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Aegis Sciences Corporation Provides Insights into Early Detection Methods of COVID-19 Variants

In collaboration with Walgreens, data analysis examines more than 300,000 COVID-19 samples during Omicron surge

NASHVILLE, Tenn., (Oct. 6, 2022)
 – A manuscript detailing an extensive analysis completed by Aegis Sciences Corporation and Walgreens was published in PLOS ONE this week. The manuscript, Validation of reduced S-gene target performance and failure for rapid surveillance of SARS-CoV-2 variants, highlights a unique methodology developed through work by both organizations to create a more comprehensive early warning system during periods of emerging new viral variants.

Throughout the COVID-19 pandemic, Aegis Sciences Corporation and Walgreens collaborated to provide timely access to testing resources and published near real-time trends on viral spread through the Walgreens COVID-19 Index. This interactive tracking tool from Walgreens, powered by testing data from Aegis Sciences Corporation, was among the first to uniquely identify the spread of current and emerging variants in near real time.

Public health organizations have utilized various methods to identify and characterize new mutations of SARS-CoV-2. This information is used to inform the public about variants that are potentially more transmissible or that could contribute to increased risk of severe illness. Additionally, close attention has been paid to certain variants of concern, such as Alpha and certain Omicron lineages, that cause uncommon patterns of results identified through polymerase chain reaction, or PCR, testing. Commonly referred to as “S-Gene Target Failure,” the result pattern is at times used as a proxy to identify transmission of new variants.

“Continued collaboration throughout the development, implementation, and maintenance of the COVID-19 Index has allowed us to explore the available data beyond reporting positive and negative results,” said Dr. Matthew Hardison, senior vice president of lab operations at Aegis Sciences Corporation.“These analyses and validations gave us the opportunity to identify the shift in new emerging variant infections better than other presumptive methods and may allow us to more comprehensively identify these changes in the future.”

Through a comparison of PCR and WGS results during the Alpha and Omicron waves, the Aegis and Walgreens teams identified an improved mechanism that allows for enhanced early surveillance of emerging variants beyond assessing for S-Gene Target Failure alone. In doing so, they were able to predict emergence of new variants sooner, such as BA.1 and BA.2, prior to confirmation of presence of these variants through slower sequencing processes. Using this new method, they believe that they will have an improved ability to identify transitions from one variant to the next at certain points moving into the future.

“COVID has demonstrated the need for multiple surveillance tools to fully and quickly track community spread so that individuals and local governments can respond with appropriate mitigation,” said Michael Taitel, PhD, Senior Director, Healthcare and Clinical Analytics for Walgreens. “Our collaboration with Aegis allowed us to leverage our collective data assets, including the nationwide COVID testing in place at our stores, in order to better monitor and help improve public health.”

The development of novel tools to expedite identification of emerging variants will be critical during the transition into an endemic phase. Collaborative efforts between laboratories and health care providers to identify unique trends within large, shared datasets can provide support for public health decision-making.

About Aegis Sciences Corporation

Founded in 1990, Aegis Sciences Corporation is a laboratory sciences company based in Nashville, Tenn., that provides science-driven testing and consulting services to health care providers, pharmaceutical companies, professional and amateur sports organizations, leading college and university athletic programs, Fortune 500 corporations, and government agencies throughout the United States. Since launching COVID-19 testing in April 2020, Aegis has quickly increased testing capacity to meet the needs of communities across the United States. To date, Aegis has performed over 13 million COVID-19 tests and is the leading provider of SARS-CoV-2 genome sequencing results in the United States. For more information, please visit