Estimating virus occurrence using Bayesian modeling in multiple drinking water systems of the United States

Water, Water Everywhere, but Every Drop Unique: Challenges in the Science to Understand the Role of Contaminants of Emerging Concern in the Management of Drinking Water Supplies

The protection and management of water resources continues to be challenged by multiple and ongoing factors such as shifts in demographic, social, economic, and public health requirements. Physical limitations placed on access to potable supplies include natural and human-caused factors such as aquifer depletion, aging infrastructure, saltwater intrusion, floods, and drought. These factors, although varying in magnitude, spatial extent, and timing, can exacerbate the potential for contaminants of concern (CECs) to be present in sources of drinking water, infrastructure, premise plumbing and associated tap water. This monograph examines how current and emerging scientific efforts and technologies increase our understanding of the range of CECs and drinking water issues facing current and future populations. It is not intended to be read in one sitting, but is instead a starting point for scientists wanting to learn more about the issues surrounding CECs. This text discusses the topical evolution CECs over time (Section 1), improvements in measuring chemical and microbial CECs, through both analysis of concentration and toxicity (Section 2) and modeling CEC exposure and fate (Section 3), forms of treatment effective at removing chemical and microbial CECs (Section 4), and potential for human health impacts from exposure to CECs (Section 5). The paper concludes with how changes to water quantity, both scarcity and surpluses, could affect water quality (Section 6). Taken together, these sections document the past 25 years of CEC research and the regulatory response to these contaminants, the current work to identify and monitor CECs and mitigate exposure, and the challenges facing the future.

Occurrence of human pathogenic viruses in drinking water and in its sources: A review

Since many waterborne diseases are caused by human pathogenic viruses, virus monitoring of drinking water (DW) and DW sources is crucial for public health. Therefore, the aim of this review was to describe the occurrence of human pathogenic viruses in DW and DW sources; the occurrence of two viruses proposed as novel indicators of human faecal contamination (Pepper mild mottle virus and Tobacco mosaic virus) was also reported. This research was focused on articles that assessed viral occurrence using molecular methods in the surface water used for DW production (SW-D), groundwater used for DW production (GW-D), DW and bottled-DW (BW). A total of 1544 studies published in the last 10 years were analysed, and 79 were ultimately included. In considering the detection methods, filtration is the most common concentration technique, while quantitative polymerase chain reaction is the most common quantification technique. Regarding virus occurrence in SW-D, GW-D, and DW, high percentages of positive samples were reported for adenovirus, polyomavirus and Pepper mild mottle virus. Viral genomes were frequently detected in SW-D and rarely in GW-D, suggesting that GW-D may be a safe DW source. Viral genomes were also detected in DW, posing a possible threat to human health. The lowest percentages of positive samples were found in Europe, while the highest were found in Asia and South America. Only three articles assessed viral occurrence in BW. This review highlights the lack of method standardization and the need for legislation updates.

Surfactant Treatment for Efficient Gene Detection of Enteric Viruses and Indicators in Surface Water Concentrated by Ultrafiltration

The hollow fiber ultrafiltration (HFUF)-based microbial concentration method is widely applied for monitoring pathogenic viruses and microbial indicators in environmental water samples. However, the HFUF-based method can co-concentrate substances that interfere with downstream molecular processes-nucleic acid extraction, reverse transcription (RT), and PCR. These inhibitory substances are assumed to be hydrophobic and, therefore, expected to be excluded by a simple surfactant treatment before the silica membrane-based RNA extraction process. In this study, the efficacy and limitations of the sodium deoxycholate (SD) treatment were assessed by quantifying a process control and indigenous viruses using 42 surface water samples concentrated with HFUF. With some exceptions, which tended to be seen in samples with high turbidity (> 4.0 NTU), virus recovery by the ultrafiltration method was sufficiently high (> 10%). RNA extraction-RT-quantitative PCR (RT-qPCR) efficiency of the process control was insufficient (10%) for 30 of the 42 HFUF concentrates without any pretreatments, but it was markedly improved for 21 of the 30 inhibitory concentrates by the SD treatment. Detection rates of indigenous viruses were also improved and no substantial loss of viral RNA was observed. The SD treatment was particularly effective in mitigating RT-qPCR inhibition, although it was not effective in improving RNA extraction efficiency. The methodology is simple and easily applied. These findings indicate that SD treatment can be a good alternative to sample dilution, which is widely applied to mitigate the effect of RT-qPCR inhibition, and can be compatible with other countermeasures.

