Variations among Viruses in Influent Water and Effluent Water at a Wastewater Plant over One Year as Assessed by Quantitative PCR and Metagenomics

Distinct distribution of HEV-3 subtypes across humans, animals, and environmental waters in Sweden

We previously observed a notable discrepancy in the distribution of HEV-3 subtypes between wastewater and clinical samples in Sweden. To confirm this observation and comprehensively elucidate HEV-3 circulation patterns across humans, animals, and environmental waters in Sweden, we analysed the HEV genetic diversity in archived wastewater samples between late 2016 and early 2018, clinical cases between 2012 and 2024, and all available Swedish sequences from the NCBI Virus database. HEV RNA was detected in all archived wastewater samples, with subtype 3c being the only subtype identified. In typed clinical cases, subtypes 3f (45/126) and 3c (44/126) were nearly equally distributed, though regional dominance varied. When incorporating human sequences from other Swedish studies, subtype 3f became dominant (75/168). Analysis of all available sequences revealed that 3f (113/136) was the dominant subtype in Sus scrofa (pigs and wild boars), while 3c (30/33) was dominant in environmental waters. These findings highlight the complex transmission dynamics of HEV-3 in Sweden. The near-absence of 3c in Swedish domestic pigs and wild boars, despite its high proportion in clinical cases, raises the question about the source of human 3c infection. In addition, the near-exclusive detection of 3c in wastewater suggests potential differences in viral shedding, disease severity of HEV-3 subtypes, or alternative host sources. This study emphasizes the importance of integrated One Health surveillance to track HEV circulation across reservoirs.

Epidemiological and Molecular Surveillance of Aichi Virus A at Different Stages of Sewage Treatment: A One-Year Study in the Southeast of Brazil

Enteric viruses, such as the Aichi virus (AiV), pose a potential health risk due to their high excretion rates through fecal elimination, limited removal during treatment processes, and prolonged survival, highlighting the need to assess the potential for exposure and disease transmission through sanitation systems. This study investigated the prevalence of AiV at three key stages of sewage treatment in the city of São José do Rio Preto, São Paulo state, Brazil, as well as its viral concentrations, infectious potential, and molecular characterization. The data were also analyzed for potential correlations with reported diarrheal disease cases in the city and the physicochemical properties of sewage. The methodology employed included Nested PCR, qPCR, Sanger Sequencing, and phylogenetic analysis, as well as infectivity testing in cell cultures. The prevalence of AiV throughout the year in raw sewage samples was 90.4%, 78.8% in post-anaerobic biological treatment, and 71.1% in post-chemical treatment, totaling 125 positive samples out of 156, being characterized as AiV genotype A. The virus also demonstrated persistence and infectious potential at all three stages analyzed. The AiV-A mean concentration ranged from 2.05 log10 to 4.64 GC/mL, 2.31 to 4.72 log10 GC/mL, and 2.13 to 2.85 log10 GC/mL for the same treatment stages, respectively. A significant difference (p ≤ 0.05) suggests higher viral concentrations in summer at the three sewage process points analyzed, while lower viral concentrations were observed in post-chemical treatment samples (p ≤ 0.01). Additionally, no statistically significant relationship was observed between the virus occurrence in samples and cases of acute diarrheal diseases in the city. In conclusion, this study highlights that much remains to be understood about AiV while providing valuable insights into the relationship between AiV, environmental factors, and public health.

In-depth comparison of untargeted and targeted sequencing for detecting virus diversity in wastewater

Sequencing approaches may enable monitoring of a broad range of viruses in wastewater, including potential emerging and non-reportable human viruses. Considering the fact that metagenomic sequencing may be non-specific for low-abundance human viruses, integration of viral amplification and enrichment strategies are proposed to enhance the accurate detection of a broad range of human viruses in municipal wastewater. In this study, we focused on the in-depth comparison analysis of three untargeted amplification methods (Multiple Displace Amplification [MDA], Reverse Transcription - MDA [RT-MDA], and a PCR-based random amplification [PCR-based]) and one targeted method (Twist Comprehensive Viral Research Panel [TWIST]) for detecting virus diversity in wastewater. In addition, we included the comparisons of two extraction kits (Qiagen QIAamp VIRAL RNA Mini Kit and ZymoBIOMICSTM DNA/RNA Minipre Kit) and four virus identification tools (Diamond blast, Kraken2, VirSorter2 and geNomad) for a systematic study. Performances of Qiagen and Zymo extraction kits in recovering viruses and human viruses in wastewater were comparable. By the three untargeted methods we detected 12,808 contigs with lengths longer than 10,000 bp. No contig longer than 10,000 bp was detected by the targeted method. Presence of human viruses were analyzed further by comparing the viral contigs against a custom Swiss-Prot human virus database. There were 45 viruses that are potentially associated with human health found in wastewater, 8 of them were unique to the targeted method and 7 of them were unique to the three untargeted methods. Four enteric viruses Mamastrovirus, Norovirus, Rotavirus and Sapovirus were detected with high abundance in samples prepared with the targeted method. Dimensional scaling analysis demonstrated the divergent virus and human virus communities from the untargeted and targeted methods. Patterns of virus and human virus populations identified by Kraken2 and geNomad were similar. Presence of selected viruses (SARS-CoV-2 [N1&N2], SC2, RSV, Norovirus GI and GII) were confirmed with ddPCR. This work indicates integration of untargeted and targeted sequencing methods, and complementary ddPCR can ensure the accurate detection of known and novel viruses using wastewater surveillance.

Virus detection in influent, activated sludge, and effluent from municipal wastewater treatment plants using composite and grab samples in Finland

Wastewater-based surveillance has been commonly used as a monitoring tool for public health. Also, viruses present in wastewater can pose a health risk. In this study, we screened enterovirus, rhinovirus, norovirus GI and GII, pan-adenovirus, and gastroenteritis-causing adenovirus F40/41 in different wastewater sample types using reverse transcription quantitative polymerase chain reaction and quantitative polymerase chain reaction. We analyzed composite influent samples (N = 22), grab influent samples (N = 20), composite effluent samples (N = 78), grab effluent samples (N = 21), and activated sludge samples (N = 34) collected from six municipal wastewater treatment plants in the Pirkanmaa region of Finland. We detected the viruses in the influent to discover if they had the potential to be monitored using wastewater-based surveillance. In addition, we studied viruses in effluent and activated sludge to detect viruses that persisted in treatment processes. Furthermore, all sample types were compared to discover differences in the viral contents of different wastewater sample types. We detected all the studied viruses in influent, while in activated sludge, we detected enterovirus, pan-adenovirus, and adenovirus F40/41, and in effluent enterovirus, norovirus GI and GII, pan-adenovirus, and adenovirus F40/41 were identified. In addition, the relative amount of all the viruses was the highest in the influent. Our study also showed that composite sampling was a more representative and sensitive method for virus monitoring in wastewater than grab sampling, as the relative amount of the viruses present in composite samples was higher than in grab samples. Since we found abundant viruses in effluent, further studies are required to assess their infectivity and potential health risks as environmental pollutants.

