Virus Reduction during Advanced Bardenpho and Conventional Wastewater Treatment Processes

Development and comparative assessment of RT-qPCR and duplex RT-LAMP assays for the monitoring of Aichi virus A (AiV-A) in untreated wastewater samples

Diverse enteric pathogens, transmitted through human and animal feces, can cause gastroenteritis. Enteric viruses, such as human Aichi virus, specifically genotype A (AiV-A), are emerging pathogens that cause illnesses even at low doses and are spreading globally. This research developed a reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay targeting the 3CD junction and a reverse transcription colorimetric loop-mediated isothermal amplification (RT-cLAMP) duplex assay targeting junctions 2BC and 3CD of the AiV-A genome for rapid and sensitive detection of this virus in metropolitan and regional wastewater samples in Queensland, Australia. The performance of these assays was evaluated using control materials and by analyzing wastewater samples. In serially diluted control materials, RT-qPCR provided quantifiable data (mean 1.51 log10 GC/2 μL of nucleic acid) down to a dilution of 1 × 10-5 pg/μL. In comparison, the duplex RT-cLAMP assay detected down to 1 × 10-4 pg/μL, indicating that its sensitivity was one order of magnitude less than that of RT-qPCR. Of the 38 wastewater samples from 38 metropolitan and regional wastewater treatment plants (WWTPs) in Queensland, Australia, 21 (55.3 %) tested positive by RT-qPCR with concentrations ranging from 3.60 to 6.23 log10 GC/L. In contrast, only 15 (39.5 %) of 38 wastewater samples were positive using the duplex RT-cLAMP assay. The methods demonstrated substantial qualitative agreement (κ = 0.730), with a concordance of 86.5 %, demonstrating the reliability of RT-cLAMP for detecting AiV-A in wastewater samples. The duplex RT-cLAMP assay, despite demonstrating reduced detection sensitivity, has proven effective and holds promise as a supplementary approach, especially in settings with limited resources where rapid and affordable testing is crucial.

The fate of severe acute respiratory syndrome coronavirus-2 and pepper mild mottle virus at various stages of wastewater treatment process

This study investigated the efficiency of the treatment processes of wastewater treatment plants (WWTPs) to remove severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and pepper mild mottle virus (PMMoV) from the wastewater and sewage sludge, as well as the influence of the mode of operation on the quality of the treated wastewater. SARS-CoV-2 and PMMoV were detected and quantified at different stages of the wastewater and sludge treatment process of three major WWTPs in Stockholm, Sweden. The results showed that primary, biological, and advanced membrane treatment processes are effective in removing SARS-CoV-2 from the wastewater with removal efficiencies of 99-100 % for all WWTPs, while the virus was accumulated in the primary and waste-activated sludges due to higher affinity to biosolids. Operation strategies such as bypass reintroduced the virus into the treated wastewater. The WWTPs achieved relatively low PMMoV removal efficiencies (63-87 %) most probably due to the robust capsid structure of the virus. Anaerobic digestion could not completely remove SARS-CoV-2 and PMMoV from the sludge leading to increased levels of SARS-CoV-2 and PMMoV in dewatered sludge. The study gives an overview of WWTPs' role in tackling pathogen spread in society in the event of a pandemic and disease breakout.

A framework for integrating wastewater-based epidemiology and public health

Wastewater-based epidemiology (WBE) is an environmental approach to monitor community health through the analysis of sewage. The COVID-19 pandemic catalyzed scientists and public health professionals to revisit WBE as a tool to optimize resource allocation to mitigate disease spread and prevent outbreaks. Some studies have highlighted the value of WBE programs that coordinate with public health professionals; however, the details necessary for implementation are not well-characterized. To respond to this knowledge gap, this article documents the framework of a successful WBE program in Arizona, titled Wastewater Analysis for Tactical Epidemiological Response Systems (WATERS), detailing the developed structure and methods of communication that enabled public health preparedness and response actions. This communication illustrates how program operations were employed to reduce outbreak severity. The structure outlined here is customizable and may guide other programs in the implementation of WBE as a public health tool.

Virus surrogates throughout a full-scale advanced water reuse system

Water reuse as an alternative water supply is increasing throughout the world due to water stress and scarcity; however, there are no standard practices for monitoring virus pathogens in such systems. This study aimed to identify suitable surrogates for virus fate, transport, and removal throughout a water reuse scheme. Various microbial targets (11 viruses, two phage, and three bacteria) were monitored using molecular and culture methods across all treatment stages in a wastewater reclamation facility and advanced water treatment facility. Criteria were established for identifying suitable surrogates, which included reliable detection, observable fate and transport, calculable log-reduction values (LRVs), correlations with other targets, and various morphological types. In total, five viruses (PMMoV, AiV, GII NoV, AdV, FRNA GII) met these stringent criteria and were suggested as potential virus surrogates. These surrogates enabled successful comparison of assigned versus actual LRVs throughout a water reuse scheme. Results suggest that virus pathogens are effectively removed throughout water reuse treatment and the suggested surrogates can be utilized for monitoring treatment performance and ensuring public health safety. This study provides a framework that water utilities across the world can reference for establishing virus monitoring practices.

Non-potable water reuse and the public health risks from protozoa and helminths: a case study from a city with a semi-arid climate

The study estimated the risk due to Cryptosporidium, Giardia, and Ascaris, associated with non-potable water reuse in the city of Jaipur, India. The study first determined the exposure dose of Cryptosporidium, Giardia, and Ascaris based on various wastewater treatment technologies for various scenarios of reuse for six wastewater treatment plants (WWTPs) in the city. The exposure scenarios considered were (1) garden irrigation; (2) working and lounging in the garden; and (3) consumption of crops irrigated with recycled water. The estimated annual risk of infection varied between 8.57 × 10-7 and 1.0 for protozoa and helminths, respectively. The order of treatment processes, in decreasing order of annual risk of infection, was found to be: moving-bed bioreactor (MBBR) technology > activated sludge process (ASP) technology > sequencing batch reactor (SBR) technology. The estimated annual risk was found to be in this order: Ascaris > Giardia > Cryptosporidium. The study also estimated the maximum allowable concentration (Cmax) of pathogen in the effluent for a benchmark value of annual infection of risk equal to 1:10,000, the acceptable level of risk used for drinking water. The estimated Cmax values were found to be 6.54 × 10-5, 1.37 × 10-5, and 2.89 × 10-6 (oo) cysts/mL for Cryptosporidium, Giardia, and Ascaris, respectively.

Inactivation of phage phiX174 by UV254 and free chlorine: Structure impairment and function loss

Disinfection is widely applied in water and wastewater treatment to inactivate viruses. However, the inactivation mechanism associated with viral structural alteration during disinfection is still not clear. In this work, inactivation of bacteriophage phiX174 by ultraviolet radiation (UV₂₅₄) and free chlorine (FC), two most commonly used disinfection processes, was studied at the molecular level to investigate the relationship between phiX174 genome impairment and virus inactivation, and the correlation between protein impairment and function loss. Double-layer agar technique, quantitative real-time polymerase chain reaction (qPCR), real-time reverse transcription-polymerase chain reaction (RT-qPCR), and liquid chromatography-tandem mass spectrometry techniques (LC-MS/MS), together with structure impairment and function experiments were implemented to quantitatively analyze the inactivation and damage to genome and proteins of phiX174. Results showed that UV₂₅₄ and FC could effectively inactivate phiX174 at the practical doses (UV₂₅₄ dose of 30 mJ/cm², and FC of 1-3 mg/L) used in water treatment plants, accompanied with the damage to viral genome and proteins. Specifically, a UV₂₅₄ irradiation dose of 9.6 mJ/cm², and FC at an initial concentration of 1 mg/L at 4 min could lead to a 4-log₁₀ inactivation. Nevertheless, the combination of these two methods at selected doses played no significant synergistic disinfection effect. During UV₂₅₄ disinfection, the proportion of phiX174 with damaged genome was similar with that of the inactivated phiX174. In addition, UV₂₅₄ and FC could disrupt proteins of phiX174 such as H protein, thereby hindering the physiological function associated with these proteins. With these findings, it is suggested that UV₂₅₄ and FC disinfection could hinder the injection of the viral genome into host cells, thus resulting in the inactivation of phiX174. This work provides a comprehensive study of the inactivation mechanism of phiX174, which can enhance the applicability of UV₂₅₄ and FC in water treatment plants, and facilitate the design and optimization of disinfection technologies for virus control in drinking water and wastewater worldwide to ensure the biosafety.

