Implementation of Practical Surface SARS-CoV-2 Surveillance in School Settings

Victor J. Cantú; Pedro Belda-Ferre; Rodolfo A. Salido; Rebecca Tsai; Brett Austin; William Jordan; Menka Asudani; Amanda Walster; Celestine G. Magallanes; Holly Valentine; Araz Manjoonian; Carrissa Wijaya; Vinton Omaleki; Karenina Sanders; Stefan Aigner; Nathan A. Baer; Maryann Betty; Anelizze Castro-Martínez; Willi Cheung; Evelyn S. Crescini; Peter De Hoff; Emily Eisner; Abbas Hakim; Bhavika Kapadia; Alma L. Lastrella; Elijah S. Lawrence; Toan T. Ngo; Tyler Ostrander; Shashank Sathe; Phoebe Seaver; Elizabeth W. Smoot; Aaron F. Carlin; Gene W. Yeo; Louise C. Laurent; Anna Liza Manlutac; Rebecca Fielding-Miller; Rob Knight

doi:10.1128/msystems.00103-22

mSystems (Aug 2022)

Implementation of Practical Surface SARS-CoV-2 Surveillance in School Settings

Victor J. Cantú,
Pedro Belda-Ferre,
Rodolfo A. Salido,
Rebecca Tsai,
Brett Austin,
William Jordan,
Menka Asudani,
Amanda Walster,
Celestine G. Magallanes,
Holly Valentine,
Araz Manjoonian,
Carrissa Wijaya,
Vinton Omaleki,
Karenina Sanders,
Stefan Aigner,
Nathan A. Baer,
Maryann Betty,
Anelizze Castro-Martínez,
Willi Cheung,
Evelyn S. Crescini,
Peter De Hoff,
Emily Eisner,
Abbas Hakim,
Bhavika Kapadia,
Alma L. Lastrella,
Elijah S. Lawrence,
Toan T. Ngo,
Tyler Ostrander,
Shashank Sathe,
Phoebe Seaver,
Elizabeth W. Smoot,
Aaron F. Carlin,
Gene W. Yeo,
Louise C. Laurent,
Anna Liza Manlutac,
Rebecca Fielding-Miller,
Rob Knight

Affiliations

Victor J. Cantú: Department of Bioengineering, University of California San Diego, La Jolla, California, USA
Pedro Belda-Ferre: Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Rodolfo A. Salido: Department of Bioengineering, University of California San Diego, La Jolla, California, USA
Rebecca Tsai: Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Brett Austin: San Diego County Public Health Lab, San Diego, California, USA
William Jordan: San Diego County Public Health Lab, San Diego, California, USA
Menka Asudani: San Diego County Public Health Lab, San Diego, California, USA
Amanda Walster: San Diego County Public Health Lab, San Diego, California, USA
Celestine G. Magallanes: Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
Holly Valentine: Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
Araz Manjoonian: Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
Carrissa Wijaya: Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
Vinton Omaleki: Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
Karenina Sanders: Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Stefan Aigner: 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
Maryann Betty: 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
Willi Cheung: 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
Peter De Hoff: 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
Abbas Hakim: Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Bhavika Kapadia: 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
Elijah S. Lawrence: Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, 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
Tyler Ostrander: Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Shashank Sathe: Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, 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
Elizabeth W. Smoot: Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, 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, La Jolla, California, USA
Gene W. Yeo: Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
Louise C. Laurent: Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
Anna Liza Manlutac: San Diego County Public Health Lab, San Diego, California, USA
Rebecca Fielding-Miller: Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, California, USA
Rob Knight: Department of Bioengineering, University of California San Diego, La Jolla, California, USA

DOI: https://doi.org/10.1128/msystems.00103-22
Journal volume & issue: Vol. 7, no. 4

Abstract

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ABSTRACT Surface sampling for SARS-CoV-2 RNA detection has shown considerable promise to detect exposure of built environments to infected individuals shedding virus who would not otherwise be detected. Here, we compare two popular sampling media (VTM and SDS) and two popular workflows (Thermo and PerkinElmer) for implementation of a surface sampling program suitable for environmental monitoring in public schools. We find that the SDS/Thermo pipeline shows superior sensitivity and specificity, but that the VTM/PerkinElmer pipeline is still sufficient to support surface surveillance in any indoor setting with stable cohorts of occupants (e.g., schools, prisons, group homes, etc.) and may be used to leverage existing investments in infrastructure. IMPORTANCE The ongoing COVID-19 pandemic has claimed the lives of over 5 million people worldwide. Due to high density occupancy of indoor spaces for prolonged periods of time, schools are often of concern for transmission, leading to widespread school closings to combat pandemic spread when cases rise. Since pediatric clinical testing is expensive and difficult from a consent perspective, we have deployed surface sampling in SASEA (Safer at School Early Alert), which allows for detection of SARS-CoV-2 from surfaces within a classroom. In this previous work, we developed a high-throughput method which requires robotic automation and specific reagents that are often not available for public health laboratories such as the San Diego County Public Health Laboratory (SDPHL). Therefore, we benchmarked our method (Thermo pipeline) against SDPHL’s (PerkinElmer) more widely used method for the detection and prediction of SARS-CoV-2 exposure. While our method shows superior sensitivity (false-negative rate of 9% versus 27% for SDPHL), the SDPHL pipeline is sufficient to support surface surveillance in indoor settings. These findings are important since they show that existing investments in infrastructure can be leveraged to slow the spread of SARS-CoV-2 not in just the classroom but also in prisons, nursing homes, and other high-risk, indoor settings.

Published in mSystems

ISSN: 2379-5077 (Online)
Publisher: American Society for Microbiology
Country of publisher: United States
LCC subjects: Science: Microbiology
Website: https://journals.asm.org/journal/msystems

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