Development of Visual Loop-Mediated Isothermal Amplification Assays for Foodborne Hepatitis A Virus

(1) Background: There are many cases of human disease caused by the hepatitis A virus contamination of aquatic products, so the development of the rapid detection of hepatitis A virus in aquatic products is crucial. (2) Methods: In this study, we developed three visual loop-mediated isothermal amplification methods for the rapid and intuitive detection of hepatitis A virus in aquatic products. New specific LAMP primers were designed for the HAV-specific VP1 protein shell. (1) HNB dye was added to the LAMP reaction system. After the reaction, the color of the reaction mixture changed from violet to sky blue, showing a positive result. (2) Cresol red dye was added to the LAMP reaction system, and a positive result was indicated by orange, while a negative result was indicated by purple. (3) By labeling FIP with biotin and LF with 6-FAM, the amplified product simultaneously contained biotin and 6-FAM, which bound to the anti-biotin antibody on the gold nanoparticles on the lateral flow dipstick (LFD). Subsequently, biotin was further combined with the anti-fam antibody on the T-line of the test strip to form a positive test result. (3) Results: The three visual LAMP methods were highly specific for HAV. The sensitivity of the visual assay was 2.59 × 100 copies/μL. The positive detection ratio for 155 bivalve shellfish samples was 8.39%, which was the same as that for RT-qPCR. The three visual LAMP methods established in our work have better sensitivity than the international gold standard, and their operation is simple and requires less time. (4) Conclusions: The results can be obtained by eye color comparison and lateral flow dipsticks. Without the use of large-scale instrumentation, the sensitivity is the same as that of RT-qPCR. The test strips are lightweight, small in size, and easy to carry; they are suitable for emergency detection, on-site monitoring, field sampling, or remote farms and other non-laboratory environments for rapid identification.

Seasonality of enteric viruses and correlation of hepatitis a virus in wastewater with clinical cases

Human adenovirus F41 (HAdV-41), norovirus genogroup II (HNV-GII), rotavirus group A (RVA), and hepatitis A virus (HAV) are responsible for millions of illnesses every year in Canada. Wastewater-based epidemiology is one way to monitor the prevalence of these underreported (HAV) and non-reportable (HAdV-41, HNV-GII, RVA) food and waterborne enteric viruses. In this study, we monitored the presence of these four viruses in wastewater over 16 months from September 2022 until December 2023 using samples from two locations in southern Ontario. Viruses in 286 wastewater samples were concentrated using PEG precipitation and quantified using a multiplex RT-qPCR assay for HAdV-41, HNV-GII, and RVA, and a singleplex RT-qPCR assay for HAV. In agreement with historical clinical data, HNV-GII and RVA had seasonal peaks in wastewater in the winter (HNV-GII, up to 1.09 × 103 gene copies (GC)/mL) and spring (RVA, up to 1.20 × 102 GC/mL). The concentration of HAdV-41 in wastewater had a significant seasonal peak in the fall of 2022 (up to 4.65 × 104 GC/mL) that was not repeated in the fall of 2023. The detection of HAV in 24 of 127 samples was correlated with four clinical cases in one sewershed with a one-week wastewater lead time.

National survey of the rat hepatitis E virus in rodents in Spain, 2022 to 2023

BackgroundRat hepatitis E virus (ratHEV) is an emerging virus causing acute and chronic hepatitis in humans. Rats are the main natural reservoir of this pathogen. Large-scale studies assessing ratHEV circulation in rodents in Spain are lacking.AimWe aimed to determine the prevalence of ratHEV in rats in Spain and evaluate potential transmission risk to humans.MethodsWe designed a cross-sectional nationwide study where black (Rattus rattus) and Norway (R. norvegicus) rats were collected and analysed between 2022 and 2023 for ratHEV infection using real-time (RT)-qPCR testing of liver tissue. Sequencing and analysis of ratHEV shedding in faeces were carried out in positive animals.ResultsRatHEV was detected in 125 of the 481 rats analysed, supposing a prevalence of 26.0% (95 CI%: 22.3-30.1). Positive rats were found in urban (25.6%), and farm (29.8%) settings. Black rats (31.3%) had 1.5 times higher odds of being infected by the virus than Norway rats (22.5%) (p = 0.049). Significantly higher prevalence of ratHEV was detected in rodents sampled from southern (31.9%) than northern (17.8%) Spain (p = 0.003). Viral RNA was detected in faeces from 45.5% of infected rats. Phylogenetic analysis evidenced a wide genetic diversity of ratHEV sequences, some showing high homology with ratHEV strains found in patients from Spain.ConclusionsCirculation of ratHEV appears to be heterogeneous and the virus appears to be endemic among rat populations in Spain, highlighting the possible risk of zoonotic transmission of this emerging virus in this country.

Can Wastewater Surveillance Enhance Genomic Tracking of Climate-Driven Pathogens?

Climate change heightens the threat of infectious diseases in Europe, necessitating innovative surveillance methods. Based on 390 scientific papers, for the first time, this review associates climate-related pathogens, data related to their presence in wastewater, and associated available genomic detection methods. This deep analysis reveals a wide range of pathogens that can be tracked through methods such as quantitative and digital PCR, as well as genomic pathogen enrichment in combination with sequencing and metagenomics. Nevertheless, significant gaps remain in the development of methods, particularly for vector-borne pathogens, and in their general harmonization relating to performance criteria. By offering an overview of recent advancements while identifying critical gaps, we advocate for collaborative research and validation to integrate detection techniques into surveillance frameworks. This will enhance public health resilience against emerging infectious diseases driven by climate change.

Assessing the prevalence of human enteric viruses in hospital wastewater to evaluate the effectiveness of wastewater treatment systems

In this experiment, we employed Real-time PCR(RT-PCR) and metagenomic Next-Generation Sequencing (mNGS) techniques to detect the presence of Norovirus, Rotavirus Group A, Adenovirus Group F, and Astrovirus in untreated sewage from three major hospitals. A comparison with clinical lab test outcomes revealed Norovirus as having the highest infection rate, followed by Adenovirus Group F and Rotavirus Group A. Despite not testing for Astrovirus in clinical labs, its sewage detection rate was surpassed only by Norovirus, suggesting a potentially high clinical infection rate. Further analysis of these viruses in treated sewage revealed that chlorination failed to eliminate the virus, maintaining viral concentrations in the treated sewage between 10^2 and 10^3 copies/ml. Even though nucleic acid testing methods fail to detect viral actions, the possible danger they present to public safety should not be ignored. During this experiment, viral nucleic acid was extracted directly from the samples without prior concentration. This method, unlike conventional virus detection post-concentration, bypasses concerns such as recovery efficiency, offering a clearer representation of virus concentrations in water samples and facilitating easier operation.

First detection of Hepatitis E virus (Rocahepevirus ratti) in French urban wastewater: Potential implications for human contamination

Hepatitis E virus (HEV) is considered as an emerging zoonotic pathogen circulating in a wide range of animals. In recent decades, the genus Paslahepevirus frequently isolated in pigs were the most involved in human clinical practice. In addition, the genus Rocahepevirus have been isolated in rodents, and transmission to humans is increasingly reported worldwide, although gaps remain regarding the exposure factors. In this study, the presence of HEV was investigated in urban wastewater, swine slaughterhouse wastewater and river waters, in a geographical area where its circulation had previously been reported. In addition to the expected detection of Paslahepevirus in almost all waters samples collected, Rocahepevirus strains were detected with the same frequencies in urban and river waters, at concentrations up to 40-fold higher. No Rocahepeviruses were detected in swine slaughterhouse wastewater. This is the first study demonstrating the presence of Rocahepevirus in French wastewater. Although no evidence of transmission was reported among patients followed for a suspected HEV infection in the same area between April 2019 and October 2023 (i.e. 135/3078 serological tests positive for anti-HEV IgM detection; 46/822 blood samples positive for Paslahepevirus genome detection but none for Rocahepevirus), the circulation of Rocahepevirus in waters in such concentrations raises the question of the possible zoonotic transmission to human. Indeed, the waterborne transmission of HEV is now well documented in industrialized countries, and the exploration of the growing number of human infections in Europe involving Rocahepevirus has not until now made it possible to clarify the transmission routes.

