Decay of SARS-CoV-2 and surrogate murine hepatitis virus RNA in untreated wastewater to inform application in wastewater-based epidemiology

Monitoring human arboviral diseases through wastewater surveillance: Challenges, progress and future opportunities

Arboviral diseases are caused by a group of viruses spread by the bite of infected arthropods. Amongst these, dengue, Zika, west nile fever and yellow fever cause the greatest economic and social impact. Arboviral epidemics have increased in frequency, magnitude and geographical extent over the past decades and are expected to continue increasing with climate change and expanding urbanisation. Arboviral prevalence is largely underestimated, as most infections are asymptomatic, nevertheless existing surveillance systems are based on passive reporting of loosely defined clinical syndromes with infrequent laboratory confirmation. Wastewater-based surveillance (WBS), which has been demonstrated to be useful for monitoring diseases with significant asymptomatic populations including COVID19 and polio, could be a useful complement to arboviral surveillance. We review the current state of knowledge and identify key factors that affect the feasibility of monitoring arboviral diseases by WBS to include viral shedding loads by infected persons, the persistence of shed arboviruses and the efficiency of their recovery from sewage. We provide a simple model on the volume of wastewater that needs to be processed for detection of arboviruses, in face of lower arboviral shedding rates. In all, this review serves to reflect on the key challenges that need to be addressed and overcome for successful implementation of arboviral WBS.

Predicting the dispersal of SARS-CoV-2 RNA from the wastewater treatment plant to the coast

Viral pathogens including SARS-CoV-2 RNA have been detected in wastewater treatment effluent, and untreated sewage overflows, that pose an exposure hazard to humans. We assessed whether SARS-CoV-2 RNA was likely to have been present in detectable quantities in UK rivers and estuaries during the first wave of the Covid-19 pandemic. We simulated realistic viral concentrations parameterised on the Camel and Conwy catchments (UK) and their populations, showing detectable SARS-CoV-2 RNA concentrations for untreated but not for treated loading, but also being contingent on viral decay, hydrology, catchment type/shape, and location. Under mean or low river flow conditions, viral RNA concentrated within the estuaries allowing for viral build-up and caused a lag by up to several weeks between the peak in community infections and the viral peak in the environment. There was an increased hazard posed by SARS-CoV-2 RNA with a T 90 decay rate >24 h, as the estuarine build-up effect increased. High discharge events transported the viral RNA downstream and offshore, increasing the exposure risk to coastal bathing waters and shellfisheries - although dilution in this case reduced viral concentrations well below detectable levels. Our results highlight the sensitivity of exposure to viral pathogens downstream of wastewater treatment, across a range of viral loadings and catchment characteristics - with implications to environmental surveillance.

Development of passive samplers for the detection of SARS-CoV-2 in sewage and seawater: Application for the monitoring of sewage

Recent studies have shown that passive sampling is a promising tool for SARS-CoV-2 detection for wastewater-based epidemiology (WBE) application. We have previously developed passive sampling of viruses using polymer membranes in seawater. Even though SARS-CoV-2 was not detected yet in seawater, passive sampling could be optimized for future application in coastal areas close to wastewater treatment plant (WWTP). The aim of this study was to optimize passive sampling of SARS-CoV-2 in sewage and seawater by selecting a suitable membrane, to determine whether the quantities of virus increase over time, and then to determine if passive sampling and traditional sampling are correlated when conducted in a wastewater treatment plant. Nylon and Zetapor allowed the detection of heat inactivated SARS-CoV-2 and of the Porcine Epidemic Diarrhea Virus (PEDV), a coronavirus surrogate, in wastewater and seawater spiked with these 2 viruses, showing an increase in detection between 4 h and 24 h of immersion and significantly higher recoveries of both viruses with nylon in seawater (15%) compared to wastewater (4%). On wastewater samples, both membranes detected the virus, the recovery rate was of about 3% for freshly collected samples, and no significant difference was found between SARS-CoV-2 genome concentration on Zetapor and that in water. In sewage spiked seawater, similar concentrations of genome were found on both membranes, with a mean recovery rate of 16% and 11% respectively for nylon and Zetapor. A 3-weeks monitoring with passive sampler allowed the detection of viruses in the influent of a WWTP with a frequency of 100% and 76% for SARS-CoV-2 and norovirus GII respectively. Passive and traditional sampling gave the same evolution of the SARS-CoV-2 concentration over time. All these results confirmed the interest of passive sampling for virus detection and its potential application for monitoring in the wastewater system for targeted public health actions.

Effect of inactivating RNA viruses by coupled UVC and UVA LEDs evaluated by a viral surrogate commonly used as a genetic vector

RNA viruses are ubiquitous in nature, many of which can cause severe infectious syndromes to humanity, e.g., the SARS-CoV-2 virus. Ultraviolet (UV) radiation has been widely studied for inactivating various species of microorganisms, including viruses. The most applicable UV light for viruses ranges from 200nm to 280nm in wavelength, i.e., UVC. More recently, the synergy of UVA light with UVC has been studied in disinfecting bacteria in polluted water. However, little attention has been paid to studying viral inactivation by coupled UVC and UVA LEDs. The necessity of such research is to find an effective and economical solution for the LEDs of these two bands. Along this track, we attempt to tackle two major challenges. The first is to find a suitable viral surrogate that can safely be used in ordinary labs. In this aspect, lentivirus is commonly used as a genetic vector and has been selected to surrogate RNA viruses. Another is to determine the effective dosage of the coupled UVC and UVA light. To this end, the surrogate lentivirus was irradiated by 280nm (UVC) LEDs, 365nm (UVA) LEDs, and their combination at various doses. Survival rates were detected to compare the efficacy of various options. Moreover, the viral RNA damage was detected by RT-qPCR to disclose the mechanism of viral death. The results have shown that for the same duration of irradiation, the effect of the full-power 280nm LEDs is equivalent to that of the half-power 280nm LEDs combined with a suitable radiant power of the 365nm LEDs. The observations have been further confirmed by the effect of damaging the viral RNA by either the 280nm or 365nm light. In conclusion, the experimental results provide clear evidence of alleviating the requirement of UVC LEDs in viral inactivation by substituting them partially with UVA LEDs.

Identification and quantification of bioactive compounds suppressing SARS-CoV-2 signals in wastewater-based epidemiology surveillance

Recent SARS-CoV-2 wastewater-based epidemiology (WBE) surveillance have documented a positive correlation between the number of COVID-19 patients in a sewershed and the level of viral genetic material in the wastewater. Efforts have been made to use the wastewater SARS-CoV-2 viral load to predict the infected population within each sewershed using a multivariable regression approach. However, reported clear and sustained variability in SARS-CoV-2 viral load among treatment facilities receiving industrial wastewater have made clinical prediction challenging. Several classes of molecules released by regional industries and manufacturing facilities, particularly the food processing industry, can significantly suppress the SARS-CoV-2 signals in wastewater by breaking down the lipid-bilayer of the membranes. Therefore, a systematic ranking process in conjugation with metabolomic analysis was developed to identify the wastewater treatment facilities exhibiting SARS-CoV-2 suppression and identify and quantify the chemicals suppressing the SARS-COV-2 signals. By ranking the viral load per diagnosed case among the sewersheds, we successfully identified the wastewater treatment facilities in Missouri, USA that exhibit SARS-CoV-2 suppression (significantly lower than 5 × 1011 gene copies/reported case) and determined their suppression rates. Through both untargeted global chemical profiling and targeted analysis of wastewater samples, 40 compounds were identified as candidates of SARS-CoV-2 signal suppressors. Among these compounds, 14 had higher concentrations in wastewater treatment facilities that exhibited SARS-CoV-2 signal suppression compared to the unsuppressed control facilities. Stepwise regression analyses indicated that 4-nonylphenol, palmitelaidic acid, sodium oleate, and polyethylene glycol dioleate are positively correlated with SARS-CoV-2 signal suppression rates. Suppression activities were further confirmed by incubation studies, and the suppression kinetics for each bioactive compound were determined. According to the results of these experiments, bioactive molecules in wastewater can significantly reduce the stability of SARS-CoV-2 genetic marker signals. Based on the concentrations of these chemical suppressors, a correction factor could be developed to achieve more reliable and unbiased surveillance results for wastewater treatment facilities that receive wastewater from similar industries.