Applicability of crAssphage as a performance indicator for viral reduction during activated sludge wastewater treatment

A major threat to water quality is the discharge of human-derived wastewater, which can cause waterborne illnesses associated with enteric viruses. A poor association exists between fecal indicator bacteria and virus fate in the environment, especially during wastewater treatment. In the current study, the potential of using a novel human gut bacteriophage crAssphage as a wastewater treatment process indicator was evaluated. Using qPCR, influent and effluent wastewater samples of two wastewater treatment plants were analyzed for crAssphage and human viruses including human bocavirus (HBoV), human adenovirus (HAdV), and human polyomavirus (HPyV). All samples were positive for crAssphage. The annual crAssphage concentrations varied between 1.45E + 04 and 2.39E + 08 gc/l in influent samples and from 1.25E + 04 to 7.88E + 06 gc/l in effluent samples. Human viruses concentrations were some orders of magnitude lower than that of crAssphage. Data demonstrated a significant correlation between crAssphage, HAdV, and HPyV during the wastewater treatment process, suggesting that crAssphage and human viral pathogens have similar removal mechanisms. Ultimately, this work concludes that crAssphage could be a performance indicator for viral reduction in the wastewater treatment process.

Pepper Mild Mottle Virus: An Infectious Pathogen in Pepper Production and a Potential Indicator of Domestic Water Quality

Pepper (Capsicum spp.; Family: Solanaceae; 2n = 24) is an important crop cultivated worldwide for the consumption of its fresh and dried processed fruits. Pepper fruits are used as raw materials in a wide variety of industrial processes. As a multipurpose vegetable crop, there is a need to increase the yield. However, yield productivity of pepper is severely constrained by infectious plant pathogens, including viruses, bacteria, fungi, and oomycetes. The pepper mild mottle virus (PMMoV) is currently one of the most damaging pathogens associated with yield losses in pepper production worldwide. In addition to impacts on pepper productivity, PMMoV has been detected in domestic and aquatic water resources, as well as in the excreta of animals, including humans. Therefore, PMMoV has been suggested as a potential indicator of domestic water quality. These findings present additional concerns and trigger the need to control the infectious pathogen in crop production. This review provides an overview of the distribution, economic impacts, management, and genome sequence variation of some isolates of PMMoV. We also describe genetic resources available for crop breeding against PMMoV.

Quantitative Assessment of Microbial Pathogens and Indicators of Wastewater Treatment Performance for Safe and Sustainable Water Reuse in India

Currently, there is no data on the molecular quantification of microbial indicators of recycled water quality in India. In this study, multiple microbial pathogens and indicators of water quality were evaluated at three wastewater treatment plants located in two Indian cities (New Delhi and Jaipur) to determine the treatment performance and suitability of recycled water for safe and sustainable reuse applications. Real-time polymerase chain reaction (PCR) was used for the rapid evaluation of six human pathogens and six microbial indicators of fecal contamination. Among the microbial indicators, pepper mild mottle virus (PMMoV), F⁺RNA-GII bacteriophage, Bacteroides thetaiotamicron, and four human pathogens (Norovirus genogroups I & II, Giardia, and Campylobacter coli) were detected in all of the influent samples analyzed. This work suggests that the raw influents contain lower levels of noroviruses and adenoviruses and higher levels of Giardia compared to those reported from other geographic regions. Overall, the efficacy of the removal of microbial targets was over 93% in the final effluent samples, which is consistent with reports from across the world. PMMoV and Giardia were identified as the best microbial targets, from the microbial indicators spanning across bacteria, bacteriophages, DNA/RNA viruses, and protozoan parasites, by which to evaluate treatment performance and recycled water quality in Indian settings, as they were consistently present at high concentrations in untreated wastewater both within and across the sites. Also, they showed a strong correlation with other microbial agents in both the raw influent and in the final effluent. These findings provide valuable insights into the use of culture-independent molecular indicators that can be used to assess the microbial quality of recycled water in Indian settings. IMPORTANCE Wastewater treatment plants (WWTPs) have rapidly increased in India during the last decade. Nonetheless, there are only a few labs in India that can perform culture-based screening for microbial quality. In the last 2 years of the pandemic, India has witnessed a sharp increase in molecular biology labs. Therefore, it is evident that culture-independent real-time PCR will be increasingly used for the assessment of microbial indicators/pathogens in wastewater, especially in resource-limited settings. There is no data available on the molecular quantitation of microbial indicators from India. There is an urgent need to understand and evaluate the performance of widely used microbial indicators via molecular quantitation in Indian WWTPs. Our findings lay the groundwork for the molecular quantitation of microbial indicators in WWTPs in India. We have screened for 12 microbial targets (indicators and human pathogens) and have identified pepper mild mottle virus (PMMoV) and Giardia as the best molecular microbiological indicators in Indian settings.

Microbial Water Quality through a Full-Scale Advanced Wastewater Treatment Demonstration Facility

The fates of viruses, bacteria, and antibiotic resistance genes during advanced wastewater treatment are important to assess for implementation of potable reuse systems. Here, a full-scale advanced wastewater treatment demonstration facility (ozone, biological activated carbon filtration, micro/ultrafiltration, reverse osmosis, and advanced oxidation) was sampled over three months. Atypically, no disinfectant residual was applied before the microfiltration step. Microbial cell concentrations and viability were assessed via flow cytometry and adenosine triphosphate (ATP). Concentrations of bacteria (16S rRNA gene), viruses (human adenovirus and JC polyomavirus), and antibiotic resistance genes (sul1 and bla _TEM ) were assessed via quantitative PCR following the concentration of large sample volumes by dead-end ultrafiltration. In all membrane filtration permeates, microbial concentrations were higher than previously reported for chloraminated membranes, and log₁₀ reduction values were lower than expected. Concentrations of 16S rRNA and sul1 genes were reduced by treatment but remained quantifiable in reverse osmosis permeate. It is unclear whether sul1 in the RO permeate was from the passage of resistance genes or new growth of microorganisms, but the concentrations were on the low end of those reported for conventional drinking water distribution systems. Adenovirus, JC polyomavirus, and bla _TEM genes were reduced below the limit of detection (∼10^-2 gene copies per mL) by microfiltration. The results provide insights into how treatment train design and operation choices affect microbial water quality as well as the use of flow cytometry and ATP for online monitoring and process control.

A probabilistic assessment of microbial infection risks due to occupational exposure to wastewater in a conventional activated sludge wastewater treatment plant

Exposure to pathogens during wastewater treatment could result in significant health risks. In this paper, a probabilistic approach for assessing the risks of microbial infection for workers in an activated sludge wastewater treatment plant is presented. A number of exposure routes were modelled, including hand-to-mouth and droplet ingestion of untreated wastewater, droplet ingestion and inhalation of aerosols after secondary treatment, and ingestion of sludge during drying. Almost all workers exposed to untreated wastewater could be infected with the three selected potential pathogens of pathogenic E. coli, Norovirus and Cryptosporidium spp. Hand-to-mouth ingestion is the single most significant route of exposure at the head of works. There is also a risk of infections resulting from ingestion of droplets or inhalation of aerosols at the aeration tanks or contaminated hands at the clarifiers during secondary wastewater treatment. For sludge, the risks of infection with Norovirus was found to be the highest due to accidental ingestion (median risks of 2.2 × 10^-2(±3.3 × 10^-3)). Regardless of the point and route of exposure, Norovirus and Cryptosporidium spp. presented the highest risks. The study finds that occupational exposure to wastewater at wastewater treatment plants can result in significant viral and protozoan infections. This risk assessment framework can be used to establish and measure the success of risk reduction measures in wastewater treatment plants. These measures could include the use of personal protective equipment and adherence to strict personal hygiene.

A comparative study of flow cytometry-sorted communities and shotgun viral metagenomics in a Singapore municipal wastewater treatment plant

Traditional or "bulk" viral enrichment and amplification methods used in viral metagenomics introduce unavoidable bias in viral diversity. This bias is due to shortcomings in existing viral enrichment methods and overshadowing by the more abundant viral populations. To reduce the complexity and improve the resolution of viral diversity, we developed a strategy coupling fluorescence-activated cell sorting (FACS) with random amplification and compared this to bulk metagenomics. This strategy was validated on both influent and effluent samples from a municipal wastewater treatment plant using the Modified Ludzack-Ettinger (MLE) process as the treatment method. We found that DNA and RNA communities generated using bulk samples were mostly different from those derived following FACS for both treatments before and after MLE. Before MLE treatment, FACS identified five viral families and 512 viral annotated contigs. Up to 43% of mapped reads were not detected in bulk samples. Nucleo-cytoplasmic large DNA viral families were enriched to a greater extent in the FACS-coupled subpopulations compared with bulk samples. FACS-coupled viromes captured a single-contig viral genome associated with Anabaena phage, which was not observed in bulk samples or in FACS-sorted samples after MLE. These short metagenomic reads, which were assembled into a high-quality draft genome of 46 kbp, were found to be highly dominant in one of the pre-MLE FACS annotated virome fractions (57.4%). Using bulk metagenomics, we identified that between Primary Settling Tank and Secondary Settling Tank viromes, Virgaviridae, Astroviridae, Parvoviridae, Picobirnaviridae, Nodaviridae, and Iridoviridae were susceptible to MLE treatment. In all, bulk and FACS-coupled metagenomics are complementary approaches that enable a more thorough understanding of the community structure of DNA and RNA viruses in complex environmental samples, of which the latter is critical for increasing the sensitivity of detection of viral signatures that would otherwise be lost through bulk viral metagenomics.

