tetano
Editor, Senior Moderator
Sci Total Environ
. 2022 Jan 20;805:149877.
doi: 10.1016/j.scitotenv.2021.149877. Epub 2021 Aug 25.
Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance
Warish Ahmed[SUP] 1 [/SUP], Stuart L Simpson[SUP] 2 [/SUP], Paul M Bertsch[SUP] 3 [/SUP], Kyle Bibby[SUP] 4 [/SUP], Aaron Bivins[SUP] 4 [/SUP], Linda L Blackall[SUP] 5 [/SUP], Sílvia Bofill-Mas[SUP] 6 [/SUP], Albert Bosch[SUP] 7 [/SUP], João Brandão[SUP] 8 [/SUP], Phil M Choi[SUP] 9 [/SUP], Mark Ciesielski[SUP] 10 [/SUP], Erica Donner[SUP] 11 [/SUP], Nishita D'Souza[SUP] 12 [/SUP], Andreas H Farnleitner[SUP] 13 [/SUP], Daniel Gerrity[SUP] 14 [/SUP], Raul Gonzalez[SUP] 15 [/SUP], John F Griffith[SUP] 16 [/SUP], Pradip Gyawali[SUP] 17 [/SUP], Charles N Haas[SUP] 18 [/SUP], Kerry A Hamilton[SUP] 19 [/SUP], Hapuarachchige Chanditha Hapuarachchi[SUP] 20 [/SUP], Valerie J Harwood[SUP] 21 [/SUP], Rehnuma Haque[SUP] 22 [/SUP], Greg Jackson[SUP] 23 [/SUP], Stuart J Khan[SUP] 24 [/SUP], Wesaal Khan[SUP] 25 [/SUP], Masaaki Kitajima[SUP] 26 [/SUP], Asja Korajkic[SUP] 27 [/SUP], Giuseppina La Rosa[SUP] 28 [/SUP], Blythe A Layton[SUP] 29 [/SUP], Erin Lipp[SUP] 30 [/SUP], Sandra L McLellan[SUP] 31 [/SUP], Brian McMinn[SUP] 27 [/SUP], Gertjan Medema[SUP] 32 [/SUP], Suzanne Metcalfe[SUP] 3 [/SUP], Wim G Meijer[SUP] 33 [/SUP], Jochen F Mueller[SUP] 34 [/SUP], Heather Murphy[SUP] 35 [/SUP], Coleen C Naughton[SUP] 36 [/SUP], Rachel T Noble[SUP] 10 [/SUP], Sudhi Payyappat[SUP] 37 [/SUP], Susan Petterson[SUP] 38 [/SUP], Tarja Pitkänen[SUP] 39 [/SUP], Veronica B Rajal[SUP] 40 [/SUP], Brandon Reyneke[SUP] 25 [/SUP], Fernando A Roman Jr[SUP] 36 [/SUP], Joan B Rose[SUP] 12 [/SUP], Marta Rusiñol[SUP] 41 [/SUP], Michael J Sadowsky[SUP] 42 [/SUP], Laura Sala-Comorera[SUP] 33 [/SUP], Yin Xiang Setoh[SUP] 20 [/SUP], Samendra P Sherchan[SUP] 43 [/SUP], Kwanrawee Sirikanchana[SUP] 44 [/SUP], Wendy Smith[SUP] 3 [/SUP], Joshua A Steele[SUP] 16 [/SUP], Rosalie Sabburg[SUP] 45 [/SUP], Erin M Symonds[SUP] 46 [/SUP], Phong Thai[SUP] 34 [/SUP], Kevin V Thomas[SUP] 34 [/SUP], Josh Tynan[SUP] 34 [/SUP], Simon Toze[SUP] 3 [/SUP], Janelle Thompson[SUP] 47 [/SUP], Andy S Whiteley[SUP] 48 [/SUP], Judith Chui Ching Wong[SUP] 20 [/SUP], Daisuke Sano[SUP] 49 [/SUP], Stefan Wuertz[SUP] 50 [/SUP], Irene Xagoraraki[SUP] 51 [/SUP], Qian Zhang[SUP] 42 [/SUP], Amity G Zimmer-Faust[SUP] 16 [/SUP], Orin C Shanks[SUP] 27 [/SUP]
Affiliations
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.
Keywords: COVID-19; False negative; False positive; RT-PCR; SARS-CoV-2; Surveillance; Wastewater.