Occurrence of SARS-CoV-2 in excreta, sewage, and environment: epidemiological significance and potential risks

The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in patients' excreta raises the issue of its occurrence and fate in sewage. This review has focused on the presence of the SARS-CoV-2 in human excreta, wastewater, sewage sludge, and river waters. It explored the potential use of the wastewater-based epidemiology approach to report on the situation of current and eventual future SARS-CoV-2 outbreaks. The main concern of the occurrence of SARS-CoV-2 in the environment is the public health risks at sites of sewage products disposal and reuse, especially in low-income countries with inadequate sanitation, where direct discharge and reuse of raw sewage are common practices. The review also addressed the role sewage-irrigated agriculture can have in SARS-CoV-2 spread in the environmental compartments reached through sewage products application. An overview was made on the interest of sewage management, water safety, and hygienic practices for controlling the environmental dissemination of SARS-CoV-2.

Application of human RNase P normalization for the realistic estimation of SARS-CoV-2 viral load in wastewater: A perspective from Qatar wastewater surveillance

The apparent uncertainty associated with shedding patterns, environmental impacts, and sample processing strategies have greatly influenced the variability of SARS-CoV-2 concentrations in wastewater. This study evaluates the use of a new normalization approach using human RNase P for the logic estimation of SARS-CoV-2 viral load in wastewater. SARS-CoV-2 variants outbreak was monitored during the circulating wave between February and August 2021. Sewage samples were collected from five major wastewater treatment plants and subsequently analyzed to determine the viral loads in the wastewater. SARS-CoV-2 was detected in all the samples where the wastewater Ct values exhibited a similar trend as the reported number of new daily positive cases in the country. The infected population number was estimated using a mathematical model that compensated for RNA decay due to wastewater temperature and sewer residence time, and which indicated that the number of positive cases circulating in the population declined from 765,729 ± 142,080 to 2,303 ± 464 during the sampling period. Genomic analyses of SARS-CoV-2 of thirty wastewater samples collected between March 2021 and April 2021 revealed that alpha (B.1.1.7) and beta (B.1.351) were among the dominant variants of concern (VOC) in Qatar. The findings of this study imply that the normalization of data allows a more realistic assessment of incidence trends within the population.

Sources, fates and treatment strategies of typical viruses in urban sewage collection/treatment systems: A review

The ongoing coronavirus pandemic (COVID-19) throughout the world has severely threatened the global economy and public health. Due to receiving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a wide variety of sources (e.g., households, hospitals, slaughterhouses), urban sewage treatment systems are regarded as an important path for the transmission of waterborne viruses. This review presents a quantitative profile of the concentration distribution of typical viruses within wastewater collection systems and evaluates the influence of different characteristics of sewer systems on virus species and concentration. Then, the efficiencies and mechanisms of virus removal in the units of wastewater treatment plants (WWTPs) are summarized and compared, among which the inactivation efficiencies of typical viruses by typical disinfection approaches under varied operational conditions are elucidated. Subsequently, the occurrence and removal of viruses in treated effluent reuse and desalination, as well as that in sewage sludge treatment, are discussed. Potential dissemination of viruses is emphasized by occurrence via aerosolization from toilets, the collection system and WWTP aeration, which might have a vital role in the transmission and spread of viruses. Finally, the frequency and concentration of viruses in reclaimed water, the probability of infection are also reviewed for discussing the potential health risks.

A Review of the Presence of SARS-CoV-2 in Wastewater: Transmission Risks in Mexico

The appearance of SARS-CoV-2 represented a new health threat to humanity and affected millions of people; the transmission of this virus occurs through different routes, and one of them recently under debate in the international community is its possible incorporation and spread by sewage. Therefore, the present work's research objectives are to review the presence of SARS-CoV-2 in wastewater throughout the world and to analyze the coverage of wastewater treatment in Mexico to determine if there is a correlation between the positive cases of COVID-19 and the percentages of treated wastewater in Mexico as well as to investigate the evidence of possible transmission by aerosol sand untreated wastewater. Methodologically, a quick search of scientific literature was performed to identify evidence the presence of SARS-CoV-2 RNA (ribonucleic acid) in wastewater in four international databases. The statistical information of the positive cases of COVID-19 was obtained from data from the Health Secretary of the Mexican Government and the Johns Hopkins Coronavirus Resource Center. The information from the wastewater treatment plants in Mexico was obtained from official information of the National Water Commission of Mexico. The results showed sufficient evidence that SARS-CoV-2 remains alive in municipal wastewater in Mexico. Our analysis indicates that there is a low but significant correlation between the percentage of treated water and positive cases of coronavirus r = -0.385, with IC (95%) = (-0.647, -0.042) and p = 0.030; this result should be taken with caution because wastewater is not a transmission mechanism, but this finding is useful to highlight the need to increase the percentage of treated wastewater and to do it efficiently. In conclusions, the virus is present in untreated wastewater, and the early detection of SAR-CoV-2 could serve as a bioindicator method of the presence of the virus. This could be of great help to establish surveillance measures by zones to take preventive actions, which to date have not been considered by the Mexican health authorities. Unfortunately, wastewater treatment systems in Mexico are very fragile, and coverage is limited to urban areas and non-existent in rural areas. Furthermore, although the probability of contagion is relatively low, it can be a risk for wastewater treatment plant workers and people who are close to them.

Investigation on Potential ESKAPE Surrogates for 222 and 254 nm Irradiation Experiments

Background

Due to the increase in multidrug-resistant pathogens, it is important to investigate further antimicrobial options. In order not to have to work directly with pathogens, the investigation of possible surrogates is an important aspect. It is examined how suitable possible surrogate candidates for ESKAPE pathogens are for UVC applications. In addition, the inactivation sensitivities to 222 and 254 nm radiation are compared in relation.

Methods

Non-pathogenic members (Enterococcus mundtii, Staphylococcus carnosus, Acinetobacter kookii, Pseudomonas fluorescens and Escherichia coli) of genera of ESKAPE strains were photoinactivated in PBS with irradiation wavelengths of 222 and 254 nm (no non-pathogenic Klebsiella was available). Log reduction doses were determined and compared to published photoinactivation results on ESKAPE pathogens. It was assumed that non-pathogenic bacteria could be designated as surrogates for one wavelength and one ESKAPE strain, if the doses were between the 25 and 75% quantiles of published log reduction dose of the corresponding pathogen.

Results

For all non-pathogen relatives (except A. kookii), higher average log reduction doses were required for irradiation at 222 nm than at 254 nm. Comparison by boxplot revealed that five of eight determined log reduction doses of the possible surrogates were within the 25 and 75% quantiles of the data for ESKAPE pathogens. The measured log reduction dose for non-pathogenic E. coli was above the 75% quantile at 222 nm, and the log reduction dose for S. carnosus was below the 25% quantile at 254 nm.

Conclusion

For more than half of the studied cases, the examined ESKAPE relatives in this study can be applied as surrogates for ESKAPE pathogens. Because of lack of data, no clear statement could be made for Enterococcus faecalis at 222 nm and Acinetobacter baumannii at both wavelengths.

Back-estimation of norovirus infections through wastewater-based epidemiology: A systematic review and parameter sensitivity

The amount of norovirus RNA (Ribonucleic Acid) in raw wastewater, collected from a wastewater treatment plant (WWTP), can provide an indication of disease prevalence within the sampled catchment. However, an accurate back-estimation might be impeded by the uncertainties from in-sewer/in-sample degradation of viral RNA, variable shedding magnitude, and difficulties in measurement within raw wastewater. The current study reviewed the published literature regarding the factors of norovirus shedding, viral RNA decay in wastewater, and the occurrence of norovirus RNA in raw wastewater based on molecular detection. Sensitivity analysis for WBE back-estimation was conducted using the reported data of the factors mentioned above considering different viral loads in wastewater samples. It was found that the back-estimation is more sensitive to analytical detection uncertainty than shedding variability for norovirus. Although seasonal temperature change can lead to variation of decay rates and may influence the sensitivity of this pathogen-specific parameter, decay rates of norovirus RNA contribute negligibly to the variance in estimating disease prevalence, based on the available data from decay experiments in bulk wastewater under different temperatures. However, the effects of in-sewer transportation on viral RNA decay and retardation by sewer biofilms on pipe surfaces are largely unknown. Given the highest uncertainty from analytical measurement by molecular methods and complexity of in-sewer processes that norovirus experienced during the transportation to WWTP, future investigations are encouraged to improve the accuracy of viral RNA detection in wastewater and delineate viral retardation/interactions with wastewater biofilms in real sewers.

