Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance

The Science of The Total Environment, Год журнала: 2021, Номер 805, С. 149877 - 149877

Опубликована: Авг. 25, 2021

Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide early warning signal COVID-19 infections a community. The capacity world's environmental microbiology virology laboratories SARS-CoV-2 RNA characterization increasing rapidly. However, there are no standardized protocols or harmonized quality assurance control (QA/QC) procedures surveillance. This paper technical review factors that cause false-positive false-negative errors wastewater, culminating recommended strategies be implemented to identify mitigate some these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, virus concentration efficient extraction, PCR inhibition assessment, inclusion sample processing controls, considerations RT-PCR assay selection data interpretation. Clear interpretation guidelines (e.g., determination positive negative samples) critical, particularly when low. Corrective confirmatory actions must place inconclusive results diverging from current trends initial onset reemergence community). It also prudent perform interlaboratory comparisons ensure results' reliability interpretability prospective retrospective analyses. this aim improve detection applications. A silver lining pandemic efficacy continues demonstrated during global crisis. In future, should play important role range other communicable diseases.

Язык: Английский

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Wastewater concentrations of human influenza, metapneumovirus, parainfluenza, respiratory syncytial virus, rhinovirus, and seasonal coronavirus nucleic-acids during the COVID-19 pandemic: a surveillance study

The Lancet Microbe, Год журнала: 2023, Номер 4(5), С. e340 - e348

Опубликована: Март 22, 2023

Respiratory disease is a major cause of morbidity and mortality; however, surveillance for circulating respiratory viruses passive biased. Wastewater-based epidemiology has been used to understand SARS-CoV-2, influenza A, syncytial virus (RSV) infection rates at community level but not investigate other viruses. We aimed use wastewater-based viral occurrence.A retrospective study was carried out large wastewater treatment plant located in California, USA. Using droplet digital RT-PCR, we measured RNA concentrations A B viruses, RSV B, parainfluenza (1-4) rhinovirus, seasonal coronaviruses, metapneumovirus solids three times per week 17 months (216 samples) between Feb 1, 2021, June 21, 2022. Novel probe-based RT-PCR assays non-influenza targets were developed validated. compared positivity infections from clinical specimens submitted California Sentinel Clinical Laboratories (sentinel laboratories) assess concordance the two datasets.We detected all tested solids. Human rhinovirus (median concentration 4300 [0-9500] copies gram dry weight) human coronaviruses (35 000 [17 000-56 000]) found highest concentrations. Concentrations correlated significantly positively with associated diseases sentinel laboratories (tau 0·32-0·57, p<0·0009); only exceptions which rarely Measurements indicated coronavirus OC43 dominated whereas 3 among during period. decreased noticeably after omicron BA.1 surge suggesting connection changes behaviour transmission viruses.Wastewater-based can be obtain information on circulation localised, without need test many individuals because single sample represents entire contributing community. Results available within 24 h collection, generating real time inform public health responses, decision making, individual modifications.CDC Foundation.

Язык: Английский

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Respiratory Syncytial Virus (RSV) RNA in Wastewater Settled Solids Reflects RSV Clinical Positivity Rates

Environmental Science & Technology Letters, Год журнала: 2022, Номер 9(2), С. 173 - 178

Опубликована: Янв. 12, 2022

Wastewater-based epidemiology (WBE) uses concentrations of infectious agent targets in wastewater to infer infection trends the contributing community. To date, WBE has been used gain insight into gastrointestinal diseases, but its application respiratory diseases limited. Here, we report that syncytial virus (RSV) genomic ribonucleic acid can be detected settled solids at two publicly owned treatment works. We further show concentration is strongly associated (Kendalls tau = 0.65–0.77, p < 10–7) with clinical positivity rates for RSV sentinel laboratories across state 2021, a year anomalous seasonal disease. Given infections have similar presentations COVID-19, life threatening some, and immunoprophylaxis distribution vulnerable people based on outbreak identification, represents an important tool augment current surveillance public health response efforts.

Язык: Английский

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Droplet-based digital PCR (ddPCR) and its applications

TrAC Trends in Analytical Chemistry, Год журнала: 2022, Номер 158, С. 116897 - 116897

Опубликована: Дек. 24, 2022

Язык: Английский

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Application of digital PCR for public health-related water quality monitoring

The Science of The Total Environment, Год журнала: 2022, Номер 837, С. 155663 - 155663

Опубликована: Май 4, 2022

Язык: Английский

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Human viral nucleic acids concentrations in wastewater solids from Central and Coastal California USA

Scientific Data, Год журнала: 2023, Номер 10(1)

Опубликована: Июнь 22, 2023

Abstract We measured concentrations of SARS-CoV-2, influenza A and B virus, respiratory syncytial virus (RSV), mpox human metapneumovirus, norovirus GII, pepper mild mottle nucleic acids in wastewater solids at twelve treatment plants Central California, USA. Measurements were made daily for up to two years, depending on the plant. using digital droplet (reverse-transcription–) polymerase chain reaction (RT-PCR) following best practices making environmental molecular biology measurements. These data can be used better understand disease occurrence communities contributing wastewater.