Infectious Pepper Mild Mottle Virus and Human Adenoviruses as Viral Indices in Sewage and Water Samples

The objective of this study was to compare human adenoviruses (HAdVs) genome and infectivity, polyomaviruses (JC and BK) genome (JCPyVs) and (BKPyVs), Pepper Mild Mottle Virus (PMMoV) genome and infectivity, and infectious bacteriophages as viral indices for sewage and water samples. One hundred and forty-four samples were collected from inlets and outlets of water and wastewater treatment plants (WTPs), and WWTPs within Greater Cairo from October 2015 till March 2017. Two methods of viral concentration [Aluminium hydroxide (Al(OH)₃) precipitation method and adsorption-elution technique followed by organic flocculation method] were compared to determine which of them was the best method to concentrate viruses from sewage and water. Although samples with only one litre volume were concentrated using Al(OH)₃ precipitation method and the same samples with larger volumes (5-20 L) were concentrated using the adsorption-elution technique followed by the organic flocculation method, a non-significant difference was observed between the efficiency of the two methods in all types of samples except for the drinking water samples. Based on the qualitative prevalence of studied viruses in water and wastewater samples, the number of genome copies and infectious units in the same samples, resistance to treatment processes in water and wastewater treatment plants, higher frequency of both adenoviruses and PMMoV genomes as candidate viral indices in treated sewage and drinking water was observed. The problem of having a viral genome as indices of viral pollution is that it does not express the recent viral pollution because of the longer survivability of the viral genome than the infectious units in water and wastewater. Both infectious adenovirus and infectious phiX174 bacteriophage virus showed similar efficiencies as indices for viral pollution in drinking water and treated sewage samples. On the other hand, qualitative detection of infectious PMMoV failed to express efficiently the presence/absence of infectious enteric viruses in drinking water samples. Infectious adenoviruses and infectious bacteriophage phiX174 virus may be better candidates than adenoviruses genome, polyomaviruses genome, and PMMoV genome and infectivity as viral indices for water and wastewater.

CrAssphage as an indicator of human-fecal contamination in water environment and virus reduction in wastewater treatment

Viral indicators of human-fecal contamination in wastewaters and environmental waters have been getting much attention in the past decade. Cross-assembly phage (crAssphage) is the most abundant DNA virus in human feces. Recently, the usefulness of crAssphage as a microbial source tracking and water quality monitoring tool for human-fecal contamination has been highlighted. Here, we conducted a comprehensive review on crAssphage in water, focusing on detection methodology, concentration range in various waters and wastewaters, specificity to human-fecal contamination, and reduction in wastewater treatment systems. This review highlights that crAssphage is globally distributed in wastewaters and various fecal-contaminated water bodies at high concentrations without seasonal fluctuations. CrAssphage is highly specific to human-fecal contamination and is rarely found in animal feces. It also has a good potential as a performance indicator to ensure virus reduction in wastewater treatment systems. Accordingly, crAssphage could be an effective tool for monitoring of human-fecal contamination and potential presence of fecal pathogenic microbes in environmental waters. Bridging the research gaps highlighted in this review would make crAssphage a powerful tool to support the control of water-related health risks.

Role of pepper mild mottle virus as a tracking tool for fecal pollution in aquatic environments

The plant pathogen pepper mild mottle virus (PMMoV) has recently been proposed as a water quality indicator, it is a RNA virus belonging to the genus Tobamovirus in the family Virgoviridae that causes harm to the pepper crops. After consuming processed food products containing infected peppers, such as hot sauces, PMMoV is excreted in high concentrations in feces; therefore, this is the most common RNA virus, constantly found in the feces of humans. The fecal-oral pathway is emerging as an environmental problem. The presence of high concentrations of pathogens associated with human excreta in environmental waters or water reuse supplies poses a threat to public health. Due to the difficulty in determining the presence of pathogens effectively in water, attempts to monitor microbial water quality often use surrogates or indicator organisms that can be easily detected; therefore, PMMoV is used as a viral surrogate in aquatic environment. This paper describes the incidence and persistence of PMMoV in aquatic environments and in waste treatment plants and its usefulness for quantifying virus reductions by advanced water treatment technologies. In recent research, SARS-CoV-2 was reported to be found in wastewater and utilized for the purpose of monitoring coronavirus illness outbreaks. Since PMMoV is readily identified in the human feces and can also serve as an indicator of human waste, the determined PMMoV concentrations may be utilized to give the normalized report of the SARS-CoV-2 concentration, so that, the amount of human waste found in the wastewater can be taken into consideration.

Occurrence of bacterial and viral fecal markers in municipal sewage sludge and their removal during sludge conditioning processes

Fecal contamination in wastewater treatment system may pose severe threats to human health, but the detailed contamination of fecal bacterial and viral pathogens in municipal sewage sludge remains unclear. In addition, it is also unclear how sludge conditioning treatments would impact the distribution of fecal markers in conditioned sewage sludge. Before addressing these two issues, the possible polymerase chain reaction (PCR) inhibition effect when determining the abundances of fecal markers in both sludge solids and sludge supernatants should be solved, and methods of effectively concentrating fecal markers from sludge supernatant should also be developed. In the present study, we found that the serial tenfold dilution effectively reduced the PCR inhibition effect when determining the abundances of fecal markers including cross-assembly phages (CrAssphage), JC polyomavirus (JCPyV), human-specific HF183 bacteroides (HF183), human BK polyomavirus (BKPyV), human adenovirus (HAdV) and Escherichia coli (EC), while the utilization of negatively charged HA membrane was effective to recover fecal markers from sludge supernatant. The results of a six-month monitoring revealed that gene markers of CrAssphage, JCPyV, HF183, BKPyV, HAdV, and EC can be detected in municipal sewage sludge collected from a local wastewater treatment plant. Among the investigated four chemical conditioning methods, i.e., chemical conditioning with polyacrylamide (PAM), Fe[III]/CaO, or Fenton's reagent, and chemical acidification conditioning, chemical conditioning with Fenton's reagent was much more effective than the other three conditioning methods to reduce the abundances of fecal markers in the supernatant and solid of conditioned sewage sludge. Furthermore, the investigated fecal markers in the conditioned sewage sludge can be simultaneously attenuated by employing suitable conditioning methods, consequently reducing the associated environmental risks.

Review and Meta‐Analysis: SARS‐CoV‐2 and Enveloped Virus Detection in Feces and Wastewater

Detection and quantification of viruses supplies key information on their spread and allows risk assessment for public health. In wastewater, existing detection methods have been focusing on non‐enveloped enteric viruses due to enveloped virus transmission, such as coronaviruses, by the fecal‐oral route being less likely. Since the beginning of the SARS‐CoV‐2 pandemic, interest and importance of enveloped virus detection in wastewater has increased. Here, quantitative studies on SARS‐CoV‐2 occurrence in feces and raw wastewater and other enveloped viruses via quantitative real‐time reverse transcription polymerase chain reaction (RT‐qPCR) during the early stage of the pandemic until April 2021 are reviewed, including statistical evaluation of the positive detection rate and efficiency throughout the detection process involving concentration, extraction, and amplification stages. Optimized and aligned sampling protocols and concentration methods for enveloped viruses, along with SARS‐CoV‐2 surrogates, in wastewater environments may improve low and variable recovery rates providing increased detection efficiency and comparable data on viral load measured across different studies.

Quantification of human enteric viruses as alternative indicators of fecal pollution to evaluate wastewater treatment processes

We investigated the potential use and quantification of human enteric viruses in municipal wastewater samples of Winnipeg (Manitoba, Canada) as alternative indicators of contamination and evaluated the processing stages of the wastewater treatment plant. During the fall 2019 and winter 2020 seasons, samples of raw sewage, activated sludge, effluents, and biosolids (sludge cake) were collected from the North End Sewage Treatment Plant (NESTP), which is the largest wastewater treatment plant in the City of Winnipeg. DNA (Adenovirus and crAssphage) and RNA enteric viruses (Pepper mild mottle virus, Norovirus genogroups GI and GII, Rotavirus Astrovirus, and Sapovirus) as well as the uidA gene found in Escherichia coli were targeted in the samples collected from the NESTP. Total nucleic acids from each wastewater treatment sample were extracted using a commercial spin-column kit. Enteric viruses were quantified in the extracted samples via quantitative PCR using TaqMan assays. Overall, the average gene copies assessed in the raw sewage were not significantly different (p-values ranged between 0.1023 and 0.9921) than the average gene copies assessed in the effluents for DNA and RNA viruses and uidA in terms of both volume and biomass. A significant reduction (p-value ≤ 0.0438) of Adenovirus and Noroviruses genogroups GI and GII was observed in activated sludge samples compared with those for raw sewage per volume. Higher GCNs of enteric viruses were observed in dewatered sludge samples compared to liquid samples in terms of volume (g of sample) and biomass (ng of nucleic acids). Enteric viruses found in gene copy numbers were at least one order of magnitude higher than the E. coli marker uidA, indicating that enteric viruses may survive the wastewater treatment process and viral-like particles are being released into the aquatic environment. Viruses such as Noroviruses genogroups GI and GII, and Rotavirus were detected during colder months. Our results suggest that Adenovirus, crAssphage, and Pepper mild mottle virus can be used confidently as complementary viral indicators of human fecal pollution.

