New Variant: Omicron

I hope you all had a wonderful Thanksgiving!

Unfortunately, I have some concerning news on the COVID front. The WHO has identified a new variant, currently called B.1.1.529. The variant likely first arose in South Africa, but has already spread to several countries in Southern Africa as well as at least Hong Kong and Israel. It has an estimated 32 mutations in the Spike protein alone. The new variant has been assigned the Greek letter Omicron (O).

Omicron is currently estimated to be 500% (6x) more infectious than Delta. For reference, Delta was just 60% more infectious than Alpha. Because of the many mutations in the Spike protein, the new variant may evade current vaccinations.

Since Omicron is so new, there isn’t yet information on fatality rate. Historically, new viruses in a group tend to be more infectious and less pathogenic (disease causing) than previous versions.

Most outlets will never talk about Antibody Dependent Enhancement, but a new variant with a very different Spike protein has the potential to trigger the ADE pathway. I might recommend that you take more precautions until more is known.

The President has suggested that anyone who hasn’t been vaccinated should do so now. I disagree. Because of the possibility of ADE, vaccination may even be worse for you than not being vaccinated. Until we know more, take additional precautions regardless of vaccination status.

My precautions are:
1) Wear an N95, KN95, or KF94 mask indoors in public. These masks are rated to filter out 95% of viral particles. In my opinion, surgical masks and especially neck gators are nearly worthless in these settings.
2) Keep 6 ft away from others. (I basically ignore this one if other precautions are in place, especially on an airplane!)
3) Avoid indoor gatherings, especially ones in which singing or shouting is likely.
4) Outdoor gatherings are fine, even without masks, if everyone maintains a distance. I have hosted several outdoor gatherings.
5) While many restaurants are open for limited indoor seating, I personally am still not comfortable eating indoors at a restaurant. I enjoy eating outdoors at restaurants, however.
6) I never take my mask off on the plane, and find an isolate spot in the airport to eat or drink on layovers.
7) If you find you can’t do any of the above, try to produce as much ventilation for yourself as possible. Sit next an an open window, choose larger rather than smaller indoor areas, or use a number 10 Honeywell air filter in your home or office. You can even make a virus filter out of a box fan and a number 10 filter.

Because Omicron is new, and may trigger the Antibody Dependent Enhancement pathway, vaccination may be either worthless or even detrimental. We’ll just have to see. Even vaccinated people should be more careful until we know more.

This story is early and evolving, and will let you know when I have substantial information to share.

Updated November 29th, 2021:

There is a little more news about the Omicron Variant. South African Doctor Angelique Coetzee was the first Doctor to alert health care authorities about the new variant. She says that symptoms are more mild than for previous versions, causing severe fatigue for a new days, but no cough and no loss of smell and taste. She cautions that most of her patients are relatively young and healthy, so she can’t yet say how symptoms will be for older patients.

Worse or Better?: With a huge number of mutations (34 in the Spike protein alone) the Omicron variant has the potential to be much worse than previous versions, because it may trigger the Antibody Dependent Pathway and make infections worse for those who have already had COVID. It is also likely to at least partially elude vaccination, putting us back to square one in terms of vaccination efforts. Omicron is also 6x more infectious than Delta.

The Omicron variant has 53 mutations relative to the original Wuhan strain. 34 of these are in the Spike protein. Delta has only 9 mutations in the Spike protein. Photo is from the Stanford University Variants Genome Viewer.

On the other hand, there is currently a chance that Omicron may be a blessing in disguise. IF symptoms are truly mild, and the fatality rate from Omicron is very low, the variant may spread very quickly and infect large populations with a mild disease, giving them safe immunity.

So at this point, there is a broad range of potential outcomes. I know many of you are “over it” and are living life normally at this point. However, I urge some increased caution at this moment, until we know more about the new variant. It will probably take a few weeks before we know how things will go.

At this point, I do not recommend strict lockdowns as practiced last year. Last years lockdowns did not prevent the spread of SARS-2, and had many more negative impacts. I recommend instead protecting your self from infections by taking the precautions listed above.

The United States and several other governments have put restrictions in place for travel to South Africa. The South African government is complaining that they are being punished for being transparent about the virus. I have mixed thinking about this. South Africa is to be greatly commended for being open and sharing information about Omicron, unlike the Chinese government when this all started. However, I do think it is warranted to be cautious regarding travel. We should take a pause while we access the situation.

I predict, however, that as countries sequence virus detected in patients, they will soon discover that Omicron is already wide spread. It may already be too late for travel restrictions to have a big impact. The new variant has already been detected in Israel, Hong Kong, the UK, the Netherlands, Portugal, and many other European countries. Given the extreme contagiousness of the new variant, it is likely already wide spread.
UPDATE: December 1st, 1:00 pm
Just hours ago, California Public Health and the CDC have announced that a patient with the Omicron variant has been detected in California. They had returned from South African on the 22nd, and the case was detected on the 29th.
UPDATE: December 2nd, 2021
2 more cases of Omicron have been detected, in Minnesota and Colorado. The case in California and Colorado were in individuals who were fully vaccinated. All individuals so far have had mild symptoms.

Don’t fear, but be smart,

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