Multiple lineages of SARS-CoV-2 have been identified featuring distinct sets of genetic changes that confer to the virus higher transmissibility and ability to evade existing immunity. The continuous ...evolution of SARS-CoV-2 may pose challenges for current treatment options and diagnostic tools. In this study, we have first evaluated the performance of the 14 WHO-recommended real-time reverse transcription (RT)-PCR assays currently in use for the detection of SARS-CoV-2 and found that only one assay has reduced performance against Omicron. We then developed a new duplex real-time RT-PCR assay based on the amplification of two ultra-conserved elements present within the SARS-CoV-2 genome. The new duplex assay successfully detects all of the tested SARS-CoV-2 variants of concern (including Omicron sub-lineages BA.4 and BA.5) from both clinical and wastewater samples with high sensitivity and specificity. The assay also functions as a one-step droplet digital RT-PCR assay. This new assay, in addition to clinical testing, could be adopted in surveillance programs for the routine monitoring of SARS-CoV-2's presence in a population in wastewater samples. Positive results with our assay in conjunction with negative results from an Omicron-specific assay may provide timely indication of the emergence of a novel SARS-CoV-2 variant in a certain community and thereby aid public health interventions.
Abstract Background Wastewater surveillance (WWS) acts as a vigilant sentinel system for communities, analysing sewage to protect public health by detecting outbreaks and monitoring trends in ...pathogens and contaminants. To achieve a thorough comprehension of present and upcoming practices and to identify challenges and opportunities for standardisation and improvement in WWS methodologies, two EU surveys were conducted targeting over 750 WWS laboratories across Europe and other regions. The first survey explored a diverse range of activities currently undertaken or planned by laboratories. The second survey specifically targeted methods and quality controls utilised for SARS-CoV-2 surveillance. Results The findings of the two surveys provide a comprehensive insight into the procedures and methodologies applied in WWS. In Europe, WWS primarily focuses on SARS-CoV-2 with 99% of the survey participants dedicated to this virus. However, the responses highlighted a lack of standardisation in the methodologies employed for monitoring SARS-CoV-2. The surveillance of other pathogens, including antimicrobial resistance, is currently fragmented and conducted by only a limited number of laboratories. Notably, these activities are anticipated to expand in the future. Survey replies emphasise the collective recognition of the need to enhance the accuracy of results in WWS practices, reflecting a shared commitment to advancing precision and effectiveness in WWS methodologies. Conclusions These surveys identified a lack of standardised common procedures in WWS practices and the need for quality standards and reference materials to enhance the accuracy and reliability of WWS methods in the future. In addition, it is important to broaden surveillance efforts beyond SARS-CoV-2 to include other emerging pathogens and antimicrobial resistance to ensure a comprehensive approach to protecting public health.
To better understand local water quality pollution by organic contaminants and how it affects communities around the world, “The Gems of Water” project aims to build a co-creative global
...scientist-citizen
approach, actively engaging citizens and connecting them to scientists and to advanced water monitoring tools. The project applies the Stir Bar Sorptive Extraction technique with an advanced wide-screening method, used to assess the occurrence of agrochemicals, industrial compounds and pharmaceuticals in surface and groundwaters. In collaboration between Coral Conservation and the Joint Research Centre (JRC) of the European Commission, a study was conducted to identify contamination patterns which could be affecting the coral reef by investigating water quality in local rivers in the south Caribbean region of Costa Rica, an area characterized by agricultural activities linked to bananas production. Coral Conservation is a youth-led non-governmental organization focused on activities for the conservation and protection of the coral reef. Sampling locations for the study were jointly determined with members of the Coral Conservation group and included 13 sampling points from 3 different rivers and 2 wells. The pilot study allowed evaluation of the workflow for
scientist-citizen
collection of water quality data, whereby participants from the local community conduct sampling and extraction activities, while the wide-screening analysis of about 230 contaminants is performed at the JRC Water Laboratory. Considering the lessons learned through the Costa Rican pilot case, in this paper we discuss the elements required for successful
scientist-citizen
projects. Challenges are described and outlooks provided to improve citizens’ engagement projects and others participatory water quality monitoring activities. “The Gems of Water” project contributes to data collection of rarely monitored compounds in rural and remote areas through a
scientist-citizen
approach, addressing knowledge gaps on water quality and building bridges between science and society. The outlook is for such an innovative approach to support bottom-up management actions which can lead to alternative solutions in water quality management.