Corrigendum to: "High prevalence of hepatitis E and rat hepatitis E viruses in wastewater in Gothenburg, Sweden" [One Health, volume 19, article number 100882]

[This corrects the article DOI: 10.1016/j.onehlt.2024.100882.].

High prevalence of hepatitis E and rat hepatitis E viruses in wastewater in Gothenburg, Sweden

Hepatitis E virus (HEV) and Rat Hepatitis E virus (RHEV), recognized for their zoonotic potential, pose significant public health concerns. Our previous research identified both viruses in effluent wastewater in Gothenburg, Sweden. However, there are lingering inquiries regarding the prevalence and genetic diversity of these viruses in influent wastewater, as well as the utility of wastewater surveillance in elucidating their community circulation dynamics. To address these knowledge gaps, we conducted weekly collection of wastewater samples at the Rya wastewater treatment plant in Gothenburg throughout 2023. The concentrations of HEV and RHEV were quantified using quantitative polymerase chain reaction (qPCR). Additionally, two semi/nested-PCR were utilized to amplify viral strains. Furthermore, HEV strains from patients within the same region, as well as other regions in Sweden in 2023, were incorporated into the analysis. Remarkably, we observed a high prevalence of HEV (86%) and RHEV (98%) in wastewater samples, with the majority of HEV sequences identified as subtype 3c/i (9/12). In contrast, HEV subtype 3f was the most sequenced among clinical patient samples (6/12). Notably, previously unreported HEV-3b and unclassified strains were detected in wastewater. Almost all RHEV strains (20/21) were clustered into European groups, with none of the RHEV genetically close to strains previously found in human cases. The notable discordance in prevalence and identified subtypes of HEV-3 in wastewater compared to clinical samples suggests either a significant underdiagnosis of HEV infections or differences in viral loads and shedding durations among humans between HEV-3 subtypes. This underscores the urgent need for improved diagnostic techniques and heightened awareness of HEV transmission dynamics. Furthermore, the consistent detection of RHEV in wastewater underscores the necessity for further investigations to assess the potential role of RHEV in hepatitis cases of unknown etiology, given that most currently available clinical diagnostic assays fail to detect RHEV.

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.

Multisite community-scale monitoring of respiratory and enteric viruses in the effluent of a nursing home and in the inlet of the local wastewater treatment plant

The aim of this study was to evaluate whether community-level monitoring of respiratory and enteric viruses in wastewater can provide a comprehensive picture of local virus circulation. Wastewater samples were collected weekly at the wastewater treatment plant (WWTP) inlet and at the outlet of a nearby nursing home (NH) in Burgundy, France, during the winter period of 2022/2023. We searched for the pepper mild mottle virus as an indicator of fecal content as well as for the main respiratory viruses [severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza, and respiratory syncytial virus] and enteric viruses (rotavirus, sapovirus, norovirus, astrovirus, and adenovirus). Samples were analyzed using real-time reverse transcription PCR-based methods. SARS-CoV-2 was the most frequently detected respiratory virus, with 66.7% of positive samples from the WWTP and 28.6% from the NH. Peaks of SARS-CoV-2 were consistent with the chronological incidence of infections recorded in the sentinel surveillance and the nearby hospital databases. The number of positive samples was lower in the NH than in WWTP for the three respiratory viruses. Enteric viruses were frequently detected, most often sapovirus and norovirus genogroup II, accounting both for 77.8% of positive samples in the WWTP and 57.1% and 37%, respectively, in the NH. The large circulation of sapovirus was unexpected in particular in the NH. Combined wastewater surveillance using simple optimized methods can be a valuable tool for monitoring viral circulation and may serve as a suitable early warning system for identifying both local outbreaks and the onset of epidemics. These results encourage the application of wastewater-based surveillance (WBS) to SARS-CoV2, norovirus, and sapovirus.IMPORTANCEWBS provides valuable information on the spread of epidemic viruses in the environment using appropriate and sensitive detection methods. By monitoring the circulation of viruses using reverse transcription PCR methods in wastewater from the inlet of a wastewater treatment plant and the outlet of a nearby retirement home (connected to the same collective sewer network), we aimed to demonstrate that implementing combined WBS at key community sites allows effective detection of the occurrence of respiratory (influenza, respiratory syncytial virus, and SARS-CoV-2) and enteric (norovirus, rotavirus, and sapovirus) virus infections within a given population. This analysis on a localized scale provided new information on the viral circulation in the two different sites. Implementing WBS to monitor the circulation or the emergence of infectious diseases is an important means of alerting the authorities and improving public health management. WBS could participate actively to the health of humans, animals, and the environment.

Surveillance of Emerging Rodent-Borne Pathogens in Wastewater in Taiwan: A One Health Approach

Leptospirosis and hantavirus syndrome are two major rodent-borne diseases in Taiwan. Rocahepevirus ratii (RHEV), a virus closely related to hepatitis E virus (HEV, Paslahepevirus balayani), is emerging and has been reported to cause hepatitis in humans. We employed wastewater-based epidemiology to actively monitor rodent-borne pathogens, and the correlations with human cases were evaluated. Wastewater was collected using grab sampling at 11 sites along a sewer system including influents and effluents at a wastewater treatment plant in Tamsui, New Taipei City, Taiwan, monthly during June 2023 to May 2024. The presence of pathogens was examined by reverse transcription-polymerase chain reaction (RT-PCR). The result showed an overall positivity rate of 38.2% (50/131). Leptospira was detected most often (48/131, 36.6%), and RHEV and hantaviruses were found once each during the study period. Sequencing identified Leptospira interrogans close to isolates from rodents and human cases, while sequences of hantavirus and RHEV were most similar to isolates from rodents. No significant correlation was found with human cases or positive samples for rodent DNA. Here, we present an example of a One Health approach applying wastewater to environmental surveillance for the early detection and prevention of emerging diseases.

Development of a wastewater based infectious disease surveillance research system in South Korea

Wastewater-based epidemiology has been used in pathogen surveillance for microorganisms at the community level. This study was conducted to determine the occurrence and trends of infectious pathogens in sewage from Yongin city and the relationships between these pathogens and the incidence of infectious diseases in the community. From December 2022 to November 2023, we collected inflow water from six wastewater treatment plants in Yongin city twice a month. The analyzed microorganisms included 15 respiratory viruses, 7 pneumonia-causing bacteria, 19 acute diarrhea-causing pathogens, SARS-CoV-2, Zika virus, hepatitis A virus, poliovirus, Mpox, and measles. They were detected through real-time PCR and conventional PCR. The concentrations of 9 pathogens among them were additionally analyzed using quantitative real time PCR. The correlation was confirmed through statistical analysis with the rate of detection for pathogens reported by the Korea Disease Control and Prevention Agency. Influenza A virus, human adenovirus, and human rhinovirus were moderately correlated (rho values of 0.45 to 0.58). Campylobacter spp. and sapovirus were strong correlated (rho values of 0.62, 0.63). Enteropathogenic E. coli, human coronavirus, and norovirus GII were very strong correlated (rho values of 0.86 to 0.92). We were able to identify the prevalence of respiratory viral infections, pneumonia, and acute diarrhea-causing pathogens in the community through wastewater-based epidemiology data. This study will be helpful in establishing a system for future surveillance of infectious diseases present in sewage.

Rotavirus in Water Environments: A Systematic Review and Meta-Analysis

Background

Despite the adoption of rotavirus vaccines, sporadic outbreaks of the virus have been reported in many parts of the world. These outbreaks are facilitated by several factors including the ease of transmission of rotavirus through water environments. This systematic review aimed to determine the global prevalence of rotavirus in water environments.

