The World Health Organization (WHO) on Nov. 26 declared a new COVID-19 variant, called omicron, a variant of concern because of its many mutations and initial evidence that suggests the variant may more easily reinfect people. Since the WHO’s announcement, the variant has been detected in more than 20 countries, including the United States.
Is there a new test to detect the omicron variant?
No, there isn’t a new test to detect the omicron variant. A molecular test already used to find COVID-19 infections can signal a potential omicron infection, which is confirmed through a process called genomic sequencing.
WHAT WE FOUND
The bottom line is one of the common tests already used to find COVID-19 infections can also help identify omicron, and then it’s confirmed using genomic sequencing, just like other variants such as delta.
Here’s that scientific explanation:
Polymerase chain reaction (PCR) tests detect genetic material from the SARS-CoV-2 virus that causes COVID-19. They are the “gold standard” test for diagnosing COVID-19, according to the Cleveland Clinic.
The WHO says there is a widely-used PCR test, the Thermo Fisher TaqPath, that can be used as a marker to identify the omicron variant. The test targets three genes, one of which is not detected when there is a positive test for the omicron variant, according to the WHO. This is called “S gene dropout” or “S gene target failure.”
“One of the genetic mutations in the spike protein, we can flag it from one of the specific PCR tests that we use to diagnose this infection,” Richard Lessells, an infectious diseases specialist at the University of KwaZulu-Natal in South Africa, said during a press conference with the country’s health officials on Nov. 25.
The alpha variant, which was first detected in September 2020, also has the “S gene dropout” characteristic. But given alpha’s low prevalence throughout the world, the WHO said a sudden increase in “S gene dropout” test results may be indicative of the omicron variant.
“You can get a sense before you do the whole genome sequencing of what proportion of the samples that are testing positive might be this variant,” Lessells said.
But the PCR test is not enough to confirm an omicron case. Confirmation is done through genome sequencing, a laboratory process that decodes the genes of the SARS-CoV-2 virus. It’s how the U.S. and other countries throughout the world confirm COVID-19 infections are of a specific variant. The method is used to confirm delta variant cases, which still represent 99% of COVID-19 cases in the U.S, and it is being used to confirm potential omicron variant infections.
“Genomic sequencing allows scientists to identify SARS-CoV-2 and monitor how it changes over time into new variants, understand how these changes affect the characteristics of the virus, and use this information to better understand how it might impact health,” the Centers for Disease Control and Prevention (CDC) says.
The WHO advised countries with genome sequencing capabilities to sequence “a representative subset” of COVID-19 cases to help determine how far the omicron variant has spread globally.
The U.S. is sequencing about 80,000 samples per week, which is about one in every seven PCR-positive cases, CDC director Dr. Rochelle Walensky said during a White House briefing on Nov. 30. Earlier this year, the U.S. was sequencing only about 8,000 samples per week.
“We have the tools and surveillance in place to identify the omicron variant,” Walensky said.
The Food and Drug Administration (FDA) said, based on a preliminary review, it believes rapid tests and other PCR tests widely used in the U.S. will remain effective at identifying positive COVID-19 cases involving the omicron variant, even if they don’t directly flag a potential omicron infection.