11/29/2021
OMICRON VARIANT OF COVID-19
I am very concerned about the new Variant, called Omicron (also known as B.1.1.52), being reported in the news. Here is some information about Omicron.
Background:
B.1.1.529, now labeled Omicron, was identified in a specimen collected from a patient from South Africa on November 2nd. It was reported to the WHO on November 24th. This variant has over 50 mutations compared to the original Covid-19 viral strain, with 32 of those mutations occurring in the Spike protein, which both binds to human cells, and has antibodies (from prior infections and immunizations) bind to it. Therefore, big changes in this protein are of concern, both for potential for increased spread, and for resistance to immunity from vaccination or prior infection.
Omicron’s mutations look worrisome. The Delta variant had two mutations in the region of the Spike protein called the Receptor Binding Domain (RBD), the portion that binds to human cells, and presumbably this contributed to its higher transmissibility. Omicron has ten.
At about the same time this variant was identified, there was a tremendous increase in the number of cases of Covid-19 in South Africa. The number of cases to begin with in South Africa were relatively low, 200 or 300 new cases a day. This spiked up to 2000 – 3000 over the course of a couple of days. With a fairly low baseline, it’s hard to tell what a spike means, as it could just be some statistical noise, but it certainly is a concern. Now, at this point, it’s not know whether the increased cases are due to Omicron or not, and it will be a few more days before we find this out. We do know that many of the cases in the region surrounding Johannesburg and Pretoria are due to Omicron, which increases the level of worry about this.
How did this variant start?
No-one knows for sure. However, given both the large number of untreated HIV patients in South Africa, and the very large number of mutations, it seems likely that the Covid-19 virus replicated in an uninhibited manor in a highly immunosuppressed AIDS patient, resulted in the accumulation of such number of mutations.
Where is Omicron now?
It seems to be concentrated in South Africa in the Gauteng Province surrounding Pretoria and Johannesburg, although the full extent of the spread is not clear at present. Isolated cases have been identified in several countries now, including Belgium, Australia, Britain, Italy, the Czech Republic, Germany, and Hong Kong. Thirteen proven cases, out of a total of 61 Covid-19 positive cases, were identified on two airplanes from South Africa that arrived in the Netherlands two days ago. I’m not aware if the remaining 48 have been tested for Omicron or not. There are no reported cases in the United States right now, but there will be soon.
Why the Travel Interdictions?
Well, this started in Europe, with Britain being the first nation to halt travel from Southern Africa, followed rapidly by other countries imposing travel bans, quarantines, or both. Europe is already struggling with Covid-19, with hospitals in many nations currently overwhelmed, so the presence of another problematic variant could be catastrophic. Other countries, including the US, followed the European lead.
Basically, the travel interdictions just buy a little time to figure out whether this variant is really as worrisome as it seems, and to plan for other measures that might be needed to slow the spread.
How much do we need to worry?
We don’t know at this point. While the structure and mutations of Omicron are very concerning, and the situation in South Africa are concerning, it’s really too early to know how concerned we need to be. There have been some other variants that initially looked to be worrisome, but never spread enough to be a problem. We’ll likely know within the next two weeks. I do think it is unlikely that Omicron will be completely resistant to vaccine-mediated immunity; Vaccination will probably provide some degree of protection against severe infection and death.
What can I do to protect myself?
Get vaccinated! Even if Omicron is partially vaccine-resistant, vaccines will likely provide some degree of protection. Get the primary vaccines, and get a booster when eligible.
Continue masking in high-risk environments, such as poorly ventilated indoor spaces (and avoid such spaces whenever possible, even if masked, as masking provides inadequate protection against aerosolized transmission). Limit your exposure to unvaccinated individuals. Continue to socially distance when appropriate and feasible.