Methodology

Comprehensive Boolean searches were conducted in PubMed, SCOPUS, and Web of Science. A total of 75 eligible studies were included in the study, from which data was extracted for both systematic review and meta-analysis. Extracted prevalence data was grouped according to six water categories: drinking water, untreated sewage, treated sewage, surface water, groundwater, and others. A single-group prevalence meta-analysis was conducted in RStudio version 4.3.3 subjecting the data to the random-effects model.

Results

The included studies were conducted in 32 countries that span 5 continents: Africa, Asia, Europe, North America, and South America. The pooled prevalence of rotavirus in water environments was 40.86%. Among the individual water environments, untreated sewage had the highest prevalence (68.27%), followed by treated sewage (53.07%), surface water (33.40%), groundwater (25.64%) and drinking water (9.46%). Continental stratification of the prevalence data was as follows: Africa (51.75%), Asia (32.48%), Europe (55.90%), North America (41.80%), and South America (28.51%).

Conclusion

There is a high prevalence of rotavirus in water environments, especially in untreated sewage, and in Europe. Further research is needed to find more efficient methods that can effectively eliminate rotavirus to insignificant levels in water environments.

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preamplification pipelines (specific to RNA viruses, DNA viruses or both) for viral genome sequencing using spiked-in Phosphate Buffered Saline and sewage samples containing known concentrations of viruses. We found that compared to the pipeline targeting all genome types, the RNA pipeline performed better in detecting RNA viruses in both spiked and unspiked sewage samples, allowing the detection of various mammalian viruses including members from the Reoviridae, Picornaviridae, Astroviridae and Caliciviridae. However, the DNA-specific pipeline did not improve the detection of mammalian DNA viruses. We also measured viral recovery by quantitative reverse transcription polymerase chain reaction and assessed the impact of genetic background (non-viral genetic material) on viral coverage. Our results indicate that viral recoveries were generally lower in sewage (average of 11.0%) and higher in Phosphate Buffered Saline (average of 23.4%) for most viruses. Additionally, spiked-in viruses showed lower genome coverage in sewage, demonstrating the negative effect of genetic background on sequencing. Finally, correlation analysis revealed a relationship between virus concentration and genome normalized reads per million, indicating that viral metagenomic sequencing can be semiquantitative.

Advances in wastewater analysis revealing the co-circulating viral trends of noroviruses and Omicron subvariants

Co-presence of enveloped and non-enveloped viruses is common both in community circulation and in wastewater. Community surveillance of infections requires robust methods enabling simultaneous quantification of multiple viruses in wastewater. Using enveloped SARS-CoV-2 Omicron subvariants and non-enveloped norovirus (NoV) as examples, this study reports a robust method that integrates electronegative membrane (EM) concentration, viral inactivation, and RNA preservation (VIP) with efficient capture and enrichment of the viral RNA on magnetic (Mag) beads, and direct detection of RNA on the beads. This method provided improved viral recoveries of 80 ± 4 % for SARS-CoV-2 and 72 ± 5 % for Murine NoV. Duplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays with newly designed degenerate primer-probe sets offered high PCR efficiencies (90-91 %) for NoV (GI and GII) targets and were able to detect as few as 15 copies of the viral RNA per PCR reaction. This technique, combined with duplex detection of NoV and multiplex detection of Omicron, successfully quantified NoV (GI and GII) and Omicron variants in the same sets of 94 influent wastewater samples collected from two large wastewater systems between July 2022 and June 2023. The wastewater viral RNA results showed temporal changes of both NoV and Omicron variants in the same wastewater systems and revealed an inverse relationship of their emergence. This study demonstrated the importance of a robust analytical platform for simultaneous surveillance of enveloped and non-enveloped viruses in wastewater. The ability to sensitively determine multiple viral pathogens in wastewater will advance applications of wastewater surveillance as a complementary public health tool.

Wastewater-Based Epidemiology for Viral Surveillance from an Endemic Perspective: Evidence and Challenges

Wastewater-based epidemiology (WBE) is currently used to monitor not only the spread of the viral SARS-CoV-2 pandemic but also that of other viruses in endemic conditions, particularly in the absence of syndromic surveillance. The continuous monitoring of sewage requires high expenditure and significant time investments, highlighting the need for standardized methods and structured monitoring strategies. In this context, we conducted weekly wastewater monitoring in northwestern Tuscany (Italy) and targeted human adenovirus (HAdV), norovirus genogroup II (NoVggII), enterovirus (EV), and SARS-CoV-2. Samples were collected at the entrances of treatment plants and concentrated using PEG/NaCl precipitation, and viral nucleic acids were extracted and detected through real-time reverse transcription qPCR. NoVggII was the most identified target (84.4%), followed by HAdV, SARS-CoV-2, and EV. Only HAdV and EV exhibited seasonal peaks in spring and summer. Compared with data that were previously collected in the same study area (from February 2021 to September 2021), the results for SARS-CoV-2 revealed a shift from an epidemic to an endemic pattern, at least in the region under investigation, which was likely due to viral mutations that led to the spreading of new variants with increased resistance to summer environmental conditions. In conclusion, using standardized methods and an efficient monitoring strategy, WBE proves valuable for viral surveillance in pandemic and epidemic scenarios, enabling the identification of temporal-local distribution patterns that are useful for making informed public health decisions.

Occurrence and fate of CECs (OMPs, ARGs and pathogens) during decentralised treatment of black water and grey water

Decentralised wastewater treatment is becoming a suitable strategy to reduce cost and environmental impact. In this research, the performance of two technologies treating black water (BW) and grey water (GW) fractions of urban sewage is carried out in a decentralised treatment of the wastewater produced in three office buildings. An Anaerobic Membrane Bioreactor (AnMBR) treating BW and a Hybrid preanoxic Membrane Bioreactor (H-MBR) containing small plastic carrier elements, treating GW were operated at pilot scale. Their potential on reducing the release of contaminants of emerging concern (CECs) such as Organic Micropollutants (OMPs), Antibiotic Resistance Genes (ARGs) and pathogens was studied. After 226 d of operation, a stable operation was achieved in both systems: the AnMBR removed 92.4 ± 2.5 % of influent COD, and H-MBR removed 89.7 ± 3.5 %. Regarding OMPs, the profile of compounds differed between BW and GW, being BW the matrix with more compounds detected at higher concentrations (up to μg L-1). For example, in the case of ibuprofen the concentrations in BW were 23.63 ± 3.97 μg L-1, 3 orders of magnitude higher than those detected in GW. The most abundant ARGs were sulfonamide resistant genes (sul1) and integron class 1 (intl1) in both BW and GW. Pathogenic bacteria counts were reduced between 1 and 3 log units in the AnMBR. Bacterial loads in GW were much lower than in BW, being no bacterial re-growth observed for the GW effluents after treatment in the H-MBR. None of the selected enteric viruses was detected in GW treatment line.

Isolation and characterization of novel plasmid-dependent phages infecting bacteria carrying diverse conjugative plasmids

IMPORTANCE

This work was undertaken because plasmid-dependent phages can reduce the prevalence of conjugative plasmids and can be leveraged to prevent the acquisition and dissemination of ARGs by bacteria. The two novel phages described in this study, Lu221 and Hi226, can infect Escherichia coli, Salmonella enterica, Kluyvera sp. and Enterobacter sp. carrying conjugative plasmids. This was verified with plasmids carrying resistance determinants and belonging to the most common plasmid families among Gram-negative pathogens. Therefore, the newly isolated phages could have the potential to help control the spread of ARGs and thus help combat the antimicrobial resistance crisis.