Язык: Английский

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More than a Tripledemic: Influenza A Virus, Respiratory Syncytial Virus, SARS-CoV-2, and Human Metapneumovirus in Wastewater during Winter 2022–2023

Environmental Science & Technology Letters, Год журнала: 2023, Номер 10(8), С. 622 - 627

Опубликована: Июль 20, 2023

Wastewater monitoring can provide insights into respiratory disease occurrence in communities that contribute to the wastewater system. Using daily measurements of RNA influenza A (IAV), syncytial virus (RSV), and human metapneumovirus (HMPV), as well SARS-CoV-2 solids from eight publicly owned treatment works Greater San Francisco Bay Area California between July 2022 early 2023, we identify a "tripledemic" when concentrations IAV, RSV, peaked at approximately same time. HMPV was also widely circulating. We designed novel hydrolysis probe RT-PCR assays for different IAV subtype markers discern dominant circulating H3N2. show data be used onset offset events. This information insight epidemiology timely, localized inform hospital staffing clinical decision making respond viruses. Whereas RSV events were mostly regionally coherent, displayed patterns.

Язык: Английский

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Detection of Hemagglutinin H5 Influenza A Virus Sequence in Municipal Wastewater Solids at Wastewater Treatment Plants with Increases in Influenza A in Spring, 2024

Environmental Science & Technology Letters, Год журнала: 2024, Номер 11(6), С. 526 - 532

Опубликована: Май 20, 2024

Prospective influenza A (IAV) RNA monitoring at 190 wastewater treatment plants (WWTPs) across the US identified increases in IAV concentrations 59 spring 2024, after typical seasonal period, coincident with identification of highly pathogenic avian (subtype H5N1) circulating dairy cattle US. We developed and validated a hydrolysis-probe RT-PCR assay for quantification H5 hemagglutinin gene. applied it retrospectively to samples from four WWTPs where springtime were one WWTP they not. The marker was detected all coinciding not without an increase. Positive are located states confirmed outbreaks influenza, H5N1 clade 2.3.4.4b, cattle. Concentrations gene approached overall virus concentrations, suggesting large fraction inputs subtypes. At positive WWTPs, industrial discharges containing animal waste, including milk byproducts, permitted discharge into sewers. Our findings demonstrate that can detect animal-associated contributions highlight need consider agricultural wastewater. This work illustrates monitoring's value comprehensive surveillance, influenzas currently thought be primarily found animals important implications human health.

Язык: Английский

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SARS-CoV-2 RNA is enriched by orders of magnitude in primary settled solids relative to liquid wastewater at publicly owned treatment works

Environmental Science Water Research & Technology, Год журнала: 2022, Номер 8(4), С. 757 - 770

Опубликована: Янв. 1, 2022

We compared SARS-CoV-2 RNA concentrations in primary settled solids and raw wastewater samples matched date to investigate the relationship between two matrices.

Язык: Английский

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A framework for standardized qPCR-targets and protocols for quantifying antibiotic resistance in surface water, recycled water and wastewater

Critical Reviews in Environmental Science and Technology, Год журнала: 2022, Номер 52(24), С. 4395 - 4419

Опубликована: Янв. 16, 2022

Water environments are increasingly recognized as a conduit for the spread of antibiotic resistance, but there is need to standardize resistance monitoring protocols ensure comparability across studies. Quantitative polymerase chain reaction (qPCR) attractive sensitive means quantifying genes (ARGs) and has been applied broadly over past two decades various water matrices. QPCR avoids challenges biases associated with culture-based methods, providing reproducible highly measure ARGs carried bacterial community. However, numerous quality assurance other aspects that be addressed measurements representative comparable Here we conducted critical review identify gene targets most commonly measured by qPCR quantify in surface water, recycled wastewater assess corresponding protocols. Identified monitored samples included sul1, tetA, intI1, given their abundance tendency correlate anthropogenic inputs, vanA blaCTX-M, more rarely detected, clinically-relevant targets. We identified 117 peer-reviewed studies meeting search criteria application these assays matrices interest systematically assessed protocols, including sample collection concentration, DNA extraction, primer/probe specificity, amplification conditions, amplicon length, PCR inhibition evaluation, limit detection/quantification. Gene copy numbers reported were further compared assay matrix. Based on this comprehensive recommend assays, standardized workflows, reporting five target genes.

Язык: Английский

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