Comparison of five polyethylene glycol precipitation procedures for the RT-qPCR based recovery of murine hepatitis virus, bacteriophage phi6, and pepper mild mottle virus as a surrogate for SARS-CoV-2 from wastewater

Polyethylene glycol (PEG) precipitation is one of the conventional methods for virus concentration. This technique has been used to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. The procedures and seeded surrogate viruses were different among implementers; thus, the reported whole process recovery efficiencies considerably varied among studies. The present study compared five PEG precipitation procedures, with different operational parameters, for the RT-qPCR-based whole process recovery efficiency of murine hepatitis virus (MHV), bacteriophage phi6, and pepper mild mottle virus (PMMoV), and molecular process recovery efficiency of murine norovirus using 34 raw wastewater samples collected in Japan. The five procedures yielded significantly different whole process recovery efficiency of MHV (0.070%-2.6%) and phi6 (0.071%-0.51%). The observed concentration of indigenous PMMoV ranged from 8.9 to 9.7 log (8.2 × 108 to 5.6 × 109) copies/L. Interestingly, PEG precipitation with 2-h incubation outperformed that with overnight incubation partially due to the difference in molecular process recovery efficiency. The recovery load of MHV exhibited a positive correlation (r = 0.70) with that of PMMoV, suggesting that PMMoV is the potential indicator of the recovery efficiency of SARS-CoV-2. In addition, we reviewed 13 published studies and found considerable variability between different studies in the whole process recovery efficiency of enveloped viruses by PEG precipitation. This was due to the differences in operational parameters and surrogate viruses as well as the differences in wastewater quality and bias in the measurement of the seeded load of surrogate viruses, resulting from the use of different analytes and RNA extraction methods. Overall, the operational parameters (e.g., incubation time and pretreatment) should be optimized for PEG precipitation. Co-quantification of PMMoV may allow for the normalization of SARS-CoV-2 RNA concentration by correcting for the differences in whole process recovery efficiency and fecal load among samples.

Selected Mechanistic Aspects of Viral Inactivation by Peracetic Acid

Peracetic acid (PAA) is an alternative to traditional wastewater disinfection as it has a high oxidation potential without producing chlorinated disinfection byproducts. Reports have shown the effectiveness of PAA to reduce waterborne viruses, but the mechanism of inactivation is understudied. This study evaluated PAA consumption by amino acids and nucleotides that are the building blocks of both viral capsids and genomes. Cysteine (>1.7 min^-1) and methionine (>1.2 min^-1) rapidly consumed PAA, while cystine (1.9 × 10^-2 min^-1) and tryptophan (1.4 × 10^-4 min^-1) reactions occurred at a slower rate. All other amino acids and nucleotides did not react significantly (p < 0.05) with PAA during experiments. Also, PAA treatment did not result in significant (p < 0.05) reductions of purified RNA from MS2 bacteriophage and murine norovirus. Data in this study suggest that PAA effectively inactivates viruses by targeting susceptible amino acids on capsid proteins and does not readily damage viral genomes. Knowledge of virus capsid structures and protein compositions can be used to qualitatively predict the relative resistance or susceptibility of virus types to PAA. Capsid structures containing a higher total number of target amino acids may be more susceptible to PAA reactions that damage structural integrity resulting in inactivation.

Study on the influence of operational and management processes of a water reclamation plant since COVID-19 situation

Reusing treated wastewater can effectively alleviate water shortages and water contamination problems but depends on ensuring the safety of the reclaimed water that is produced. The operating and management conditions for water reclamation plants in China have been changed since the outbreak of the COVID-19 epidemic in China at the end of 2019 to prevent emerging viruses being spread through wastewater treatment processes and the reclaimed water that is produced. Removal of pathogens and trace organic compounds (e.g., pharmaceuticals and personal care products and endocrine disrupting chemicals) in a real water reclamation plant after the start of COVID-19 epidemic was studied. Disinfection byproduct formation caused by chlorine being added to meet disinfection requirements was also assessed. The pathogenic microorganism concentrations in effluent were <2 (most probable number)/L, and the removal rates for most trace organic compounds were >80% when advanced treatments were performed using ozone, ultraviolet light, and chlorine doses of 2 mg/L, 20.5 mJ/cm², and 2-3 mg/L, respectively. The main disinfection byproduct produced at a chlorine dose of 2 mg/L and a residence time of 1 h was chloroform (at concentrations <15 μg/L). The results indicated that the water reclamation processes with modified conditions gave high pathogen and trace organic compound removal rates and reasonably well-controlled disinfection byproduct concentrations.

Advanced Oxidation Processes for Water and Wastewater Viral Disinfection. A Systematic Review

Water and wastewater virological quality is a significant public health issue. Viral agents include emerging and re-emerging pathogens characterized by extremely small size, and high environmental stability. Since the mainly used conventional disinfection methods are usually not able to achieve complete disinfection of viral and other microbial targets, in real water and wastewater matrices, effective strategies for the treatment, use and reuse of water and the development of next-generation water supply systems are required. The scope of the present systematic review was to summarize research data on the application of advanced oxidation processes (AOPs) for viral disinfection of water and wastewater. A literature survey was conducted using the electronic databases PubMed, Scopus, and Web of Science. This comprehensive research yielded 23 records which met the criteria and were included and discussed in this review. Most of the studies (14/23) used only MS2 bacteriophage as an index virus, while the remaining studies (9/23) used two or more viral targets, including phages (MS2, T4, T7, phiX174, PRD-1, S2, ϕB124-14, ϕcrAssphage) and/or Adenovirus, Aichivirus, Norovirus (I, II, IV), Polyomavirus (JC and BK), Sapovirus, Enterovirus, Coxsackievirus B3, Echovirus, and Pepper mild mottle virus. The vast majority of the studies applied a combination of two or more treatments and the most frequently used process was ultraviolet light-hydrogen peroxide (UV/H₂O₂) advanced oxidation. The review is expected to highlight the potential of the AOPs for public health protection from the waterborne viral exposure.

An optimized and robust PEG precipitation method for detection of SARS-CoV-2 in wastewater

Wastewater-based epidemiology is currently being utilized to monitor the dissemination of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), on a population scale. The detection of SARS-CoV-2 in wastewater is highly influenced by methodologies used for its isolation, concentration and RNA extraction. Although various viral concentration methods are currently employed, including polyethylene glycol (PEG) precipitation, adsorption-extraction, ultracentrifugation and ultrafiltration, to our knowledge, none of these methods have been standardized for use with a variety of wastewater matrices and/or different kits for RNA extraction and quantification. To address this, wastewater with different physical characteristics was seeded with gamma-irradiated SARS-CoV-2 and used to test the efficiency of PEG precipitation and adsorption-extraction to concentrate the virus from three physiochemically different wastewater samples, sourced from three distinct wastewater plants. Efficiency of viral concentration and RNA extraction was assessed by reverse-transcriptase polymerase chain reaction and the recovery yields calculated. As co-purification of inhibitors can be problematic for subsequent detection, two commonly used commercial master mixes were assessed for their sensitivity and efficiency to detect two SARS-CoV-2 target nucleocapsid (N) gene sequences. Recovery rates varied greatly between wastewater matrices and concentration methods, with the highest and most reproducible recovery rates (46.6-56.7%) observed when SARS-CoV-2 was precipitated with PEG and detected by the Luna® Universal master mix. The adsorption-extraction method was less effective (0-21.7%). This study demonstrates that PEG precipitation is the more robust method, which translates well to varying wastewater matrices, producing consistent and reproducible recovery rates. Furthermore, it is compatible with different kits for RNA extraction and quantitation.

Occurrence of various viruses and recent evidence of SARS-CoV-2 in wastewater systems

Viruses are omnipresent and persistent in wastewater, which poses a risk to human health. In this review, we summarise the different qualitative and quantitative methods for virus analysis in wastewater and systematically discuss the spatial distribution and temporal patterns of various viruses (i.e., enteric viruses, Caliciviridae (Noroviruses (NoVs)), Picornaviridae (Enteroviruses (EVs)), Hepatitis A virus (HAV)), and Adenoviridae (Adenoviruses (AdVs))) in wastewater systems. Then we critically review recent SARS-CoV-2 studies to understand the ongoing COVID-19 pandemic through wastewater surveillance. SARS-CoV-2 genetic material has been detected in wastewater from France, the Netherlands, Australia, Italy, Japan, Spain, Turkey, India, Pakistan, China, and the USA. We then discuss the utility of wastewater-based epidemiology (WBE) to estimate the occurrence, distribution, and genetic diversity of these viruses and generate human health risk assessment. Finally, we not only promote the prevention of viral infectious disease transmission through wastewater but also highlight the potential use of WBE as an early warning system for public health assessment.