Inactivation and genome damage of rotavirus and a human norovirus surrogate by monochloramine treatment and sequential application with UV

The inactivation efficacy by monochloramine for disinfecting gastroenteritis-causing rotaviruses (RV) and Tulane viruses (TV), a surrogate for noroviruses, were evaluated in this study. In addition, the strategies for improving the disinfection efficiency of monochloramine by raising the temperature and sequentially implementing UV irradiation were investigated. The results showed that monochloramine was more effective in the inactivation of TV than RV. Additionally, the inactivation rate constants of RV and TV by monochloramine at 35 °C were improved approximately by 46% and 100%, respectively, compared to those at 25 °C. Moreover, applying UV irradiation before monochloramine enhanced the inactivation efficacy of RV and TV by 63% and 72% compared to monochloramine alone (UV: 6 mJ/cm², NH₂Cl: 60 ppm × min). Furthermore, the synergistic effect was observed during the RV inactivation by the sequential process. Especially, higher than 0.5 log₁₀ reductions of RV VP1 genome contributed to the synergistic effect in sequential treatment, while less than 0.1 log₁₀ reductions of RV VP1 genome were observed during UV alone (13 mJ/cm²) or monochloramine alone (94 ppm × min). The genome damage might be the primary mechanism of generating synergy in sequential treatment for the inactivation of RV. By comparison, no synergistic effect was discovered for the inactivation of TV due to high susceptibility to monochloramine and UV. The findings on the inactivation efficacy and mechanism for improvement will contribute to a wide application of monochloramine for virus inactivation in water treatment and distribution systems.

Evaluation of reduction efficiencies of pepper mild mottle virus and human enteric viruses in full-scale drinking water treatment plants employing coagulation-sedimentation-rapid sand filtration or coagulation-microfiltration

Here, we evaluated the reduction efficiencies of indigenous pepper mild mottle virus (PMMoV, a potential surrogate for human enteric viruses to assess virus removal by coagulation-sedimentation-rapid sand filtration [CS-RSF] and coagulation-microfiltration [C-MF]) and representative human enteric viruses in four full-scale drinking water treatment plants that use CS-RSF (Plants A and B) or C-MF (Plants C and D). First, we developed a virus concentration method by using an electropositive filter and a tangential-flow ultrafiltration membrane to effectively concentrate and recover PMMoV from large volumes of water: the recovery rates of PMMoV were 100% when 100-L samples of PMMoV-spiked dechlorinated tap water were concentrated to 20 mL; even when spiked water volume was 2000 L, recovery rates of >30% were maintained. The concentrations of indigenous PMMoV in raw and treated water samples determined by using this method were always above the quantification limit of the real-time polymerase chain reaction assay. We therefore were able to determine its reduction ratios: 0.9-2.7-log10 in full-scale CS-RSF and 0.7-2.9-log10 in full-scale C-MF. The PMMoV reduction ratios in C-MF at Plant C (1.0 ± 0.3-log10) were lower than those in CS-RSF at Plants A (1.7 ± 0.5-log10) and B (1.4 ± 0.7-log10), despite the higher ability of MF for particle separation in comparison with RSF owing to the small pore size in MF. Lab-scale virus-spiking C-MF experiments that mimicked full-scale C-MF revealed that a low dosage of coagulant (polyaluminum chloride [PACl]) applied in C-MF, which is determined mainly from the viewpoint of preventing membrane fouling, probably led to the low reduction ratios of PMMoV in C-MF. This implies that high virus reduction ratios (>4-log10) achieved in previous lab-scale virus-spiking C-MF studies are not necessarily achieved in full-scale C-MF. The PMMoV reduction ratios in C-MF at Plant D (2.2 ± 0.6-log10) were higher than those at Plant C, despite similar coagulant dosages. In lab-scale C-MF, the PMMoV reduction ratios increased from 1-log10 (with PACl [basicity 1.5], as at Plant C) to 2-4-log10 (with high-basicity PACl [basicity 2.1], as at Plant D), suggesting that the use of high-basicity PACl probably resulted in higher reduction ratios of PMMoV at Plant D than at Plant C. Finally, we compared the reduction ratios of indigenous PMMoV and representative human enteric viruses in full-scale CS-RSF and C-MF. At Plant D, the concentrations of human norovirus genogroup II (HuNoV GII) in raw water were sometimes above the quantification limit; however, whether its reduction ratios in C-MF were higher than those of PMMoV could not be judged since reduction ratios were >1.4-log10 for HuNoV GII and 2.3-2.9-log10 for PMMoV. At Plant B, the concentrations of enteroviruses (EVs) and HuNoV GII in raw water were above the quantification limit on one occasion, and the reduction ratios of EVs (>1.2-log10) and HuNoV GII (>1.5-log10) in CS-RSF were higher than that of PMMoV (0.9-log10). This finding supports the usefulness of PMMoV as a potential surrogate for human enteric viruses to assess virus removal by CS-RSF.

