Simultaneous detection of SARS-CoV-2, influenza A, respiratory syncytial virus, and measles in wastewater by multiplex RT-qPCR

The Science of The Total Environment, Год журнала: 2023, Номер 889, С. 164261 - 164261

Опубликована: Май 17, 2023

Язык: Английский

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Wastewater-based monitoring of SARS-CoV-2 at UK airports and its potential role in international public health surveillance

PLOS Global Public Health, Год журнала: 2023, Номер 3(1), С. e0001346 - e0001346

Опубликована: Янв. 19, 2023

It is well established that air travel plays a key role in the global spread of many enteric and respiratory diseases, including COVID-19. Even with restrictions (e.g. mask wearing, negative COVID-19 test prior to departure), SARS-CoV-2 may be transmitted by asymptomatic or pre-symptomatic individuals carrying virus. Due limitation current clinical surveillance approaches, complementary methods need developed allow estimation frequency entry across international borders. Wastewater-based epidemiology (WBE) represents one such approach, allowing unbiased sampling carriage passenger cohorts entering via airports. In this study, we monitored sewage samples from terminals (n = 150) aircraft 32) at three major airports UK for 1–3 weeks March 2022. As raw were more turbid than typical municipal wastewater, used beef extract treatment followed polyethylene glycol (PEG) precipitation concentrate viruses, reverse transcription quantitative PCR (RT-qPCR) detection faecal indicator virus, crAssphage. All taken sewers arrival Heathrow Bristol airports, 85% sites Edinburgh airport, positive SARS-CoV-2. This suggests high prevalence among passengers and/or airport staff members. Samples derived also showed 93% positivity. No difference viral was found before after lifted. Our results suggest WBE useful tool monitoring transfer rate human pathogens other disease-causing agents borders should form part wider efforts monitor contain future disease outbreaks.

Язык: Английский

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Wastewater-based epidemiology for comprehensive community health diagnostics in a national surveillance study: Mining biochemical markers in wastewater

Journal of Hazardous Materials, Год журнала: 2023, Номер 450, С. 130989 - 130989

Опубликована: Фев. 16, 2023

This manuscript showcases results from a large scale and comprehensive wastewater-based epidemiology (WBE) study focussed on multi-biomarker suite analysis of both chemical biological determinants in 10 cities towns across England equating to population ∼7 million people. Multi-biomarker analysis, describing city metabolism, can provide holistic understanding encompass all human, human-derived, activities single model: lifestyle choices (e.g. caffeine intake, nicotine) through health status prevalence pathogenic organisms, usage pharmaceuticals as proxy for non-communicable disease, NCD, conditions or infectious disease status), exposure harmful chemicals due environmental industrial sources pesticide intake via contaminated food exposure). Population normalised daily loads (PNDLs) many markers were found, extent, driven by the size contributing wastewater (especially NCDs). However, there are several exceptions providing insights into that inform either various communities unintentional hazardous chemicals: e.g. very high PNDLs ibuprofen Hull resulting its direct disposal (confirmed ibuprofen/2-hydroxyibuprofen ratios) bisphenol A (BPA) Hull, Lancaster Portsmouth likely related discharge. An importance tracking endogenous such 4-hydroxy-2-nonenal-mercapturic acid (HNE-MA, an oxidative stress marker) generic marker was observed increased levels HNE-MA seen at Barnoldswick treatment plant coincided with higher-than-average paracetamol SARS-CoV-2 this community. virus found be highly variable. Being prevalent nationwide during sampling, presence extent community driven. The same applies fecal virus, crAssphage, which is urban communities. In contrast, norovirus enterovirus showed much higher variability sites investigated, clear cases localized outbreaks some while maintaining low other locations. conclusion, clearly demonstrates potential WBE integrated assessment help target validate policy interventions aimed improving public wellbeing.

Язык: Английский

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Identification and genome sequencing of an influenza H3N2 variant in wastewater from elementary schools during a surge of influenza A cases in Las Vegas, Nevada

The Science of The Total Environment, Год журнала: 2023, Номер 872, С. 162058 - 162058

Опубликована: Фев. 8, 2023

Real-time surveillance of infectious diseases at schools or in communities is often hampered by delays reporting due to resource limitations and infrastructure issues. By incorporating quantitative PCR genome sequencing, wastewater has been an effective complement public health the community building-scale for pathogens such as poliovirus, SARS-CoV-2, even monkeypox virus. In this study, we asked whether programs elementary could be leveraged detect RNA from influenza viruses shed wastewater. We monitored A B viral six January May 2022. Quantitative led identification three schools, which coincided with lifting COVID-19 restrictions a surge infections Las Vegas, Nevada, USA. performed sequencing RNA, leading 2021–2022 vaccine-resistant (H3N2) 3C.2a1b.2a.2 subclade. next tested samples treatment plant that serviced but were unable presence A/B RNA. Together, our results demonstrate utility near-source detection local transmission potential investigated further paired school-level incidence data.