Metagenomic and viromic data mining reveals viral threats in biologically treated domestic wastewater

Activated sludge (AS), a common biological secondary treatment process in wastewater treatment plants (WWTPs), is known to remove a large spectrum of microorganisms. Yet little is known about its effect on the entire viral community. After compiling 3 Tbp of next-generation sequencing (NGS) metagenomic/viromic datasets consisted of 119 sub-datasets of influent, effluent, and AS samples from 27 WWTPs, viral removal efficacy is evaluated through data mining. The normalized abundance of viruses suggests effluents exhibit the highest viral prevalence (3.21 ± 3.26%, n = 13) followed by the AS (0.48 ± 0.25%, n = 57) and influents (0.23 ± 0.17%, n = 17). In contrast, plasmids, representing genetic element of bacteria, show higher average prevalence (0.73 ± 0.82%, n = 17) in influents than those of the AS (0.63 ± 0.26%, n = 57) and effluents (0.35 ± 0.42%, n = 13). Furthermore, the abundance-occupancy analysis identifies 142 core phage viruses and 17 non-phages core viruses, including several pathogenic viruses in the AS virome. The persistent occurrence of pathogenic viruses, coupled with non-favorable virus removal by the AS treatment, reveals the hidden virus threats in biologically treated domestic wastewater. The mechanisms for why viruses persist and the possibility that WWTPs are potential hotspots for viral survival deserve attention.

Estimating the minimum number of SARS-CoV-2 infected cases needed to detect viral RNA in wastewater: To what extent of the outbreak can surveillance of wastewater tell us?

There is increasing interest in wastewater-based epidemiology (WBE) of SARS-CoV-2 RNA to serve as an early warning system for a community. Despite successful detection of SARS-CoV-2 RNA in wastewaters sampled from multiple locations, there is still no clear idea on the minimal number of cases in a community that are associated with a positive detection of the virus in wastewater. To address this knowledge gap, we sampled wastewaters from a septic tank (n = 57) and biological activated sludge tank (n = 52) located on-site of a hospital. The hospital is providing treatment for SARS-CoV-2 infected patients, with the number of hospitalized patients per day known. It was observed that depending on which nucleocapsid gene is targeted by means of RT-qPCR, a range of 253-409 positive cases out of 10,000 persons are required prior to detecting RNA SARS-CoV-2 in wastewater. There was a weak correlation between N1 and N2 gene abundances in wastewater with the number of hospitalized cases. This correlation was however not observed for N3 gene. The frequency of detecting N1 and N2 gene in wastewater was also higher than that for N3 gene. Furthermore, nucleocapsid genes of SARS-CoV-2 were detected at lower frequency in the partially treated wastewater than in the septic tank. In particular, N1 gene abundance was associated with water quality parameters such as total organic carbon and pH. In instances of positive detection, the average abundance of N1 and N3 genes in the activated sludge tank were reduced by 50 and 70% of the levels detected in septic tank, suggesting degradation of the SARS-CoV-2 gene fragments already occurring in the early stages of the wastewater treatment process.

Pepper Mild Mottle Virus as Indicator of Pollution: Assessment of Prevalence and Concentration in Different Water Environments in Italy

Pepper mild mottle virus (PMMoV), a plant pathogenic virus belonging to the family Virgoviridae, has been proposed as a potential viral indicator for human faecal pollution in aquatic environments. The present study investigated the occurrence, amount and diversity of PMMoV in water environments in Italy. A total of 254 water samples, collected between 2017 and 2019 from different types of water, were analysed. In detail, 92 raw sewage, 32 treated sewage, 16 river samples, 9 estuarine waters, 20 bathing waters, 67 groundwater samples and 18 drinking waters were tested. PMMoV was detected in 79% and 75% of untreated and treated sewage samples, respectively, 75% of river samples, 67% and 25% of estuarine and bathing waters and 13% of groundwater samples. No positive was detected in drinking water. The geometric mean of viral concentrations (genome copies/L) was ranked as follows: raw sewage (2.2 × 10⁶) > treated sewage (2.9 × 10⁵) > river waters (6.1 × 10²) > estuarine waters (4.8 × 10²) > bathing waters (8.5 × 10¹) > groundwater (5.9 × 10¹). A statistically significant variation of viral loads could be observed between raw and treated sewage and between these and all the other water matrices. PMMoV occurrence and viral loads did not display seasonal variation in raw sewage nor correlation with faecal indicator bacteria in marine waters and groundwater. This study represents the first report on the occurrence and quantification PMMoV in different water environments in Italy. Further studies are required to evaluate the suitability of PMMoV as a viral indicator for human faecal pollution and for viral pathogens in waters.

Inactivation of Pepper Mild Mottle Virus in Water by Cold Atmospheric Plasma

Water scarcity is one of the greatest threats for human survival and quality of life, and this is increasingly contributing to the risk of human, animal and plant infections due to waterborne viruses. Viruses are transmitted through polluted water, where they can survive and cause infections even at low concentrations. Plant viruses from the genus Tobamovirus are highly mechanically transmissible, and cause considerable damage to important crops, such as tomato. The release of infective tobamoviruses into environmental waters has been reported, with the consequent risk for arid regions, where these waters are used for irrigation. Virus inactivation in water is thus very important and cold atmospheric plasma (CAP) is emerging in this field as an efficient, safe, and sustainable alternative to classic waterborne virus inactivation methods. In the present study we evaluated CAP-mediated inactivation of pepper mild mottle virus (PMMoV) in water samples. PMMoV is a very resilient water-transmissible tobamovirus that can survive transit through the human digestive tract. The efficiency of PMMoV inactivation was characterized for infectivity and virion integrity, and at the genome level, using test plant infectivity assays, transmission electron microscopy, and molecular methods, respectively. Additionally, the safety of CAP treatment was determined by testing the cytotoxic and genotoxic properties of CAP-treated water on the HepG2 cell line. 5-min treatment with CAP was sufficient to inactivate PMMoV without introducing any cytotoxic or genotoxic effects in the in-vitro cell model system. These data on inactivation of such stable waterborne virus, PMMoV, will encourage further examination of CAP as an alternative for treatment of potable and irrigation waters, and even for other water sources, with emphasis on inactivation of various viruses including enteric viruses.

Performance of viral and bacterial genetic markers for sewage pollution tracking in tropical Thailand

Identifying sewage contamination via microbial source tracking (MST) marker genes has proven useful for effective water quality management worldwide; however, performance evaluations for these marker genes in tropical areas are limited. Therefore, this research evaluated four human-associated MST marker genes (human polyomaviruses (JC and BK viruses [HPyVs]), bacteriophage crAssphage (CPQ_056), Lachnospiraceae Lachno3, and Bacteroides BacV6-21) for tracking sewage pollution in aquatic environments of Thailand. The viral marker genes, HPyV and crAssphage were highly sensitive and specific to sewage from onsite wastewater treatment plants (OWTPs; n = 19), with no cross-detection in 120 composite swine, cattle, chicken, duck, goat, sheep, and buffalo fecal samples. The bacterial marker genes, Lachno3 and BacV6-21, demonstrated high sensitivity but moderate specificity; however, using both markers could improve specificity to >0.80 (max value of 1.00). The most abundant markers in OWTP samples were Lachno3 and BacV6-21 (5.42-8.02 and nondetect-8.05 log₁₀ copies/100 mL), crAssphage (5.28-7.38 log₁₀ copies/100 mL), and HPyVs (3.66-6.53 log₁₀ copies/100 mL), respectively. Due to their increased specificity, the abundance of viral markers were further investigated in environmental waters, in which HPyVs showed greater levels (up to 4.33 log₁₀ copies/100 mL) and greater detection rates (92.7%) in two coastal beaches (n = 41) than crAssphage (up to 3.51 log₁₀ copies/100 mL and 56.1%). HPyVs were also found at slightly lower levels (up to 5.10 log₁₀ copies/100 mL), but at higher detection rates (92.6%), in a freshwater canal (n = 27) than crAssphage (up to 5.21 log₁₀ copies/100 mL and 88.9%). HPyVs and crAssphage marker genes were identified as highly sensitive and specific for tracking sewage pollution in aquatic environments of Thailand. This study underlines the importance of characterizing and validating MST markers in host groups and environmental waters before including them in a water quality management toolbox.

Assessment of socioeconomic inequality based on virus-contaminated water usage in developing countries: A review

Water is an essential resource required for various human activities such as drinking, cooking, and other recreational activities. While developed nations have made significant improvement in providing adequate quality water and sanitation devoid of virus contaminations to a significant percentage of the residences, many of the developing countries are still lacking in these regards, leading to many death cases among the vulnerable due to ingestion of virus-contaminated water and other waterborne pathogens. However, the recent global pandemic of COVID-19 seems to have changed the paradigm by reawakening the importance of water quality and sanitation, and focusing more attention on the pervasive effect of the use of virus-contaminated water as it can be a potential driver for the spread of the virus and other waterborne diseases, especially in developing nations that are characterized by low socioeconomic development. Therefore, this review assessed the socioeconomic inequalities related to the usage of virus-contaminated water and other waterborne pathogens in developing countries. The socioeconomic factors attributed to the various waterborne diseases due to the use of virus-contaminated water in many developing countries are poverty, the standard of living, access to health care facilities, age, gender, and level of education. Some mitigation strategies to address the viral contamination of water sources are therefore proposed, while future scope and recommendations on tackling the essential issues related to socioeconomic inequality in developing nations are highlighted.