Artificial neural network-based estimation of COVID-19 case numbers and effective reproduction rate using wastewater-based epidemiology

As a cost-effective and objective population-wide surveillance tool, wastewater-based epidemiology (WBE) has been widely implemented worldwide to monitor the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentration in wastewater. However, viral concentrations or loads in wastewater often correlate poorly with clinical case numbers. To date, there is no reliable method to back-estimate the coronavirus disease 2019 (COVID-19) case numbers from SARS-CoV-2 concentrations in wastewater. This greatly limits WBE in achieving its full potential in monitoring the unfolding pandemic. The exponentially growing SARS-CoV-2 WBE dataset, on the other hand, offers an opportunity to develop data-driven models for the estimation of COVID-19 case numbers (both incidence and prevalence) and transmission dynamics (effective reproduction rate). This study developed artificial neural network (ANN) models by innovatively expanding a conventional WBE dataset to include catchment, weather, clinical testing coverage and vaccination rate. The ANN models were trained and evaluated with a comprehensive state-wide wastewater monitoring dataset from Utah, USA during May 2020 to December 2021. In diverse sewer catchments, ANN models were found to accurately estimate the COVID-19 prevalence and incidence rates, with excellent precision for prevalence rates. Also, an ANN model was developed to estimate the effective reproduction number from both wastewater data and other pertinent factors affecting viral transmission and pandemic dynamics. The established ANN model was successfully validated for its transferability to other states or countries using the WBE dataset from Wisconsin, USA.

Persistence of Coronavirus Surrogates on Meat and Fish Products during Long-Term Storage

Multiple pathways of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission have been examined, and the role of contaminated foods as a source of SARS-CoV-2 exposure has been suggested. As many cases of SARS-CoV-2 have been linked to meat processing plants, it may be that conditions in live animal markets and slaughterhouses or meat processing plant procedures transfer viral particles to meat, poultry, and seafood during animal slaughter, processing, storage, or transport. Because of the potential for contamination of foods such as beef, chicken, pork, or fish, the goal of this study was to evaluate the survival of a lipid enveloped RNA bacteriophage, phi 6, as well as two animal coronaviruses, murine hepatitis virus (MHV) and transmissible gastroenteritis virus (TGEV), as SARS-CoV-2 surrogates for their survival under various meat and fish cold-storage conditions over 30 days. Viral surrogates differed in survival, depending on food product and temperature, but overall, viruses survived for extended periods of time at high concentrations at both refrigerated and frozen temperatures. The ability of SARS-CoV-2 viral surrogates like Phi 6 and animal coronaviruses to survive for varying extents on some meat and fish products when stored refrigerated or frozen is a significant and concerning finding. Continued efforts are needed to prevent contamination of foods and food processing surfaces, worker hands, and food processing utensils such as knives, and there is a need to better address the lack of or inadequate disinfection of these foods prior to meat packaging. IMPORTANCE The ability of SARS-CoV-2 viral surrogates like Phi 6 and animal coronaviruses to survive for long periods on meat and fish products at cold temperatures emphasizes the need for rigorous and sustained food sanitation and hygiene in the harvest, transport, processing, and distribution of these foods.

Development of an efficient wastewater testing protocol for high-throughput country-wide SARS-CoV-2 monitoring

Wastewater-based surveillance has been widely used as a non-intrusive tool to monitor population-level transmission of COVID-19. Although various approaches are available to concentrate viruses from wastewater samples, scalable methods remain limited. Here, we sought to identify and evaluate SARS-CoV-2 virus concentration protocols for high-throughput wastewater testing. A total of twelve protocols for polyethylene glycol (PEG) precipitation and four protocols for ultrafiltration-based approaches were evaluated across two phases. The first phase entailed an initial evaluation using a small sample set, while the second phase further evaluated five protocols using wastewater samples of varying SARS-CoV-2 concentrations. Permutations in the pre-concentration, virus concentration and RNA extraction steps were evaluated. Among PEG-based methods, SARS-CoV-2 virus recovery was optimal with 1) the removal of debris prior to processing, 2) 2 h to 24 h incubation with 8% PEG at 4 °C, 3) 4000 xg or 14,000 xg centrifugation, and 4) a column-based RNA extraction method, yielding virus recovery of 42.4-52.5%. Similarly, the optimal protocol for ultrafiltration included 1) the removal of debris prior to processing, 2) ultrafiltration, and 3) a column-based RNA extraction method, yielding a recovery of 38.2%. This study also revealed that SARS-CoV-2 RNA recovery for samples with higher virus concentration were less sensitive to changes in the PEG method, but permutations in the PEG protocol could significantly impact virus yields when wastewater samples with lower SARS-CoV-2 RNA were used. Although both PEG precipitation and ultrafiltration methods resulted in similar SARS-CoV-2 RNA recoveries, the former method is more cost-effective while the latter method provided operational efficiency as it required a shorter turn-around-time (PEG precipitation, 9-23 h; Ultrafiltration, 5 h). The decision on which method to adopt will thus depend on the use-case for wastewater testing, and the need for cost-effectiveness, sensitivity, operational feasibility and scalability.

A systematic review on the occurrence, fate, and remediation of SARS-CoV-2 in wastewater

The COVID-19 has been declared a pandemic by the World Health Organization. Along with impairing the respiratory system, it also affects the gastrointestinal system. By reviewing experiments on the wastewater analysis for the detection of coronavirus, this study explores the fate, persistence, and various remediation strategies for the virus removal from the wastewater. The results indicated that the virus can be detected in the wastewater samples, feces, and sewage, even before the onset of symptoms. Coronavirus can be a potential panzootic disease, as several mammalian species get infected by the deadly virus. The disinfection strategies used earlier for the treatment of wastewater are not sufficient for the removal of viruses from the wastewater. Therefore, concerted efforts should be made to understand their fate, sources, and occurrence in the environmental matrices. To prevent the spread of the panzootic disease, revised guidelines should be issued for the remediation of the virus. Recent viral remediation methods such as membrane bioreactors and advanced oxidation methods can be used. Therefore, the present review puts a light on the current knowledge on the occurrence of coronaviruses in wastewater, the possible sources, fate, and removal strategies.

Detection of SARS-CoV-2 RNA throughout wastewater treatment plants and a modeling approach to understand COVID-19 infection dynamics in Winnipeg, Canada

Although numerous studies have detected SARS-CoV-2 RNA in wastewater and attempted to find correlations between the concentration of SARS-CoV-2 RNA and the number of cases, no consensus has been reached on sample collection and processing, and data analysis. Moreover, the fate of SARS-CoV-2 in wastewater treatment plants is another issue, specifically regarding the discharge of the virus into environmental settings and the water cycle. The current study monitored SARS-CoV-2 RNA in influent and effluent wastewater samples with three different concentration methods and sludge samples over six months (July to December 2020) to compare different virus concentration methods, assess the fate of SARS-CoV-2 RNA in wastewater treatment plants, and describe the potential relationship between SARS-CoV-2 RNA concentrations in influent and infection dynamics. Skimmed milk flocculation (SMF) resulted in 15.27 ± 3.32% recovery of an internal positive control, Armored RNA, and a high positivity rate of SARS-CoV-2 RNA in stored wastewater samples compared to ultrafiltration methods employing a prefiltration step to eliminate solids in fresh wastewater samples. Our results suggested that SARS-CoV-2 RNA may predominate in solids, and therefore, concentration methods focusing on both supernatant and solid fractions may result in better recovery. SARS-CoV-2 RNA was detected in influent and primary sludge samples but not in secondary and final effluent samples, indicating a significant reduction during primary and secondary treatments. SARS-CoV-2 RNA was first detected in influent on September 30th, 2020. A decay-rate formula was applied to estimate initial concentrations of late-processed samples with SMF. A model based on shedding rate and new cases was applied to estimate SARS-CoV-2 RNA concentrations and the number of active shedders. Inferred sensitivity of observed and modeled concentrations to the fluctuations in new cases and test-positivity rates indicated a potential contribution of newly infected individuals to SARS-CoV-2 RNA loads in wastewater.

