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  • drmarkmurphy

An Omicron Primer: How a variant with a name like a bad transformer has changed the COVID narrative

Updated: Dec 31, 2021

A few weeks ago, after nearly two years of doom and gloom, I finally wrote an optimistic column in my local newspaper about the COVID 19 pandemic—a sort of “light at the end of the tunnel” piece, reminding everyone how far we’d come since last year.

My timing, as is often the case, turned out to be impeccably bad.

Several days after that article ran, we started getting reports from South Africa about the emergence of a new, highly mutated COVID-19 strain which might have resistance to the current vaccines. That strain, which we now know as omicron, has since exemplified the adage about “the best laid plans,” forcing governments all over the world to rethink their strategies in dealing with what has proved to be a particularly stubborn virus. ( ).

To be fair, I did say in my earlier newspaper piece that we would never reach the viral nirvana of herd immunity with COVID-19, as the SARS CoV-2 virus has been “too contagious, too adaptive and too pervasive” for that. I just didn’t expect to be proved prescient in such a definitive fashion so soon.

The omicron variant sounds like the name of a second-tier Michael Crichton novel, or an evil Transformer (which I guess it is, in a way). We are still learning about it, but out of an abundance of caution, governments around the world responded to the omicron news with travel restrictions even as stock markets plunged, all of which led most of us to sigh and wonder when the hell all of this was going to end.

What do we really know about omicron? The omicron variant (originally called B 1.1.529) is unique in that it has over 30 different mutations. Some of the mutations are among those which can make the virus more contagious; others may make it more vaccine resistant. The specific nature of those mutations is what caused the World Health Organization to recently designate it a “variant of concern.” The variant has spread all over the world since it was first identified on November 24, including the United States, which recorded its first omicron case on December 1st. By December 18, omicron was the dominant strain in the United States, comprising 73% of all isolates identified—and it was even more prevalent in the Northwest and Southeast, where it was isolated in 95% of reported cases as of that date ( ). In South Africa, where only 25% of the population is vaccinated, the omicron variant led to incredibly rapid increases in COVID-19 cases, with a 592% rise in cases in a single week between November 20 and November 27. Similar increases were recently seen in the state of Florida, which saw a 320% increase in COVID cases between December 17 and December 23. Omicron clearly has a transmission advantage over the previously dominant delta variant, with one researcher suggesting that omicron may be able to infect 3-6 times as many people over the same time period ( Ominously, it has also shown a high propensity to reinfect persons with prior COVID infection—far more so than with the prior beta and delta variants ( ).

By the way, the term “omicron,” from the letter in the Greek alphabet, was chosen because the prior two letters, nu and xi, were potentially confusing (“nu’ was too easily confused with “new,” while Xi is a common Chinese surname) ( ).

How does COVID 19 with the omicron variant differ from prior mutations? Well, to start with, it can make you ill more rapidly. For the original alpha variant, the incubation period—the time from exposure to symptomatic illness—was 2-14 days, with an average of 5 days. The delta variant shortened that interval to 4 days. Omicron has an even shorter incubation period—about three days, by current estimates. It also seems to replicate faster than prior variants, producing much greater viral loads in a shorter time frame. Interestingly, the symptoms of omicron-related COVID disease are different than the more “classic” COVID-19 illness symptoms. Patients with omicron infections describe runny nose, headache, fatigue, sneezing, and a sore throat as their major symptoms. This contrasts with the previously described “classic” COVID 19 symptoms of a dry cough, fever and a loss of smell or taste described with earlier variants. The symptoms of COVID-19 patients infected with the omicron variant are therefore remarkably similar to those of the common cold—making testing of anyone with upper respiratory symptoms of paramount importance if one hopes to limit viral spread.

There is some good news on the omicron front: Two studies, one out of Scotland and another from South Africa, show that the omicron variant is significantly less likely to result in hospitalization than prior variants. The Scottish study, published by researchers at the University of Edinburgh, showed that persons infected with omicron are two-thirds less likely to require hospitalization than persons infected with the delta variant ( ). Similar findings were seen in the South African study, which showed the omicron-infected COVID patients were 70-80% less likely to require in-hospital care ( ).

