# SARS-CoV-2 genomic surveillance using rapid point of care COVID-19 antigen tests at public test sites in California

## TL;DR

California used rapid antigen tests at public sites to collect SARS-CoV-2 genomes, enabling large-scale genomic surveillance and contributing significantly to state and national sequencing efforts.

## Contribution

Demonstrates successful statewide genomic surveillance using antigen tests, expanding accessibility and coverage in rural and urban areas.

## Key findings

- 14,088 SARS-CoV-2 genomes were successfully sequenced from antigen tests with a 92.9% success rate.
- The program contributed 13.9% of California's and 2.7% of the US's SARS-CoV-2 sequences during the period.
- In one rural region, the program generated 69% of all SARS-CoV-2 sequences.

## Abstract

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.