Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance
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 Respira...
| Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2022 |
| País: | España |
| Institución: | Consejo Superior de Investigaciones Científicas (CSIC) |
| Repositorio: | DIGITAL.CSIC. Repositorio Institucional del CSIC |
| OAI Identifier: | oai:digital.csic.es:10261/257769 |
| Acceso en línea: | http://hdl.handle.net/10261/257769 |
| Access Level: | acceso abierto |
| Palabra clave: | COVID-19 SARS-CoV-2 Wastewater Surveillance False positive False negative RT-PCR |
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Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillanceAhmed, WarishSimpson, StuartBertsch, PaulBibby, KyleBivins, AaronBlackall, LindaBofill-Mas, SílviaBosch, AlbertBrandão, JoaoChoi, PhilCiesielski, MarkDonner, EricaD'Souza, NishitaFarnleitner, AndreasGerrity, DanielGonzález, RaúlGriffith, JohnGyawali, PradipHaas, CharlesHamilton, KerryHapuarachchi, ChandithaHarwood, ValerieHaque, RehnumaJackson, GregKhan, StuartKhan, WesaalKitajima, MasaakiKorajkic, AsjaLa Rosa, GiuseppinaLayton, BlytheLipp, ErinMcLellan, Sandra L.McMinn, BrianMedema, GertjanMetcalfe, SuzanneMeijer , WimMueller, JochenMurphy, HeatherNaughton, ColleenNoble, Rachel T.Payyappat, SudhiPetterson, SusanPitkanen, TarjaRajal, VerónicaReyneke, BrandonRomán, FernandoRose, JoanRusiñol, MartaSadowsky, MichaelSala-Comorera, LauraSetoh, Yin XiangSherchan, SamendraSirikanchana, KwanraweeSmith, WendySteele, JoshuaSabburg, RosalieSymonds, ErinThai, PhongThomas, KevinTynan, JoshToze, SimonThompson, JanelleWhiteley, AndyWong, JudithSano, DaisukeWuertz, StefanXagoraraki, IreneZhang, QianZimmer-Faust, AmityShanks, OrinCOVID-19SARS-CoV-2WastewaterSurveillanceFalse positiveFalse negativeRT-PCRWastewater 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.Peer reviewedElsevier BVConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202220222022info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_dcae04bcPublisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/257769reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttps://doi.org/10.1016/j.scitotenv.2021.149877Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2577692026-05-22T06:33:51Z |
| dc.title.none.fl_str_mv |
Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance |
| title |
Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance |
| spellingShingle |
Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance Ahmed, Warish COVID-19 SARS-CoV-2 Wastewater Surveillance False positive False negative RT-PCR |
| title_short |
Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance |
| title_full |
Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance |
| title_fullStr |
Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance |
| title_full_unstemmed |
Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance |
| title_sort |
Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance |
| dc.creator.none.fl_str_mv |
Ahmed, Warish Simpson, Stuart Bertsch, Paul Bibby, Kyle Bivins, Aaron Blackall, Linda Bofill-Mas, Sílvia Bosch, Albert Brandão, Joao Choi, Phil Ciesielski, Mark Donner, Erica D'Souza, Nishita Farnleitner, Andreas Gerrity, Daniel González, Raúl Griffith, John Gyawali, Pradip Haas, Charles Hamilton, Kerry Hapuarachchi, Chanditha Harwood, Valerie Haque, Rehnuma Jackson, Greg Khan, Stuart Khan, Wesaal Kitajima, Masaaki Korajkic, Asja La Rosa, Giuseppina Layton, Blythe Lipp, Erin McLellan, Sandra L. McMinn, Brian Medema, Gertjan Metcalfe, Suzanne Meijer , Wim Mueller, Jochen Murphy, Heather Naughton, Colleen Noble, Rachel T. Payyappat, Sudhi Petterson, Susan Pitkanen, Tarja Rajal, Verónica Reyneke, Brandon Román, Fernando Rose, Joan Rusiñol, Marta Sadowsky, Michael Sala-Comorera, Laura Setoh, Yin Xiang Sherchan, Samendra Sirikanchana, Kwanrawee Smith, Wendy Steele, Joshua Sabburg, Rosalie Symonds, Erin Thai, Phong Thomas, Kevin Tynan, Josh Toze, Simon Thompson, Janelle Whiteley, Andy Wong, Judith Sano, Daisuke Wuertz, Stefan Xagoraraki, Irene Zhang, Qian Zimmer-Faust, Amity Shanks, Orin |
