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Whitney O, Kennedy LC, Fan VB, Hinkle A, Kantor R, Greenwald H, Crits-Christoph A, Al-Shayeb B, Chaplin M, Maurer AC, Tjian R, Nelson KL. Sewage, Salt, Silica, and SARS-CoV-2 (4S): An Economical Kit-Free Method for Direct Capture of SARS-CoV-2 RNA from Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:4880-4888. [PMID: 33759506 PMCID: PMC8009096 DOI: 10.1021/acs.est.0c08129] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/01/2021] [Accepted: 03/11/2021] [Indexed: 05/19/2023]
Abstract
Wastewater-based epidemiology is an emerging tool to monitor COVID-19 infection levels by measuring the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. There remains a need to improve wastewater RNA extraction methods' sensitivity, speed, and reduce reliance on often expensive commercial reagents to make wastewater-based epidemiology more accessible. We present a kit-free wastewater RNA extraction method, titled "Sewage, Salt, Silica and SARS-CoV-2" (4S), that employs the abundant and affordable reagents sodium chloride (NaCl), ethanol, and silica RNA capture matrices to recover sixfold more SARS-CoV-2 RNA from wastewater than an existing ultrafiltration-based method. The 4S method concurrently recovered pepper mild mottle virus (PMMoV) and human 18S ribosomal subunit rRNA, which have been proposed as fecal concentration controls. The SARS-CoV-2 RNA concentrations measured in three sewersheds corresponded to the relative prevalence of COVID-19 infection determined via clinical testing. Lastly, controlled experiments indicate that the 4S method prevented RNA degradation during storage of wastewater samples, was compatible with heat pasteurization, and in our experience, 20 samples can be processed by one lab technician in approximately 2 h. Overall, the 4S method is promising for effective, economical, and accessible wastewater-based epidemiology for SARS-CoV-2, providing another tool to fight the global pandemic.
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Affiliation(s)
- Oscar
N. Whitney
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720-1710, United States
| | - Lauren C. Kennedy
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Vinson B. Fan
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720-1710, United States
| | - Adrian Hinkle
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Rose Kantor
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Hannah Greenwald
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Alexander Crits-Christoph
- Department
of Plant and Microbial Biology, University
of California, Berkeley, California 94720-1710, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - Basem Al-Shayeb
- Department
of Plant and Microbial Biology, University
of California, Berkeley, California 94720-1710, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - Mira Chaplin
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Anna C. Maurer
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720-1710, United States
| | - Robert Tjian
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720-1710, United States
- The
Howard Hughes Medical Institute, University
of California Berkeley, Berkeley, California 94720, United States
| | - Kara L. Nelson
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
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Whitney ON, Kennedy LC, Fan VB, Hinkle A, Kantor R, Greenwald H, Crits-Christoph A, Al-Shayeb B, Chaplin M, Maurer AC, Tjian R, Nelson KL. Sewage, Salt, Silica, and SARS-CoV-2 (4S): An Economical Kit-Free Method for Direct Capture of SARS-CoV-2 RNA from Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021. [PMID: 33759506 DOI: 10.17504/protocols.io.biwfkfbn] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Wastewater-based epidemiology is an emerging tool to monitor COVID-19 infection levels by measuring the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. There remains a need to improve wastewater RNA extraction methods' sensitivity, speed, and reduce reliance on often expensive commercial reagents to make wastewater-based epidemiology more accessible. We present a kit-free wastewater RNA extraction method, titled "Sewage, Salt, Silica and SARS-CoV-2" (4S), that employs the abundant and affordable reagents sodium chloride (NaCl), ethanol, and silica RNA capture matrices to recover sixfold more SARS-CoV-2 RNA from wastewater than an existing ultrafiltration-based method. The 4S method concurrently recovered pepper mild mottle virus (PMMoV) and human 18S ribosomal subunit rRNA, which have been proposed as fecal concentration controls. The SARS-CoV-2 RNA concentrations measured in three sewersheds corresponded to the relative prevalence of COVID-19 infection determined via clinical testing. Lastly, controlled experiments indicate that the 4S method prevented RNA degradation during storage of wastewater samples, was compatible with heat pasteurization, and in our experience, 20 samples can be processed by one lab technician in approximately 2 h. Overall, the 4S method is promising for effective, economical, and accessible wastewater-based epidemiology for SARS-CoV-2, providing another tool to fight the global pandemic.
