COVID Transmissions for 12-3-2021
Up close and personal with Omicron
Greetings from an undisclosed location in my apartment. Welcome to COVID Transmissions.
It has been 747 days since the first documented human case of COVID-19. The 747 is, in my opinion, the most iconic passenger aircraft of the 20th century, and so this milestone warrants a break from the usual format for this space.
Today’s issue is dominated by Omicron. News of it right in my back yard—and some analysis of how it got there. Then, I talk about evidence that it might evade prior immunity.
Take this one seriously, folks. It’s not a reason to panic, but it’s a reason to protect yourselves. Get a booster if that’s an option for you. Wear high quality masks. Don’t take unnecessary risks.
And while you’re doing all that, please try to enjoy the weekend.
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Now, let’s talk COVID.
More Omicron detected in the US
It started with one case connected to AnimeNYC, a convention here in my home town. That case was found in another state, but it has uncovered a cluster of cases that originated there. Governor Hochul reported that 5 more cases have been identified: https://www.usatoday.com/story/news/health/2021/12/02/global-covid-cases-biden-winter-plan-omicron-coronavirus-updates/8830774002/
This whole thing is giving me flashbacks to February 2020. I’m sure there are many more cases of this in the US than we realize. Maybe hundreds or even thousands. This is community transmission at this point. We are not talking about spread that happened with someone who traveled abroad; these are cases acquired domestically in the US through a large gathering.
AnimeNYC had the following COVID-19 rules: https://animenyc.com/coronavirus/
They required vaccination and face coverings, but their vaccination requirement leaves a lot to be desired. There is no requirement to be fully vaccinated, and attendees could come pretty much immediately after getting their first dose. Unvaccinated people 5-12 years old needed a negative PCR test within 3 days before the event, which isn’t the worst thing, but can miss some cases. Attendees under 5 did not need to test or to be vaccinated.
All of this is not ideal in my opinion and it is clear that it backfired. The vaccination requirement should have been full vaccination, and everyone should have had to take a rapid antigen test every morning of the event. Vaccines prevent disease much better than they prevent transmission, and rapid antigen tests help prevent transmission. The universal mask policy was wise, but in general, people are not using high enough quality masks. Research has taught us that surgical masks are better than the cloth masks that most folks are using. In a huge gathering, the organizers should be providing higher quality masks.
Many of my criticisms on this originate with NYC recommendations. The city only requires one dose of vaccination for certain indoor gatherings. It also has mask recommendations that I feel are out of date.
The sum total of all this is that I think a contributor to the cluster forming is poor COVID-19 control policies. However, Omicron was always going to be here. It didn’t need to spread at a massive convention, and I wish it hadn’t, but I think it was going to be in the US whether this happened or not.
Discussion aside, the city is now recommending that if you attended AnimeNYC, you should get tested for COVID-19 as soon as possible:
If this applies to you, please heed this recommendation. You could be helping reshape the curve of the emergence of this variant in the US by doing so.
South Africa offers evidence that Omicron can evade existing immunity
This recent preprint is concerning: https://www.medrxiv.org/content/10.1101/2021.11.11.21266068v2
In this paper, the authors looked at the chance (hazard ratio) of reinfection after prior COVID-19, with older variants and also with Omicron. The paper uses a somewhat confusing metric (hazard ratio for reinfection vs primary infection), and I am not sure the design is great. Infections are not disease, and it’s a bit confusing to interpret the risk of reinfection as compared to primary infection. If primary infection is protective, you would expect this risk to be very low, so I think this paper must have done some modeling that I don’t understand very well, because it suggested that the risk of reinfection with prior variants was as high as 70% of the risk of primary infection. That doesn’t seem right to me.
Regardless, the risk of reinfection with Omicron in their modeling was a lot higher than that, and that’s what catches my eye. Even if their model is a bit strange, the suggestion here is that it is more likely for Omicron to cause reinfections than other variants. This suggests that Omicron might meaningfully escape preexisting immunity.
However, it doesn’t guarantee that. Infection alone is not a good measure of protection, or of lack of protection. If you get infected and don’t get sick or transmit to anyone else, I would say you’re protected. So we have to take this result with a grain of salt.
However, it could also mean that either protection from disease, or restriction of transmission, is compromised by Omicron. This could be true of vaccine-induced or infection-induced immunity. We’ll need to keep an eye on this.
What am I doing to cope with the pandemic? This:
Thinking about Omicron
Look, I’m a virus nerd. This is an interesting variant. Sometimes, my “recreation” is learning new things about viruses. So I’ve been studying the incredibly dense image in this tweet:
A lot of the changes in the spike protein impact the range of animals that the virus can infect! That’s amazing! It’s not great news practically, but as a matter of studying virus evolution…wow!
You might have some questions or comments! Join the conversation, and what you say will impact what I talk about in the next issue. You can also email me if you have a comment that you don’t want to share with the whole group.
Part of science is identifying and correcting errors. If you find a mistake, please tell me about it.
Though I can’t correct the emailed version after it has been sent, I do update the online post of the newsletter every time a mistake is brought to my attention.
No corrections since last issue.
See you all next time. And don’t forget to share the newsletter if you liked it.
Always,
JS
Isn't it likely that, as time goes on, that the most successful mutations will result in a virus that is more transmissible, but causes milder (non-fatal) illness? If I remember my evolutionary theory correctly, this combination would result in the most favorable set of characteristics for any parasitic entity (i.e., "don't kill the host").
And the con was in NYC, where (based on my visit last month) there are free rapid antigen tests widely available. I saw a stand advertising them outside Queens Center mall. It seems pretty easy to get tested in NYC on a regular basis.