Addressing the global water quality challenges requires collaborative efforts, multidisciplinary approaches, and innovative solutions. Here we report on the success of a special collective ...intelligence “hackathon event,” organized by five United Nations agencies and the European Commission, with the aim of reinventing engagement with diverse experts and stakeholders to tackle real-world challenges in water quality monitoring and assessment. Participants from diverse backgrounds and regions convened to devise inventive solutions in four key challenge areas, including (1) transformation of water quality data into water stewardship action, (2) empowering citizen scientists to improve water quality, (3) incorporation of Indigenous communities and their water quality knowledge in global information systems, and (4) routine monitoring of antimicrobial resistance in water. The hackathon approach fosters collective intelligence in a safe, creative and collaborative environment, enabling participants to harness their collective knowledge, expertise and skills. Key outcomes were conceptualizing practical frameworks and tailored toolboxes for diverse water quality innovations to improve monitoring, empower communities, and support policy-making. Emphasis was placed on the purpose and value of interdisciplinary collaborations to address complex global challenges, showcasing synergies between technology, environmental science, and social engagement. Hackathons are catalysts for collaborative innovation which unlock future endeavors in harnessing collective intelligence to safeguard our most precious resource – water.
•71 water samples from the Danube River and its tributaries were analysed.•Most relevant micropollutants were benzotriazoles, pharmaceuticals, organophosphorus compounds, and PFOS/A.•PFOS ...concentrations exceed its environmental quality standard (EQS).•Concentrations and loads are similar for the years 2007 and 2013.
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In the third Joint Danube Survey (JDS3), emerging organic contaminants were analysed in the dissolved water phase of samples from the Danube River and its major tributaries. Analyses were performed using solid-phase extraction (SPE) followed by ultra-high-pressure liquid chromatography triple-quadrupole mass spectrometry (UHPLC-MS-MS) and gas chromatography–mass spectrometry (GC–MS). The polar organic compounds analysed by UHPLC-MS-MS were 1H-benzotriazole, methylbenzotriazoles, carbamazepine, 10,11-dihydro-10,11-dihydroxy-carbamazepine, diclofenac, sulfamethox-azole, 2,4-D (2,4-dichlorophenoxyacetic acid), MCPA (2-methyl-4-chlorophenoxyacetic acid), metolachlor, cybutryne (irgarol), terbutryn, DEET (N,N-diethyl-m-toluamide), and several perfluoroalkyl acids (C6–C9; C8=perfluorooctanoic acid (PFOA)) and perfluorooctansulfonic acid (PFOS). In addition, several organophosphorus flame retardants were analysed by GC-MS. The most relevant compounds identified in the 71 water samples, in terms of highest median and maximum concentrations, were 1H-benzotriazole, tris(1-chloro-2-propyl)phosphate (TCPP), methylbenzotriazoles, carbama-zepine and its metabolite, DEET, sulfamethoxazole, tris(isobutyl)phosphate (TiBP), tris(2-chloroethyl)phosphate (TCEP), PFOA, PFOS and diclofenac. The concentrations of these compounds in the samples were generally below the environmental quality standard (EQS) threshold values, with the exception of PFOS, the concentration of which exceeded the annual average water EQS limit of 0.65ng/L along the whole river, and also exceeded the fish biota EQS of 9.1μg/kg. In addition, the proposed EQS for diclofenac, of 0.1μg/L, was exceeded in the Arges River in Romania (255ng/L).
