SARS-CoV-2 genomic surveillance using rapid point of care COVID-19 antigen tests at public test sites in California
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.
Authors
- Arturo González
- Jeremy Brown (ORCID: https://orcid.org/0000-0002-9941-7759)
- Ellen L. Bouchard (ORCID: https://orcid.org/0000-0003-1891-740X)
- Kathleen Jacobson (ORCID: https://orcid.org/0000-0002-4988-2329)
- Christina Morales (ORCID: https://orcid.org/0000-0001-5813-7219)
- Richard W. Michelmore (ORCID: https://orcid.org/0000-0002-7512-592X)
- Lutz Froenicke
- Siranoosh Ashtari
- Charlotte B. Acharya (ORCID: https://orcid.org/0000-0001-6010-5566)
- Stephenie Liu
- Ryan T. Davis (ORCID: https://orcid.org/0000-0003-0036-4085)
- Eric M. Foote (ORCID: https://orcid.org/0009-0007-3058-3306)
- Vanessa K. Rashbrook
- Debra A. Wadford (ORCID: https://orcid.org/0000-0002-8630-427X)
- Phacharee Arunleung (ORCID: https://orcid.org/0000-0002-2446-4227)
- Elizabeth F. Baylis
- John Bell (ORCID: https://orcid.org/0000-0003-2055-8274)
- Natalie Hnyp
- Alyssa Laxamana
- Jacob Conston
Institutions
- California Department of Public Health (US)
- University of California, Davis (US)
- Stanford University (US)
Publication Details
- Journal
- Frontiers in Public Health
- Published
- 2025-07-25
- DOI
- https://doi.org/10.3389/fpubh.2025.1620651
- Primary Topic
- SARS-CoV-2 and COVID-19 Research
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Centers for Disease Control and Prevention
- University of California, Davis
- Genome Center, University of California, Davis