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

Nature Communications
Isobel RoutledgeIsabel Rodriguez-Barraquer

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.

References

May 10, 2000·Preventive Veterinary Medicine·I A GardnerM T Collins
Sep 28, 2010·Journal of Medical Virology·Gannon C MakWilina Lim
Oct 27, 2010·PloS One·Don BandaranayakeUNKNOWN 2009 H1N1 Serosurvey Investigation Team
Oct 25, 2012·Emerging Infectious Diseases·Katja HoschlerMaria Zambon
Jan 26, 2017·Lancet·C Jessica E MetcalfBryan T Grenfell
Feb 23, 2020·The Lancet Infectious Diseases·Ensheng DongLauren Gardner
Jun 9, 2020·ELife·Michael J MinaBryan T Grenfell
Jun 17, 2020·Emerging Infectious Diseases·Hannah ClaphamClarence C Tam
Jul 8, 2020·EClinicalMedicine·Daniel PanManish Pareek
Aug 6, 2020·Journal of General Internal Medicine·Cary P GrossMarcella Nunez-Smith
Aug 9, 2020·The Lancet Infectious Diseases·Rahul K AroraDavid L Buckeridge
Aug 22, 2020·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Gabriel ChamieDiane V Havlir
Aug 28, 2020·Nature·Takehiro TakahashiAkiko Iwasaki
Sep 19, 2020·Nature Communications·Dianna L NgCharles Y Chiu

❮ Previous
Next ❯

Software Mentioned

Stan
Google Cloud Geocoding API
R
SCALE
IT
SCALE IT
- IT for Continuous ActionabLe Epidemiologic Intelligence of T...
ggmap R package

Related Concepts

Related Feeds

BioHub - Researcher Network

The Chan-Zuckerberg Biohub aims to support the fundamental research and develop the technologies that will enable physicians to cure, prevent, or manage all diseases in our childrens' lifetimes. The CZ Biohub brings together researchers from UC Berkeley, Stanford, and UCSF. Find the latest research from the CZ Biohub researcher network here.

Related Papers

Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America
Michael P Busch, Mars Stone
American Journal of Public Health
T J Dondero, J W Curran
Virus Information Exchange Newsletter for South-East Asia and the Western Pacific
S KumariT J John
© 2021 Meta ULC. All rights reserved