Not All PCR Tests Are the Same: The Value of Variant-Specific Assays in Detecting New SARS-CoV-2 Variants

September 22, 2022

As SARS-CoV-2 variants continue to evolve, identifying new variants with adaptive diagnostic tools is critical to containing the ongoing COVID-19 pandemic.

Several concerning lineages classified as variants of concerts (VOCs) are associated with higher transmissibility, virulence, or the ability to evade the immune response acquired by prior infection or vaccination. The mutations in the viral genome of these variants are associated with a change in viral fitness or are unique to their lineage and can be used as genetic markers for genotyping.

Addressing these new variants, namely the most recent Omicron variants, demands constant surveillance and the use of high-quality real-time polymerase chain reaction tests (RT-qPCR) with RNA extraction and genotyping abilities.

COVID-19 RT-qPCR tests cannot only detect the virus’s genetic information but also quantify the amount of that genetic information that is present in a sample.

Flow Heath’s Applied Biosystems TaqPath COVID-19 Combo Kit from Thermo Fisher Scientific is designed to detect the presence of the virus at very low levels and uses an algorithm to provide a positive or negative result.

Further, The TaqPath test provides a complete workflow from viral RNA extraction from up to 94 specimens and genetic analysis. It can detect the presence of antibodies against the spike (S), nucleocapsid (N), and Orf1ab (ORF1ab) proteins.

With the emergence of Omicron, it’s been observed that the S gene target has been impacted in PCR tests by the presence of the 69-70del mutation. This has caused an S gene dropout or S gene target failure.

Most PCR tests are unable to distinguish this specific deletion in the spike. However, due to the multi-target test design of Taqpath, the overall test performance of the assay is not impacted by this mutation.

The multi-target feature further solidifies the National Institutes of Health's statement that reverse transcription polymerase chain reaction-based diagnostic tests (which detect viral nucleic acids) are the gold standard for detecting current SARS-CoV-2 infection.

For more information, connect with us at or call (323) 905-0125 Monday-Friday, 8am-5pm PT.

FDA Fact Sheet and Instructions
Fact Sheet:

related blog posts