Broad virus inactivation using inorganic micro/nano-particulate materials

Inorganic materials can provide a set of tools to decontaminate solid, liquid or air containing viral particles. The use of disinfectants can be limited or not practical in scenarios where continuous cleaning is not feasible. Physicochemical differences between viruses raise the need for effective formulations for all kind of viruses. In the present work we describe two types of antimicrobial inorganic materials: i) a novel soda-lime glass (G3), and ii) kaolin containing metals nanoparticles (Ag or CuO), as materials to disable virus infectivity. Strong antiviral properties can be observed in G3 glass, and kaolin-containing nanoparticle materials showing a reduction of viral infectivity close to 99%. in the first 10 ​min of contact of vesicular stomatitis virus (VSV). A potent virucidal activity is also present in G3 and kaolin containing Ag or CuO nanoparticles against all kinds of viruses tested, reducing more than 99% the amount of HSV-1, Adenovirus, VSV, Influenza virus and SARS-CoV-2 exposed to them. Virucidal properties could be explained by a direct interaction of materials with viruses as well as inactivation by the presence of virucidal elements in the material lixiviates. Kaolin-based materials guarantee a controlled release of active nanoparticles with antiviral activity. Current coronavirus crisis highlights the need for new strategies to remove viruses from contaminated areas. We propose these low-cost inorganic materials as useful disinfecting antivirals in the actual or future pandemic threats.

A Bayesian inference approach to quantify average pathogen loads in farmyard manure and slurry using open-source Irish datasets

Farm-to-fork quantitative microbial risk assessments (QMRA) typically start with a preliminary estimate of initial concentration (C_initial) of microorganism loading at farm level, consisting of an initial estimate of prevalence (P) and the resulting pathogen levels in animal faeces. An average estimation of the initial concentration of pathogens can be achieved by combining P estimates in animal populations and the levels of pathogens in colonised animals' faeces and resulting cumulative levels in herd farmyard manure and slurry (FYM&S). In the present study, 14 years of data were collated and assessed using a Bayesian inference loop to assess the likely P of pathogens. In this regard, historical and current survey data exists on P estimates for a number of pathogens, including Cryptosporidium parvum, Mycobacterium avium subspecies paratuberculosis (MAP), Salmonella spp., Clostridium spp., Campylobacter spp., pathogenic E. coli, and Listeria monocytogenes in several species (cattle, pigs, and sheep) in Ireland. The results revealed that Cryptosporidium spp. has potentially the highest mean P (P_mean) (25.93%), followed by MAP (15.68%) and Campylobacter spp. (8.80%) for cattle. The P_mean of E. coli is highest (7.42%) in pigs, while the P_mean of Clostridium spp. in sheep was estimated to be 7.94%. C_initial for Cryptosporidium spp., MAP., Salmonella spp., Clostridium spp., and Campylobacter spp. in cattle faeces were derived with an average of 2.69, 4.38, 4.24, 3.46, and 3.84 log₁₀ MPN g ^-1, respectively. Average C_initial of Cryptosporidium spp., Salmonella spp., Clostridium spp., and E. coli in pig slurry was estimated as 1.27, 3.12, 3.02, and 4.48 log₁₀ MPN g ^-1, respectively. It was only possible to calculate the average C_initial of Listeria monocytogenes in sheep manure as 1.86 log₁₀ MPN g ^-1. This study creates a basis for future farm-to-fork risk assessment models to base initial pathogen loading values for animal faeces and enhance risk assessment efforts.