Язык: Английский

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Examining the stability of viral RNA and DNA in wastewater: Effects of storage time, temperature, and freeze-thaw cycles

Water Research, Год журнала: 2024, Номер 259, С. 121879 - 121879

Опубликована: Июнь 3, 2024

Wastewater-based epidemiology (WBE) has been demonstrably successful as a relatively unbiased tool for monitoring levels of SARS-CoV-2 virus circulating in communities during the COVID-19 pandemic. Accumulated biobanks wastewater samples allow retrospective exploration spatial and temporal trends public health indicators such chemicals, viruses, antimicrobial resistance genes, possible emergence novel human or zoonotic pathogens. We investigated resilience to time, temperature, freeze-thaw cycles, plus optimal storage conditions maintain stability genetic material (RNA/DNA) viral +ssRNA (Envelope - E, Nucleocapsid N Spike protein S genes SARS-CoV-2), dsRNA (Phi6 phage) circular dsDNA (crAssphage) wastewater. Samples consisted (i) processed extracted samples, (ii) distilled water (iii) raw, unprocessed samples. were stored at -80 °C, -20 4 20 °C 10 days, going through up cycles (once per day). Sample was measured using reverse transcription quantitative PCR, automated electrophoresis, short-read whole genome sequencing. Exploring different areas demonstrated that gene showed greater sensitivity than E genes. Investigating surrogate normalisation viruses Phi6 remains stable comparison laboratory setting crAssphage resilient temperature variation. Recovery raw significantly when which supported by sequencing data all both time negatively impacted metrics. Historical extracts re-quantified 12, 14 16 months after original quantification no major changes. This study highlights importance fast processing extraction following are robust range temperatures.

Язык: Английский

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The Inhibition and Variability of Two Different RT-qPCR Assays Used for Quantifying SARS-CoV-2 RNA in Wastewater

Food and Environmental Virology, Год журнала: 2023, Номер 15(1), С. 71 - 81

Опубликована: Фев. 15, 2023

Faecal shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its subsequent detection in wastewater turned the spotlight onto wastewater-based epidemiology (WBE) for monitoring coronavirus-disease 2019 (COVID-19) pandemic. WBE SARS-CoV-2 has been deployed 70 countries, providing insights into disease prevalence, forecasting spatiotemporal tracking emergence variants. Wastewater, however, is a complex sample matrix containing numerous reverse transcription quantitative PCR (RT-qPCR) inhibitors whose concentration diversity are influenced by factors including population size, surrounding industry agriculture climate. Such differences RT-qPCR inhibitor profile likely to impact quality data produced potentially produce erroneous results.To help determine possible assay on quality, two assays employed different laboratories within UK's programme were assessed Cefas laboratory Weymouth, UK. The based Fast Virus (FV) qScript (qS) chemistries using same primers probes, but at concentrations under cycling conditions. Bovine serum albumin MgSO4 also added FV reaction mixture. Two-hundred eighty-six samples analysed, an external control RNA (EC RNA)-based method was used measure inhibition. Compared with qS, showed 40.5% reduction mean inhibition 57.0% inter-sample variability. A 4.1-fold increase quantification seen relative qS; partially due (1.5-fold) efficiency use dsDNA standard. Analytical variability reduced 51.2% while qS increased number negative 2.6-fold. This study indicates importance thorough optimisation RT-qPCR-based which should be performed selection representative physiochemical properties wastewater. Furthermore, inhibition, analytical key considerations during optimisation. standardised framework validation procedures formed concessions emergency response situations that would allow flexibility process address difficult balance between urgency availability resources.

