ORIGINAL RESEARCH article
Front. Public Health
Sec. Infectious Diseases: Epidemiology and Prevention
Volume 13 - 2025 | doi: 10.3389/fpubh.2025.1620651
This article is part of the Research TopicInnovative Approaches for the Early Detection and Rapid Response to Biothreat and Emerging Infectious AgentsView all articles
SARS-CoV-2 genomic surveillance using rapid point of care COVID-19 antigen tests at public test sites in California
Provisionally accepted
Eric M Foote1,2
Ellen Bouchard1
Charlotte Bell Acharya3
Elizabeth F Baylis1
John Bell1
Christina Morales1Phacharee Arunleung1Andreina Urrutia Gonzalez3Jacob Conston3Stephenie Liu4Ryan Davis3,4Jeremy Brown3Natalie Hnyp3Siranoosh Ashtari3
Alyssa Laxamana3Vanessa Rashbrook3
Lutz Froenicke3Kathleen Jacobson1
Richard Michelmore3
Debra A. Wadford1*- 1California Department of Public Health, Richmond, United States
- 2Stanford University School of Medicine, Stanford, United States
- 3University of California, Davis, Davis, United States
- 4University of California Davis Health, Davis, United States
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California’s SARS-CoV-2 genomic surveillance program (California COVIDNet) developed whole genomic sequencing (WGS) capability from positive COVID-19 antigen tests to maintain genomic surveillance from public test sites. Over 4-months, COVIDNet sourced specimens from positive COVID-19 antigen tests from 142 California public test sites in 43 counties. Successful WGS was defined as at least 83% reference coverage with a minimum 20x genomic read depth. There were 14,088 SARS-CoV-2 genomes obtained from positive antigen tests with a success rate of 92.9%. The program generated 13.9% of SARS-CoV-2 sequences in California and 2.7% of sequences in the US during the program operation period. In one rural region, 69% of all SARS-CoV-2 sequences were generated by the program. California successfully transitioned SARS-CoV-2 WGS on a statewide scale to specimens sourced from positive antigen tests. Community-based testing coupled with a comprehensive genomic surveillance program provides a statewide strategy applicable to other pathogens of public health significance.
Keywords: SARS-CoV-2, COVID-19 rapid antigen test, whole genome sequencing, population viral genomic epidemiology, Genomic surveillance
Received: 30 Apr 2025; Accepted: 14 Jul 2025.
Copyright: © 2025 Foote, Bouchard, Acharya, Baylis, Bell, Morales, Arunleung, Gonzalez, Conston, Liu, Davis, Brown, Hnyp, Ashtari, Laxamana, Rashbrook, Froenicke, Jacobson, Michelmore and Wadford. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Debra A. Wadford, California Department of Public Health, Richmond, United States
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