Water-soluble polar organic contaminants are discharged by rivers, cities, and ships into the oceans. Little is known on the fate, pollution effects, and thresholds of toxic chemical mixtures in the ...marine environment. A new trace analytical method was developed for the multi-compound analysis of polar organic chemical contaminants in marine waters. The method is based on automated solid-phase extraction (SPE) of one-liter water samples followed by ultrahigh-pressure liquid chromatography triple-quadrupole linear ion-trap mass spectrometry (UHPLC–QTRAP
®
MS). Marine water samples from the open Adriatic Sea taken 16 km offshore from Venice (Italy) were analyzed. Method limits of quantification (LOQs) in the low picogram per liter (pg/l) concentration range were achieved. Among the 67 target chemicals analyzed, 45 substances could be detected above the LOQ. The chemicals detected at the highest concentrations were caffeine (up to 367 ng/l), nitrophenol (36 ng/l), 2,4-dinitrophenol (34 ng/l), 5-methyl-1
H
-benzotriazole (18.5 ng/l), sucralose (11 ng/l), 1
H
-benzotriazole (9.2 ng/l), terbuthylazine (9 ng/l), alachlor (7.7 ng/l), atrazine-desisopropyl (6.6 ng/l), diethyltoluamide (DEET) (5.0 ng/l), terbuthylazine-desethyl (4.3 ng/l), metolachlor (2.8 ng/l), perfluorooctanoic acid (PFOA) (2.5 ng/l), perfluoropentanoic acid (PFPeA) (2.3 ng/l), linuron (2.3 ng/l), perfluorohexanoic acid (PFHxA) (2.2 ng/l), diuron (2.0 ng/l), perfluorohexane sulfonate (PFHxS) (1.6 ng/l), simazine (1.6 ng/l), atrazine (1.5 ng/l), and perfluorooctane sulfonate (PFOS) (1.3 ng/l). Higher concentrations were detected during summer due to increased levels of tourist activity during this period.
•Going beyond measuring the total SARS-CoV-2 RNA concentration in wastewater.•Integrating genome sequencing to wastewater-based epidemiology.•Approach to obtain high-quality and full coverage of ...SARS-CoV-2 genome.•The genome sequencing method used worked for all wastewater samples.•Diversity of SARS-CoV-2 VOCs in 54 European municipalities revealed through genome sequencing of wastewater samples.
For community-level monitoring, the European Commission under the EU Sewage Sentinel System recommends wastewater-based SARS-CoV-2 surveillance. Tracking SARS-CoV-2 variants in a community is pivotal for appropriate public health response. Genome sequencing of SARS-CoV-2 in wastewater samples for tracking variants is challenging, often resulting in low coverage genome sequences, thereby impeding the detection of the SARS-CoV-2 mutations. Therefore, we aimed at high-coverage SARS-CoV-2 genome sequences from sewage samples which we successfully accomplished. This first pan-European surveillance compared the mutation profiles associated with the variants of concerns: B.1.1.7, P.1, B.1.351 and B.1.617.2 across 20 European countries, including 54 municipalities. The results highlight that SARS-CoV-2 variants detected in the wastewater samples mirror the variants profiles reported in clinical data. This study demonstrated that >98% coverage of SARS-CoV-2 genomic sequences is possible and can be used to track SARS-CoV-2 mutations in wastewater to support identifying variants circulating in a city at the community level.