Assessment of socioeconomic inequality based on virus-contaminated water usage in developing countries: A review

Water is an essential resource required for various human activities such as drinking, cooking, and other recreational activities. While developed nations have made significant improvement in providing adequate quality water and sanitation devoid of virus contaminations to a significant percentage of the residences, many of the developing countries are still lacking in these regards, leading to many death cases among the vulnerable due to ingestion of virus-contaminated water and other waterborne pathogens. However, the recent global pandemic of COVID-19 seems to have changed the paradigm by reawakening the importance of water quality and sanitation, and focusing more attention on the pervasive effect of the use of virus-contaminated water as it can be a potential driver for the spread of the virus and other waterborne diseases, especially in developing nations that are characterized by low socioeconomic development. Therefore, this review assessed the socioeconomic inequalities related to the usage of virus-contaminated water and other waterborne pathogens in developing countries. The socioeconomic factors attributed to the various waterborne diseases due to the use of virus-contaminated water in many developing countries are poverty, the standard of living, access to health care facilities, age, gender, and level of education. Some mitigation strategies to address the viral contamination of water sources are therefore proposed, while future scope and recommendations on tackling the essential issues related to socioeconomic inequality in developing nations are highlighted.

Viruses in wastewater: occurrence, abundance and detection methods

This paper presents an updated and comprehensive review on the different methods used for detection and quantification of viruses in wastewater treatment systems. The analysis of viability of viruses in wastewater and sludge is another thrust of this review. Recent studies have mostly focused on determining the abundance and diversity of viruses in wastewater influents, in samples from primary, secondary, and tertiary treatment stages, and in final effluents. A few studies have also examined the occurrence and diversity of viruses in raw and digested sludge samples. Recent efforts to improve efficiency of virus detection and quantification methods in the complex wastewater and sludge matrices are highlighted in this review. A summary and a detailed comparison of the pre-treatment methods that have been utilized for wastewater and sludge samples are also presented. The role of metagenomics or sequencing analysis in monitoring wastewater systems to predict disease outbreaks, to conduct public health surveillance, to assess the efficiency of existing treatment systems in virus removal, and to re-evaluate current regulations regarding pathogenic viruses in wastewater is discussed in this paper. Challenges and future perspectives in the detection of viruses, including emerging and newly emerged viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in wastewater systems are discussed in this review.

First detection of SARS-CoV-2 RNA in wastewater in North America: A study in Louisiana, USA

We investigated the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater samples in southern Louisiana, USA. Untreated and treated wastewater samples were collected on five occasions over a four-month period from January to April 2020. The wastewater samples were concentrated via ultrafiltration (Method A), and an adsorption-elution method using electronegative membranes (Method B). SARS-CoV-2 RNA was detected in 2 out of 15 wastewater samples using two reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays (CDC N1 and N2). None of the secondary treated and final effluent samples tested positive for SARS-CoV-2 RNA. To our knowledge, this is the first study reporting the detection of SARS-CoV-2 RNA in wastewater in North America, including the USA. However, concentration methods and RT-qPCR assays need to be refined and validated to increase the sensitivity of SARS-CoV-2 RNA detection in wastewater.

Recent advances in nitrous oxide production and mitigation in wastewater treatment

Nitrous oxide (N₂O) emitted from wastewater treatment plants has caused widespread concern. Over the past decade, people have made tremendous efforts to discover the microorganisms responsible for N₂O production, elucidate metabolic pathways, establish production models and formulate mitigation strategies. The ultimate goal of all these efforts is to shed new light on how N₂O is produced and how to reduce it, and one of the best ways is to find key opportunities by integrating the information obtained. This review article critically evaluates the knowledge gained in the field within a decade, especially in N₂O production microbiology, biochemistry, models and mitigation strategies, with a focus on denitrification. Previous research has greatly deepened the understanding of the N₂O generation mechanism, but further efforts are still needed due to the lack of standardized methodology for establishing N₂O mitigation strategies in full-scale systems. One of the challenges seems to be to convert the denitrification process from a net N₂O source into an effective sink, which is recommended as a key opportunity to reduce N₂O production in this review.

Reduction of Human Enteric and Indicator Viruses at a Wastewater Treatment Plant in Southern Louisiana, USA

This study assessed wastewater quality through the quantification of four human enteric viruses and the applicability of pepper mild mottle virus (PMMoV) and tobacco mosaic virus (TMV) as indicators of viral reduction during wastewater treatment. Thirty-three samples were collected from three steps of a wastewater treatment plant in Southern Louisiana, USA for a year between March 2017 and February 2018. Noroviruses of genogroup I were the most prevalent human enteric viruses in influent samples. The concentrations of PMMoV in influent samples (5.9 ± 0.7 log₁₀ copies/L) and biologically treated effluent samples (5.9 ± 0.5 log₁₀ copies/L) were significantly higher than those of TMV (P < 0.05), and the reduction ratio of PMMoV (1.0 ± 0.8 log₁₀) was found comparable to those of TMV and Aichi virus 1. Because of the high prevalence, high correlations with human enteric viruses, and lower reduction ratios, PMMoV was deemed an appropriate indicator of human enteric viral reduction during wastewater treatment process.

The Effectiveness of Activated Sludge Procedure and UV-C254 in Norovirus Inactivation in a Tunisian Industrial Wastewater Treatment Plant

The molecular detection of Norovirus GI and Norovirus GII in the Tunisian industrial wastewater treatment plant of Charguia I was conducted to test the effectiveness of secondary biological treatment using the activated sludge procedure and the UV-C₂₅₄ tertiary treatment radiation using a UV disinfection prototype to upgrade the quality of the purified wastewater. A total of 140 sewage samples were collected from the two lines of sewage treatment procedures. Norovirus GI and Norovirus GII have been found and quantified using Real-Time Reverse Transcription Polymerase Chain Reaction (qRT-PCR) in 66.4 and 86.4% of the collected wastewater samples. The Norovirus GI and GII mean concentration values got in the treated effluents showed a significant decrease of Norovirus viral content rates detected from upstream to downstream of activated sludge procedures and at the output of UV-C₂₅₄ treatment. These findings characterise and denote for the first time the effectiveness of biological and UV-C254 treatment for Norovirus GI and Norovirus GII removal in Tunis City, northern Tunisia. Also, these data underlined the fact that purified sewage makes up a route of gastroenteritis virus transmission and a cause of viral gastroenteritis associated with water-borne and food-borne outbreaks.

Viral indicators for tracking domestic wastewater contamination in the aquatic environment

Waterborne enteric viruses are an emerging cause of disease outbreaks and represent a major threat to global public health. Enteric viruses may originate from human wastewater and can undergo rapid transport through aquatic environments with minimal decay. Surveillance and source apportionment of enteric viruses in environmental waters is therefore essential for accurate risk management. However, individual monitoring of the >100 enteric viral strains that have been identified as aquatic contaminants is unfeasible. Instead, viral indicators are often used for quantitative assessments of wastewater contamination, viral decay and transport in water. An ideal indicator for tracking wastewater contamination should be (i) easy to detect and quantify, (ii) source-specific, (iii) resistant to wastewater treatment processes, and (iv) persistent in the aquatic environment, with similar behaviour to viral pathogens. Here, we conducted a comprehensive review of 127 peer-reviewed publications, to critically evaluate the effectiveness of several viral indicators of wastewater pollution, including common enteric viruses (mastadenoviruses, polyomaviruses, and Aichi viruses), the pepper mild mottle virus (PMMoV), and gut-associated bacteriophages (Type II/III FRNA phages and phages infecting human Bacteroides species, including crAssphage). Our analysis suggests that overall, human mastadenoviruses have the greatest potential to indicate contamination by domestic wastewater due to their easy detection, culturability, and high prevalence in wastewater and in the polluted environment. Aichi virus, crAssphage and PMMoV are also widely detected in wastewater and in the environment, and may be used as molecular markers for human-derived contamination. We conclude that viral indicators are suitable for the long-term monitoring of viral contamination in freshwater and marine environments and that these should be implemented within monitoring programmes to provide a holistic assessment of microbiological water quality and wastewater-based epidemiology, improve current risk management strategies and protect global human health.

