Since the initial COVID-19 outbreak in 2020, the SARS-CoV-2 virus has mutated, resulting in a range of variants such as Alpha, Beta, Delta and, most recently, Omicron. While much about Omicron remains uncertain, public health organizations and medical professionals are watching the potential impacts of this new variant closely, warranting the question — what makes it different? And, how concerned should we be about both Omicron and future mutations or variants?
To help increase understanding of the Omicron variant and how we can prevent its spread, Manoj Gandhi, M.D., Ph.D., Thermo Fisher’s senior director of medical affairs, Genetic Sciences, recently spoke with the BBC on the essential role of testing in response to emerging variants. Dr. Gandhi highlighted the impact of surveilling the viral genome, the informative “S gene dropout” finding, and why public health organizations around the world are calling on labs to take advantage of a distinctive feature of Thermo Fisher Scientific’s TaqPath COVID-19 Diagnostic testing solution.*
As Dr. Gandhi explained, we can examine test patterns originally noted with the Alpha variant to gain insight into the Omicron variant. Certain COVID-19 tests are designed to analyze multiple areas within the viral genome to deliver a positive or negative result. According to Dr. Gandhi, this redundancy is built into multiplex tests, so even if the virus mutates the test can still detect its presence. The TaqPath COVID-19 diagnostic testing solution, for example, analyzes three parts of the genome: the orf1a/1b region, the S gene, and the N gene. While each of these regions holds significance to the virus’s ability to be infectious, the S gene has proven to be an essential tool for tracing COVID-19 infections and identifying changes to SARS-CoV-2.
The S gene encodes for a spike protein, which is a key feature of the virus that allows for entry into healthy human cells and subsequent infection . In December of 2020, experts started seeing an unusual pattern in COVID-19 tests, where the result would be positive for SARS-CoV-2, but the S gene part of the test would be negative. This “S gene dropout” became a key feature in identifying the Alpha variant. Labs and public health officials soon realized the TaqPath test offers a unique advantage when examining COVID-19 test results, as it can easily detect the S gene dropout and be used to proactively flag samples for confirmatory sequencing.
When scientists began seeing a similar S gene pattern in November of 2021, the initial thought was that the Alpha variant was reemerging. However, after closer examination, experts found a variety of mutations across the genome that are not present in previously identified variants, ultimately leading to the discovery of Omicron .
While Dr. Gandhi says it is still too early to draw specific conclusions about the Omicron variant’s impact on the pandemic, the many mutations present raise concerns that the virus will continue to mutate and potentially evade vaccine-mediated protection. Early data indicates that current vaccines and boosters are not as effective against Omicron as they are against previous variants, but the increased number of antibodies in the body from vaccine doses helps protect against severe Omicron infections and hospitalization .
Dr. Gandhi also says we can expect the COVID-19 virus to continue to mutate and evolve, finding new ways to infect people and evade vaccines. At the same time, our collective immunity will likely continue to adjust to the changing virus. Similar to the flu, as COVID-19 becomes endemic, experts predict that in the future, we will likely see some years with severe infections, and some years that have a lower incidence of infections and milder disease . Regardless, the only way to reliably track these mutations and predict future COVID-19 outbreaks is by testing and sequencing SARS-CoV-2.
For more information on Omicron, variants, and the importance of testing, please listen to the full BBC podcast featuring Dr. Gandhi. To learn more about COVID-19 mutations and the importance of surveillance, visit https://www.thermofisher.com/covid19mutations.
*For Emergency Use Authorization (EUA) only. For prescription use only. For in vitro diagnostic use. Regulatory requirements vary by country; products may not be available in your geographic area.
 Why S-Gene Sequencing is Key for SARS-CoV-2 Surveillance
 Science Brief: Omicron (B.1.1.529) Variant
 Omicron Variant: What You Need to Know
 What will it be like when COVID-19 becomes endemic? | News | Harvard T.H. Chan School of Public Health