. 2022 Jan 20;805:149877.
doi: 10.1016/j.scitotenv.2021.149877. Epub 2021 Aug 25.
Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance
Warish Ahmed[SUP] 1 [/SUP], Stuart L Simpson[SUP] 2 [/SUP], Paul M Bertsch[SUP] 3 [/SUP], Kyle Bibby[SUP] 4 [/SUP], Aaron Bivins[SUP] 4 [/SUP], Linda L Blackall[SUP] 5 [/SUP], Sílvia Bofill-Mas[SUP] 6 [/SUP], Albert Bosch[SUP] 7 [/SUP], João Brandão[SUP] 8 [/SUP], Phil M Choi[SUP] 9 [/SUP], Mark Ciesielski[SUP] 10 [/SUP], Erica Donner[SUP] 11 [/SUP], Nishita D'Souza[SUP] 12 [/SUP], Andreas H Farnleitner[SUP] 13 [/SUP], Daniel Gerrity[SUP] 14 [/SUP], Raul Gonzalez[SUP] 15 [/SUP], John F Griffith[SUP] 16 [/SUP], Pradip Gyawali[SUP] 17 [/SUP], Charles N Haas[SUP] 18 [/SUP], Kerry A Hamilton[SUP] 19 [/SUP], Hapuarachchige Chanditha Hapuarachchi[SUP] 20 [/SUP], Valerie J Harwood[SUP] 21 [/SUP], Rehnuma Haque[SUP] 22 [/SUP], Greg Jackson[SUP] 23 [/SUP], Stuart J Khan[SUP] 24 [/SUP], Wesaal Khan[SUP] 25 [/SUP], Masaaki Kitajima[SUP] 26 [/SUP], Asja Korajkic[SUP] 27 [/SUP], Giuseppina La Rosa[SUP] 28 [/SUP], Blythe A Layton[SUP] 29 [/SUP], Erin Lipp[SUP] 30 [/SUP], Sandra L McLellan[SUP] 31 [/SUP], Brian McMinn[SUP] 27 [/SUP], Gertjan Medema[SUP] 32 [/SUP], Suzanne Metcalfe[SUP] 3 [/SUP], Wim G Meijer[SUP] 33 [/SUP], Jochen F Mueller[SUP] 34 [/SUP], Heather Murphy[SUP] 35 [/SUP], Coleen C Naughton[SUP] 36 [/SUP], Rachel T Noble[SUP] 10 [/SUP], Sudhi Payyappat[SUP] 37 [/SUP], Susan Petterson[SUP] 38 [/SUP], Tarja Pitkänen[SUP] 39 [/SUP], Veronica B Rajal[SUP] 40 [/SUP], Brandon Reyneke[SUP] 25 [/SUP], Fernando A Roman Jr[SUP] 36 [/SUP], Joan B Rose[SUP] 12 [/SUP], Marta Rusiñol[SUP] 41 [/SUP], Michael J Sadowsky[SUP] 42 [/SUP], Laura Sala-Comorera[SUP] 33 [/SUP], Yin Xiang Setoh[SUP] 20 [/SUP], Samendra P Sherchan[SUP] 43 [/SUP], Kwanrawee Sirikanchana[SUP] 44 [/SUP], Wendy Smith[SUP] 3 [/SUP], Joshua A Steele[SUP] 16 [/SUP], Rosalie Sabburg[SUP] 45 [/SUP], Erin M Symonds[SUP] 46 [/SUP], Phong Thai[SUP] 34 [/SUP], Kevin V Thomas[SUP] 34 [/SUP], Josh Tynan[SUP] 34 [/SUP], Simon Toze[SUP] 3 [/SUP], Janelle Thompson[SUP] 47 [/SUP], Andy S Whiteley[SUP] 48 [/SUP], Judith Chui Ching Wong[SUP] 20 [/SUP], Daisuke Sano[SUP] 49 [/SUP], Stefan Wuertz[SUP] 50 [/SUP], Irene Xagoraraki[SUP] 51 [/SUP], Qian Zhang[SUP] 42 [/SUP], Amity G Zimmer-Faust[SUP] 16 [/SUP], Orin C Shanks[SUP] 27 [/SUP]
Affiliations
- PMID: 34818780
- DOI: 10.1016/j.scitotenv.2021.149877
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.
Keywords: COVID-19; False negative; False positive; RT-PCR; SARS-CoV-2; Surveillance; Wastewater.