Spatial and temporal profiles of enteric viruses in the coastal waters of Tokyo Bay during and after a series of rainfall events

Recreational activities in coastal waters that are polluted by enteric viruses can result in gastroenteritis etc. In this study, the pollution profiles of enteric viruses were examined in the coastal area of Tokyo Bay, Japan, by collecting 57 water samples from three different depths (0.5 m, 3.0 m, and 5.0 m) during and after a series of heavy rainfall events. Vertically spatial and temporal changes in the concentrations of NoV genogroup I (GI) and genogroup II (GII), pepper mild mottle virus (PMMoV), and Aichi virus (AiV) were determined using quantitative reverse transcription-polymerase chain reaction, while those of the bacterial indicator, Escherichia coli, and F-specific RNA bacteriophages (FRNA phages) were monitored using culture methods. PMMoV was highly abundant (1.4 × 10⁴-6.8 × 10⁶ genome copies/L), whereas the concentrations of the other enteric viruses were relatively low (AiV, 1.3 × 10²-2.9 × 10⁴; GI, 2.9 × 10-5.6 × 10³; GII, 2.5 × 10-1.2 × 10⁴ genome copies/L). All of the viruses showed lower fluctuations in concentration than E. coli, which increased up to 460-fold after the rainfall event and then decreased over the subsequent two weeks. The maximum vertical difference in E. coli concentration was observed immediately after the rainfall. The E. coli reached the surface and then gradually spread down, whereas the virus concentrations exhibited few fluctuations due to the remaining effects of the previous combined sewer overflows. These findings indicate that viruses have a relatively long retention period over fecal indicator bacteria in this coastal area.

Reduction of erythromycin resistance gene erm(F) and class 1 integron-integrase genes in wastewater by Bardenpho treatment

Wastewaters routinely contain antibiotic-resistant bacteria (ARB) and genes (ARG) that are removed to a varying degree during wastewater treatment. This study investigated the removal of the erythromycin ribosome methylase class F (erm(F)) and class 1 integron-integrase (intI1) genes at each stage from two water resource recovery facilities in southern Arizona. Although genes were significantly reduced by Bardenpho treatment, erm(F) and intI1 were still observed in ≥ 9 and 7 out of 12 secondary effluent samples. Primary processes via sedimentation or dissolved air flotation, as well as chlorine disinfection, did not significantly impact erm(F) and intI1 concentrations. Therefore, Bardenpho treatment was critical to reduce erm(F) and intI1. Concentrations of erm(F) and intI1 were compared with each other and other markers for anthropogenic pollution. Results from this study support intI1 as one suitable marker to measure erythromycin resistance genes in wastewater, as intI1 was found at higher concentrations, persisted more throughout treatment, and correlated with erm(F) at nearly every treatment stage. PRACTITIONER POINTS: Bardenpho treatment was the key process responsible for the reduction of intI1 and erm(F) genes during wastewater treatment. Primary treatment and chlorine disinfection did not impact erm(F) and intI1 gene concentrations. The intI1 gene is a suitable marker for measuring erm(F) genes in wastewater.

Potential indicators of virus transport and removal during soil aquifer treatment of treated wastewater effluent

Increased water demands have led to a notable interest in the use of treated wastewater for reuse. Typically, this results from the implementation of advanced treatment of final effluent from wastewater treatment plants prior to reuse for potable or non-potable purposes. Soil aquifer treatment (SAT) is a natural treatment process in which water from sources of varying quality is infiltrated into the soil to further improve its quality. The goal of this study was to determine the log₁₀ reduction values (LRVs) of viruses naturally present in treated effluent and evaluate two potential indicators of virus removal and transport, pepper mild mottle virus (PMMoV) and crAssphage, during SAT of treated effluent. Groundwater was sampled at three wells with different attributes within the Sweetwater Recharge Facility (SWRF) in Tucson, AZ. These sites vary greatly in operational parameters such as effluent infiltration rates and wetting/drying cycles, which may influence virus removal efficiency. Detection of adenovirus, enterovirus, PMMoV, and crAssphage were determined by qPCR/RT-qPCR and log₁₀ reduction values (LRVs) were determined. PMMoV and crAssphage were detected in groundwater associated with a set of recharge basins that exhibited shorter wetting/drying cycles and faster infiltration rates. LRVs for crAssphage and PMMoV at this site ranged from 3.9 to 5.8, respectively. Moreover, PMMoV was detected downflow of the SAT sites, indicating the potential degradation of microbial groundwater quality in the region surrounding managed aquifer recharge facilities. Overall, PMMoV and crAssphage showed potential as conservative process indicators of virus removal during SAT, particularly for attribution of LRV credits. Moreover, the detection of these viruses indicated the potential influence of wetting/drying cycles on virus removal by SAT, a parameter that has not yet been studied with respect to biological contaminants.

Environmental and Adaptive Changes Necessitate a Paradigm Shift for Indicators of Fecal Contamination

Changes in the occurrence, distribution, and seasonal variation of waterborne pathogens due to global climate change may increase the risk of human exposure to these microorganisms, thus heightening the need for more reliable surveillance systems. Routine monitoring of drinking water supplies and recreational waters is performed using fecal indicator microorganisms, such as Escherichia coli , Enterococcus spp., and coliphages. However, the presence and numbers of these indicators, especially E. coli and Enterococcus spp., do not correlate well with those of other pathogens, especially enteric viruses, which are a major cause of waterborne outbreaks associated with contaminated water and food, and recreational use of lakes, ponds, rivers, and estuarine waters. For that reason, there is a growing need for a surveillance system that can detect and quantify viral pathogens directly in water sources to reduce transmission of pathogens associated with fecal transmission. In this review, we present an updated overview of relevant waterborne enteric viruses that we believe should be more commonly screened to better evaluate water quality and to determine the safety of water use and reuse and of epidemiological data on viral outbreaks. We also discuss current methodologies that are available to detect and quantify these viruses in water resources. Finally, we highlight challenges associated with virus monitoring. The information presented in this review is intended to aid in the assessment of human health risks due to contact with water sources, especially since current environmental and adaptive changes may be creating the need for a paradigm shift for indicators of fecal contamination.

Comparative fate of CrAssphage with culturable and molecular fecal pollution indicators during activated sludge wastewater treatment

Wastewater treatment plants are typically monitored using fecal indicator bacteria to ensure adequate microbial water quality of the treated effluent. Fecal indicator bacteria exhibit poor correlation with virus fate in the environment, including during wastewater treatment. Viral-based microbial source tracking methods have the potential to overcome this limitation. The recently discovered human gut bacteriophage crAssphage is a promising viral human fecal indicator. In this current study, primary influent, primary effluent, secondary effluent, and final effluent of a conventional activated sludge wastewater treatment plant were analyzed for a suite of fecal indicators to evaluate the suitability of crAssphage as a wastewater process indicator for virus removal. CrAssphage was the most abundant fecal indicator measured through the wastewater treatment process. Culturable and molecular bacterial fecal pollution indicators showed higher removal than viral fecal pollution indicators, including crAssphage, confirming the necessity of a viral-specific fecal monitoring target. CrAssphage was strongly correlated with adenovirus and polyomavirus molecular indicators through the wastewater treatment process. Literature comparison demonstrated site-specific removal of molecular fecal indicators during wastewater treatment highlighting the need for local performance validation. The high abundance of crAssphage and correlation with pathogenic viruses suggests the potential suitability of crAssphage as a viral fecal pollution process indicator during wastewater treatment.

Applicability of crAssphage, pepper mild mottle virus, and tobacco mosaic virus as indicators of reduction of enteric viruses during wastewater treatment

This study was conducted to evaluate the applicability of crAssphage, pepper mild mottle virus (PMMoV), and tobacco mosaic virus (TMV) as indicators of the reduction of human enteric viruses during wastewater treatment. Thirty-nine samples were collected from three steps at a wastewater treatment plant (raw sewage, secondary-treated sewage, and final effluent) monthly for a 13-month period. In addition to the three indicator viruses, eight human enteric viruses [human adenoviruses, JC and BK polyomaviruses, Aichi virus 1 (AiV-1), enteroviruses, and noroviruses of genogroups I, II, and IV] were tested by quantitative PCR. Indicator viruses were consistently detected in the tested samples, except for a few final effluents for crAssphage and TMV. The mean concentrations of crAssphage were significantly higher than those of most tested viruses. The concentrations of crAssphage in raw sewage were positively correlated with the concentrations of all tested human enteric viruses (p <0.05), suggesting the applicability of crAssphage as a suitable indicator to estimate the concentrations of human enteric viruses in raw sewage. The reduction ratios of AiV-1 (1.8 ± 0.7 log₁₀) were the lowest among the tested viruses, followed by TMV (2.0 ± 0.3 log₁₀) and PMMoV (2.0 ± 0.4 log₁₀). Our findings suggested that the use of not only AiV-1 and PMMoV but also TMV as indicators of reductions in viral levels can be applicable during wastewater treatment.

