrix, and a secondarily treated WW (a real WW matrix). Third, as WW is generally discharged into the marine environment after treatment, the safety of PDI-treated WW was assessed through the determination of the viability of native marine water microorganisms after their contact with the PDI-treated effluent. Overall, the results showed that, when used as a surrogate for SARS-CoV-2, phage φ6 remains viable in different environmental conditions for a considerable period. Moreover, PDI proved to be an efficient approach in the inactivation of the viruses, and the PDI-treated effluent showed no toxicity to native aquatic microorganisms under realistic dilution conditions, thus endorsing PDI as an efficient and safe tertiary WW disinfection method. Although all studies were performed with phage φ6, which is considered a suitable model of SARS-CoV-2, further studies using SARS-CoV-2 are necessary; nevertheless, the findings show the potential of PDI for controlling SARS-CoV-2 in WW.

SARS-CoV-2 in wastewater: From detection to evaluation

SARS-CoV-2 presence in wastewater has been reported in several studies and has received widespread attention among the Wastewater-based epidemiology (WBE) community. Such studies can potentially be used as a proxy for early warning of potential COVID-19 outbreak, or as a mitigation measure for potential virus transmission via contaminated water. In this review, we summarized the latest understanding on the detection, concentration, and evaluation of SARS-CoV-2 in wastewater. Importantly, we discuss factors affecting the quality of wastewater surveillance ranging from temperature, pH, starting concentration, as well as the presence of chemical pollutants. These factors greatly affect the reliability and comparability of studies reported by various communities across the world. Overall, this review provides a broadly encompassing guidance for epidemiological study using wastewater surveillance.

Wastewater Surveillance for SARS-CoV-2 RNA in Canada

Wastewater surveillance for SARS-CoV-2 RNA is a relatively recent adaptation of long-standing wastewater surveillance for infectious and other harmful agents. Individuals infected with COVID-19 were found to shed SARS-CoV-2 in their faeces. Researchers around the world confirmed that SARS-CoV-2 RNA fragments could be detected and quantified in community wastewater. Canadian academic researchers, largely as volunteer initiatives, reported proof-of-concept by April 2020. National collaboration was initially facilitated by the Canadian Water Network.

Many public health officials were initially skeptical about actionable information being provided by wastewater surveillance even though experience has shown that public health surveillance for a pandemic has no single, perfect approach. Rather, different approaches provide different insights, each with its own strengths and limitations. Public health science must triangulate among different forms of evidence to maximize understanding of what is happening or may be expected. Well-conceived, resourced, and implemented wastewater-based platforms can provide a cost-effective approach to support other conventional lines of evidence. Sustaining wastewater monitoring platforms for future surveillance of other disease targets and health states is a challenge. Canada can benefit from taking lessons learned from the COVID-19 pandemic to develop forward-looking interpretive frameworks and capacity to implement, adapt, and expand such public health surveillance capabilities.