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Wastewater testing could also be used as an early-warning sign if the virus returns. Wastewater testing could also be used as an early-warning sign if the virus returns. A bird's eye view of a water cleaning plant purifying sewage water, Netherlands

Tracking SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant to naturally acquired or vaccine-induced immunity. To monitor New York City (NYC) for the presence of novel variants, we deep sequence most of the receptor binding domain coding sequence of the S protein of SARS-CoV-2 isolated from the New York City wastewater. Here we report detecting increasing frequencies of novel cryptic SARS-CoV-2 lineages not recognized in GISAID’s EpiCoV database. These lineages contain mutations that had been rarely observed in clinical samples, including Q493K, Q498Y, E484A, and T572N and share many mutations with the Omicron variant of concern. Some of these mutations expand the tropism of SARS-CoV-2 pseudoviruses by allowing infection of cells expressing the human, mouse, or rat ACE2 receptor. Finally, pseudoviruses containing the spike amino acid sequence of these lineages were resistant to different classes of receptor binding domain neutralizing monoclonal antibodies. We offer several hypotheses for the anomalous presence of these lineages, including the possibility that these lineages are derived from unsampled human COVID-19 infections or that they indicate the presence of a non-human animal reservoir. To monitor the presence of novel SARS-CoV-2 variants in New York City, Smyth et al. perform deep-sequencing of the receptor binding domain of S protein in wastewater samples and find novel cryptic lineages containing mutations affecting ACE2-tropism and showing decreased neutralization by antibodies.

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 log 10 ) were the lowest among the tested viruses, followed by TMV (2.0 ± 0.3 log 10 ) and PMMoV (2.0 ± 0.4 log 10 ). 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.

Water resources contamination has a worldwide impact and is a cause of global concern. The need for provision of clean water is becoming more and more demanding. Nanotechnology may support effective strategies for the treatment, use and reuse of water and the development of next-generation water supply systems. The excellent properties and effectiveness of nanomaterials make them particularly suitable for water/wastewater treatment. This review provides a comprehensive overview of the main categories of nanomaterials used in catalytic processes (carbon nanotubes/graphitic carbon nitride (CNT/g-C3N4) composites/graphene-based composites, metal oxides and composites, metal–organic framework and commercially available nanomaterials). These materials have found application in the removal of different categories of pollutants, including pharmaceutically active compounds, personal care products, organic micropollutants, as well as for the disinfection of bacterial, viral and protozoa microbial targets, in water and wastewater matrices. Apart from reviewing the characteristics and efficacy of the aforementioned nanoengineered materials for the removal of different pollutants, we have also recorded performance limitations issues (e.g., toxicity, operating conditions and reuse) for their practical application in water and wastewater treatment on large scale. Research efforts and continuous production are expected to support the development of eco-friendly, economic and efficient nanomaterials for real life applications in the near future.

We measured severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in primary sewage sludge in the New Haven, Connecticut, USA, metropolitan area during the Coronavirus Disease 2019 (COVID-19) outbreak in Spring 2020. SARS-CoV-2 RNA was detected throughout the more than 10-week study and, when adjusted for time lags, tracked the rise and fall of cases seen in SARS-CoV-2 clinical test results and local COVID-19 hospital admissions. Relative to these indicators, SARS-CoV-2 RNA concentrations in sludge were 0–2 d ahead of SARS-CoV-2 positive test results by date of specimen collection, 0–2 d ahead of the percentage of positive tests by date of specimen collection, 1–4 d ahead of local hospital admissions and 6–8 d ahead of SARS-CoV-2 positive test results by reporting date. Our data show the utility of viral RNA monitoring in municipal wastewater for SARS-CoV-2 infection surveillance at a population-wide level. In communities facing a delay between specimen collection and the reporting of test results, immediate wastewater results can provide considerable advance notice of infection dynamics. Testing sewage for the novel coronavirus reveals epidemiological trends.

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases 1 – 3 . SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing 4 , 5 . Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission. Emerging SARS-CoV-2 variants of concern were detected early and multiple cases of virus spread not captured by clinical genomic surveillance were identified using high-resolution wastewater and clinical sequencing.

Summary In recent decades, considerable effort has been devoted to finding microbial source‐tracking (MST) markers that are suitable to assess the health risks of faecally polluted waters, with no universal marker reported so far. In this study, the abundance and prevalence of a crAssphage‐derived DNA marker in wastewaters of human and animal origins were studied by a new qPCR assay with the ultimate aim of assessing its potential as an MST marker. crAssphage showed up to 106 GC/ml in the sewage samples of human origin, in both the total DNA and the viral DNA fraction. In wastewaters containing animal faecal remains, 39% of the samples were negative for the presence of the crAssphage sequence, while those showing positive results (41% of the samples) were at least 1 log10 unit lower than the samples of human origin. Noteworthy, the log10 values of the ratio (R) crAssphage (GC/ml)/Escherichia coli (CFU/ml) varied significantly depending on the human or animal origin (R > 1.5 for human samples and R < −1.5 for animal wastewater samples. This study opens the way for further research to explore if different specific animal variants of crAssphage exist and whether other zones of the crAssphage genome are better suited to source discrimination. High numbers of crAssphage was detected by qPCR in wastewaters with human fecal pollution although it was detected in pig, cow and poultry wastewaters for the first time. Hoewever, the log10 ratio crAssphage/E. coli allowed the precise detection of human fecal pollution.

As clinical specimens are collected and analyzed less for SARS-CoV-2, variant detection in wastewater provides a readily accessible and rich source of information on SARS-CoV-2 evolution. The detection of pathogen targets in wastewater samples using PCR assays is a sensitive, cost-effective way to monitor the levels of infectious diseases, like SARS-CoV-2, in a community. Unfortunately, because PCR-based methods are typically not used to distinguish between viral variants, most wastewater testing labs must rely on more expensive, time-consuming, and resource-intensive sequencing methods for these results. Building upon recent developments for variant detection using quantitative PCR, we developed and assessed a novel, customizable digital PCR-based genotyping method for SARS-CoV-2 variant detection in wastewater, which is more rapid, cost-effective, and accessible than sequencing. We characterize the method and offer insights for improvement in future implementations.

The SARS-CoV-2 can be excreted in feces and can reach sewage systems. Determining the presence of infective viral particles in feces and sewage is necessary to take adequate control measures and to elucidate new routes of transmission. Here, we have developed a sample concentration methodology that allows us to maintain viral infectivity. Feces of COVID-19 patients and wastewater samples have been analyzed both by molecular methods and cell culture. Our results show no evidence of infective viral particles, suggesting that fecal–oral transmission is not a primary route. However, larger-scale efforts are needed, especially with the emergence of new viral variants.

Research groups around the globe are looking to see whether urban wastewater monitoring can be integrated into surveillance systems for SARS-CoV-2 and other pathogens.