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In the year 2010, effluents from 90 European wastewater treatment plants (WWTPs) were analyzed for 156 polar organic chemical contaminants. The analyses were complemented by effect-based monitoring ...approaches aiming at estrogenicity and dioxin-like toxicity analyzed by in vitro reporter gene bioassays, and yeast and diatom culture acute toxicity optical bioassays. Analyses of organic substances were performed by solid-phase extraction (SPE) or liquid–liquid extraction (LLE) followed by liquid chromatography tandem mass spectrometry (LC-MS-MS) or gas chromatography high-resolution mass spectrometry (GC-HRMS). Target microcontaminants were pharmaceuticals and personal care products (PPCPs), veterinary (antibiotic) drugs, perfluoroalkyl substances (PFASs), organophosphate ester flame retardants, pesticides (and some metabolites), industrial chemicals such as benzotriazoles (corrosion inhibitors), iodinated x-ray contrast agents, and gadolinium magnetic resonance imaging agents; in addition biological endpoints were measured. The obtained results show the presence of 125 substances (80% of the target compounds) in European wastewater effluents, in concentrations ranging from low nanograms to milligrams per liter. These results allow for an estimation to be made of a European median level for the chemicals investigated in WWTP effluents. The most relevant compounds in the effluent waters with the highest median concentration levels were the artificial sweeteners acesulfame and sucralose, benzotriazoles (corrosion inhibitors), several organophosphate ester flame retardants and plasticizers (e.g. tris(2-chloroisopropyl)phosphate; TCPP), pharmaceutical compounds such as carbamazepine, tramadol, telmisartan, venlafaxine, irbesartan, fluconazole, oxazepam, fexofenadine, diclofenac, citalopram, codeine, bisoprolol, eprosartan, the antibiotics trimethoprim, ciprofloxacine, sulfamethoxazole, and clindamycine, the insect repellent N,N′-diethyltoluamide (DEET), the pesticides MCPA and mecoprop, perfluoroalkyl substances (such as PFOS and PFOA), caffeine, and gadolinium.
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•Effluents of 90 European wastewater treatment plants analyzed for 156 micropollutants.•Largest EU wide monitoring survey on WWTP effluents ever performed in Europe.•Organophosphate esters, pharmaceuticals, antibiotics, perfluoroalkyl substances.•Artificial sweeteners, benzotriazoles, pesticides.•Effect-based monitoring approaches applied.
Wastewater-based severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surveillance of Frankfurt Airport by genome sequencing was used to detect SARS-CoV-2 variants entering the region. In ...November 2021, we found all characteristic mutations of Omicron in wastewater originating from Frankfurt Airport before the first confirmed clinical report from an arriving passenger on 26 November 2021.
•586 of the studied 2362 contaminants were detected in the Danube River Basin.•Risk assessment prioritized 12 legacy and 33 emerging contaminants.•The 33 emerging contaminants are Danube River Basin ...Specific Pollutants.•20 performance indicators were checked in wastewater treatment plants.•The plants showed medium or efficient removal for 70% of the studied compounds.
A state-of-the-art wide-scope target screening of 2,362 chemicals and their transformation products (TPs) was performed in samples collected within the Joint Danube Survey 4 (JDS4) performed in 2019. The analysed contaminants of emerging concern (CECs) included three major categories: plant protection products (PPPs), industrial chemicals and pharmaceuticals and personal care products (PPCPs). In total, 586 CECs were detected in the samples including 158 PPPs, 71 industrial chemicals, 348 PPCPs, and 9 other chemicals. A wide-variety of sample matrices were collected including influent and effluent wastewater, groundwater, river water, sediment and biota. Forty-five CECs (19 PPPs, 8 industrial chemicals, 18 PPCPs) were detected at levels above their ecotoxicological thresholds (lowest predicted no-effect concentration (PNEC) values) in one or more of the investigated environmental compartments, indicating potential adverse effects on the impacted ecosystems. Among them 12 are legacy substances; 33 are emerging and qualify as potential Danube River Basin Specific Pollutants (RBSPs). Moreover, the efficiency of the wastewater treatment plants (WWTPs) was evaluated using 20 selected performance indicator chemicals. WWTPs showed effective removal (removal rate ≥80%) and medium removal (removal rate 25–80%) for 6 and 8 of the indicator chemicals, respectively. However, numerous contaminants passed the WWTPs with a lower removal rate. Further investigation on performance of WWTPs is suggested at catchment level to improve their removal efficiency. WWTP effluents are proven to be one of the major sources of contaminants in the Danube River Basin (DRB). Other sources include sewage discharges, industrial and agricultural activities. Continuous monitoring of the detected CECs is suggested to ensure water quality of the studied area.
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