| author |
Ahmed, Warish |
| author_facet |
Ahmed, Warish Simpson, Stuart Bertsch, Paul Bibby, Kyle Bivins, Aaron Blackall, Linda Bofill-Mas, Sílvia Bosch, Albert Brandão, Joao Choi, Phil Ciesielski, Mark Donner, Erica D'Souza, Nishita Farnleitner, Andreas Gerrity, Daniel González, Raúl Griffith, John Gyawali, Pradip Haas, Charles Hamilton, Kerry Hapuarachchi, Chanditha Harwood, Valerie Haque, Rehnuma Jackson, Greg Khan, Stuart Khan, Wesaal Kitajima, Masaaki Korajkic, Asja La Rosa, Giuseppina Layton, Blythe Lipp, Erin McLellan, Sandra L. McMinn, Brian Medema, Gertjan Metcalfe, Suzanne Meijer , Wim Mueller, Jochen Murphy, Heather Naughton, Colleen Noble, Rachel T. Payyappat, Sudhi Petterson, Susan Pitkanen, Tarja Rajal, Verónica Reyneke, Brandon Román, Fernando Rose, Joan Rusiñol, Marta Sadowsky, Michael Sala-Comorera, Laura Setoh, Yin Xiang Sherchan, Samendra Sirikanchana, Kwanrawee Smith, Wendy Steele, Joshua Sabburg, Rosalie Symonds, Erin Thai, Phong Thomas, Kevin Tynan, Josh Toze, Simon Thompson, Janelle Whiteley, Andy Wong, Judith Sano, Daisuke Wuertz, Stefan Xagoraraki, Irene Zhang, Qian Zimmer-Faust, Amity Shanks, Orin |
| author_role |
author |
| author2 |
Simpson, Stuart Bertsch, Paul Bibby, Kyle Bivins, Aaron Blackall, Linda Bofill-Mas, Sílvia Bosch, Albert Brandão, Joao Choi, Phil Ciesielski, Mark Donner, Erica D'Souza, Nishita Farnleitner, Andreas Gerrity, Daniel González, Raúl Griffith, John Gyawali, Pradip Haas, Charles Hamilton, Kerry Hapuarachchi, Chanditha Harwood, Valerie Haque, Rehnuma Jackson, Greg Khan, Stuart Khan, Wesaal Kitajima, Masaaki Korajkic, Asja La Rosa, Giuseppina Layton, Blythe Lipp, Erin McLellan, Sandra L. McMinn, Brian Medema, Gertjan Metcalfe, Suzanne Meijer , Wim Mueller, Jochen Murphy, Heather Naughton, Colleen Noble, Rachel T. Payyappat, Sudhi Petterson, Susan Pitkanen, Tarja Rajal, Verónica Reyneke, Brandon Román, Fernando Rose, Joan Rusiñol, Marta Sadowsky, Michael Sala-Comorera, Laura Setoh, Yin Xiang Sherchan, Samendra Sirikanchana, Kwanrawee Smith, Wendy Steele, Joshua Sabburg, Rosalie Symonds, Erin Thai, Phong Thomas, Kevin Tynan, Josh Toze, Simon Thompson, Janelle Whiteley, Andy Wong, Judith Sano, Daisuke Wuertz, Stefan Xagoraraki, Irene Zhang, Qian Zimmer-Faust, Amity Shanks, Orin |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72] |
| dc.subject.none.fl_str_mv |
COVID-19 SARS-CoV-2 Wastewater Surveillance False positive False negative RT-PCR |
| topic |
COVID-19 SARS-CoV-2 Wastewater Surveillance False positive False negative RT-PCR |
| description |
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. |
| publishDate |
2022 |
| dc.date.none.fl_str_mv |
2022 2022 2022 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/article http://purl.org/coar/resource_type/c_dcae04bc Publisher's version info:eu-repo/semantics/publishedVersion |
| format |
article |
| status_str |
publishedVersion |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10261/257769 |
| url |
http://hdl.handle.net/10261/257769 |
| dc.language.none.fl_str_mv |
Inglés |
| language_invalid_str_mv |
Inglés |
| dc.relation.none.fl_str_mv |
https://doi.org/10.1016/j.scitotenv.2021.149877 Sí |
| dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess |
| eu_rights_str_mv |
openAccess |
| dc.publisher.none.fl_str_mv |
Elsevier BV |
| publisher.none.fl_str_mv |
Elsevier BV |
| dc.source.none.fl_str_mv |
reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC instname:Consejo Superior de Investigaciones Científicas (CSIC) |
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Consejo Superior de Investigaciones Científicas (CSIC) |
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DIGITAL.CSIC. Repositorio Institucional del CSIC |
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DIGITAL.CSIC. Repositorio Institucional del CSIC |
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1869403855732604928 |
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15,81155 |