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December 18, 2021

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The SARS-CoV-2 Omicron Variant

COVID-19 Resources

On November 26, 2021, the World Health Organization designated a new variant of concern – B.1.1.529.  Keeping with the Greek alphabet naming, this variant is now called the Omicron variant.

What were the Primary Triggers for the Omicron Designation?

The primary triggers for the WHO designation of VOC for Omicron were as follows.

  1. After its initial detection on November 9, 2021, the variant has rapidly expanded in prevalence in South Africa. In the Johannesburg are, COVID admissions spiked from about 300 daily to almost 3,000 daily in a two-week period from November 16 to November 28, 2021, coinciding with the detection of the variant.
  2. There is a coalescence of known and potentially dangerous mutations in critical locations of the Omicron genome. These mutations could promote changes in infectivity, virulence and vaccine escape.
  3. The pandemic in South Africa has been mostly represented by four surges. Each surge has been due to a new variant taking over the primary viral circulation. The first two were the initial waves of SARS-CoV-2; the third was the Delta wave. The current fourth surge of new cases has coincided with the detection of Omicron. The proportion of Omicron variants in some locations is rapidly replacing the Delta variant.
  1. Significant surges of COVID-19 admissions have been noted in the Johannesburg area and elsewhere from under 300 daily to about 3,000. This has also coincided with the detection of Omicron.
  2. The Omicron variant has now been detected in multiple nations globally. This includes the United States.
  3. Over 30 new mutations have concentrated in the spike protein itself (out 50 new mutations overall). This has been significant enough for some PCR tests to now test negative for the spike or S-protein of SARS-CoV-2, while still testing positive for the nuclear or N-proteins. That indicates a substantial alteration in the affinity of specific antibodies to the spike protein. This has potential implications not just for testing, but for vaccines and monoclonal antibody treatments of Omicron.

Omicron Variant Mutation

One of the most critical issues with the Omicron variant is the number and nature of the mutations in its genome. SARS-CoV-2 variants develop mainly by antigenic shift and antigenic drift. The virus needs a large unprotected population (unvaccinated) to reach a high level of virus replication in order to quickly accumulate mutations. While some of the 50 new mutations are novel, we do not yet know if there is significant impact. Some have been identified in other variants and are known to enhance transmission, vaccine escape and virulence; however, other variants have some of the same mutations and have not taken over.

The spike protein is critical in the attachment and, therefore, the transmission and infectivity of the SARS-CoV-2 virus. This is why the spike protein has been the target of COVID-19 vaccines. Blocking the spike protein with antibodies keeps it from attaching and entering human cells. Omicron has at least 30 new mutations in the spike protein – and these have altered the structure of the specific spike proteins targeted by the vaccine antibodies. Research suggests a higher level of spike protein alteration with Omicron than with previous variants. This will impact the efficacy of our current vaccines, as was the case with the Delta variant.

Omicron Variant Transmission

Regarding the ability of Omicron to spread, there are suggestions that it may spread at least as well, or even better, than the Delta variant. This is based on the observation that Omicron seems to have replaced Delta in some locations. But it is important to note that there are multiple other epidemiologic factors that could cause this. This is why global teams have been deployed to study Omicron’s transmission characteristics.

Omicron and COVID-19 Vaccines

One of the primary questions is how will Omicron impact the efficacy of our current COVD-19 vaccines. While information is forthcoming, there are reports that the great majority of admissions in South Africa are in unvaccinated people, suggesting a likely impact from vaccines. Additionally, as with previous variants, evidence-based vaccine recommendations continue to outweigh the unsubstantiated claims that natural immunity provides adequate protection – particularly with Omicron, as there appear to be lower possible protections than with previous variants.

If the spike protein has significant changes, the efficacy of antibodies created by our vaccines will be altered and probably made less effective. Our current vaccines make such huge amounts of antibodies that all our vaccines have remained very effective for all variants. Laboratory studies are underway now to evaluate the impact of Omicron on neutralizing antibodies made by vaccines. While we expect some vaccine efficacy decrease, the most likely result will be that the mRNA and DNA (Adenovirus) vaccines will continue to prevent most serious COVID-19 cases and mortality from Omicron. Sampling and research is being conducted to discover the relationship with breakthrough cases (those who have been vaccinated); however, most of these cases appear to be mild.

What should our Response to Omicron be at this Phase?

Being proactive is part of what we do when we try to protect patients, our loved ones and ourselves. The Omicron variant has worrisome characteristics, but we have encountered difficult variants before. Continue to practice common public health measures, such as wearing a mask in public, social distancing, avoiding large crowds, washing your hands, covering coughs and staying home if you are sick. In addition, please get vaccinated if you have not already, and receive your booster shot if you are eligible and able.

This is a rapidly changing issue. Stay informed and keep up with our COVID-19 resources.