Targeted community wastewater surveillance for SARS-CoV-2 and Mpox virus during a festival mass-gathering event

Wastewater surveillance has emerged recently as a powerful approach to understanding infectious disease dynamics in densely populated zones. Wastewater surveillance, while promising as a public health tool, is often hampered by slow turn-around times, complex analytical protocols, and resource-intensive techniques. In this study, we evaluated an affinity capture method and microfluidic digital PCR as a rapid approach to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), mpox (formerly known as monkeypox) virus, and fecal indicator, pepper mild mottle virus (PMMoV) in wastewater during a mass-gathering event. Wastewater samples (n = 131) were collected from residential and commercial manholes, pump stations, and a city's wastewater treatment plant. The use of Nanotrap® Microbiome Particles and microfluidic digital PCR produced comparable results to other established methodologies, with reduced process complexity and analytical times, providing same day results for public health preparedness and response. Using indigenous SARS-CoV-2 and PMMoV in wastewater, the average viral recovery efficiency was estimated at 10.1 %. Both SARS-CoV-2 N1 and N2 genes were consistently detected throughout the sampling period, with increased RNA concentrations mainly in wastewater samples collected from commercial area after festival mass gatherings. The mpox virus was sporadically detected in wastewater samples during the surveillance period, without distinct temporal trends. SARS-CoV-2 RNA concentrations in the city's wastewater mirrored the city's COVID-19 cases, confirming the predictive properties of wastewater surveillance. Wastewater surveillance continues to be beneficial for tracking diseases that display gastrointestinal symptoms, including SARS-CoV-2, and can be a powerful tool for sentinel surveillance. However, careful site selection and a thorough understanding of community dynamics are necessary when performing targeted surveillance during temporary mass-gathering events as potential confirmation bias may occur.

Rocahepevirus ratti as an Emerging Cause of Acute Hepatitis Worldwide

The hepatitis E virus (HEV) is a widespread human infection that causes mainly acute infection and can evolve to a chronic manifestation in immunocompromised individuals. In addition to the common strains of hepatitis E virus (HEV-A), known as Paslahepevirus balayani, pathogenic to humans, a genetically highly divergent rat origin hepevirus (RHEV) can cause hepatitis possessing a potential risk of cross-species infection and zoonotic transmission. Rocahepevirus ratti, formerly known as Orthohepevirus C, is a single-stranded RNA virus, recently reassigned to Rocahepevirus genus in the Hepeviridae family, including genotypes C1 and C2. RHEV primarily infects rats but has been identified as a rodent zoonotic virus capable of infecting humans through the consumption of contaminated food or water, causing both acute and chronic hepatitis cases in both animals and humans. This review compiles data concluding that 60% (295/489) of RHEV infections are found in Asia, being the continent with the highest zoonotic and transmission potential. Asia not only has the most animal cases but also 16 out of 21 human infections worldwide. Europe follows with 26% (128/489) of RHEV infections in animals, resulting in four human cases out of twenty-one globally. Phylogenetic analysis and genomic sequencing will be employed to gather global data, determine epidemiology, and assess geographical distribution. This information will enhance diagnostic accuracy, pathogenesis understanding, and help prevent cross-species transmission, particularly to humans.

Surveillance for rat hepatitis E in wastewater networks, Italy

IMPORTANCE

Hepatitis E virus (HEV) infection constitutes a significant health problem worldwide. In recent years, in addition to the zoonotic HEV3 and HEV4, emerging highly divergent hepevirus of rat origin (rat HEV [RHEV]) has been associated with human acute and chronic hepatitis. As environmental surveillance can be a complementary tool to explore emerging viruses of human and rodent origin, we investigated the epidemiology and the genetic variability of RHEV targeting 14 wastewater treatment plants in an Italian geographic area considered a hot spot for HEV infection in humans. Our results revealed that RHEV is a significant component of the wastewater microbiota with viral RNA detected in 43.9% of the specimens tested, adding further evidence to the need to investigate more in depth the real burden of RHEV infections in humans.

Measures against COVID-19 affected the spread of human enteric viruses in a Swedish community, as found when monitoring wastewater

The quantification of viral genomes in wastewater reflects the prevalence of viral infections within the community. Knowledge of how the spread of common enteric viruses in the community was affected by the Swedish COVID-19 interventions is limited. To investigate this, the weekly wastewater samples collected for monitoring SARS-CoV-2 throughout the COVID-19 pandemic at the Rya sewage treatment plant in Gothenburg were also analyzed for adenovirus, norovirus GII, astrovirus, and rotavirus. The amount of each viral genome was quantified by real-time-qPCR and compared with the quantity of these viral genomes in wastewater from 2017. The results showed that the winter seasonality of norovirus GII and rotavirus in wastewater observed in 2017 was interrupted shortly after the introduction of the COVID-19 interventions, and they remained at low level throughout the pandemic. The circulation pattern of astrovirus and adenovirus was less affected. When the COVID-19 restrictions were lifted in 2022, a dramatic increase was observed in the amount of norovirus GII, rotavirus, and adenovirus genomes in wastewater. The changes in abundance and seasonality of some viruses identified through wastewater monitoring were consistent with changes in the number of patients diagnosed with these viruses. These findings suggest that moderate intervention to prevent COVID-19 significantly reduced the spread of some enteric viruses in the community. The results show that wastewater monitoring is a valuable tool for detecting the spread and outbreaks of viral infections that may cause gastroenteritis also when people do not seek medical help, such as during the COVID-19 pandemic.

The Virucidal Effect of the Chlorination of Water at the Initial Phase of Disinfection May Be Underestimated If Contact Time Calculations Are Used

For the microbiological safety of drinking water, disinfection methods are used to remove or inactivate microorganisms. Chlorine and chlorine dioxide are often used as disinfectants in drinking water treatment plants (DWTPs). We investigated the effectiveness of these chemicals in inactivate echovirus 30 (E30), simian 11 rotavirus (RV SA11), and human adenovirus type 2 (HAdV2) in purified water from a DWTP. Within two minutes of contact, chlorine dioxide inactivated E30 by 4-log10, RV SA11 by 3-log10, and HAdV2 could not be detected, while chlorine reduced E30 by 3-log10, RV SA11 by 2-3log10, and HAdV2 by 3-4log10. However, viral genomes could be detected for up to 2 h using qPCR. The CT method, based on a combination of disinfectant concentration and contact time, during such a short initial phase, is problematic. The high concentrations of disinfectant needed to neutralize organic matter may have a strong immediate effect on virus viability. This may lead to the underestimation of disinfection and overdosing of disinfectants in water with organic contamination. These results are useful for the selection of disinfection systems for reuse of treated wastewater and in the risk assessment of water treatment processes using chlorine and chlorine dioxide.

Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria

Effective infectious disease surveillance in high-risk regions is critical for clinical care and pandemic preemption; however, few clinical diagnostics are available for the wide range of potential human pathogens. Here, we conduct unbiased metagenomic sequencing of 593 samples from febrile Nigerian patients collected in three settings: i) population-level surveillance of individuals presenting with symptoms consistent with Lassa Fever (LF); ii) real-time investigations of outbreaks with suspected infectious etiologies; and iii) undiagnosed clinically challenging cases. We identify 13 distinct viruses, including the second and third documented cases of human blood-associated dicistrovirus, and a highly divergent, unclassified dicistrovirus that we name human blood-associated dicistrovirus 2. We show that pegivirus C is a common co-infection in individuals with LF and is associated with lower Lassa viral loads and favorable outcomes. We help uncover the causes of three outbreaks as yellow fever virus, monkeypox virus, and a noninfectious cause, the latter ultimately determined to be pesticide poisoning. We demonstrate that a local, Nigerian-driven metagenomics response to complex public health scenarios generates accurate, real-time differential diagnoses, yielding insights that inform policy.

Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs?

