Omicron Arrives in the US amid Continuing COVID Mutation

Experts have been burning through Greek letters as new strains of the virus continue to emerge worldwide, prompting renewed concerns.

Viruses adapt by mutating, and new variants and strains of a virus are expected to occur over time. RNA viruses typically have higher mutation rates than DNA viruses, although coronaviruses are usually less prone to it. Mutation is a change in genomic sequence; a variant is a version of virus that has one or more mutations in its genome. If a mutation has a competitive advantage over the original or a prior iteration, the variant that is more robust may take over.

When SARS-CoV-2, the virus that causes COVID-19, was discovered, we recognized that it was a race to get an effective vaccine distributed and administered to try to contain and hopefully eliminate the virus. We failed, and SARS-CoV-2 has thus been thriving globally, surge after surge.

Initially, people were referring to variants by the country of origin. This was considered off-putting, so they developed a different methodology based on lineage (e.g., B.1.1.7, P.1., B.1.617.2). Very quickly, authorities recognized that those alphanumeric combinations would not slip off the tongue, so they decided to utilize the Greek alphabet instead. They skipped “nu” because they were worried people would interpret it as “new,” and skipped “xi” because it is a common Chinese surname (spelling is the same, although the pronunciation is different).

There are currently 11 named variants. There are also four categories of variants:

• Variants Being Monitored (VBM): The Centers for Disease Control and Prevention (CDC) monitors all variants circulating in the United States;
• Variants of Interest (VOI): A variant that has been causing community transmission or clusters, with specific genetic markers associated with changes to receptor binding, reduced neutralization by antibodies, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity;
• Variants of Concern (VOC): Variants that have demonstrated increase in transmissibility, more severe disease, significant neutralization by antibodies, decreased effectiveness of treatments or vaccines, or an inability to diagnostically detect; and
• Variants of High Consequence (VOHC): There is clear evidence that prevention measures or medical countermeasures (diagnostic testing, vaccine effectiveness, therapeutics) have reduced effectiveness, or that more severe clinical disease and increased hospitalizations are resulting.

There have been five VOCs, including the Delta variant (B.1.617.2). When Delta emerged, it very rapidly squeezed out all the other variants due to its enhanced transmissibility.

Omicron (B.1.2.529) was first reported to the World Health Organization (WHO) on Nov. 24, after isolation in a patient in South Africa. It was classified as a VOC two days later. We are waiting to see what happens in the next few weeks to see if it gets upgraded to a VOHC. It has a high number of mutations, including more than 30 affecting the spike protein.

At least 40 countries have detected Omicron as of Dec. 6, and it has been detected in 17 states (in one week!) so far. It is eliciting travel bans. I am not sure what good this does – it is like closing the barn door after the horse has run out. The U.S. started restricting travel from multiple southern African countries on Monday, Dec. 6, but it only relates to non-U.S. citizens. Between now and then, many cases could be imported, and I am pretty confident that American citizens will be just as capable of contracting and dispersing the variant as a South African citizen.

There are many unanswered questions about this new variant, the answers to which will be determined over the next few weeks and months:

• Is Omicron more transmissible (i.e., contagious)? It has some of the same mutations of Delta, so it is expected that it will be highly transmissible. The current impression is that Omicron may be even more transmissible.
• Is it more or less virulent? (e.g., does it cause more severe disease, more hospitalizations, more deaths?) Thus far, the disease seems to be milder, but there are some confounding variables. Most Omicron infections have been detected in younger individuals, who often have milder disease. It will take more cases to assess severity, and hospitalization and death always lag after onset and progression of symptoms. It would be great if Omicron resulted in milder illness and edged out more virulent strains. It would be ideal to end up with endemic mild coronavirus disease.
• Will the current vaccines be protective against this variant (or will there be immune evasion or escape)? An Omicron-specific vaccine booster would take several months to manufacture, test for safety, distribute, and administer.
• Can people who already had COVID-19 contract another case with the Omicron variant, and if so, how soon after the first case (i.e., reinfection)?
• What measures should be (or, more likely, should have been) taken? New York Governor Kathy Hochul declared a state of emergency that proactively boosts hospital capacity and deals with staffing shortages, despite a very good vaccination rate (90 percent overall, but significantly lower upstate compared to downstate).

We have been playing catch-up with COVID-19 throughout the whole pandemic. One would think we would have learned lessons about how to confront and combat this virus. The most reliable tools we have are masks, social distancing, and vaccination. There has been a slight uptick in vaccination in response to Omicron fears, but only 59.9 percent of the U.S. population is fully vaccinated, and only 23 percent have received their boosters.

My analogy is that of a fire. If there is a forest fire, pouring water on the brush and vegetation can impede its growth, but if it gets hot enough, even wet wood will burn. Vaccines are the water, and we are the ground vegetation. Dry wood burns first and hottest, but wet wood can still combust.

An additional observation for you. President Biden had a garden-variety upper respiratory infection (URI) last week. My stepsister just told me that my brother-in-law recently had a cold, too. In 2020, I didn’t know a soul who contracted any infection other than COVID-19. In communities with widespread acceptance and practice of mask-wearing, minor respiratory infections were exceedingly rare. Now that people are no longer wearing masks and washing their hands obsessively, URIs are back with a vengeance. We are expecting a brutal influenza season. Personally, I hate having colds, and I haven’t been sick since March 2020, when I had COVID-19. I may never give up wearing a mask.

Even if Omicron isn’t completely averted by vaccination, there is evidence that there will be some effectiveness. That’s somewhat encouraging. I implore you to get vaccinated, get boosted, and get your flu shot. Get tested when indicated. Stay home if you are feeling under the weather. As the holiday season approaches, please stay healthy and safe.

Programming Note: Listen to Dr. Erica Remer live every Tuesday when she co-hosts Talk Ten Tuesdays with Chuck Buck, 10 Eastern.

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Branswell H, The name game for coronavirus variants just got a little easier, STATNews, May 31, 2021. https://www.statnews.com/2021/05/31/the-name-game-for-coronavirus-variants-just-got-a-little-easier/

SARS-CoV-2 Variant Classifications and Definitions, CDC, October 4, 2021. https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html#anchor_1632158885160

Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern, WHO, November 26, 2021. https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern