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

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Ahmed , W , Simpson , S L , Bertsch , P M , Bibby , K , Bivins , A , Blackall , L L , Bofill-Mas , S , Bosch , A , Brandao , J , Choi , P M , Ciesielski , M , Donner , E , D'Souza , N , Farnleitner , A H , Gerrity , D , Gonzalez , R , Griffith , J F , Gyawali , P , Haas , C N , Hamilton , K A , Hapuarachchi , H C , Harwood , V J , Haque , R , Jackson , G , Khan , S J , Khan , W , Kitajima , M , Korajkic , A , La Rosa , G , Layton , B A , Lipp , E , McLellan , S L , McMinn , B , Medema , G , Metcalfe , S , Meijer , W G , Mueller , J F , Murphy , H , Naughton , C C , Noble , R T , Payyappat , S , Petterson , S , Pitkänen , T , Rajal , V B , Reyneke , B , Jr , F A R , Rose , J B , Rusinol , M , Sadowsky , M J , Sala-Comorera , L , Setoh , Y X , Sherchan , S P , Sirikanchana , K , Smith , W , Steele , J A , Subburg , R , Symonds , E M , Thai , P , Thomas , K , Tynan , J , Toze , S , Thompson , J , Whiteley , A S , Wong , J C C , Sano , D , Wuertz , S , Xagoraraki , I , Zhang , Q , Zimmer-Faust , A G & Shanks , O C 2022 , ' Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance ' , The Science of the Total Environment , vol. 805 , 149877 . https://doi.org/10.1016/j.scitotenv.2021.149877

Title: Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance
Author: Ahmed, Warish; Simpson, Stuart L.; Bertsch, Paul M.; Bibby, Kyle; Bivins, Aaron; Blackall, Linda L.; Bofill-Mas, Silvia; Bosch, Albert; Brandao, Joao; Choi, Phil M.; Ciesielski, Mark; Donner, Erica; D'Souza, Nishita; Farnleitner, Andreas H.; Gerrity, Daniel; Gonzalez, Raul; Griffith, John F.; Gyawali, Pradip; Haas, Charles N.; Hamilton, Kerry A.; Hapuarachchi, Hapuarachchige Chandithal; Harwood, Valerie J.; Haque, Rehnuma; Jackson, Greg; Khan, Stuart J.; Khan, Wesaal; Kitajima, Masaaki; Korajkic, Asja; La Rosa, Giuseppina; Layton, Blythe A.; Lipp, Erin; McLellan, Sandra L.; McMinn, Brian; Medema, Gertjan; Metcalfe, Suzanne; Meijer, Wim G.; Mueller, Jochen F.; Murphy, Heather; Naughton, Coleen C.; Noble, Rachel T.; Payyappat, Sudhi; Petterson, Susan; Pitkänen, Tarja; Rajal, Veronica B.; Reyneke, Brandon; Jr, Fernando A. Roman; Rose, Joan B.; Rusinol, Marta; Sadowsky, Michael J.; Sala-Comorera, Laura; Setoh, Yin Xiang; Sherchan, Samendra P.; Sirikanchana, Kwanrawee; Smith, Wendy; Steele, Joshua A.; Subburg, Rosalie; Symonds, Erin M.; Thai, Phong; Thomas, Kevin; Tynan, Josh; Toze, Simon; Thompson, Janelle; Whiteley, Andy S.; Wong, Judith Chui Ching; Sano, Daisuke; Wuertz, Stefan; Xagoraraki, Irene; Zhang, Qian; Zimmer-Faust, Amity G.; Shanks, Orin C.
Contributor: University of Helsinki, Helsinki One Health (HOH)
Date: 2022-01-20
Language: eng
Number of pages: 20
Belongs to series: The Science of the Total Environment
ISSN: 0048-9697
URI: http://hdl.handle.net/10138/335519
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. Crown Copyright (C) 2021 Published by Elsevier B.V.
Subject: COVID-19
SARS-CoV-2
Wastewater
Surveillance
False positive
False negative
RT-PCR
REAL-TIME PCR
GUIDELINES MINIMUM INFORMATION
DROPLET DIGITAL PCR
ENVIRONMENTAL SURVEILLANCE
INTERNAL CONTROLS
NUCLEIC-ACIDS
CORONAVIRUS
VIRUS
DNA
CONTAMINATION
11832 Microbiology and virology
1172 Environmental sciences
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