SARS-CoV-2 shedding sources in wastewater and implications for wastewater-based epidemiology

Wastewater-based epidemiology (WBE) approach for COVID-19 surveillance is largely based on the assumption of SARS-CoV-2 RNA shedding into sewers by infected individuals. Recent studies found that SARS-CoV-2 RNA concentration in wastewater (CRNA) could not be accounted by the fecal shedding alone. This study aimed to determine potential major shedding sources based on literature data of CRNA, along with the COVID-19 prevalence in the catchment area through a systematic literature review. Theoretical CRNA under a certain prevalence was estimated using Monte Carlo simulations, with eight scenarios accommodating feces alone, and both feces and sputum as shedding sources. With feces alone, none of the WBE data was in the confidence interval of theoretical CRNA estimated with the mean feces shedding magnitude and probability, and 63% of CRNA in WBE reports were higher than the maximum theoretical concentration. With both sputum and feces, 91% of the WBE data were below the simulated maximum CRNA in wastewater. The inclusion of sputum as a major shedding source led to more comparable theoretical CRNA to the literature WBE data. Sputum discharging behavior of patients also resulted in great fluctuations of CRNA under a certain prevalence. Thus, sputum is a potential critical shedding source for COVID-19 WBE surveillance.

Detection of SARS-CoV-2 RNA in wastewater and importance of population size assessment in smaller cities: An exploratory case study from two municipalities in Latvia

Wastewater-based epidemiology (WBE) has regained global importance during the COVID-19 pandemic. The mobility of people and other factors, such as precipitation and irregular inflow of industrial wastewater, are complicating the estimation of the disease prevalence through WBE, which is crucial for proper crisis management. These estimations are particularly challenging in urban areas with moderate or low numbers of inhabitants in situations where movement restrictions are not adopted (as in the case of Latvia) because residents of smaller municipalities tend to be more mobile and less strict in following the rules and measures of disease containment. Thus, population movement can influence the outcome of WBE measurements significantly and may not reflect the actual epidemiological situation in the respective area. Here, we demonstrate that by combining the data of detected SARS-CoV-2 RNA copy number, 5-hydroxyindoleacetic acid (5-HIAA) analyses in wastewater and mobile call detail records it was possible to provide an accurate assessment of the COVID-19 epidemiological situation in towns that are small (COVID-19 28-day cumulative incidence r = 0.609 and 35-day cumulative incidence r = 0.89, p < 0.05) and medium-sized towns (COVID-19 21-day cumulative incidence r = 0.997, 28-day cumulative incidence r = 0.98 and 35-day cumulative incidence r = 0.997, p < 0.05). This is the first study demonstrating WBE for monitoring COVID-19 outbreaks in Latvia. We demonstrate that the application of population size estimation measurements such as total 5-HIAA and call detail record data improve the accuracy of the WBE approach.

A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities

The COVID-19 pandemic has stimulated wastewater-based surveillance, allowing public health to track the epidemic by monitoring the concentration of the genetic fingerprints of SARS-CoV-2 shed in wastewater by infected individuals. Wastewater-based surveillance for COVID-19 is still in its infancy. In particular, the quantitative link between clinical cases observed through traditional surveillance and the signals from viral concentrations in wastewater is still developing and hampers interpretation of the data and actionable public-health decisions. We present a modelling framework that includes both SARS-CoV-2 transmission at the population level and the fate of SARS-CoV-2 RNA particles in the sewage system after faecal shedding by infected persons in the population. Using our mechanistic representation of the combined clinical/wastewater system, we perform exploratory simulations to quantify the effect of surveillance effectiveness, public-health interventions and vaccination on the discordance between clinical and wastewater signals. We also apply our model to surveillance data from three Canadian cities to provide wastewater-informed estimates for the actual prevalence, the effective reproduction number and incidence forecasts. We find that wastewater-based surveillance, paired with this model, can complement clinical surveillance by supporting the estimation of key epidemiological metrics and hence better triangulate the state of an epidemic using this alternative data source.

Monitoring SARS-CoV-2 in the Wastewater and Rivers of Tapachula, a Migratory Hub in Southern Mexico

The COVID-19 pandemic has been monitored by applying different strategies, including SARS-CoV-2 detection with clinical testing or through wastewater-based epidemiology (WBE). We used the latter approach to follow SARS-CoV-2 dispersion in Tapachula city, located in Mexico's tropical southern border region. Tapachula is a dynamic entry point for people seeking asylum in Mexico or traveling to the USA. Clinical testing facilities for SARS-CoV-2 monitoring are limited in the city. A total of eighty water samples were collected from urban and suburban rivers and sewage and a wastewater treatment plant over 4 months in Tapachula. We concentrated viral particles with a PEG-8000-based method, performed RNA extraction, and detected SARS-CoV-2 particles through RT-PCR. We considered the pepper mild mottle virus as a fecal water pollution biomarker and analytical control. SARS-CoV-2 viral loads (N1 and N2 markers) were quantified and correlated with official regional statistics of COVID-19 bed occupancy and confirmed cases (r > 91%). Our results concluded that WBE proved a valuable tool for tracing and tracking the COVID-19 pandemic in tropical countries with similar water temperatures (21-29 °C). Monitoring SARS-CoV-2 through urban and suburban river water sampling would be helpful in places lacking a wastewater treatment plant or water bodies with sewage discharges.

Monitoring COVID-19 through SARS-CoV-2 quantification in wastewater: progress, challenges and prospects

Wastewater-Based Epidemiology (WBE) is widely used to monitor the progression of the current SARS-CoV-2 pandemic at local levels. In this review, we address the different approaches to the steps needed for this surveillance: sampling wastewaters (WWs), concentrating the virus from the samples and quantifying them by qPCR, focusing on the main limitations of the methodologies used. Factors that can influence SARS-CoV-2 monitoring in WWs include: (i) physical parameters as temperature that can hamper the detection in warm seasons and tropical regions, (ii) sampling methodologies and timetables, being composite samples and Moore swabs the less variable and more sensitive approaches, (iii) virus concentration methodologies that need to be feasible and practicable in simpler laboratories and (iv) detection methodologies that should tend to use faster and cost-effective procedures. The efficiency of WW treatments and the use of WWs for SARS-CoV-2 variants detection are also addressed. Furthermore, we discuss the need for the development of common standardized protocols, although these must be versatile enough to comprise variations among target communities. WBE screening of risk populations will allow for the prediction of future outbreaks, thus alerting authorities to implement early action measurements.

Emergence of SARS-CoV-2 Alpha lineage and its correlation with quantitative wastewater-based epidemiology data

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) gave rise to an international public health emergency in 3 months after its emergence in Wuhan, China. Typically for an RNA virus, random mutations occur constantly leading to new lineages, incidental with a higher transmissibility. The highly infective alpha lineage, firstly discovered in the UK, led to elevated mortality and morbidity rates as a consequence of Covid-19, worldwide. Wastewater surveillance proved to be a powerful tool for early detection and subsequent monitoring of the dynamics of SARS-CoV-2 and its variants in a defined catchment. Using a combination of sequencing and RT-qPCR approaches, we investigated the total SARS-CoV-2 concentration and the emergence of the alpha lineage in wastewater samples in Vienna, Austria linking it to clinical data. Based on a non-linear regression model and occurrence of signature mutations, we conclude that the alpha variant was present in Vienna sewage samples already in December 2020, even one month before the first clinical case was officially confirmed and reported by the health authorities. This provides evidence that a well-designed wastewater monitoring approach can provide a fast snapshot and may detect the circulating lineages in wastewater weeks before they are detectable in the clinical samples. Furthermore, declining 14 days prevalence data with simultaneously increasing SARS-CoV-2 total concentration in wastewater indicate a different shedding behavior for the alpha variant. Overall, our results support wastewater surveillance to be a suitable approach to spot early circulating SARS-CoV-2 lineages based on whole genome sequencing and signature mutations analysis.

Factors influencing SARS-CoV-2 RNA concentrations in wastewater up to the sampling stage: A systematic review

Wastewater-based surveillance (WBS) for SARS-CoV-2 RNA is a promising complementary approach to monitor community viral circulation. A myriad of factors, however, can influence RNA concentrations in wastewater, impeding its epidemiological value. This article aims to provide an overview and discussion of factors up to the sampling stage that impact SARS-CoV-2 RNA concentration estimates in wastewater. To this end, a systematic review was performed in three databases (MEDLINE, Web of Science and Embase) and two preprint servers (MedRxiv and BioRxiv). Two authors independently screened and selected articles published between January 1, 2019 and May 4, 2021. A total of 22 eligible articles were included in this systematic review. The following factors up to sampling were identified to have an influence on SARS-CoV-2 RNA concentrations in wastewater and its interpretation: (i) shedding-related factors, including faecal shedding parameters (i.e. shedding pattern, recovery, rate, and load distribution), (ii) population size, (iii) in-sewer factors, including solid particles, organic load, travel time, flow rate, wastewater pH and temperature, and (iv) sampling strategy. In conclusion, factors influencing SARS-CoV-2 RNA concentration estimates in wastewater were identified and research gaps were discussed. The identification of these factors supports the need for further research on WBS for COVID-19.