Язык: Английский

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Comparative assessment of Nanotrap and polyethylene glycol-based virus concentration in wastewater samples

FEMS Microbes, Год журнала: 2024, Номер 5

Опубликована: Янв. 1, 2024

Abstract Wastewater-based epidemiology is now widely used in many countries for the routine monitoring of SARS-CoV-2 and other viruses at a community level. However, efficient sample processing technologies are still under investigation. In this study, we compared performance novel Nanotrap® Microbiome Particles (NMP) concentration method to commonly polyethylene glycol (PEG) precipitation concentrating from wastewater their subsequent quantification sequencing. For this, first spiked with SARS-CoV-2, influenza measles norovirus found that NMP recovered 0.4%–21% them depending on virus type, providing consistent reproducible results. Using PEG methods, monitored A B viruses, RSV, enteroviruses GI GII crAssphage using quantitative PCR (qPCR)-based methods next-generation Good viral recoveries were observed highly abundant both methods; however, was more successful recovery low-abundance present wastewater. Furthermore, samples processed successfully sequenced than those method. Virus enhanced by high volumes when applied. Overall, our results suggest rapid easy targets wastewater, whereas may be suited analysis next generation

Язык: Английский

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Optimization and performance evaluation of an automated filtration method for the recovery of SARS-CoV-2 and other viruses in wastewater

The Science of The Total Environment, Год журнала: 2023, Номер 882, С. 163487 - 163487

Опубликована: Апрель 15, 2023

A rapid virus concentration method is needed to get high throughput. Reliable results of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) detection in wastewater are necessary for applications wastewater-based epidemiology. In this study, an automated filtration using a concentrating pipette (CP Select; Innovaprep) was applied detect SARS-CoV-2 samples with several modifications increase its sensitivity and The performance the CP Select compared other methods (polyethylene glycol precipitation direct capture silica column) evaluate applicability wastewater. RNA successfully detected six eight method, whereas could all samples. Enteric viruses, such as noroviruses genogroups I (NoVs-GI) II (NoVs-GII) enteroviruses, were tested, resulting 100 % NoVs-GII methods. As NoVs-GI gave comparable number This study showed that optimized less sensitive than methods, applicable or recover viruses

Язык: Английский

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Comparison of the methods for isolation and detection of SARS-CoV-2 RNA in municipal wastewater

Frontiers in Public Health, Год журнала: 2023, Номер 11

Опубликована: Март 7, 2023

Coronavirus SARS-CoV-2 is a causative agent responsible for the current global pandemic situation known as COVID-19. Clinical manifestations of COVID-19 include wide range symptoms from mild (i.e., cough, fever, dyspnea) to severe pneumonia-like respiratory symptoms. has been demonstrated be detectable in stool patients. Waste-based epidemiology (WBE) shown promising approach early detection and monitoring local population performed via collection, isolation, viral pathogens environmental sources.In order select optimal protocol epidemiological region Turiec, Slovakia, we (1) compared methods separation including virus precipitation by polyethylene glycol (PEG), purification ultrafiltration (Vivaspin®) subsequent isolation NucleoSpin RNA Virus kit (Macherey-Nagel), direct wastewater (Zymo Environ Water Kit); (2) evaluated impact water freezing on SARS- CoV-2 separation, detection; (3) role filtration stability; (4) determined appropriate reverse transcription-droplet digital PCR (RT-ddPCR) real-time quantitative polymerase chain reaction (RT-qPCR) (targeting same genes, i.e., RdRp gene E) samples.(1) Usage Zymo Kit provided superior quality isolated comparison with both ultracentrifugation PEG precipitation. Freezing samples significantly reduces yield. Filtering counterproductive when used. According specificity sensitivity, RT-ddPCR outperforms RT-qPCR.The results our study suggest that WBE valuable warning alert represents non-invasive monitor pathogens, thus protects public health regional national level. In addition, have sensitivity testing nearer limit can improved selecting combination enrichment, methods.

Язык: Английский

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Near-source passive sampling for monitoring viral outbreaks within a university residential setting

Epidemiology and Infection, Год журнала: 2024, Номер 152

Опубликована: Янв. 1, 2024

Abstract Wastewater-based epidemiology (WBE) has proven to be a powerful tool for the population-level monitoring of pathogens, particularly severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For assessment, several wastewater sampling regimes and methods viral concentration have been investigated, mainly targeting SARS-CoV-2. However, use passive samplers in near-source environments range viruses is still under-investigated. To address this, samples were taken at four locations student hall residence. These chosen as an exemplar due their high population density perceived risk disease transmission. Viruses investigated SARS-CoV-2 its variants concern (VOCs), influenza viruses, enteroviruses. Sampling was conducted either morning, where place overnight (17 h) during day, with exposure 7 h. We demonstrated usefulness detection VOCs using quantitative polymerase chain reaction (qPCR) next-generation sequencing (NGS). Furthermore, outbreaks A sporadic enteroviruses (some associated enterovirus D68 coxsackieviruses) identified among resident population, providing evidence near-source, in-sewer health communities.

Язык: Английский

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