RT-PCR Diagnostic Testing Differentiating Between Seasonal Influenza and COVID-19

This article was last updated on April 16, 2022

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A recent announcement from the Centers for Disease Control and Prevention warrants a closer look since it may explain some of the issues that appeared during the 2021 influenza season.

Here is a Lab Alert from the CDC dated July 21, 2021:

The CDC is pre-warning clinic laboratories and testing sites that, effective January 1, 2022, the CDC is withdrawing its request to the Food and Drug Administration for the Emergency Use Authorization of its CDC 2019-Novel Coronavirus Real-Time RT-PCR Diagnostic Panel which was originally approved for use on February 4, 2020.  Test sites are advised to use one of the other 250 RT-PCR COVID-19 authorized molecular diagnostic tools as shown on this screen capture (which shows only a few of the approved tests) with the soon-to-be withdrawn CDC product highlighted:

Here is the key phrase of the CDC's Lab Alert:

"CDC encourages laboratories to consider adoption of a multiplexed method that can facilitate detection and differentiation of SARS-CoV-2 and influenza viruses. Such assays can facilitate continued testing for both influenza and SARS-CoV-2 and can save both time and resources as we head into influenza season."

It would appear that the CDC's own RT-PCR diagnostic equipment is not capable of differentiating  between influenza and COVID-19 and, as such, is being withdrawn from service before the 2022 influenza season begins.

This issue with the RT-PCR testing equipment may go a long way to explaining why there were very few positive tests for influenza over the 2021 season as shown here:

…when compared to the 2019 and 2020 influenza seasons as shown here (note the dramatic change in the y-axis scale):

This begs two questions since the entire narrative of the COVID-19 pandemic was built on the foundation of the RT-PCR tests: 

1.) How many of the tests that were positive for the SARS-CoV-2 virus were actually detecting the virus that causes seasonal influenza during the 2021 flu season?

2.) How many of the other 250 RT-PCR COVID-19 molecular diagnostic tools that have been in use throughout the pandemic have the same issue of differentiating between the two viruses?

I'm guessing that we'll never know.

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