Reduction and discharge of SARS-CoV-2 RNA in Chicago-area water reclamation plants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA is commonly excreted in the feces and urine of infected individuals and is, therefore, detected in wastewaters where infection is present in the surrounding population. Water reclamation plants (WRPs) that treat these wastewaters commonly discharge treated effluents into the surrounding environment, yet little is known about the removal or persistence of SARS-CoV-2 RNA through wastewater treatment systems and potential for eventual release into the environment. We collected 361 24-hour composite influent and effluent samples from seven WRPs in the Greater Chicago Area in Illinois. Samples were collected over a period of 21 weeks for three large WRPs (with design max flows of 1.89-2.32 billion gallons per day and serving a combined population of 4.62 million people) and 11 weeks for four smaller WRPs (with design max flows of 96.3-186 million gallons per day and serving a combined population of >0.5 million people). A total of two of the larger WRPs implemented seasonal disinfection (using UV light or chlorination/dechlorination) for 8 weeks of this sampling period. SARS-CoV-2 RNA was quantified in the influent and effluent samples by reverse-transcription quantitative PCR (RT-qPCR) of the N1 and N2 targets of the nucleocapsid (N) gene. Although SARS-CoV-2 RNA was regularly detected in influent and effluent from all WRPs, viral RNA concentrations in the effluent samples were considerably lower, with mean effluent: influent gene copy concentration ratios ranging from 1:160 to 1:2.95 between WRPs. Samples collected while disinfection was active vs. inactive did not show any significant difference in the portion of RNA persisting through the treatment process (P > .05).

Persistence of SARS-CoV-2 RNA in wastewater after the end of the COVID-19 epidemics

Although the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely detected in wastewater in many countries to track the COVID-19 pandemic development, it is still a lack of clear understanding of the persistence of SARS-CoV-2 in raw sewage, especially after the end of the COVID-19 pandemic event. To fill this knowledge gap, this study conducted a field trial on the SARS-CoV-2 presence in various wastewater facilities after the end of the COVID-19 epidemics in Beijing. The result showed that the wastewater treatment facility is a large SARS-CoV-2 repository. The viral RNA was still present in hospital sewage for 15 days and was continually detected in municipal WWTPs for more than 19 days after the end of the local COVID-19 epidemics. The T90 values of the SARS-CoV-2 RNA in raw wastewater were 17.17-8.42 days in the wastewater at 4 ℃ and 26 ℃, respectively, meaning that the decay rates of low titer viruses in raw sewage were much faster. The results confirmed that the SARS-CoV-2 RNA could persist in wastewater for more than two weeks, especially at lower temperatures. The sewage systems would be a virus repository and prolong the presence of the residual SARS-CoV-2 RNA. The study could enhance further understanding of the presence of SARS-CoV-2 RNA in raw wastewater.

Coronaviruses and SARS-CoV-2 in sewerage and their removal: Step by step in wastewater treatment plants

The fate of Coronaviruses (CoVs) and in particular SARS-CoV-2 in wastewater treatment plants (WWTPs) has not been completely understood yet, but an adequate knowledge on the removal performances in WWTPs could help to prevent waterborne transmission of the virus that is still under debate. CoVs and SARS-CoV-2 are discharged from faeces into the sewer network and reach WWTPs within a few hours. This review presents the fate of SARS-CoV-2 and other CoVs in the primary, secondary and tertiary treatments of WWTPs as well as in sludge treatments. The viral loads decrease progressively along with the treatments from 20 to 3.0E+06 GU/L (Genomic Units/L) in the influent wastewater to concentrations below 2.50E+05 GU/L after secondary biological treatments and finally to negative concentrations (below detection limit) in disinfected effluents. Reduction of CoVs is due to (i) natural decay under unfavourable conditions (solids, microorganisms, temperature) for relatively long hydraulic retention times and (ii) processes of sedimentation, filtration, predation, adsorption, disinfection. In primary and secondary settling, due to the hydrophobic properties, a partial accumulation of CoVs may occur in the separated sludge. In secondary treatment (i.e. activated sludge) CoVs and SARS-CoV-2 loads can be reduced only by about one logarithm (∼90%). To enhance this removal, tertiary treatment with ultrafiltration (Membrane Bioreactors) and chemical disinfection or UV light is needed. CoVs and SARS-CoV-2 in the sludge (1.2E+04-4.6E+08 GU/L) can be inactivated significantly in the thermophilic digestion (55 °C), while mesophilic temperatures (33-37 °C) are not efficient. Additional studies are required to investigate the infectivity of SARS-CoV-2 in WWTPs, especially in view of increasing interest in wastewater reclamation and reuse.

Decay of four enteric pathogens and implications to wastewater-based epidemiology: Effects of temperature and wastewater dilutions

Measurement of pathogens in raw wastewater from a population within certain sewer catchments can provide quantitative information on public health status within the sampled urban area. This so-called wastewater-based epidemiology (WBE) approach has the potential of becoming a powerful tool to monitor pathogen circulation and support timely intervention during outbreaks. However, many WBE studies failed to account for the pathogen decay during wastewater transportation in back calculating the disease prevalence. Various sewer process factors, including water temperature and infiltration/inflow, can lead to the variation of pathogen decay rates. This paper firstly reviewed the effects of temperature and types of water, i.e., wastewater, freshwater, and saline water, on the decay of four selected enteric pathogens, i.e., Campylobacter, Salmonella, Norovirus, and Adenovirus. To elucidate the importance of the pathogen decay rates (measured by culture and molecular methods) to WBE, a sensitivity analysis was conducted on the back-calculation equation for infection prevalence with decay rates collected from published literature. It was found that WBE back-calculation is more sensitive to decay rates under the condition of high wastewater temperature (i.e., over 25 °C) or if wastewater is diluted by saline water (i.e., sewer infiltration or use of seawater as an alternative source of freshwater constituting around 1/3 household water demand in some cities). Stormwater dilution of domestic wastewater (i.e., sewer inflow might achieve 10 times volumetric dilution) was shown to play a role in increasing the sensitivity of WBE back-calculation to bacterial pathogens, but not viral pathogens. Hence, WBE back-calculation in real sewers should account for in-sewer decay of specific pathogen species under different wastewater temperatures and dilutions. Overall, this review contributes to a better understanding of pathogen decay in wastewater which can lead to improved accuracy of WBE back-calculation.

Human viruses lurking in the environment activated by excessive use of COVID-19 prevention supplies

Due to extensive COVID-19 prevention measures, millions of tons of chemicals penetrated into natural environment. Alterations of human viruses in the environment, the neglected perceiver of environmental fluctuations, remain obscure. To decipher the interaction between human viruses and COVID-19 related chemicals, environmental samples were collected on March 2020 from surroundings of designated hospitals and receivers of wastewater treatment plant effluent in Wuhan. The virus community and chemical concentration were respectively unveiled in virtue of virome and ultra-high-performance liquid chromatography-tandem mass spectrometry. The complex relationship between virus and chemical was ulteriorly elaborated by random forest model. As an indicator, environmental viruses were corroborated to sensitively reflect the ecological disturbance originated from pandemic prevention supplies. Chemicals especially trihalomethanes restrained the virus community diversity. Confronting this adverse scenario, Human gammaherpesvirus 4 and Orf virus with resistance to trihalomethanes flourished while replication potential of Macacine alphaherpesvirus 1 ascended under glucocorticoids stress. Consequently, human viruses lurking in the environment were actuated by COVID-19 prevention chemicals, which was a constant burden to public health in this ongoing pandemic. Besides, segments of SARS-CoV-2 RNA were detected near designated hospitals, suggesting environment as a missing link in the transmission route. This research innovatively underlined the human health risk of pandemic prevention supplies from the virus - environment interaction, appealing for monitoring of environmental viruses in long term.