Demonstrating the reduction of enteric viruses by drinking water treatment during snowmelt episodes in urban areas

This study investigates short-term fluctuations in virus concentrations in source water and their removal by full-scale drinking water treatment processes under different source water conditions. Transient peaks in raw water faecal contamination were identified using in situ online β-d-glucuronidase activity monitoring at two urban drinking water treatment plants. During these peaks, sequential grab samples were collected at the source and throughout the treatment train to evaluate concentrations of rotavirus, adenovirus, norovirus, enterovirus, JC virus, reovirus, astrovirus and sapovirus by reverse transcription and real-time quantitative PCR. Virus infectivity was assessed through viral culture by measurement of cytopathic effect and integrated cell culture qPCR. Virus concentrations increased by approximately 0.5-log during two snowmelt/rainfall episodes and approximately 1.0-log following a planned wastewater discharge upstream of the drinking water intake and during a β-d-glucuronidase activity peak in dry weather conditions. Increases in the removal of adenovirus and rotavirus by coagulation/flocculation processes were observed during peak virus concentrations in source water, suggesting that these processes do not operate under steady-state conditions but dynamic conditions in response to source water conditions. Rotavirus and enterovirus detected in raw and treated water samples were predominantly negative in viral culture. At one site, infectious adenoviruses were detected in raw water and water treated by a combination of ballasted clarification, ozonation, GAC filtration, and UV disinfection operated at a dose of 40 mJ cm^-2. The proposed sampling strategy can inform the understanding of the dynamics associated with virus concentrations at drinking water treatment plants susceptible to de facto wastewater reuse.

Suitability of pepper mild mottle virus as a human enteric virus surrogate for assessing the efficacy of thermal or free-chlorine disinfection processes by using infectivity assays and enhanced viability PCR

Evaluating the efficacy of disinfection processes to inactivate human enteric viruses is important for the prevention and control of waterborne diseases caused by exposure to those viruses via drinking water. Here, we evaluated the inactivation of two representative human enteric viruses (adenovirus type 40 [AdV] and coxsackievirus B5 [CV]) by thermal or free-chlorine disinfection. In addition, we compared the infectivity reduction ratio of a plant virus (pepper mild mottle virus [PMMoV], a recently proposed novel surrogate for human enteric viruses for the assessment of virus removal by coagulation‒rapid sand filtration and membrane filtration) with that of the two human enteric viruses to assess the suitability of PMMoV as a human enteric virus surrogate for use in thermal and free-chlorine disinfection processes. Finally, we examined whether conventional or enhanced viability polymerase chain reaction (PCR) analysis using propidium monoazide (PMA) or improved PMA (PMAxx) with or without an enhancer could be used as alternatives to infectivity assays (i.e., plaque-forming unit method for AdV and CV; local lesion count assay for PMMoV) for evaluating virus inactivation by disinfection processes. We found that PMMoV was more resistant to heat treatment than AdV and CV, suggesting that PMMoV is a potential surrogate for these two enteric viruses with regard to thermal disinfection processes. However, PMMoV was much more resistant to chlorine treatment compared with AdV and CV (which is chlorine-resistant) (CT value for 4-log₁₀ inactivation: PMMoV, 84.5 mg-Cl₂·min/L; CV, 1.15-1.19 mg-Cl₂·min/L), suggesting that PMMoV is not useful as a surrogate for these enteric viruses with regard to free-chlorine disinfection processes. For thermal disinfection, the magnitude of the signal reduction observed with PMAxx-Enhancer-PCR was comparable with the magnitude of reduction in infectivity, indicating that PMAxx-Enhancer-PCR is a potential alternative to infectivity assay. However, for free-chlorine disinfection, the magnitude of the signal reduction observed with PMAxx-Enhancer-PCR was smaller than the magnitude of the reduction in infectivity, indicating that PMAxx-Enhancer-PCR underestimated the efficacy of virus inactivation (i.e., overestimated the infectious virus concentration) by chlorine treatment. Nevertheless, among the PCR approaches examined in the present study (PCR alone, PMA-PCR or PMAxx-PCR either with or without enhancer), PMAxx-Enhancer-PCR provided the most accurate assessment of the efficacy of virus inactivation by thermal or free chlorine disinfection processes.

