Fact check: Genomic sequencing, not PCR testing, detects COVID-19 variants

The claim: COVID-19 variants can't be detected because PCR tests can't discern different strains

During the coronavirus pandemic, polymerase chain reaction, or PCR, testing has been an invaluable tool to diagnose new COVID-19 cases. But some social media users are casting doubt on the test's ability to detect coronavirus variants. 

"How can a rise in certain variants be detected when test kits do not decipher between different variant strains?" reads text in a meme published July 24 on Facebook. The image shows a still from the 1971 musical "Willy Wonka & the Chocolate Factory," a popular meme format.

"This meme challenged me to do some quick research," one Facebook user commented. "There (is) literally nothing out there explaining how they know or even track variants."

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That's wrong – public health officials are tracking coronavirus variants. They're just not using PCR tests to do it.

Since the start of the pandemic, scientists worldwide have used genetic surveillance networks to keep track of new coronavirus mutations. That genetic sequencing, not PCR testing, detects variants of the virus.  

USA TODAY reached out to the Facebook user who shared the post for comment. 

PCR tests diagnose, genomic sequencing finds variants 

The post makes it seem like PCR tests are the primary way scientists try to detect coronavirus variants. But that's not the case.

"All the PCR test will tell you is whether you test positive for COVID-19, but it doesn't specify. It is not sophisticated enough to tell you specific variants of the virus," Erich Fogg, director of walk-in services and COVID-19 testing for York Hospital in Maine, told WMTW, an ABC News affiliate TV station.

A lab assistant points at charts of a sequenced COVID-19 virus at the Wellcome Sanger Institute that is operated by Genome Research in Cambridge, Thursday, March 4, 2021.

A PCR test looks for the presence of viral genetic material in someone's body. If a PCR test returns positive, a patient's sample will typically go through a more detailed analysis called genomic sequencing. This technique decodes the coronavirus' genome, searching for any new mutations – or ones that match known variants. 

This sort of testing not only informs public health experts about emerging variants, but also helps track a virus' transmission. For example, if two people share viral sequences with little to no genetic differences, it's likely one transmitted the virus to the other, or that they both got the virus from a common source.

Genomic sequencing is performed in several laboratories across the U.S., including those run by state and local public health departments. The U.S. Centers for Disease Control and Prevention has also been involved in the sequencing effort through its National SARS-CoV-2 Strain Surveillance (NS3) system.

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It's important to note that not all positive PCR tests undergo genomic sequencing to detect coronavirus variants.

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The U.S. lags behind other developed countries in terms of the percentage of COVID-19 cases that are sequenced. The Biden administration announced in April that it would dedicate $1.7 billion to expanding the nation's sequencing capacity. 

Our rating: Missing context

Based on our research, we rate MISSING CONTEXT the claim that new COVID-19 variants can't be detected since PCR tests can't discern different strains, because without additional information it is misleading. PCR tests can only tell if someone is positive or negative for the coronavirus. Positive samples, however, typically go through a more sophisticated analysis called genomic sequencing, which can discern whether a sample contains a new or a known COVID-19 variant. 

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Our fact-check work is supported in part by a grant from Facebook.