Will the current vaccines be effective? The preliminary data from South Africa have shown a

higher rate of breakthrough omicron infections among those who have previously been vaccinated. The

CEOs of both Moderna and Pfizer have expressed concerns that their current vaccines may be less

effective against omicron. However, the South African data also indicate that the vaccines are still

effective in preventing severe disease, with most hospitalizations there coming among those who were

unvaccinated. Non-antibody components of the immune system, such as cell-mediated immunity

(involving T-cells and natural killer cells), are not as likely to be impacted by the omicron mutations and

can still be helpful in preventing severe disease ( ).

Booster shots of existing raise antibody levels to a much higher levels, and those elevated antibody levels

seem to confer greater resistance to infection with omicron. An Israeli study recently published in the

New England Journal of Medicine showed a 10-fold decrease in infection in boosted individuals across all

age groups and an 18-fold decrease in “severe illness” requiring hospitalization among boosted individuals

( ). Data like these have led Israel to allow a

fourth shot (second booster) among individuals over 60 and health care workers

Recently published data from Great Britain showed that persons recently boosted with an mRNA

\vaccine had 60% protection against infection with the omicron variant 2-4 weeks after the booster shot

was administered. Unfortunately, 10 weeks after boosters were administered, the efficacy for a third

Pfizer dose against omicron dropped to 45%; for Moderna, the value was similar. However, Pfizer

recipients who received a Moderna booster still had 75% efficacy in protection against omicron after 9

manufacturers of the U.S.-approved COVID 19 vaccines are investigating ways that their vaccines could

be made more omicron-specific. Pfizer has stated that it could develop a tailor-made vaccine against the

How about therapeutic pharmacology treatments? We don’t have much data here. However, antibody-based treatments, such as the Regeneron infusion and a similar antibody product developed by Eli Lilly, are likely to be less effective. The newer direct antiviral medications such as those developed by Pfizer and Merck may still be quite effective, since they target areas of the virus which are not as susceptible to mutation, but at this point we simply cannot be certain ( ). The clinical trials of these drugs, which substantially reduced hospitalization and death when administered within five days of the first COVID symptoms, are very promising, and both drugs were recently approved for Emergency Use Authorization by the FDA. The Pfizer drug, for example, was nearly 90% effective in preventing COVID-related hospitalization and death (

Is omicron more severe than other strains? As noted previously, data from South Africa, Israel and Europe suggest that persons infected with omicron may be less sick than with prior iterations of SARS CoV-2 ( ). It should be noted that the omicron patients in South Africa tended to be younger, which could mitigate the severity of the virus’s effects. In addition, the true adverse outcomes from COVID-19 are often not evident until weeks after the initial infection. Still, omicron has been in the U.S. for nearly a month now, and while cases of it are skyrocketing, hospitalizations are not ( ).

How do I plan for travel and family gatherings during the omicron spike? There are several methods you can use to mitigate the risk to yourself and others during the omicron spike. First, if you haven’t done it yet, get a booster. Only one in six Americans have—but, as noted above, the booster shots can decrease your risk of getting omicron, at least for the next few months (and this spike is not likely to last that long). The optimal timing would be about two weeks prior to any anticipated exposure. Second, try to minimize your risk. This may mean avoiding crowded, poorly ventilated indoor spaces in which unmasked, closely spaced people are talking, eating or drinking (think bars or intimate restaurants) or wearing an N95 mask, as opposed to a cloth one, on airplanes. In short, we should eat outside just a little bit longer—and be aware of situations where we might be at increased risk ( ). Third, test frequently. On the day of our family’s recent Christmas Eve dinner—which was cancelled last year due to COVID-19—we mandated that everyone be tested for COVID-19 within a few hours of the dinner. This added an extra layer of protection for everyone at our gathering (all of whom were vaccinated, boosted and asymptomatic). We used the On/Go home antigen tests ( ). Given the higher viral titers seen with omicron and the short incubation periods, home antigen tests—previously maligned due to a high number of false negatives—have come into a new era of utility with omicron. PCR tests can be hard to get at times, and results can take days. That won’t cut it with a virus which spreads as rapidly as omicron. Using a rapid antigen test, which can be ordered online or purchased at your local drugstore, can be a great alternative. One word of caution: You should test as close to the event as possible. With the rapid replication rates of omicron, a person testing negative might subsequently become positive in only a few hours’ time ( ).

Although we are still learning about the omicron curveball, we must remember that we are still far better off than we were at this point two years ago, when COVID 19 was a locked black box of an illness. Today, COVID-19 is a disease we can track, test for and effectively treat, and that puts us miles ahead of where we were then. So there is still a light at the end of the proverbial tunnel. It’s just going to take a few more steps to get there.

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