Clean Water Production Enhancement through the Integration of Small-Scale Solar Stills with Solar Dish Concentrators (SDCs)—A Review

The conventional solar still, as a water treatment technique, has been reported to produce water at a low working temperature where various thermal resistance pathogens could survive in their distillate. In this work, the reviews of previous research on the quality of water produced by passive solar stills and their productivities in initial basin water temperatures were first presented and discussed. The next review discussed some recent studies on the performances of small-scale solar stills integrated with SDCs (with and without sun-tracking systems (STSs)) to observe the operating temperatures from early hours until the end of operations, daily water yield, and cost per liter. Based on these findings, it was revealed that SDCs with STSs indicated an instant increase in the absorber water temperature up to 70 °C at the starting point of the experiments in which this temperature range marked the unbearable survival of the pathogenic organisms and viruses, particularly the recent SARS-CoV-2. Furthermore, disinfection was also observed when the absorbers’ water temperature reached beyond the boiling point until the end of operations. This indicates the effectiveness of SDCs with STS in reflecting a large amount of sun’s rays and heat to the small-scale absorbers and providing higher operating absorbers temperatures compared to immobile SDCs. Daily productivities and costs per liter of the SDCs with STSs were found to be higher and lower than those of the other previous passive and active solar stills. Therefore, it is recommended that small-scale absorbers integrated with SDCs and STS can be used as a cost-effective and reliable method to produce hygienic pathogen-free water for the communities in remote and rural areas which encounter water scarcity and abundant annual bright sunshine hours.

Effect of Time and Temperature on SARS-CoV-2 in Municipal Wastewater Conveyance Systems

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.

Occurrence and decay of SARS-CoV-2 in community sewage drainage systems

The rapid spread of the coronavirus disease (COVID-19) pandemic in over 200 countries poses a substantial threat to human health. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes COVID-19, can be discharged with feces into the drainage system. However, a comprehensive understanding of the occurrence, presence, and potential transmission of SARS-CoV-2 in sewers, especially in community sewers, is still lacking. This study investigated the virus occurrence by viral nucleic acid testing in vent stacks, septic tanks, and the main sewer outlets of community where confirmed patients had lived during the outbreak of the epidemic in Wuhan, China. The results indicated that the risk of long-term emission of SARS-CoV-2 to the environment via vent stacks of buildings was low after confirmed patients were hospitalized. SARS-CoV-2 were mainly detected in the liquid phase, as opposed to being detected in aerosols, and its RNA in the sewage of septic tanks could be detected for only four days after confirmed patients were hospitalized. The surveillance of SARS-CoV-2 in sewage could be a sensitive indicator for the possible presence of asymptomatic patients in the community, though the viral concentration could be diluted more than 10 times, depending on the sampling site, as indicated by the Escherichia coli (E. coli) test. The comprehensive investigation of the community sewage drainage system is helpful to understand the occurrence characteristics of SARS-CoV-2 in sewage after excretion with feces and the feasibility of sewage surveillance for COVID-19 pandemic monitoring.

Investigation of mouse hepatitis virus strain A59 inactivation under both ambient and cold environments reveals the mechanisms of infectivity reduction following UVC exposure

The surface contamination of SARS-CoV-2 is becoming a potential source of virus transmission during the pandemic of COVID-19. Under the cold environment, the infection incidents would be more severe with the increase of virus survival time. Thus, the disinfection of contaminated surfaces in both ambient and cold environments is a critical measure to restrain the spread of the virus. In our study, it was demonstrated that the 254 nm ultraviolet-C (UVC) is an efficient method to inactivate a coronavirus, mouse hepatitis virus strain A59 (MHV-A59). The inactivation rate to MHV-A59 coronavirus was up to 99.99% when UVC doses were 2.90 and 14.0 mJ/cm² at room temperature (23 °C) and in cold environment (-20 °C), respectively. Further mechanistic study demonstrated that UVC could induce spike protein damage to partly impede virus attachment and genome penetration processes, which contributes to 12% loss of viral infectivity. Additionally, it can induce genome damage to significantly interrupt genome replication, protein synthesis, virus assembly and release processes, which takes up 88% contribution to viral inactivation. With these mechanistic understandings, it will greatly contribute to the prevention and control of the current SARS-CoV-2 transmissions in cold chains (low temperature-controlled product supply chains), public area such as airport, school, and warehouse.

Tracking the temporal variation of COVID-19 surges through wastewater-based epidemiology during the peak of the pandemic: A six-month long study in Charlotte, North Carolina

The global spread of SARS-CoV-2 has continued to be a serious concern after WHO declared the virus to be the causative agent of the coronavirus disease 2019 (COVID-19) a global pandemic. Monitoring of wastewater is a useful tool for assessing community prevalence given that fecal shedding of SARS-CoV-2 occurs in high concentrations by infected individuals, regardless of whether they are asymptomatic or symptomatic. Using tools that are part of wastewater-based epidemiology (WBE) approach, combined with molecular analyses, wastewater monitoring becomes a key piece of information used to assess trends and quantify the scale and dynamics of COVID-19 infection in a specific community, municipality, or area of service. This study investigates a six-month long SARS-CoV-2 RNA quantification in influent wastewater from four municipal wastewater treatment plants (WWTP) serving the Charlotte region of North Carolina (NC) using both RT-qPCR and RT-ddPCR platforms. Influent wastewater was analyzed for the nucleocapsid (N) genes N1 and N2. Both RT-qPCR and RT-ddPCR performed well for detection and quantification of SARS-CoV-2 using the N1 target, while for the N2 target RT-ddPCR was more sensitive. SARS-CoV-2 concentration ranged from 103 to 105 copies/L for all four plants. Both RT-qPCR and RT-ddPCR showed a significant positive correlation between SARS-CoV-2 concentrations and the 7-day rolling average of clinically reported COVID-19 cases when lagging 5 to 12 days (ρ = 0.52-0.92, p < 0.001-0.02). A major finding of this study is that RT-qPCR and RT-ddPCR generated SARS-CoV-2 data that was positively correlated (ρ = 0.569, p < 0.0001) and can be successfully used to monitor SARS-CoV-2 signals across the WWTP of different sizes and metropolitan service functions without significant anomalies.

Evaluating the Use of Alternative Normalization Approaches on SARS-CoV-2 Concentrations in Wastewater: Experiences from Two Catchments in Northern Sweden

The detection of SARS-CoV-2 RNA fragments in feces has paved the way for wastewater-based epidemiology to contribute to COVID-19 mitigation measures, with its use in a public health context still under development. As a way to facilitate data comparison, this paper explores the impact of using alternative normalization approaches (wastewater treatment plant (WWTP) flow, population size estimates (derived using total nitrogen (TN), total phosphorus (TP) and census data) and pepper mild mottle virus (PMMoV)) on the relationship between viral wastewater data and clinical case numbers. Influent wastewater samples were collected at two WWTPs in Luleå, northern Sweden, between January and March 2021. TN and TP were determined upon sample collection, with RNA analysis undertaken on samples after one freeze–thaw cycle. The strength of the correlation between normalization approaches and clinical cases differed between WWTPs (r ≤ 0.73 or r ≥ 0.78 at the larger WWTP and r ≤ 0.23 or r ≥ 0.43 at the smaller WWTP), indicating that the use of wastewater as an epidemiological tool is context-dependent. Depending on the normalization approach utilized, time-shifted analyses imply that wastewater data on SARS-CoV-2 RNA pre-dated a rise in clinical cases by 0–2 and 5–8 days, for the lager and smaller WWTPs, respectively. SARS-CoV-2 viral loads normalized to the population or PMMoV better reflect the number of clinical cases when comparing wastewater data between sewer catchments.

Ability of Essential Oil Vapours to Reduce Numbers of Culturable Aerosolised Coronavirus, Bacteria and Fungi

Transmission of pathogens present in the indoor air can occur through aerosols. This study evaluated the efficacy of an evaporated mix of essential oils to reduce the numbers of culturable aerosolized coronavirus, bacterium and fungus. The essential oil-containing gel was allowed to vaporize inside a glass chamber for 10 or 20 min. Aerosols of a surrogate of SARS-CoV-2, murine hepatitis coronavirus MHV-1, Escherichia coli or Aspergillus flavus spores were produced using a collision nebuliser and passed through the essential oil vapours, then collected on a six-stage Andersen sampler. The six-stages of the impact sampler capture aerosols in sizes ranging from 7 to 0.65 µm. The number of culturable microbes present in the aerosols collected in the different stages were enumerated and compared to the number of culturable microbes in control microbial aerosols that were not exposed to the evaporated essential oils. After 10 and 20 min evaporation, the essential oils reduced the numbers of culturable aerosolized coronavirus by 48% (log₁₀ reduction = 0.3; p = 0.002 vs. control) and 53% (log₁₀ reduction = 0.3; p = 0.001 vs. control), respectively. The essential oils vaporised for 10 min, reduced the number of viable E. coli by 51% (log₁₀ reduction = 0.3; p = 0.032 vs. control). The Aspergillus flavus spores were mostly observed in the larger aerosols (7.00 µm to 2.10 µm) and the essential oils vaporised for 10 min reduced the number of viable spores by 72% (log₁₀ reduction = 0.6; p = 0.008 vs. control). The vapours produced by a gel containing naturally occurring essential oils were able to significantly reduce the viable numbers of aerosolized coronavirus, bacteria and fungal spores. The antimicrobial gel containing the essential oils may be able to reduce aerosol transmission of microbes when used in domestic and workplace settings.

