How COVID-19 tests are staying ahead of SARS-CoV-2 variants

Thermo Fisher Scientific has been working with clinical labs and public health officials since tracking COVID-19 cases became a top priority at the start of the pandemic. From the time SARS-CoV-2 was first identified as a potential global health threat in early 2020, one of the biggest concerns has been how easily the virus seemed to spread within communities and across geographies.

As the pandemic has progressed and case counts fluctuate, multiple variants of concern have emerged that are even more transmissible than earlier strains. Delta, the most widespread variant thus far, is reportedly five times more infectious than the original strain, for example [1]. Most recently, the World Health Organization designated Omicron as a variant of concern, putting public health organizations around the globe on alert [2]. While the impact of this new version of the virus remains to be seen, it is a reminder that SARS-CoV-2 will continue to mutate with ongoing spread, leading experts to caution that future variants could be even more virulent.

Health experts warn that unvaccinated populations, in particular, are at high risk of falling sick, thereby creating a potential breeding ground for new variants and, in turn, a dangerous public health situation [3]. Due to a combination of access issues and consumer hesitancy, vaccination rates are only in the single digits in some parts of the world and, although the U.S. Food and Drug Administration (FDA) recently authorized the vaccination of children ages five and older, parents are still waiting for an option to immunize younger children.

Another concerning issue is that while vaccines have largely been shown to be effective even against new strains, there have been “breakthrough” infections in vaccinated individuals. In fact, the Centers for Disease Control and Prevention (CDC) has confirmed that fully immunized people can still get infected and spread COVID-19 [4].

It is important to understand the difference between the terms “infection” and “disease.” Vaccines don’t always prevent someone from getting infected with SARS-CoV-2, but they are highly effective at preventing someone who is infected from falling sick due to COVID-19 and having their disease progress to severe. While overall risks are reduced, no intervention is perfect, and there have been cases of people being hospitalized despite being fully vaccinated. Additionally, waning immunity post-vaccination until a booster is administered introduces the opportunity for previously vaccinated individuals to become more susceptible to infection. It is therefore extremely important to continue to seek testing in the event of illness or exposure, even for those who are vaccinated.

As COVID-19 continues to evolve, testing was designed with it to stay ahead of the changing virus. Thermo Fisher designed the multiplex COVID-19 TaqPath tests to be resilient from the start by targeting three different areas of the SARS-CoV-2 genome, ensuring the tests can detect the virus even as it mutates. This built-in redundancy was put to the test last fall when labs started noticing early evidence of the Alpha, or B.1.1.7, variant – a new COVID-19 strain that would soon start spreading around the globe. Since the test looks at multiple targets, the mutation in this strain did not affect its accuracy. In fact, labs began using what they termed the “S gene dropout,” or “S gene target failure,” as a signal to detect the presence of the Alpha variant and to track the spread of this variant in support of global surveillance efforts.

The TaqPath test and S gene dropout are proving invaluable yet again with the emergence of Omicron. As with the Alpha variant, a mutation in the spike region of the Omicron strain causes an S gene target failure when a sample is analyzed with the TaqPath multiplex test. Labs are now using this test as an early warning signal that Omicron may be present in samples. In fact, public health officials have asked labs to use Thermo Fisher’s TaqPath test to search for the Omicron variant and prioritize samples with the S gene target failure for genomic sequencing.[5]

Omicron will likely not be the last variant to emerge from COVID-19. Scientists can’t predict exactly how SARS-CoV-2 will mutate in the months ahead, but we do know existing mutations have primarily emerged in the “S” gene, or the area of the genome that codes for the virus’s notable spike protein. To account for this new understanding and ensure future availability of effective tests, Thermo Fisher developed the next generation of TaqPath COVID-19 tests to look at multiple targets across three genomic regions outside of the S gene. The TaqPath COVID-19 2.0 tests now have eight targets across three genes; the orf1a, orf1b and the N gene. The new tests’ increased redundancy safeguards their effectiveness against future SARS-CoV-2 mutations.

The health and scientific communities have made great strides in the fight against COVID-19. As more of the population gets vaccinated, there will be evolutionary pressure on the virus to mutate and form new variants. These new variants could threaten to upend that progress, but health systems, test developers, and drug and vaccine researchers are constantly adjusting course to stay ahead of the virus and put an end to this global pandemic.

To learn more about Thermo Fisher Scientific’s COVID-19 Testing Solutions, please visit https://www.thermofisher.com/covid19.

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