Antimicrobial resistance (AMR) is a global threat to human and animal health and well-being. To understand AMR dynamics, it is important to monitor resistant bacteria and resistance genes in all relevant settings. However, while monitoring of AMR has been implemented in clinical and veterinary settings, comprehensive monitoring of AMR in the environment is almost completely lacking. Yet, the environmental dimension of AMR is critical for understanding the dissemination routes and selection of resistant microorganisms, as well as the human health risks related to environmental AMR. Here, we outline important knowledge gaps that impede implementation of environmental AMR monitoring. These include lack of knowledge of the 'normal' background levels of environmental AMR, definition of high-risk environments for transmission, and a poor understanding of the concentrations of antibiotics and other chemical agents that promote resistance selection. Furthermore, there is a lack of methods to detect resistance genes that are not already circulating among pathogens. We conclude that these knowledge gaps need to be addressed before routine monitoring for AMR in the environment can be implemented on a large scale. Yet, AMR monitoring data bridging different sectors is needed in order to fill these knowledge gaps, which means that some level of national, regional and global AMR surveillance in the environment must happen even without all scientific questions answered. With the possibilities opened up by rapidly advancing technologies, it is time to fill these knowledge gaps. Doing so will allow for specific actions against environmental AMR development and spread to pathogens and thereby safeguard the health and wellbeing of humans and animals.

Viral Metagenomics as a Tool to Track Sources of Fecal Contamination: A One Health Approach

The One Health framework recognizes that human, animal, and environmental health are linked and highly interdependent. Fecal contamination of water, soil, foodstuff, and air may impact many aspects of One Health, and culture, PCR-based, and sequencing methods are utilized in the detection of fecal contamination to determine source, load, and risk to inform targeted mitigation strategies. Viruses, particularly, have been considered as fecal contamination indicators given the narrow host range many exhibit and their association with other biological contaminants. Culture- and molecular-based methods are considered the gold-standards for virus detection and for determining specific sources of fecal contamination via viral indicators. However, viral metagenomics is also being considered as a tool for tracking sources of fecal contamination. In the present review, studies tracking potential sources of fecal contamination in freshwaters, marine waters, foodstuff, soil, and air using viral metagenomics are discussed to highlight the potential of viral metagenomics for optimizing fecal source tracking. Limitations of the use of viral metagenomics to track fecal contamination sources, including sample processing, nucleic acid recovery, sequencing depth, and bioinformatics are also discussed. Finally, the present review discusses the potential of viral metagenomics as part of the toolbox of methods in a One Health approach.

Occurrence of Hepatitis A Virus in Water Matrices: A Systematic Review and Meta-Analysis

Hepatitis A is a common form of viral hepatitis. It is usually transmitted through the ingestion of contaminated food and water. This systematic review was carried out to summarise the overall prevalence of Hepatitis A virus (HAV) in different water matrices: untreated and treated wastewater, surface water, groundwater, drinking water, and others (e.g., irrigation water and floodwater). The literature search was performed in four databases: PubMed, Web of Science, Global Index Medicus, and Excerpta Medica Database. Heterogeneity (I2) was assessed using the χ2 test on the Cochran Q statistic and H parameters. A total of 200 prevalence data from 144 articles were included in this meta-analysis. The overall prevalence of HAV in water matrices was 16.7% (95% CI: 13.4−20.3). The prevalence for individual matrix was as follows: 31.4% (95% CI: 23.0−40.4) untreated wastewater, 18.0% (95% CI: 9.5−28.2) treated wastewater, 15.0% (95% CI: 10.1−20.5) surface water, 2.3% (95% CI: 0.1−6.0) in groundwater, 0.3% (95% CI: 0.0−1.7) in drinking water, and 8.5% (95% CI: 3.1−15.6) in other matrices. The prevalence was higher in low-income economies (29.0%). Africa and Eastern Mediterranean were the regions with higher HAV prevalence values. This study showed a high heterogeneity (I2 > 75%) with a significant publication bias (p value Egger test < 0.001). The results of this review suggest that water matrices could be an important route of HAV transmission even in industrialized countries, despite the lower prevalence compared to less industrialized countries, and the availability of advanced water management systems. More effective water/wastewater treatment strategies are needed in developing countries to limit the environmental circulation of HAV.

Monthly dynamics of microbial communities and variation of nitrogen-cycling genes in an industrial-scale expanded granular sludge bed reactor

Introduction

The expanded granular sludge bed (EGSB) is a major form of anaerobic digestion system during wastewater treatment. Yet, the dynamics of microbial and viral communities and members functioning in nitrogen cycling along with monthly changing physicochemical properties have not been well elucidated.

Methods

Here, by collecting the anaerobic activated sludge samples from a continuously operating industrial-scale EGSB reactor, we conducted 16S rRNA gene amplicon sequencing and metagenome sequencing to reveal the microbial community structure and variation with the ever-changing physicochemical properties along within a year.

Results

We observed a clear monthly variation of microbial community structures, while COD, the ratio of volatile suspended solids (VSS) to total suspended solids (TSS) (VSS/TSS ratio), and temperature were predominant factors in shaping community dissimilarities examined by generalized boosted regression modeling (GBM) analysis. Meanwhile, a significant correlation was found between the changing physicochemical properties and microbial communities (p <0.05). The alpha diversity (Chao1 and Shannon) was significantly higher (p <0.05) in both winter (December, January, and February) and autumn (September, October, and November) with higher organic loading rate (OLR), higher VSS/TSS ratio, and lower temperature, resulting higher biogas production and nutrition removal efficiency. Further, 18 key genes covering nitrate reduction, denitrification, nitrification, and nitrogen fixation pathways were discovered, the total abundance of which was significantly associated with the changing environmental factors (p <0.05). Among these pathways, the dissimilatory nitrate reduction to ammonia (DNRA) and denitrification had the higher abundance contributed by the top highly abundant genes narGH, nrfABCDH, and hcp. The COD, OLR, and temperature were primary factors in affecting DNRA and denitrification by GBM evaluation. Moreover, by metagenome binning, we found the DNRA populations mainly belonged to Proteobacteria, Planctomycetota, and Nitrospirae, while the denitrifying bacteria with complete denitrification performance were all Proteobacteria. Besides, we detected 3,360 non-redundant viral sequences with great novelty, in which Siphoviridae, Podoviridae, and Myoviridae were dominant viral families. Interestingly, viral communities likewise depicted clear monthly variation and had significant associations with the recovered populations (p <0.05).

Discussion

Our work highlights the monthly variation of microbial and viral communities during the continuous operation of EGSB affected by the predominant changing COD, OLR, and temperature, while DNRA and denitrification pathways dominated in this anaerobic system. The results also provide a theoretical basis for the optimization of the engineered system.

Novel Virus Identification through Metagenomics: A Systematic Review

Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.

Multiple Novel Human Norovirus Recombinants Identified in Wastewater in Pretoria, South Africa by Next-Generation Sequencing

The genogroup II genotype 4 (GII.4) noroviruses are a major cause of viral gastroenteritis. Since the emergence of the Sydney_2012 variant, no novel norovirus GII.4 variants have been reported. The high diversity of noroviruses and periodic emergence of novel strains necessitates continuous global surveillance. The aim of this study was to assess the diversity of noroviruses in selected wastewater samples from Pretoria, South Africa (SA) using amplicon-based next-generation sequencing (NGS). Between June 2018 and August 2020, 200 raw sewage and final effluent samples were collected fortnightly from two wastewater treatment plants in Pretoria. Viruses were recovered using skimmed milk flocculation and glass wool adsorption-elution virus recovery methods and screened for noroviruses using a one-step real-time reverse-transcription PCR (RT-PCR). The norovirus BC genotyping region (570-579 bp) was amplified from detected norovirus strains and subjected to Illumina MiSeq NGS. Noroviruses were detected in 81% (162/200) of samples. The majority (89%, 89/100) of raw sewage samples were positive for at least one norovirus, compared with 73% (73/100) of final effluent samples. Overall, a total of 89 different GI and GII RdRp-capsid combinations were identified, including 51 putative novel recombinants, 34 previously reported RdRp-capsid combinations, one emerging novel recombinant and three Sanger-sequencing confirmed novel recombinants.