Metal-Catalyzed Hydrolysis of RNA in Aqueous Environments

The stability of RNA in aqueous systems is critical for multiple environmental applications including evaluating the environmental fate of RNA interference pesticides and interpreting viral genetic marker abundance for wastewater-based epidemiology. In addition to biological processes, abiotic reactions may also contribute to RNA loss. In particular, some metals are known to dramatically accelerate rates of RNA hydrolysis under certain conditions (i.e., 37 °C or higher temperatures, 0.15-100 mM metal concentrations). In this study, we investigated the extent to which metals catalyze RNA hydrolysis under environmentally relevant conditions. At ambient temperature, neutral pH, and ∼10 μM metal concentrations, we determined that metals that are stronger Lewis acids (i.e., lead, copper) catalyzed single-stranded (ss)RNA, whereas metals that are weaker Lewis acids (i.e., zinc, nickel) did not. In contrast, double-stranded (ds)RNA resisted hydrolysis by all metals. While lead and copper catalyzed ssRNA hydrolysis at ambient temperature and neutral pH values, other factors such as lowering the solution pH and including inorganic and organic ligands reduced the rates of these reactions. Considering these factors along with sub-micromolar metal concentrations typical of environmental systems, we determined that both ssRNA and dsRNA are unlikely to undergo significant metal-catalyzed hydrolysis in most environmental aqueous systems.

SARS-CoV-2 RNA surveillance in large to small centralized wastewater treatment plants preceding the third COVID-19 resurgence in Bangkok, Thailand

Wastewater surveillance for SARS-CoV-2 RNA has been a successful indicator of COVID-19 outbreaks in populations prior to clinical testing. However, this has been mostly conducted in high-income countries, which means there is a dearth of performance investigations in low- and middle-income countries with different socio-economic settings. This study evaluated the applicability of SARS-CoV-2 RNA monitoring in wastewater (n = 132) to inform COVID-19 infection in the city of Bangkok, Thailand using CDC N1 and N2 RT-qPCR assays. Wastewater influents (n = 112) and effluents (n = 20) were collected from 19 centralized wastewater treatment plants (WWTPs) comprising four large, four medium, and 11 small WWTPs during seven sampling events from January to April 2021 prior to the third COVID-19 resurgence that was officially declared in April 2021. The CDC N1 assay showed higher detection rates and mostly lower Ct values than the CDC N2. SARS-CoV-2 RNA was first detected at the first event when new reported cases were low. Increased positive detection rates preceded an increase in the number of newly reported cases and increased over time with the reported infection incidence. Wastewater surveillance (both positive rates and viral loads) showed strongest correlation with daily new COVID-19 cases at 22-24 days lag (Spearman's Rho = 0.85-1.00). Large WWTPs (serving 432,000-580,000 of the population) exhibited similar trends of viral loads and new cases to those from all 19 WWTPs, emphasizing that routine monitoring of the four large WWTPs could provide sufficient information for the city-scale dynamics. Higher sampling frequency at fewer sites, i.e., at the four representative WWTPs, is therefore suggested especially during the subsiding period of the outbreak to indicate the prevalence of COVID-19 infection, acting as an early warning of COVID-19 resurgence.

Evaluation of multiple analytical methods for SARS-CoV-2 surveillance in wastewater samples

In this study, 14 virus concentration protocols based on centrifugation, filtration, polyethylene glycol (PEG) precipitation and ultrafiltration were tested for their efficacy for the quantification of SARS-CoV-2 in wastewater samples. These protocols were paired with four RNA extraction procedures resulting in a combination of 50 unique approaches. Bovine respiratory syncytial virus (BRSV) was used as a process control and seeded in each wastewater sample subjected to all 50 protocols. The recovery of BRSV obtained through the application of 50 unique approaches ranged from <0.03 to 64.7% (±1.6%). Combination of centrifugation as the solid removal step, ultrafiltration (Amicon-UF-15; 100 kDa cut-off; protocol 9) as the primary virus concentration method, and Zymo Quick-RNA extraction kit provided the highest BRSV recovery (64.7 ± 1.6%). To determine the impact of prolonged storage of large wastewater sample volume (900 mL) at -20 °C on enveloped virus decay, the BRSV seeded wastewaters samples were stored at -20 °C up to 110 days and analyzed using the most efficient concentration (protocol 9) and extraction (Zymo Quick-RNA kit) methods. BRSV RNA followed a first-order decay rate (k = 0.04/h with r2 = 0.99) in wastewater. Finally, 21 wastewater influent samples from five wastewater treatment plants (WWTPs) in southern Maryland, USA were analyzed between May to August 2020 to determine SARS-CoV-2 RNA concentrations. SARS-CoV-2 RNA was quantifiable in 17/21 (81%) of the influent wastewater samples with concentration ranging from 1.10 (±0.10) × 104 to 2.38 (±0.16) × 106 gene copies/L. Among the RT-qPCR assays tested, US CDC N1 assay was the most sensitive followed by US CDC N2, E_Sarbeco, and RdRp assays. Data presented in this study may enhance our understanding on the effective concentration and extraction of SARS-CoV-2 from wastewater.

The Detection of SARS-CoV-2 in the Environment: Lessons from Wastewater

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.

SARS-CoV-2 wastewater surveillance in Germany: Long-term RT-digital droplet PCR monitoring, suitability of primer/probe combinations and biomarker stability

In recent months, wastewater-based epidemiology (WBE) has been shown to be an important tool for early detection of SARS-CoV-2 circulation in the population. In this study, a detection methodology for SARS-CoV-2 RNA (wildtype and variants of concern) in wastewater was developed based on the detection of different target genes (E and ORF1ab) by polyethylene glycol (PEG) precipitation and digital droplet PCR. This methodology was used to determine the SARS-CoV-2 concentration and the proportion of N501Y mutation in raw sewage of the wastewater treatment plant of the city of Karlsruhe in south-western Germany over a period of 1 year (June 2020 to July 2021). Comparison of SARS-CoV-2 concentrations with reported COVID-19 cases in the catchment area showed a significant correlation. As the clinical SARS-CoV-2 official case report chain takes time, viral RNA titre trends appeared more than 12 days earlier than clinical data, demonstrating the potential of wastewater-based epidemiology as an early warning system. Parallel PCR analysis using seven primer and probe systems revealed similar gene copy numbers with E, ORF, RdRP2 and NSP9 assays. RdPP1 and NSP3 generally resulted in lower copy numbers, and in particular for N1 there was low correlation with the other assays. The occurrence of the N501Y mutation in the wastewater of Karlsruhe was consistent with the occurrence of the alpha-variant (B.1.1.7) in the corresponding individual clinical tests. In batch experiments SARS-CoV-2 RNA was stable for several days under anaerobic conditions, but the copy numbers decreased rapidly in the presence of dissolved oxygen. Overall, this study shows that wastewater-based epidemiology is a sensitive and robust approach to detect trends in the spread of SARS-CoV-2 at an early stage, contributing to successful pandemic management.

Understanding and managing uncertainty and variability for wastewater monitoring beyond the pandemic: Lessons learned from the United Kingdom national COVID-19 surveillance programmes

The COVID-19 pandemic has put unprecedented pressure on public health resources around the world. From adversity, opportunities have arisen to measure the state and dynamics of human disease at a scale not seen before. In the United Kingdom, the evidence that wastewater could be used to monitor the SARS-CoV-2 virus prompted the development of National wastewater surveillance programmes. The scale and pace of this work has proven to be unique in monitoring of virus dynamics at a national level, demonstrating the importance of wastewater-based epidemiology (WBE) for public health protection. Beyond COVID-19, it can provide additional value for monitoring and informing on a range of biological and chemical markers of human health. A discussion of measurement uncertainty associated with surveillance of wastewater, focusing on lessons-learned from the UK programmes monitoring COVID-19 is presented, showing that sources of uncertainty impacting measurement quality and interpretation of data for public health decision-making, are varied and complex. While some factors remain poorly understood, we present approaches taken by the UK programmes to manage and mitigate the more tractable sources of uncertainty. This work provides a platform to integrate uncertainty management into WBE activities as part of global One Health initiatives beyond the pandemic.

