SARS-CoV-2 Genomic Surveillance from Community-Distributed Rapid Antigen Tests, Wisconsin, USA

Area of Science:

• Public Health
• Virology
• Genomic Surveillance

Background:

• SARS-CoV-2 genomic surveillance in the US predominantly used diagnostic specimens from nucleic acid amplification-based tests.
• The waning use of these tests post-COVID-19 Public Health Emergency necessitated alternative surveillance methods.

Purpose of the Study:

• To establish a sustainable SARS-CoV-2 genomic surveillance program using freely available community rapid antigen tests (RATs).
• To assess the feasibility of sequencing SARS-CoV-2 from RATs in partnership with community organizations.

Main Methods:

• Collaboration with public health agencies and the South Central Library System in Dane County, Wisconsin.
• Collection and sequencing of SARS-CoV-2 from 227 community-sourced RAT samples between August 2023 and February 2024.
• Analysis of sequence success rates, particularly in relation to cycle threshold values.

Main Results:

• Successfully generated 127 SARS-CoV-2 genome sequences with high coverage (>90% genome, >10× depth) from RAT samples.
• Identified a correlation between lower cycle threshold values and successful sequencing.
• Demonstrated the practicality of community-based RAT collection for genomic surveillance.

Conclusions:

• Collecting and sequencing SARS-CoV-2 from RATs is a viable strategy for ongoing genomic surveillance.
• Partnerships with community sites enhance the sustainability of public health surveillance efforts.
• This approach offers a flexible alternative to traditional methods in response to changing public health landscapes.