Sequential treatment using a hydrophobic resin and gel filtration to improve viral gene quantification from highly complex environmental concentrates

Assays based on the polymerase chain reaction (PCR) are widely applied to quantify enteric viruses in aquatic environments to study their fates and potential infection risks. However, inhibitory substances enriched by virus concentration processes can result in inaccurate quantification. This study aimed to find a method for improving virus quantification by mitigating the effects of inhibitory environmental concentrates, using previous knowledge of the properties of the inhibitory substances. Performances of anion exchange resins, gel filtration, and a hydrophobic resin (DAX-8) were comparatively evaluated using poliovirus and its extracted RNA spiked into humic acid solutions. These solutions served as good representatives of the inhibitory environmental concentrates. A sequential treatment using DAX-8 resin and gel filtration produced the most favorable results, i.e., low virus losses that were stable and a reduced inhibitory effect. Furthermore, the sequential treatment was applied to another set of 15 environmental concentrates. Without the sequential treatment, serious underestimation (>4.0 log₁₀ to 1.1 log₁₀) of a molecular process control (murine norovirus) was measured for eight samples. With the treatment, the control was detected with <1.0 log₁₀ underestimation for all samples. The treatment improved the quantification of seven types of indigenous viruses. In summary, the sequential treatment is effective in improving the viral quantification in various of environmental concentrates.

Agglomeration of Viruses by Cationic Lignin Particles for Facilitated Water Purification

Virus contamination of water is a threat to human health in many countries. Current solutions for inactivation of viruses mainly rely on environmentally burdensome chemical oxidation or energy-intensive ultraviolet irradiation, which may create toxic secondary products. Here, we show that renewable plant biomass-sourced colloidal lignin particles (CLPs) can be used as agglomeration agents to facilitate removal of viruses from water. We used dynamic light scattering (DLS), electrophoretic mobility shift assay (EMSA), atomic force microscopy and transmission electron microscopy (AFM, TEM), and UV spectrophotometry to quantify and visualize adherence of cowpea chlorotic mottle viruses (CCMVs) on CLPs. Our results show that CCMVs form agglomerated complexes with CLPs that, unlike pristine virus particles, can be easily removed from water either by filtration or centrifugation. Additionally, cationic particles formed by adsorption of quaternary amine-modified softwood kraft lignin on the CLPs were also evaluated to improve the binding interactions with these anionic viruses. We foresee that due to their moderate production cost, and high availability of lignin as a side-stream from biorefineries, CLPs could be an alternative water pretreatment material in a large variety of systems such as filters, packed columns, or flocculants.

Relationship Between Inactivation and Genome Damage of Human Enteroviruses Upon Treatment by UV254, Free Chlorine, and Ozone

Quantitative PCR (qPCR) is a convenient tool for monitoring virus concentrations in water and wastewater treatment trains, though it only informs about virus presence, but not infectivity. This limitation can be overcome if the relationship between infectivity loss and genome decay induced by a given disinfectant is known. Here, we performed inactivation experiments using two human enteroviruses, Coxsackievirus B5 and Echovirus 11, with three disinfection methods: low-pressure ultraviolet light (UV₂₅₄), free chlorine (FC), and ozone. We compared the inactivation rates as measured by culturing to the decay rates of the whole genome, to evaluate the extent of qPCR-measurable genome damage as a function of inactivation. To determine genome damage, we used an approach that estimates damage across the full viral genome from the measured decay of multiple amplicons distributed across the viral genome. Correlations between inactivation and genome decay were observed for all viruses and all disinfection treatments, but results showed that even among closely related viruses, disinfection methods can damage the viral genome to different extents and that genome damage does not necessarily translate to inactivation. For both viruses, UV₂₅₄ treatment had the closest relationship between inactivation and genome decay and with ozone, the rate of genome decay exceeded the inactivation rate. Finally, for FC, the ratios between methods were vastly different between viruses. This work provides the basis to relate qPCR measurements to infectivity loss and enables the establishment of molecular monitoring tools for assessing enterovirus inactivation during disinfection treatments of water and wastewater.