SARS-CoV-2 wastewater surveillance in Germany: Long-term RT-digital droplet PCR monitoring, suitability of primer/probe combinations and biomarker stability

In recent months, wastewater-based epidemiology (WBE) has been shown to be an important tool for early detection of SARS-CoV-2 circulation in the population. In this study, a detection methodology for SARS-CoV-2 RNA (wildtype and variants of concern) in wastewater was developed based on the detection of different target genes (E and ORF1ab) by polyethylene glycol (PEG) precipitation and digital droplet PCR. This methodology was used to determine the SARS-CoV-2 concentration and the proportion of N501Y mutation in raw sewage of the wastewater treatment plant of the city of Karlsruhe in south-western Germany over a period of 1 year (June 2020 to July 2021). Comparison of SARS-CoV-2 concentrations with reported COVID-19 cases in the catchment area showed a significant correlation. As the clinical SARS-CoV-2 official case report chain takes time, viral RNA titre trends appeared more than 12 days earlier than clinical data, demonstrating the potential of wastewater-based epidemiology as an early warning system. Parallel PCR analysis using seven primer and probe systems revealed similar gene copy numbers with E, ORF, RdRP2 and NSP9 assays. RdPP1 and NSP3 generally resulted in lower copy numbers, and in particular for N1 there was low correlation with the other assays. The occurrence of the N501Y mutation in the wastewater of Karlsruhe was consistent with the occurrence of the alpha-variant (B.1.1.7) in the corresponding individual clinical tests. In batch experiments SARS-CoV-2 RNA was stable for several days under anaerobic conditions, but the copy numbers decreased rapidly in the presence of dissolved oxygen. Overall, this study shows that wastewater-based epidemiology is a sensitive and robust approach to detect trends in the spread of SARS-CoV-2 at an early stage, contributing to successful pandemic management.

Wastewater surveillance of SARS-CoV-2 in Austria: development, implementation, and operation of the Tyrolean wastewater monitoring program

Wastewater-based epidemiology (WBE) is an effective approach for tracking information on spatial distribution and temporal trends of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the community level. Herein, the development, implementation, and operation of the wastewater monitoring program serving Tyrol - a federal province of Austria - are described. The development of this program was initiated by Tyrolean health authorities at the end of the first phase of the Coronavirus disease 2019 (COVID-19) pandemic (May 2020). In close co-operation with the water sector and academic institutions, efficient and effective workflows and processes for wastewater surveillance were established. The monitoring program went into operation in November 2020. By the end of July 2021, a total of 5,270 wastewater influent samples collected at 43 sites were analyzed. The monitoring program provided valuable insights into the development of the pandemic situation in Tyrol and fulfilled several tasks that are of importance in different phases of the pandemic. It represented an early-warning system, provided independent confirmation of temporal trends in COVID-19 prevalence, enabled the assessment of the effectiveness of measures, alerted about bursts of disease activity, and provided evidence for the absence of COVID-19. These findings underline the importance of establishing national wastewater monitoring programs as a complementary source of information for efficient and effective pandemic management.

SARS-CoV-2 RNA in urban wastewater samples to monitor the COVID-19 pandemic in Lombardy, Italy (March-June 2020)

Wastewater-based viral surveillance was proposed as a promising approach to monitor the circulation of SARS-CoV-2 in the general population. The aim of this study was to develop an analytical method to detect SARS-CoV-2 RNA in urban wastewater, and apply it to follow the trends of epidemic in the framework of a surveillance network in the Lombardy region (Northern Italy). This area was the first hotspot of COVID-19 in Europe and was severely affected. Composite 24 h samples were collected weekly in eight cities from end-March to mid-June 2020 (first peak of the pandemic). The method developed and optimized, involved virus concentration using PEG centrifugation, and one-step real-time RT-PCR for analysis. SARS-CoV-2 RNA was identified in 65 (61%) out of 107 samples, and the viral concentrations (up to 2.1 E + 05 copies/L) were highest in March-April. By mid-June, wastewater samples tested negative in all the cities corresponding to the very low number of cases recorded in the same period. Viral loads were calculated considering the wastewater daily flow rate and the population served by each wastewater treatment plant, and were used for inter- city comparison. The highest viral loads were found in Brembate, Ranica and Lodi corresponding to the hotspots of the first peak of pandemic. The pattern of decrease of SARS-CoV-2 in wastewater was closely comparable to the decline of active COVID-19 cases in the population, reflecting the effect of lock-down. This study tested wastewater surveillance of SARS-CoV-2 to follow the pandemic trends in one of most affected areas worldwide, demonstrating that it can integrate ongoing virological surveillance of COVID-19, providing information from both symptomatic and asymptomatic individuals, and monitoring the effect of health interventions.

Associations between SARS-CoV-2 RNA concentrations in wastewater and COVID-19 rates in days after sampling in small urban areas of Seville: A time series study

Wastewater surveillance systems for SARS-CoV-2 can be used to support public health decisions, complementary to clinical surveillance. We examined the lead-lag associations between SARS-CoV-2 RNA copies in wastewater and COVID-19 rates in relatively small urban areas of Seville, adjusting for internal mobility, temperature, and wastewater-related variables. The association COVID-19 rates-RNA copies were statistically significant from three to 27 days after sampling. Temperature is a confounding factor for both viral RNA counts and mobility. The model that best fitted data used cases six days after sampling. A logarithmic unit increase in viral RNA count in wastewater was associated with a 26.9% increase in COVID-19 rate per 100,000 inhabitants (95% CI: 13.1-42.4%), within the urban area, six days later. Surveillance system for SARS-CoV-2 in wastewater has great potential for public health. Knowing the specific association between SARS-CoV-2 RNA copies in wastewater and COVID-19 daily rates may help to improve its performance.

Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance

Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.

Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance

Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.

Activation of TCA cycle restrains virus-metabolic hijacking and viral replication in mouse hepatitis virus-infected cells

Background

One of coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused coronavirus disease 2019 (COVID-19) pandemic and threatened worldwide. However, therapy for COVID-19 has rarely been proven to possess specific efficacy. As the virus relies on host metabolism for its survival, several studies have reported metabolic intervention by SARS-CoV-2.

Results

We investigated the coronavirus-metabolic hijacking using mouse hepatitis virus (MHV) as a surrogate for SARS-CoV-2. Based on the altered host metabolism by MHV infection, an increase of glycolysis with low mitochondrial metabolism, we tried to investigate possible therapeutic molecules which increase the TCA cycle. Endogenous metabolites and metabolic regulators were introduced to restrain viral replication by metabolic intervention. We observed that cells deprived of cellular energy nutrition with low glycolysis strongly suppress viral replication. Furthermore, viral replication was also significantly suppressed by electron transport chain inhibitors which exhaust cellular energy. Apart from glycolysis and ETC, pyruvate supplement suppressed viral replication by the TCA cycle induction. As the non-glucose metabolite, fatty acids supplement decreased viral replication via the TCA cycle. Additionally, as a highly possible therapeutic metabolite, nicotinamide riboside (NR) supplement, which activates the TCA cycle by supplying NAD+, substantially suppressed viral replication.

Conclusions

This study suggests that metabolite-mediated TCA cycle activation suppresses replication of coronavirus and suggests that NR might play a role as a novel therapeutic metabolite for coronavirus.

SARS-CoV-2 wastewater surveillance data can predict hospitalizations and ICU admissions

We measured SARS-CoV-2 RNA load in raw wastewater in Attica, Greece, by RT-qPCR for the environmental surveillance of COVID-19 for 6 months. The lag between RNA load and pandemic indicators (COVID-19 hospital and intensive care unit (ICU) admissions) was calculated using a grid search. Our results showed that RNA load in raw wastewater is a leading indicator of positive COVID-19 cases, new hospitalization and admission into ICUs by 5, 8 and 9 days, respectively. Modelling techniques based on distributed/fixed lag modelling, linear regression and artificial neural networks were utilized to build relationships between SARS-CoV-2 RNA load in wastewater and pandemic health indicators. SARS-CoV-2 mutation analysis in wastewater during the third pandemic wave revealed that the alpha-variant was dominant. Our results demonstrate that clinical and environmental surveillance data can be combined to create robust models to study the on-going COVID-19 infection dynamics and provide an early warning for increased hospital admissions.