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Mondal S, Feirer N, Brockman M, Preston MA, Teter SJ, Ma D, Goueli SA, Moorji S, Saul B, Cali JJ. A direct capture method for purification and detection of viral nucleic acid enables epidemiological surveillance of SARS-CoV-2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021. [PMID: 34252764 DOI: 10.1101/2021.05.06.21256753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Studies have demonstrated that SARS-CoV-2 RNA can be detected in the feces of infected individuals. This finding spurred investigation into using wastewater-based epidemiology (WBE) to monitor SARS-CoV-2 RNA and track the appearance and spread of COVID-19 in communities. SARS-CoV-2 is present at low levels in wastewater, making sample concentration a prerequisite for sensitive detection and utility in WBE. Whereas common methods for isolating viral genetic material are biased toward intact virus isolation, it is likely that a relatively low percentage of the total SARS-CoV-2 RNA genome in wastewater is contained within intact virions. Therefore, we hypothesized that a direct unbiased total nucleic acid(TNA) extraction method could overcome the cumbersome protocols, variability and low recovery rates associated with the former methods. This led to development of a simple, rapid, and modular alternative to existing purification methods. In an initial concentration step, chaotropic agents are added to raw sewage allowing binding of nucleic acid from free nucleoprotein complexes, partially intact, and intact virions to a silica matrix. The eluted nucleic acid is then purified using manual or semi-automated methods. RT-qPCR enzyme mixes were formulated that demonstrate substantial inhibitor resistance. In addition, multiplexed probe-based RT-qPCR assays detecting the N1, N2 (nucleocapsid) and E (envelope) gene fragments of SARS-CoV-2 were developed. The RT-qPCR assays also contain primers and probes to detect Pepper Mild Mottle Virus (PMMoV), a fecal indicator RNA virus present in wastewater, and an exogenous control RNA to measure effects of RT-qPCR inhibitors. Using this workflow, we monitored wastewater samples from three wastewater treatment plants (WWTP) in Dane County, Wisconsin. We also successfully sequenced a subset of samples to ensure compatibility with a SARS-CoV-2 amplicon panel and demonstrated the potential for SARS-CoV-2 variant detection. Data obtained here underscore the potential for wastewater surveillance of SARS-CoV-2 and other infectious agents in communities.
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Affiliation(s)
- Subhanjan Mondal
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America.
| | - Nathan Feirer
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - Michael Brockman
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - Melanie A Preston
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - Sarah J Teter
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - Dongping Ma
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - Said A Goueli
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - Sameer Moorji
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - Brigitta Saul
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - James J Cali
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
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Mondal S, Feirer N, Brockman M, Preston MA, Teter SJ, Ma D, Goueli SA, Moorji S, Saul B, Cali JJ. A direct capture method for purification and detection of viral nucleic acid enables epidemiological surveillance of SARS-CoV-2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 795:148834. [PMID: 34252764 PMCID: PMC8262391 DOI: 10.1016/j.scitotenv.2021.148834] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 05/04/2023]
Abstract
Studies have demonstrated that SARS-CoV-2 RNA can be detected in the feces of infected individuals. This finding spurred investigation into using wastewater-based epidemiology (WBE) to monitor SARS-CoV-2 RNA and track the appearance and spread of COVID-19 in communities. SARS-CoV-2 is present at low levels in wastewater, making sample concentration a prerequisite for sensitive detection and utility in WBE. Whereas common methods for isolating viral genetic material are biased toward intact virus isolation, it is likely that a relatively low percentage of the total SARS-CoV-2 RNA genome in wastewater is contained within intact virions. Therefore, we hypothesized that a direct unbiased total nucleic acid(TNA) extraction method could overcome the cumbersome protocols, variability and low recovery rates associated with the former methods. This led to development of a simple, rapid, and modular alternative to existing purification methods. In an initial concentration step, chaotropic agents are added to raw sewage allowing binding of nucleic acid from free nucleoprotein complexes, partially intact, and intact virions to a silica matrix. The eluted nucleic acid is then purified using manual or semi-automated methods. RT-qPCR enzyme mixes were formulated that demonstrate substantial inhibitor resistance. In addition, multiplexed probe-based RT-qPCR assays detecting the N1, N2 (nucleocapsid) and E (envelope) gene fragments of SARS-CoV-2 were developed. The RT-qPCR assays also contain primers and probes to detect Pepper Mild Mottle Virus (PMMoV), a fecal indicator RNA virus present in wastewater, and an exogenous control RNA to measure effects of RT-qPCR inhibitors. Using this workflow, we monitored wastewater samples from three wastewater treatment plants (WWTP) in Dane County, Wisconsin. We also successfully sequenced a subset of samples to ensure compatibility with a SARS-CoV-2 amplicon panel and demonstrated the potential for SARS-CoV-2 variant detection. Data obtained here underscore the potential for wastewater surveillance of SARS-CoV-2 and other infectious agents in communities.
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Affiliation(s)
- Subhanjan Mondal
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America.
| | - Nathan Feirer
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - Michael Brockman
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - Melanie A Preston
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - Sarah J Teter
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - Dongping Ma
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - Said A Goueli
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - Sameer Moorji
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - Brigitta Saul
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
| | - James J Cali
- Promega Corporation, 5430 E Cheryl Pkwy, Fitchburg, WI 53711, United States of America
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