Analysis of SARS-CoV-2 RNA Persistence across Indoor Surface Materials Reveals Best Practices for Environmental Monitoring Programs
Rodolfo A. Salido,
Victor J. Cantú,
Alex E. Clark,
Sandra L. Leibel,
Anahid Foroughishafiei,
Anushka Saha,
Abbas Hakim,
Alhakam Nouri,
Alma L. Lastrella,
Anelizze Castro-Martínez,
Ashley Plascencia,
Bhavika K. Kapadia,
Bing Xia,
Christopher A. Ruiz,
Clarisse A. Marotz,
Daniel Maunder,
Elijah S. Lawrence,
Elizabeth W. Smoot,
Emily Eisner,
Evelyn S. Crescini,
Laura Kohn,
Lizbeth Franco Vargas,
Marisol Chacón,
Maryann Betty,
Michal Machnicki,
Min Yi Wu,
Nathan A. Baer,
Pedro Belda-Ferre,
Peter De Hoff,
Phoebe Seaver,
R. Tyler Ostrander,
Rebecca Tsai,
Shashank Sathe,
Stefan Aigner,
Sydney C. Morgan,
Toan T. Ngo,
Tom Barber,
Willi Cheung,
Aaron F. Carlin,
Gene W. Yeo,
Louise C. Laurent,
Rebecca Fielding-Miller,
Rob Knight
Affiliations
Rodolfo A. Salido
Department of Bioengineering, University of California San Diego, La Jolla, California, USA
Victor J. Cantú
Department of Bioengineering, University of California San Diego, La Jolla, California, USA
Alex E. Clark
Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, USA
Sandra L. Leibel
Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Anahid Foroughishafiei
Department of Bioengineering, University of California San Diego, La Jolla, California, USA
Anushka Saha
Department of Bioengineering, University of California San Diego, La Jolla, California, USA
Abbas Hakim
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Alhakam Nouri
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Alma L. Lastrella
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Anelizze Castro-Martínez
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Ashley Plascencia
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Bhavika K. Kapadia
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Bing Xia
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Christopher A. Ruiz
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Clarisse A. Marotz
Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Daniel Maunder
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Elijah S. Lawrence
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Elizabeth W. Smoot
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Emily Eisner
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Evelyn S. Crescini
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Laura Kohn
Herbert Wertheim School of Public Health, University of California, La Jolla, California, USA
Lizbeth Franco Vargas
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Marisol Chacón
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Maryann Betty
Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Michal Machnicki
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Min Yi Wu
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Nathan A. Baer
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Pedro Belda-Ferre
Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Peter De Hoff
Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
Phoebe Seaver
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
R. Tyler Ostrander
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Rebecca Tsai
Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Shashank Sathe
Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
Stefan Aigner
Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
Sydney C. Morgan
Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
Toan T. Ngo
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Tom Barber
Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Willi Cheung
Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
Aaron F. Carlin
Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, USA
Gene W. Yeo
Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
Louise C. Laurent
Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, California, USA
Rebecca Fielding-Miller
Herbert Wertheim School of Public Health, University of California, La Jolla, California, USA
Rob Knight
Department of Bioengineering, University of California San Diego, La Jolla, California, USA
ABSTRACT Environmental monitoring in public spaces can be used to identify surfaces contaminated by persons with coronavirus disease 2019 (COVID-19) and inform appropriate infection mitigation responses. Research groups have reported detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces days or weeks after the virus has been deposited, making it difficult to estimate when an infected individual may have shed virus onto a SARS-CoV-2-positive surface, which in turn complicates the process of establishing effective quarantine measures. In this study, we determined that reverse transcription-quantitative PCR (RT-qPCR) detection of viral RNA from heat-inactivated particles experiences minimal decay over 7 days of monitoring on eight out of nine surfaces tested. The properties of the studied surfaces result in RT-qPCR signatures that can be segregated into two material categories, rough and smooth, where smooth surfaces have a lower limit of detection. RT-qPCR signal intensity (average quantification cycle [Cq]) can be correlated with surface viral load using only one linear regression model per material category. The same experiment was performed with untreated viral particles on one surface from each category, with essentially identical results. The stability of RT-qPCR viral signal demonstrates the need to clean monitored surfaces after sampling to establish temporal resolution. Additionally, these findings can be used to minimize the number of materials and time points tested and allow for the use of heat-inactivated viral particles when optimizing environmental monitoring methods. IMPORTANCE Environmental monitoring is an important tool for public health surveillance, particularly in settings with low rates of diagnostic testing. Time between sampling public environments, such as hospitals or schools, and notifying stakeholders of the results should be minimal, allowing decisions to be made toward containing outbreaks of coronavirus disease 2019 (COVID-19). The Safer At School Early Alert program (SASEA) (https://saseasystem.org/), a large-scale environmental monitoring effort in elementary school and child care settings, has processed >13,000 surface samples for SARS-CoV-2, detecting viral signals from 574 samples. However, consecutive detection events necessitated the present study to establish appropriate response practices around persistent viral signals on classroom surfaces. Other research groups and clinical labs developing environmental monitoring methods may need to establish their own correlation between RT-qPCR results and viral load, but this work provides evidence justifying simplified experimental designs, like reduced testing materials and the use of heat-inactivated viral particles.