Quantification and fate of plasmid-specific bacteriophages in wastewater: Beyond the F-coliphages

Plasmid-specific bacteriophages specifically infect bacteria carrying conjugal plasmids. While wastewater has been used as isolation source for such phages, to date, only the distribution and ecology of RNA phages specific to the F plasmid have been described, because they serve as a water quality indicator. Yet, several other plasmid classes have higher clinical and ecological relevance, and the distribution, fate, and ecology of the phages that target them remain uncharacterized. We aimed to (i) provide an experimental platform to quantify the abundance of plasmid-specific phages applicable to several different conjugal plasmid classes, (ii) describe the distribution of such phages in wastewater systems, and (iii) relate their abundance to plasmid abundance and to municipal wastewater treatment processes. We introduced four model conjugal plasmids, belonging to incompatibility groups IncP-1, IncN, IncHI1, or IncF into an avirulent Salmonella enterica strain, for which somatic phages are at low abundance in wastewater. These strains were used in double layer agar assays with waters from contrasting sources. Plasmid-specific phages were common in wastewater but rare in river water. Hospital wastewater contained significantly more IncP-1-, but fewer IncF- and IncN- specific phages than domestic wastewater. This pattern did not match that of plasmid abundance estimated by Inc group targeting high-throughput quantitative PCR. The comparison between influent and effluent of wastewater treatment plants revealed a reduction in phage concentration by ca. 2 log, without significant contribution of primary settling. Overall, the ubiquity of these phages hints at their importance for plasmid ecology, and can provide opportunities in water quality monitoring and in ecological management of mobile resistance genes.

Hepatitis E Virus in Water Environments: A Systematic Review and Meta-analysis

Hepatitis E virus (HEV) is responsible for acute hepatitis in humans, through foodborne, zoonotic, and waterborne transmission routes. This study aimed to assess the prevalence of HEV in water matrices. Six categories were defined: untreated and treated wastewater, surface water (river, lake, and seawater), drinking water, groundwater, and other water environments (irrigation water, grey water, reservoir water, flood water, and effluent of pig slaughterhouse). We searched PubMed, Web of Science, Global Index Medicus, and Excerpta Medica Database. Study selection and data extraction were performed by at least two independent investigators. Heterogeneity (I2) was assessed using the χ2 test on the Cochran Q statistic and H parameter. Sources of heterogeneity were explored by subgroup analysis. This study is registered with PROSPERO, number CRD42021289116. We included 87 prevalence studies from 58 papers, 66.4% of which performed in Europe. The overall prevalence of HEV in water was 9.8% (95% CI 6.4-13.7). The prevalence was higher in untreated wastewater (15.1%) and lower in treated wastewater (3.8%) and in drinking water (4.7%). In surface water, prevalence was 7.4%, and in groundwater, the percentage of positive samples, from only one study available, was 8.3%. Overall, only 36.8% of the studies reported the genotype of HEV, with genotype 3 (HEV-3) prevalent (168 samples), followed by HEV-1 (148 sample), and HEV-4 (2 samples). High-income countries were the most represented with 59/87 studies (67.8%), while only 3/87 (3.5%) of the studies were performed in low-income countries. The overall prevalence obtained of this study was generally higher in industrialized countries. Risk of bias was low in 14.9% of the studies and moderate in 85.1%. The results of this review showed the occurrence of HEV in different waters environments also in industrialized countries with sanitation and safe water supplies. While HEV transmission to humans through water has been widely demonstrated in developing countries, it is an issue still pending in industrialized countries. Better knowledge on the source of pollution, occurrence, survival in water, and removal by water treatment is needed to unravel this transmission path.

The amount of SARS-CoV-2 RNA in wastewater relates to the development of the pandemic and its burden on the health system

Virus surveillance in wastewater can be a useful indicator of the development of the COVID-19 pandemic in communities. However, knowledge about how the amount of SARS-CoV-2 RNA in wastewater relates to different data on the burden on the health system is still limited. Herein, we monitored the amount of SARS-CoV-2 RNA and the spectrum of virus variants in weekly pooled wastewater samples for two years from mid-February 2020 and compared with several clinical data. The two-year monitoring showed the weekly changes in the amount of viral RNA in wastewater preceded the hospital care needs for COVID-19 and the number of acute calls on adult acute respiratory distress by 1-2 weeks during the first three waves of COVID-19. Our study demonstrates that virus surveillance in wastewater can predict the development of a pandemic and its burden on the health system, regardless of society's test capacity and possibility of tracking infected cases.

The UV Dose Used for Disinfection of Drinking Water in Sweden Inadequately Inactivates Enteric Virus with Double-Stranded Genomes

Irradiation with ultraviolet light (UV) at 254 nm is effective in inactivating a wide range of human pathogens. In Sweden, a UV dose of 400 J/m² is often used for the treatment of drinking water. To investigate its effect on virus inactivation, enteric viruses with different genomic organizations were irradiated with three UV doses (400, 600, and 1000 J/m²), after which their viability on cell cultures was examined. Adenovirus type 2 (double-stranded DNA), simian rotavirus 11 (double-stranded RNA), and echovirus 30 (single-stranded RNA) were suspended in tap water and pumped into a laboratory-scale Aquada 1 UV reactor. Echovirus 30 was reduced by 3.6-log₁₀ by a UV dose of 400 J/m². Simian rotavirus 11 and adenovirus type 2 were more UV resistant with only 1-log₁₀ reduction at 400 J/m² and needed 600 J/m² for 2.9-log₁₀ and 3.1-log₁₀ reductions, respectively. There was no significant increase in the reduction of viral viability at higher UV doses, which may indicate the presence of UV-resistant viruses. These results show that higher UV doses than those usually used in Swedish drinking water treatment plants should be considered in combination with other barriers to disinfect the water when there is a risk of fecal contamination of the water.

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

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

Norovirus detection in wastewater and its correlation with human gastroenteritis: a systematic review and meta-analysis

Norovirus (NoV) is a major cause of sporadic cases and outbreaks of acute gastroenteritis (AGE), thereby imposing threat to health globally. It is unclear how quantitation of wastewater NoV reflects the incidence of human AGE infections; therefore, we conducted this systematic review and meta-analysis of published NoV wastewater surveillance studies. A literature search was performed, and all studies on NoV wastewater surveillance were identified. Quantitative results were evaluated. The results showed that the overall detection rate of NoV in wastewater was 82.10% (95% confidence interval [CI]: 74.22-89.92%); NoV concentration was statistically significant in terms of season (P < 0.001), with higher concentration in spring and winter. There were positive correlations between NoV GII concentration in wastewater and GII AGE cases (rs = 0.51, 95% CI: 0.18-0.74, I2 = 0%), total AGE cases (rs = 0.40, 95% CI: 0.15-0.61, I2 = 23%) and NoV outbreaks (rs = 0.47, 95% CI: 0.30-0.62, I2 = 0%). Results of cross-correlation analysis of partial data indicated that variations in GII concentration were consistent with or ahead of those in the number of AGE cases. The diversity of NoV genotypes in wastewater was elucidated, and the dominant strains in wastewater showed a consistent temporal distribution with those responsible for human AGE. Our study demonstrated the potential association of NoV detected in wastewater with AGE infections, and further studies are needed to confirm this conclusion.

