Citywide serosurveillance of the initial SARS-CoV-2 outbreak in San Francisco using electronic health records

Isobel Routledge (), Adrienne Epstein, Saki Takahashi, Owen Janson, Jill Hakim, Elias Duarte, Keirstinne Turcios, Joanna Vinden, Kirk Sujishi, Jesus Rangel, Marcelina Coh, Lee Besana, Wai-Kit Ho, Ching-Ying Oon, Chui Mei Ong, Cassandra Yun, Kara Lynch, Alan H. B. Wu, Wesley Wu, William Karlon, Edward Thornborrow, Michael J. Peluso, Timothy J. Henrich, John E. Pak, Jessica Briggs, Bryan Greenhouse and Isabel Rodriguez-Barraquer
Additional contact information
Isobel Routledge: University of California San Francisco
Adrienne Epstein: University of California San Francisco
Saki Takahashi: University of California San Francisco
Owen Janson: University of California San Francisco
Jill Hakim: University of California San Francisco
Elias Duarte: University of California San Francisco
Keirstinne Turcios: University of California San Francisco
Joanna Vinden: University of California San Francisco
Kirk Sujishi: University of California San Francisco
Jesus Rangel: University of California San Francisco
Marcelina Coh: University of California San Francisco
Lee Besana: University of California San Francisco
Wai-Kit Ho: University of California San Francisco
Ching-Ying Oon: University of California San Francisco
Chui Mei Ong: University of California San Francisco
Cassandra Yun: University of California San Francisco
Kara Lynch: University of California San Francisco
Alan H. B. Wu: University of California San Francisco
Wesley Wu: Chan Zuckerberg Biohub
William Karlon: University of California San Francisco
Edward Thornborrow: University of California San Francisco
Michael J. Peluso: University of California San Francisco
Timothy J. Henrich: University of California San Francisco
John E. Pak: Chan Zuckerberg Biohub
Jessica Briggs: University of California San Francisco
Bryan Greenhouse: University of California San Francisco
Isabel Rodriguez-Barraquer: University of California San Francisco

Nature Communications, 2021, vol. 12, issue 1, 1-9

Abstract: Abstract Serosurveillance provides a unique opportunity to quantify the proportion of the population that has been exposed to pathogens. Here, we developed and piloted Serosurveillance for Continuous, ActionabLe Epidemiologic Intelligence of Transmission (SCALE-IT), a platform through which we systematically tested remnant samples from routine blood draws in two major hospital networks in San Francisco for SARS-CoV-2 antibodies during the early months of the pandemic. Importantly, SCALE-IT allows for algorithmic sample selection and rich data on covariates by leveraging electronic health record data. We estimated overall seroprevalence at 4.2%, corresponding to a case ascertainment rate of only 4.9%, and identified important heterogeneities by neighborhood, homelessness status, and race/ethnicity. Neighborhood seroprevalence estimates from SCALE-IT were comparable to local community-based surveys, while providing results encompassing the entire city that have been previously unavailable. Leveraging this hybrid serosurveillance approach has strong potential for application beyond this local context and for diseases other than SARS-CoV-2.

Date: 2021
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DOI: 10.1038/s41467-021-23651-6

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