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Affiliation(s)
- Oscar N Whitney
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
| | - Lauren C Kennedy
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Vinson B Fan
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
| | - Adrian Hinkle
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Rose Kantor
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Hannah Greenwald
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-1710, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
| | - Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-1710, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
| | - Mira Chaplin
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Anna C Maurer
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
- The Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, United States
| | - Kara L Nelson
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
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Whitney ON, Kennedy LC, Fan VB, Hinkle A, Kantor R, Greenwald H, Crits-Christoph A, Al-Shayeb B, Chaplin M, Maurer AC, Tjian R, Nelson KL. Sewage, Salt, Silica, and SARS-CoV-2 (4S): An Economical Kit-Free Method for Direct Capture of SARS-CoV-2 RNA from Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021. [PMID: 33759506 DOI: 10.17504/protocols.io.biwekfbe] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Wastewater-based epidemiology is an emerging tool to monitor COVID-19 infection levels by measuring the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. There remains a need to improve wastewater RNA extraction methods' sensitivity, speed, and reduce reliance on often expensive commercial reagents to make wastewater-based epidemiology more accessible. We present a kit-free wastewater RNA extraction method, titled "Sewage, Salt, Silica and SARS-CoV-2" (4S), that employs the abundant and affordable reagents sodium chloride (NaCl), ethanol, and silica RNA capture matrices to recover sixfold more SARS-CoV-2 RNA from wastewater than an existing ultrafiltration-based method. The 4S method concurrently recovered pepper mild mottle virus (PMMoV) and human 18S ribosomal subunit rRNA, which have been proposed as fecal concentration controls. The SARS-CoV-2 RNA concentrations measured in three sewersheds corresponded to the relative prevalence of COVID-19 infection determined via clinical testing. Lastly, controlled experiments indicate that the 4S method prevented RNA degradation during storage of wastewater samples, was compatible with heat pasteurization, and in our experience, 20 samples can be processed by one lab technician in approximately 2 h. Overall, the 4S method is promising for effective, economical, and accessible wastewater-based epidemiology for SARS-CoV-2, providing another tool to fight the global pandemic.
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Affiliation(s)
- Oscar N Whitney
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
| | - Lauren C Kennedy
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Vinson B Fan
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
| | - Adrian Hinkle
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Rose Kantor
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Hannah Greenwald
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-1710, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
| | - Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-1710, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
| | - Mira Chaplin
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
| | - Anna C Maurer
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-1710, United States
- The Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, United States
| | - Kara L Nelson
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1710, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
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Whitney ON, Kennedy LC, Fan V, Hinkle A, Kantor R, Greenwald H, Crits-Christoph A, Al-Shayeb B, Chaplin M, Maurer AC, Tjian R, Nelson KL. Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.12.01.20242131. [PMID: 33300015 PMCID: PMC7724686 DOI: 10.1101/2020.12.01.20242131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Wastewater-based epidemiology is an emerging tool to monitor COVID-19 infection levels by measuring the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. There remains a need to improve wastewater RNA extraction methods' sensitivity, speed, and reduce reliance on often expensive commercial reagents to make wastewater-based epidemiology more accessible. We present a kit-free wastewater RNA extraction method, titled "Sewage, Salt, Silica and SARS-CoV-2" (4S), that employs the abundant and affordable reagents sodium chloride (NaCl), ethanol and silica RNA capture matrices to recover 6-fold more SARS-CoV-2 RNA from wastewater than an existing ultrafiltration-based method. The 4S method concurrently recovered pepper mild mottle virus (PMMoV) and human 18S ribosomal subunit rRNA, both suitable as fecal concentration controls. The SARS-CoV-2 RNA concentrations measured in three sewersheds corresponded to the relative prevalence of COVID-19 infection determined via clinical testing. Lastly, controlled experiments indicate that the 4S method prevented RNA degradation during storage of wastewater samples, was compatible with heat pasteurization, and could be performed in approximately 3 hours. Overall, the 4S method is promising for effective, economical, and accessible wastewater-based epidemiology for SARS-CoV-2, providing another tool to fight the global pandemic.
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Affiliation(s)
- Oscar N. Whitney
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Lauren C. Kennedy
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
| | - Vinson Fan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Adrian Hinkle
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
| | - Rose Kantor
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
| | - Hannah Greenwald
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
| | - Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, 94704, USA
| | - Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, 94704, USA
| | - Mira Chaplin
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
| | - Anna C. Maurer
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- The Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, USA
| | - Kara L. Nelson
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, 94704, USA
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