Through a comparison of PCR and whole-genome sequencing results gathered during the Alpha and Omicron waves, Aegis Sciences and Walgreens developed a mechanism for early surveillance of emerging variants beyond assessing for S-gene target failure alone.
Aegis and Walgreens scientists described the mechanism in a study published last week in PLOS One.
“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,” Michael Taitel, senior director of healthcare and clinical analytics at Walgreens, said in a statement.
“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,” he added.
Throughout the COVID-19 pandemic, Aegis and Walgreens collaborated to provide access to testing resources and published trends on the spread of the virus through the Walgreens COVID-19 Index, an interactive tracking tool based on testing data provided by Aegis.
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 (PCR) testing. Commonly referred to as S-gene target failure, the resulting pattern is at times used as a proxy to identify transmission of new variants, Aegis noted.
By identifying a mechanism that allows for early surveillance of emerging variants beyond assessing for S-gene target failure, Walgreens and Aegis predicted the emergence of new variants, such as BA.1 and BA.2, prior to the confirmation of their presence through sequencing, Aegis said.