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

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  • Ahmed, W.
    • Other Affiliation: CSIRO Land and Water
  • Simpson, S.L.
    • Other Affiliation: CSIRO Land and Water
  • Bertsch, P.M.
    • Other Affiliation: CSIRO Land and Water
  • Bibby, K.
    • Other Affiliation: University of Notre Dame
  • Bivins, A.
    • Other Affiliation: University of Notre Dame
  • Blackall, L.L.
    • Other Affiliation: University of Melbourne
  • Bofill-Mas, S.
    • Other Affiliation: University of Barcelona
  • Bosch, A.
    • Other Affiliation: University of Barcelona
  • Brandão, J.
    • Other Affiliation: National Institute of Health
  • Choi, P.M.
    • Other Affiliation: University of Queensland
  • Ciesielski, M.
    • Affiliation: Institute of Marine Sciences
  • Donner, E.
    • Other Affiliation: University of South Australia
  • D'Souza, N.
    • Other Affiliation: Michigan State University
  • Farnleitner, A.H.
    • Other Affiliation: Technische Universität Wien
  • Gerrity, D.
    • Other Affiliation: Southern Nevada Water Authority
  • Gonzalez, R.
    • Other Affiliation: Hampton Roads Sanitation District
  • Griffith, J.F.
    • Other Affiliation: Southern California Coastal Water Research Project
  • Gyawali, P.
    • Other Affiliation: Institute of Environmental Science and Research Ltd
  • Haas, C.N.
    • Other Affiliation: Drexel University
  • Hamilton, K.A.
    • Other Affiliation: Arizona State University
  • Hapuarachchi, H.C.
    • Other Affiliation: National Environment Agency
  • Harwood, V.J.
    • Other Affiliation: University of South Florida
  • Haque, R.
    • Other Affiliation: Environmental Interventions Unit
  • Jackson, G.
    • Other Affiliation: Queensland Health
  • Khan, S.J.
    • Other Affiliation: University of New South Wales
  • Khan, W.
    • Other Affiliation: Stellenbosch University
  • Kitajima, M.
    • Other Affiliation: Hokkaido University
  • Korajkic, A.
    • Other Affiliation: United States Environmental Protection Agency
  • La Rosa, G.
    • Other Affiliation: Istituto Superiore di Sanità
  • Layton, B.A.
    • Other Affiliation: Clean Water Services
  • Lipp, E.
    • Other Affiliation: University of Georgia
  • McLellan, S.L.
    • Other Affiliation: University of Wisconsin-Milwaukee
  • McMinn, B.
    • Other Affiliation: United States Environmental Protection Agency
  • Medema, G.
    • Other Affiliation: KWR Water Research Institute
  • Metcalfe, S.
    • Other Affiliation: CSIRO Land and Water
  • Meijer, W.G.
    • Other Affiliation: University College Dublin
  • Mueller, J.F.
    • Other Affiliation: University of Queensland
  • Murphy, H.
    • Other Affiliation: University of Guelph
  • Naughton, C.C.
    • Other Affiliation: University of California Merced
  • Noble, R.T.
    • Affiliation: Institute of Marine Sciences
  • Payyappat, S.
    • Other Affiliation: Sydney Water
  • Petterson, S.
    • Other Affiliation: Griffith University
  • Pitkänen, T.
    • Other Affiliation: University of Helsinki
  • Rajal, V.B.
    • Other Affiliation: Universidad Nacional de Salta
  • Reyneke, B.
    • Other Affiliation: Stellenbosch University
  • Roman, F.A., Jr
    • Other Affiliation: University of California Merced
  • Rose, J.B.
    • Other Affiliation: Michigan State University
  • Rusiñol, M.
    • Other Affiliation: Institute of Environmental Assessment & Water Research
  • Sadowsky, M.J.
    • Other Affiliation: University of Minnesota
  • Sala-Comorera, L.
    • Other Affiliation: University College Dublin
  • Setoh, Y.X.
    • Other Affiliation: National Environment Agency
  • Sherchan, S.P.
    • Other Affiliation: Tulane University
  • Sirikanchana, K.
    • Other Affiliation: Chulabhorn Research Institute
  • Smith, W.
    • Other Affiliation: CSIRO Land and Water
  • Steele, J.A.
    • Other Affiliation: Southern California Coastal Water Research Project
  • Subburg, R.
    • Other Affiliation: CSIRO Agriculture and Food
  • Symonds, E.M.
    • Other Affiliation: University of South Florida
  • Thai, P.
    • Other Affiliation: University of Queensland
  • Thomas, K.V.
    • Other Affiliation: University of Queensland
  • Tynan, J.
    • Other Affiliation: University of Queensland
  • Toze, S.
    • Other Affiliation: CSIRO Land and Water
  • Thompson, J.
    • Other Affiliation: Nanyang Technological University
  • Whiteley, A.S.
    • Other Affiliation: CSIRO Land and Water
  • Wong, J.C.C.
    • Other Affiliation: National Environment Agency
  • Sano, D.
    • Other Affiliation: Tohoku University
  • Wuertz, S.
    • Other Affiliation: Nanyang Technological University
  • Xagoraraki, I.
    • Other Affiliation: Michigan State University
  • Zhang, Q.
    • Other Affiliation: University of Minnesota
  • Zimmer-Faust, A.G.
    • Other Affiliation: Southern California Coastal Water Research Project
  • Shanks, O.C.
    • Other Affiliation: United States Environmental Protection Agency
Abstract
  • Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.
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  • Article
Rights statement
  • In Copyright
License
  • Attribution-NonCommercial-NoDerivs 4.0 International
Journal title
  • Science of the Total Environment
Journal volume
  • 805
Language
  • English
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  • Publisher
ISSN
  • 0048-9697
Publisher
  • Elsevier B.V.

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