Comparison of Predicted Microbiological Human Health Risks Associated with de Facto, Indirect, and Direct Potable Water Reuse

Increasing interest in recycling water for potable purposes makes understanding the risks associated with potential acute microbial hazards important. We compared risks from de facto reuse, indirect potable reuse (IPR), and direct potable reuse (DPR) scenarios using a previously published quantitative microbial risk assessment methodology and literature review results. The de facto reuse simulation results are compared to a Cryptosporidium spp. database collected for the Long Term 2 Enhanced Surface Water Treatment Rule's information collection rule (ICR) and to a literature review of norovirus (NoV) densities in ambient surface waters. The de facto simulation results with a treated wastewater effluent contribution of 1% in surface waters and a residence time of 30 days most closely match the ICR dataset. The de facto simulations also suggest that using NoV monitoring data from surface waters may overestimate microbial risks, compared to NoV data from raw sewage coupled with wastewater treatment reduction estimates. The predicted risks from IPR and DPR are consistently lower than those for the de facto reuse scenarios assuming the AWTFs are operating within design specifications. These analyses provide insight into the microbial risks associated with various potable reuse scenarios and highlight the need to carefully consider drinking water treatment choices when wastewater effluent is a component of any drinking water supply.

Flow cytometry applications in water treatment, distribution, and reuse: A review

Ensuring safe and effective water treatment, distribution, and reuse requires robust methods for characterizing and monitoring waterborne microbes. Methods widely used today can be limited by low sensitivity, high labor and time requirements, susceptibility to interference from inhibitory compounds, and difficulties in distinguishing between viable and non-viable cells. Flow cytometry (FCM) has recently gained attention as an alternative approach that can overcome many of these challenges. This article critically and systematically reviews for the first time recent literature on applications of FCM in water treatment, distribution, and reuse. In the review, we identify and examine nearly 300 studies published from 2000 to 2018 that illustrate the benefits and challenges of using FCM for assessing source-water quality and impacts of treatment-plant discharge on receiving waters, wastewater treatment, drinking water treatment, and drinking water distribution. We then discuss options for combining FCM with other indicators of water quality and address several topics that cut across nearly all applications reviewed. Finally, we identify priority areas in which more work is needed to realize the full potential of this approach. These include optimizing protocols for FCM-based analysis of waterborne viruses, optimizing protocols for specifically detecting target pathogens, automating sample handling and preparation to enable real-time FCM, developing computational tools to assist data analysis, and improving standards for instrumentation, methods, and reporting requirements. We conclude that while more work is needed to realize the full potential of FCM in water treatment, distribution, and reuse, substantial progress has been made over the past two decades. There is now a sufficiently large body of research documenting successful applications of FCM that the approach could reasonably and realistically see widespread adoption as a routine method for water quality assessment.

Per- and polyfluoroalkyl substances in source and treated drinking waters of the United States

Contaminants of emerging concern (CECs), including per- and polyfluoroalkyl substances (PFAS), are of interest to regulators, water treatment utilities, the general public and scientists. This study measured 17 PFAS in source and treated water from 25 drinking water treatment plants (DWTPs) as part of a broader study of CECs in drinking water across the United States. PFAS were quantitatively detected in all 50 samples, with summed concentrations of the 17 PFAS ranging from <1 ng/L to 1102 ng/L. The median total PFAS concentration was 21.4 ng/L in the source water and 19.5 ng/L in the treated drinking water. Comparing the total PFAS concentration in source and treated water at each location, only five locations demonstrated statistically significant differences (i.e. P < 0.05) between the source and treated water. When the perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) concentrations in the treated drinking water are compared to the existing US Environmental Protection Agency's PFOA and PFOS drinking water heath advisory of 70 ng/L for each chemical or their sum one DWTP exceeded the threshold. Six of the 25 DWTPs were along two large rivers. The DWTPs within each of the river systems had specific PFAS profiles, with the three DWTPs from one river being dominated by PFOA, while three DWTPs on the second river were dominated by perfluorobutyric acid (PFBA).