Thermo Fisher, Qiagen and other COVID-19 test makers prepare for oncoming omicron variant

The world received an early warning after virus sequencing efforts in South Africa and Botswana spotted the rise of a new genetic strain, now called omicron. (Maksim Tkachenko/iStock/Getty Images Plus)

With the omicron variant on the horizon, diagnostic companies are racing to determine whether the coronavirus’s latest mutations will hinder the performance of their screening tests.

Companies including Thermo Fisher Scientific, Abbott, Qiagen, Cue Health and Co-Diagnostics have stated that their PCR tests currently on the market for COVID-19 are not affected by the new strain. Meanwhile, test maker Eurofins has outlined plans to release new kits that specifically target the omicron variant.

Known scientifically as B.1.1.159, the variant has already been classified as a variant of concern by the World Health Organization, and its recent emergence has led to the reinstatement of international travel restrictions similar to those at the earliest stages of the pandemic.

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Omicron carries a larger number of mutations in the virus's spike protein—about 30 in all, including some possessed by delta and some never-before-seen changes—compared to past variants. That protein allows the coronavirus to enter human cells, but also provides a target for vaccines and treatments.

The world received an early warning after virus-sequencing efforts in South Africa and Botswana spotted the rise of the new genetic strain. Among a relatively small number of local positive samples, it quickly displaced the delta variant, which has been predominant worldwide for months.

Since then, omicron has been detected among international air travelers in Hong Kong, Europe and Canada. Scientists are still unsure whether omicron will result in more or less severe infections, or how it will ultimately interact with a person’s immunity and antibody therapies. 

After COVID-19 variants came to the fore late last year, the FDA warned healthcare professionals that their diagnostic accuracy can suffer if mutations occur within the specific areas of the RNA used by a molecular test to trigger a positive result. Tests can prepare against this by sampling from multiple regions of the virus’s genetic code at once.

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Now, using omicron’s genetic information shared among public global databases, Thermo Fisher, Abbott, Qiagen and Co-Diagnostics said they have conducted internal tests of their screeners and found they remained accurate.

In fact, the way tests interact with one particular mutation—a deletion in the string of genes making up the spike protein, previously spotted in the alpha variant—has been recommended by the WHO as an early proxy method for determining whether a positive sample can be traced back to the omicron strain.

According to Thermo Fisher, which produces a test that checks three different areas of the virus’s genetic makeup, that spike protein mutation causes one of those results to fail, while the other two come back positive—a pattern indicating a possible omicron infection, although full sequencing would still be needed for confirmation.

"The Thermo Fisher test allowed us to detect cases that may contain the new variant by identifying samples exhibiting S-gene dropout," said Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation at Stellenbosch University and the University of KwaZulu-Natal in South Africa. "This early identification is very important in helping us track and understand the spread of the B.1.1.529 variant to South Africa and the world."

Thermo Fisher is developing specific assays for its TaqMan Mutation Panel, used for research purposes. The company’s original TaqPath kit received clinical authorization from the FDA in March 2020, with an upgraded version gaining a green light this past August. 

"Like all viruses, we have always known that SARS-CoV-2 would continue to mutate and that effective testing strategies are a key to curbing the pandemic," Thermo Fisher’s chief operating officer, Mark Stevenson, said in a statement. "That is why we developed assays with additional built-in checks and balances to ensure that clinicians, researchers and public health officials would have effective tools to accurately test for COVID-19 even as the genetic makeup of the virus evolved."

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Qiagen and Co-Diagnostics, meanwhile, said their respective suites of tests will maintain their performance when put up against the omicron variant, including combination diagnostics that screen for COVID-19 alongside infections such as influenza A and B or respiratory syncytial virus.

In addition, rapid test developer Cue Health said 99.2% of the omicron sequences published match up with the ingredients used in its molecular COVID-19 test, which relies on the genes that make up the virus' inner nucleocapsid protein instead of the spike. Cue is also currently working with Google Cloud and the genomics company Helix to study COVID variants and share mutation sequencing data. 

“The best way to fight the global COVID-19 pandemic is a combination of extensive vaccinations, rigorous testing with gold-standard PCR tests, aggressive surveillance of new variants and above all compassionate treatment for those infected with the SARS-CoV-2 virus,” said Qiagen Chief Medical Officer Davide Manissero, M.D. 

“Further genomic sequencing of SARS-CoV-2 samples worldwide will vastly increase transparency and help us identify and respond to potentially dangerous mutations of the virus, while at the same time broadening the database we can use to verify if vaccines and tests continue to be effective,” Manissero added.

At the same time, Abbott has been relying on the international pandemic defense coalition it helped launch earlier this year, which maintains a global network of academic and public health researchers that share sequencing information, real-world samples and viral cultures.

After working directly with a partner in South Africa on omicron, Abbott said its rapid and PCR tests do not rely on the virus' spike proteins for detection, and said the company's assessments have determined that the variant's mutations would not harm their accuracy.

On the vaccine front, mRNA developer Moderna said it is already studying two multivalent candidates for a new booster shot designed to anticipate certain mutations including some that have carried over into the omicron variant. The company has also laid out plans to rapidly develop a new vaccine targeting the omicron variant itself.

Editor's note: This story has been updated with statements from Abbott and Cue Health.