Comprehensive comparison of chemically enhanced primary treatment and high-rate activated sludge in novel wastewater treatment plant configurations

Novel wastewater treatment plants (WWTPs) are designed to be more energy efficient than conventional plants. One approach to becoming more energy efficient is the pre-concentration of organic carbon through chemically enhanced primary treatment (CEPT) or high-rate activated sludge (HRAS). This study compares these approaches in terms of energy demand, operational costs, organic micropollutants (OMP), and virus removal efficiency. A CEPT pilot-scale plant was operated at a hydraulic retention time (HRT) of 30 min, and a lab-scale HRAS reactor was operated at an HRT of 2 h and a solid retention time (SRT) of 1 d in continuous mode. A minimum dose of 150 mg/L ferric chloride (FeCl₃) was required to achieve a threshold chemical oxygen demand (COD)-to-ammonium ratio below 2 g COD to 1 g of NH₄⁺ -N (fulfilling the requirement for a partial nitritation-anammox reactor), reaching high phosphate (PO₄^3-)-removal efficiency (>99%). A slightly lower COD recovery was attained in the HRAS reactor, due to the partial oxidation of the influent COD (15%). The lower PO₄^3- removal efficiency achieved in the HRAS configuration (13%) was enhanced to a comparable value of that achieved in CEPT by the addition of 30 mg/L FeCl₃ at the clarifier. The CEPT configuration was less energy-intensive (0.07 vs 0.13 kWh/m³ of wastewater) but had significantly higher operational costs than the HRAS-based configuration (6.0 vs 3.8 c€/m³ of wastewater). For OMPs with k_biol > 10 L/g_VSS·d, considerably higher removal efficiencies were achieved in HRAS (80-90%) than in CEPT (4-55%). For the remaining OMPs, the biotransformation efficiencies were generally higher in HRAS than in CEPT but were below 55% in both configurations. Finally, CEPT was less efficient than HRAS for virus removal. HRAS followed by FeCl₃ post-treatment appeared to be a more effective alternative than CEPT for COD pre-concentration in novel WWTPs.

Repeated pressurization as a potential cause of deterioration in virus removal by aged reverse osmosis membrane used in households

Reverse osmosis (RO) membrane is widely used for household water treatment in areas with limited access to safe drinking water; however, some studies documented deterioration in the quality of RO permeate. Repeated pressurization from intermittent operation in households is suspected to have an adverse effect on RO. This study aimed to evaluate virus removal by RO used in actual households as well as the water quality of permeate, and to elucidate the main cause of RO deterioration. We conducted a survey in households in Hanoi, Vietnam, to collect 27 membranes along with their usage history, where virus removal was investigated in laboratory. Of the used RO membranes, 22% did not show the protective level, >3 log₁₀ (99.9%) virus removal, recommended by World Health Organization. The differences in virus removal among Aichi virus, MS2 and φX-174 were <0.5 log₁₀. All membranes with estimated pressurization times of <4000 showed >3 log₁₀ virus removal, while 17% of membranes used for <3years, the manufacturers' warranty period, did not achieve the criterion. Therefore, virus removal performance may not be assured even if the users replace the membrane following the warranty period. Furthermore, more pressurized membranes exhibited significantly lower virus removal than less pressurized ones, suggesting a major role of repeated pressurization in the deterioration of RO. Coliforms were detected from 44% of the permeate of the point-of-use devices applying RO (RO-POU), raising concerns on the extrinsic contamination and regrowth of bacteria. Consequently, RO in households may deteriorate more rapidly than the manufactures' expectation due to repeated pressurization. RO in households should be replaced based on not only membrane age but also total pressurized times (i.e., 4000 times) to keep the protective level of virus removal. The deteriorated bacterial quality in RO permeate suggested the need for installing post-treatment, such as UV irradiation.

Interlaboratory Comparative Study to Detect Potentially Infectious Human Enteric Viruses in Influent and Effluent Waters

Wastewater represents the main reusable water source after being adequately sanitized by wastewater treatment plants (WWTPs). In this sense, only bacterial quality indicators are usually checked to this end, and human pathogenic viruses usually escape from both sanitization procedures and controls, posing a health risk on the use of effluent waters. In this study, we evaluated a protocol based on aluminum adsorption-precipitation to concentrate several human enteric viruses, including norovirus genogroup I (NoV GI), NoV GII, hepatitis A virus (HAV), astrovirus (HAstV), and rotavirus (RV), with limits of detection of 4.08, 4.64, 5.46 log genomic copies (gc)/L, 3.31, and 5.41 log PCR units (PCRU)/L, respectively. Furthermore, the method was applied in two independent laboratories to monitor the presence of NoV GI, NoV GII, and HAV in effluent and influent waters collected from five WWTPs at two different sampling dates. Concomitantly, a viability PMAxx-RT-qPCR was applied to all the samples to get information on the potential infectivity of both influent and effluent waters. The ranges of the titers in influent waters for NoV GI, NoV GII, RV, and HAstV were 4.80-7.56, 5.19-7.31 log gc/L, 5.41-6.52, and 4.59-7.33 log PCRU/L, respectively. In effluent waters, the titers ranged between 4.08 and 6.27, 4.64 and 6.08 log gc/L, < 5.51, and between 3.31 and 5.58 log PCRU/L. Moreover, the viral titers detected by viability RT-qPCR showed statistical differences with RT-qPCR alone, suggesting the potential viral infectivity of the samples despite some observed reductions. The proposed method could be applied in ill-equipped laboratories, due to the lack of a requirement for a specific apparatus (i.e., ultracentrifuge).

Fecal Source Tracking in A Wastewater Treatment and Reclamation System Using Multiple Waterborne Gastroenteritis Viruses

Gastroenteritis viruses in wastewater reclamation systems can pose a major threat to public health. In this study, multiple gastroenteritis viruses were detected from wastewater to estimate the viral contamination sources in a wastewater treatment and reclamation system installed in a suburb of Xi'an city, China. Reverse transcription plus nested or semi-nested PCR, followed by sequencing and phylogenetic analysis, were used for detection and genotyping of noroviruses and rotaviruses. As a result, 91.7% (22/24) of raw sewage samples, 70.8% (17/24) of the wastewater samples treated by anaerobic/anoxic/oxic (A²O) process and 62.5% (15/24) of lake water samples were positive for at least one of target gastroenteritis viruses while all samples collected from membrane bioreactor effluent after free chlorine disinfection were negative. Sequence analyses of the PCR products revealed that epidemiologically minor strains of norovirus GI (GI/14) and GII (GII/13) were frequently detected in the system. Considering virus concentration in the disinfected MBR effluent which is used as the source of lake water is below the detection limit, these results indicate that artificial lake may be contaminated from sources other than the wastewater reclamation system, which may include aerosols, and there is a possible norovirus infection risk by exposure through reclaimed water usage and by onshore winds transporting aerosols containing norovirus.

Evaluating the fate of bacterial indicators, viral indicators, and viruses in water resource recovery facilities

A year-long sampling campaign at nine water resource recovery facilities (WRRFs) was conducted to assess the treatability and fate of bacterial indicators, viral indicators, and viruses. Influent concentrations of viral indicators (male-specific and somatic coliphages) and bacterial indicators (Escherichia coli and enterococci) remained relatively constant, typically varying by one order of magnitude over the course of the year. Annual average bacterial indicator reduction ranged from 4.0 to 6.7 logs, and annual average viral indicator reduction ranged from 1.6 to 5.4 logs. Bacterial and viral indicator reduction depended on the WRRF's treatment processes, and bacterial indicator reduction was greater than viral indicator reduction for many processes. Viral reduction (adenovirus 41, norovirus GI, and norovirus GII) was more similar to viral indicator reduction than bacterial indicator reduction. Overall, this work suggests that viral indicator reduction in WRRFs is variable and depends on specific unit processes. Moreover, for the same unit treatment process, viral indicator reduction and bacterial indicator reduction can vary. PRACTITIONER POINTS: A year-long sampling campaign was conducted at nine water resource recovery facilities (WRRFs). The treatability and fate of bacterial indicators, viral indicators, and viruses were assessed. Viral indicator reduction in WRRFs is variable and depends on specific unit processes. For the same unit treatment process, viral indicator reduction and bacterial indicator reduction can vary.

Pepper mild mottle virus in wastewater in Egypt: a potential indicator of wastewater pollution and the efficiency of the treatment process

There is increasing evidence that the fecal indicator bacteria that are routinely used for testing water quality are inadequate for ensuring protection of the public health. Pepper mild mottle virus (PMMoV) has recently been suggested as an alternative indicator of human fecal contamination in water; however, in Egypt there are no data available about its occurrence and concentration in aquatic environment. The concentration of PMMoV in the influent and effluent of three wastewater treatment plants was measured using qRT-PCR over a period of one year and compared to that of human adenovirus (HAdV), which is considered an indicator for human fecal contamination. PMMoV was detected in ~ 94% of the influent samples and 78% of the effluent samples, with concentrations ranging from 3.9 × 10⁴ to 3.3 × 10⁸ genome copies/l (GC/l) in the influent and 3.9 × 10⁴ to 1.2 × 10⁷ GC/l in the effluent. Similarly, HAdV was identified in 88% and 78% of the influent and effluent samples, respectively. The HAdV concentration ranged between 1.5 × 10⁴ and 1.5 × 10⁷ GC/l for the influent and 2.6 × 10⁴ and 4.4 × 10⁶ GC/l for the effluent. No significant difference was found between the removal ratio of PMMoV and HAdV. Viral reduction of 0.2-1.9 log₁₀ and 0.2- 2.3 log₁₀ by the treatment process was observed for PMMoV and HAdV, respectively. Both viruses showed no clear seasonality. Our data support the use of PMMoV as a fecal indicator of wastewater contamination and a process indicator for the performance of the treatment process.