tetano
Editor, Senior Moderator
Front Public Health
. 2025 Jul 25:13:1620651.
doi: 10.3389/fpubh.2025.1620651. eCollection 2025. SARS-CoV-2 genomic surveillance using rapid point of care COVID-19 antigen tests at public test sites in California
Eric M Foote[SUP] 1 2 [/SUP], Ellen L Bouchard[SUP] 1 [/SUP], Charlotte B Acharya[SUP] 3 [/SUP], Elizabeth F Baylis[SUP] 1 [/SUP], John M Bell[SUP] 1 [/SUP], Christina Morales[SUP] 1 [/SUP], Phacharee Arunleung[SUP] 1 [/SUP], Andreina Urrutia Gonzalez[SUP] 3 [/SUP], Jacob Conston[SUP] 3 [/SUP], Stephenie Liu[SUP] 4 [/SUP], Ryan Davis[SUP] 4 [/SUP], Jeremy Brown[SUP] 3 [/SUP], Natalie Hnyp[SUP] 3 [/SUP], Siranoosh Ashtari[SUP] 3 [/SUP], Alyssa Laxamana[SUP] 3 [/SUP], Vanessa Rashbrook[SUP] 3 [/SUP], Lutz Froenicke[SUP] 3 [/SUP], Kathleen Jacobson[SUP] 1 [/SUP], Richard Michelmore[SUP] 3 [/SUP], Debra A Wadford[SUP] 1 [/SUP]
Affiliations
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: COVID-19 rapid antigen test; SARS-CoV-2; genomic surveillance; population viral genomic epidemiology; whole genome sequencing.
. 2025 Jul 25:13:1620651.
doi: 10.3389/fpubh.2025.1620651. eCollection 2025. SARS-CoV-2 genomic surveillance using rapid point of care COVID-19 antigen tests at public test sites in California
Eric M Foote[SUP] 1 2 [/SUP], Ellen L Bouchard[SUP] 1 [/SUP], Charlotte B Acharya[SUP] 3 [/SUP], Elizabeth F Baylis[SUP] 1 [/SUP], John M Bell[SUP] 1 [/SUP], Christina Morales[SUP] 1 [/SUP], Phacharee Arunleung[SUP] 1 [/SUP], Andreina Urrutia Gonzalez[SUP] 3 [/SUP], Jacob Conston[SUP] 3 [/SUP], Stephenie Liu[SUP] 4 [/SUP], Ryan Davis[SUP] 4 [/SUP], Jeremy Brown[SUP] 3 [/SUP], Natalie Hnyp[SUP] 3 [/SUP], Siranoosh Ashtari[SUP] 3 [/SUP], Alyssa Laxamana[SUP] 3 [/SUP], Vanessa Rashbrook[SUP] 3 [/SUP], Lutz Froenicke[SUP] 3 [/SUP], Kathleen Jacobson[SUP] 1 [/SUP], Richard Michelmore[SUP] 3 [/SUP], Debra A Wadford[SUP] 1 [/SUP]
Affiliations
- PMID: 40786158
- PMCID: PMC12331611
- DOI: 10.3389/fpubh.2025.1620651
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: COVID-19 rapid antigen test; SARS-CoV-2; genomic surveillance; population viral genomic epidemiology; whole genome sequencing.