Why the Omicron Variant Matters From a Public Health Perspective

Key Takeaways
  • Unlike previous COVID-19 variants, Omicron has a unique genetic makeup that includes 52[!] mutations – 30 of which are located on the spike protein, which is the part of the virus that enables it to enter our cells.

  • Preliminary studies indicate that Omicron spreads more than twice as fast as Delta and may be three times as likely to reinfect those that have already recovered from COVID-19.

  • S-Gene sequencing is key for SARS-CoV-2 surveillance. When a PCR test does not detect the S gene, public health officials use this as a marker to perform additional sequencing that confirms the presence of Omicron.

Just when coronavirus cases were starting to trend downward, a holiday gift arrived that no one asked for: a new SARS-CoV-2 variant called “Omicron”. This came on the heels of Thanksgiving travel — up 13% from 2020, with air travel recovering to about 91% of pre-pandemic levels.[1] The added issues around low COVID-19 booster rates and waning immunity from initial doses may have also created more opportunity for a new variant to emerge. As they say, “what doesn’t kill you makes you stronger”; in this case, what doesn’t kill you will mutate and try again.

How is Omicron different from Delta and other variants?

Since the first identified case of Omicron in November 2021, epidemiologists are still learning about the variant – how transmissible it may be, how severe the symptoms are – but some initial findings are causing concern.

Omicron appears to spread more than twice as fast as Delta and may be three times as likely to reinfect those that have already recovered from COVID-19, according to preliminary studies.[2, 3] In South Africa, it’s estimated that the infection rate of Omicron has already reached the same levels that were seen during the Delta wave six months ago.

Another possible cause for concern is Omicron’s unusual genetic makeup. Of its more than 50 mutations, 30 lie on the spike protein — the exposed part of the Sars-Cov-2 virus that binds with human cells. To put this into perspective, Omicron has ten times more mutations on the spike protein than the Delta variant, and could make the variant more transmissible. Why does this matter? Because these mutations could make the difference between Omicron evading antibodies and vaccines, or not.[4]

How are public health officials tracking the spread of Omicron?

Detecting and tracking the spread of Omicron will require a robust surveillance system. COVID tests, namely PCR tests, will be one of the most important tools in this effort.[5]

PCR tests are considered the “gold standard” of COVID testing with an accuracy rating of approximately 98%.[6] In the case of Omicron, certain PCR tests will not detect the S gene of the SARS-CoV-2 virus. This is called S gene dropout or S gene target failure. Researchers are using this as a marker to confirm the presence of Omicron through additional genome sequencing.[7,8]

Though individual patients don’t directly see that data, it gets reported to public health officials, who can then track whether Omnicron is present, how quickly it’s spreading, and how fast it has impacted case growth.
Bottom line: We are blind to what’s happening with Omicron if people are only using antigen tests, but PCR tests can help inform public health responses.

Can Vault’s PCR test identify the Omicron variant?

The Vault at-home COVID-19 saliva test is capable of detecting positive cases of COVID as well as all variants, including Omicron. Using the three-gene assay, our PCR test can detect the very likely presence of the Omicron variant, even before sequencing is complete, offering public health valuable information at a rapid pace. Additionally, both our major lab partners have sequencing available automatically.

This really is a game-changer for epidemiologists and public health efforts. Not only does it make tracking the presence of Omicron possible, but it also gives scientists more insight into the new variants’ transmissibility, severity, and responsiveness to existing vaccines. This will be critical to getting ahead of the spread (and further mutations) of Omicron.

How can I stop the spread of Omicron?

At this point, it seems that COVID is on track to become endemic. Still, getting vaccinated and testing frequently are important measures for minimizing your risk of infection and the possibility of spreading the virus to other people (which is what can cause further mutations).

We need to continue using every tool available. This means using both rapid antigen tests when you’re symptomatic and need an immediate response, as well as a confirmatory PCR testing, for the extra measure of accuracy and continued benefit to public health officials.

Additionally, we’re likely to see new advances in treatment that may make the virus more manageable and less dangerous in the future (e.g, oral COVID treatments). These advancements, combined with global vaccinations and ongoing testing, can help significantly reduce COVID case numbers.


  1. Singh, R. K. (2021, November 25). U.S. Thanksgiving air travel set to be busiest since pandemic began. Reuters. https://www.reuters.com/business/aerospace-defense/thanksgiving-travel-rush-tests-us-carriers-2021-11-24/
  2. Robbins, R. (2021, December 20). Covid News: F.D.A. Authorizes Eli Lilly Antibody Treatment for Youngest Covid Patients. The New York Times. https://www.nytimes.com/live/2021/12/03/world/omicron-variant-covid
  3. Bissada, M. (2021, December 4). Scientists Say Omicron Is Spreading Twice As Quickly As Delta In South Africa—And Could Be More Likely To Re-Infect. Forbes. https://www.forbes.com/sites/masonbissada/2021/12/03/scientists-say-omicron-is-spreading-twice-as-quickly-as-delta-in-south-africa-and-could-be-more-likely-to-re-infect/
  4. Omicron: What we know about Covid strain prompting fresh global restrictions. (2021, December 20). Financial Times. https://www.ft.com/content/42c5ff3d-e676-4076-9b9f-7243a00cba5e
  5. Stein, R., & Wroth, C. (2021, November 30). U.S. races to detect and track omicron, hampered by an unwieldy surveillance system. NPR. https://www.npr.org/sections/health-shots/2021/11/30/1059917469/omicron-variant-us-detect-track
  6. Brihn, A. (2021, May 13). Diagnostic Performance of an Antigen Test . . . Centers for Disease Control and Prevention. https://www.cdc.gov/mmwr/volumes/70/wr/mm7019a3.htm
  7. Roxby, B. P. (2022, January 4). Omicron: How do I know if I have it? BBC News. https://www.bbc.com/news/health-59460252
  8. Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern. (2021, November 26). WHO. https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern

DISCLAIMER: This article is for general information purposes only, does not constitute medical advice and is not intended to be relied upon for medical diagnosis or treatment. If you are experiencing a medical emergency, dial 911 immediately.