Comparative Analysis of COVID-19 Gene Target Dropout/Failure Results using Thermofisher TaqPath COVID-19 Combo Kit and Nextstrain CoVariants Genomic Databases.

Abstract

COVID-19 variants continue to infect thousands of people even though the end of the pandemic was announced on May 11, 2023. Nextstrain CoVariants (CoVariants) genomic databases provide detailed information about more than 31 variants of COVID-19 viruses that have been identified through genomic sequencing, showing the mutations they carry. Mutated viruses may yield a negative result for a gene target using a PCR test that has a positive COVID-19 test result. This negative gene target result is known as gene target dropout/failure, not a negative COVID-19 test result. The Centers for Disease Control and Prevention (CDC), World Health Organization (WHO), and CoVariants utilize gene target dropout/failure as a Variant of Concern (VOC) screening method until the genomic sequencing is performed. The Thermofisher TaqPath COVID-19 Combo kit (TaqPath), a real-time RT-PCR test, detects COVID-19 nucleic acids in respiratory specimens. TaqPath PCR COVID-19 target profile data was retrieved from the Tuskegee Health Disparities Diagnostic Center COVID-19 clinical laboratory. The results revealed an association between the TaqPath results date tested and CoVariants tracking announced and end dates for S gene target dropout/failure (SGTF). This study highlights the usefulness of TaqPath COVID-19 Combo Kit gene target profiles in monitoring and mitigating the spread of emerging COVID-19 variants, without genomic sequencing.