Virus removal during sewage treatment by anaerobic membrane bioreactor (AnMBR): The role of membrane fouling

Anaerobic membrane bioreactor (AnMBR) is a low-energy and promising solution for sewage treatment. During the treatment, the fouled membrane of AnMBR is recognized as an important barrier against pathogenic viruses. Here, the role of membrane fouling of an AnMBR at room temperature in the virus removal was investigated using MS2 bacteriophage as a virus surrogate. Results revealed that the virus removal efficiency of AnMBR was in the range of 0.2 to 3.6 logs, gradually increasing with the course of AnMBR operation. Virus removal efficiency was found to be significantly correlated with transmembrane pressure (R²=0.92, p<0.01), especially in the rapid fouling stage, indicating that membrane fouling was the key factor in the virus removal. The proportion of virus decreased from 52.03% to 15.04% in the membrane foulants when membrane fouling was aggravating rapidly, yet increased from 0.74% to 21.52% in the mixed liquor. Meanwhile, the permeate flux dramatically dropped. These imply that the primary rejection mechanism of virus by membrane in the slow fouling stage is the virus adsorption onto membrane, while the sieving effect is the main reason in the rapid fouling stage. Ex-situ virus rejection test unveiled that the cake layer was the main contributor to the overall virus rejection, while the greatest resistance-specific virus rejection was provided by the organic pore blocking. This paper provides operation strategies to balance enhanced virus removal and high permeate flux by regulating the membrane fouling process.

Targeted wastewater surveillance of SARS-CoV-2 on a university campus for COVID-19 outbreak detection and mitigation

Targeted wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been proposed by the United States Centers for Disease Control and Prevention's National Wastewater Surveillance System as a complementary approach to clinical surveillance to detect the presence of Coronavirus Disease 2019 (COVID-19) at high-density facilities and institutions such as university campuses, nursing homes, and correctional facilities. In this study we evaluated the efficacy of targeted wastewater surveillance of SARS-CoV-2 RNA together with individual-level testing for outbreak mitigation on a university campus during Fall 2020 semester. Wastewater samples (n = 117) were collected weekly from manholes or sewer cleanouts that receive wastewater inputs from dormitories, community-use buildings, and a COVID-19 isolation dormitory. Quantitative RT-PCR N1 and N2 assays were used to measure SARS-CoV-2 nucleocapsid genes in wastewater. Due to varying human waste input in different buildings, pepper mild mottle virus (PMMV) RNA was also measured in all samples and used to normalize SARS-CoV-2 N1 and N2 RNA wastewater concentrations. In this study, temporal trends of SARS-CoV-2 in wastewater samples mirrored trends in COVID-19 cases detected on campus. Normalizing SARS-CoV-2 RNA concentrations using human fecal indicator, PMMV enhanced the correlation between N1 and N2 gene abundances in wastewater with COVID-19 cases. N1 and N2 genes were significant predictors of COVID-19 cases in dormitories, and the N2 gene was significantly correlated with the number of detected COVID-19 cases in dormitories. By implementing several public health surveillance programs include targeted wastewater surveillance, individual-level testing, contact tracing, and quarantine/isolation facilities, university health administrators could act decisively during an outbreak on campus, resulting in rapid decline of newly detected COVID-19 cases. Wastewater surveillance of SARS-CoV-2 is a proactive outbreak monitoring tool for university campuses seeking to continue higher education practices in person during the COVID-19 pandemic.

Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types

Viral metagenomes (viromes) are a valuable untargeted tool for studying viral diversity and the central roles viruses play in host disease, ecology, and evolution. Establishing effective methods to concentrate and purify viral genomes prior to sequencing is essential for high quality viromes. Using virus spike-and-recovery experiments, we stepwise compared two common approaches for virus concentration, ultrafiltration and iron chloride flocculation, across diverse matrices: wastewater influent, wastewater secondary effluent, river water, and seawater. Viral DNA was purified by removing cellular DNA via chloroform cell lysis, filtration, and enzymatic degradation of extra-viral DNA. We found that viral genomes were concentrated 1-2 orders of magnitude more with ultrafiltration than iron chloride flocculation for all matrices and resulted in higher quality DNA suitable for amplification-free and long-read sequencing. Given its widespread use and utility as an inexpensive field method for virome sampling, we nonetheless sought to optimize iron flocculation. We found viruses were best concentrated in seawater with five-fold higher iron concentrations than the standard used, inhibition of DNase activity reduced purification effectiveness, and five-fold more iron was needed to flocculate viruses from freshwater than seawater—critical knowledge for those seeking to apply this broadly used method to freshwater virome samples. Overall, our results demonstrated that ultrafiltration and purification performed better than iron chloride flocculation and purification in the tested matrices. Given that the method performance depended on the solids content and salinity of the samples, we suggest spike-and-recovery experiments be applied when concentrating and purifying sample types that diverge from those tested here.

Human Adenovirus Molecular Characterization in Various Water Environments and Seasonal Impacts in Riyadh, Saudi Arabia

The regular monitoring of water environments is essential for preventing waterborne virus-mediated contamination and mitigating health concerns. We aimed to detect human adenovirus (HAdV) in the Wadi Hanifah (WH) and Wadi Namar (WN) lakes, King Saud University wastewater treatment plant (KSU-WWTP), Manfouha-WWTP, irrigation water (IW), and AnNazim landfill (ANLF) in Riyadh, Saudi Arabia. HAdV hexon sequences were analyzed against 71 HAdV prototypes and investigated for seasonal influence. ANLF had the highest HAdV prevalence (83.3%). Remarkably, the F species of HAdV, especially serotype 41, predominated. Daily temperature ranges (22–45 °C and 10–33 °C) influenced the significance of the differences between the locations. The most significant relationship of ANLF and IW to WH and KSU-WWTP was found at the high-temperature range (p = 0.001). Meanwhile, WN was most correlated to ANLF at the low-temperature range (p < 0.0001). Seasonal influences on HAdV prevalence were insignificant despite HAdV’s high prevalence in autumn and winter months, favoring low temperatures (high: 22–25 °C, low: 14–17 °C) at five out of six locations. Our study provides insightful information on HAdV prevalence and the circulating strains that can address the knowledge gap in the environmental impacts of viruses and help control viral diseases in public health management.

Surveillance of wastewater revealed peaks of SARS-CoV-2 preceding those of hospitalized patients with COVID-19

SARS-CoV-2 was discovered among humans in Wuhan, China in late 2019, and then spread rapidly, causing a global pandemic. The virus was found to be transmitted mainly by respiratory droplets from infected persons or by direct contact. It was also shown to be excreted in feces, why we investigated whether the virus could be detected in wastewater and if so, to which extent its levels reflects its spread in society. Samples of wastewater from the city of Gothenburg, and surrounding municipalities in Sweden were collected daily from mid-February until June 2020 at the Rya wastewater treatment plant. Flow proportional samples of wastewater were collected to ensure that comparable amounts were obtained for analysis. Daily samples were pooled into weekly samples. Virus was concentrated on a filter and analyzed by RT-qPCR. The amount of SARS-CoV-2 varied with peaks approximately every four week, preceding variations in number of newly hospitalized patients by 19-21 days. At that time virus testing for COVID-19 was limited to patients with severe symptoms. Local differences in viral spread was shown by analyzing weekly composite samples of wastewater from five sampling sites for four weeks. The highest amount of virus was found from the central, eastern, and northern parts of the city. SARS-CoV-2 was also found in the treated effluent wastewater from the WWTP discharged into the recipient, the Göta River, although with a reduction of 4-log_10. The viral peaks with regular temporal intervals indicated that SARS-CoV-2 may have a cluster spread, probably reflecting that the majority of infected persons only spread the disease during a few days. Our results are important for both the planning of hospital care and to rapidly identify and intervene against local spread of the virus.