COVID Transmissions for 12-15-2020
One year since first public vaccinations; Omicron increases its case share in the US
Greetings from an undisclosed location in my apartment. Welcome to COVID Transmissions.
It has been 759 days since the first documented human case of COVID-19. In 759, King Pepin III (“the Short”) of the Franks pushed Iberian Muslim1 forces out of Narbonne, which they had occupied for 40 years, and sent them retreating back across the Pyrenees. This marked the end of Muslim political and military entities’ inroads in Western Europe outside of Iberia.
That has nothing to do with COVID-19, but is a pretty watershed event in history.
As for COVID-19, we’ve reached the anniversary of a much more positive watershed event, one that in part relied on the scientific achievements of immigrants from a primarily Muslim country to a traditionally Christian European country: the rollout of the Pfizer-BioNTech vaccine. I generally think humans do a lot better when we work together. We’ll reflect a little on the progress of the group vaccination project.
We’ll also discuss some data on the percentage of cases in the US that are due to the Omicron variant.
Also, repeating the heads up that I will be traveling this week and there might not be a Friday issue. I will try, but my schedule is very full. Don’t be alarmed if I miss Friday.
Bolded terms are linked to the running newsletter glossary.
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Now, let’s talk COVID.
One year of vaccination
It has now been one year since the first COVID-19 vaccination of a member of the public outside of a clinical trial.2 In just over 365 days, 8.53 billion doses of COVID-19 vaccines have been administered around the world. I cannot think of a time in history when so many resources have been mobilized so rapidly to fight an infectious disease. While there are many things to criticize about human reactions to the COVID-19 pandemic, I do think we should be impressed with this achievement. It may not be the ideal that we wanted, but we can be proud to have improved on what has happened in the past.
Omicron variant cases are now 3% of US cases
According to CDC estimates, cases of infection with the Omicron variant are now 3% of cases in the US: https://covid.cdc.gov/covid-data-tracker/#variant-proportions
In New York City, where I live, apparently 13% of cases are due to this variant.
A week ago, the national case share was 1%. This appears to be rather explosive case share growth, given that the first cases were detected not very long ago, but I don’t know how realistic this increase actually is in reality, versus its appearances.
Firstly, US cases have had a pretty flat 7-day average in December after showing a distinct post-Thanksgiving jump. So while the share of Omicron variant among new cases has increased, the number of cases overall has followed patterns expected from human behavior rather than a big change in the virus. So we wouldn’t want to interpret this as Omicron being involved in a huge rise in cases—at least, not yet. Instead, if the data are meaningful over time, they suggest that Omicron is potentially beginning to displace Delta, which is still the dominant variant in the US.
That brings us to the second point, though. US sequencing surveillance was clearly insufficient to detect Omicron variant cases when they first came to the US. I don’t think we will know with certainty when this variant first arrived here, ever. The US has substantially expanded sequencing in order to detect this variant, and as a result we may be playing “catch up.”
A similar situation has occurred with many diseases. When surveillance for a disease gets better, you find more cases of it. Not because it is becoming more common, but because you were probably missing cases before. I can think of examples of this happening with non-infectious diseases like autism as well as with infectious diseases in the past. It also happened early on in the COVID-19 pandemic, when testing was insufficient in the US and it was extremely difficult to even know how many cases there were in the country overall.
It seems we didn’t expand our surveillance enough. There are a lot of mistakes that keep repeating themselves.
So, as we expand sequencing surveillance, the question becomes—are we detecting growth in Omicron prevalence, or are we actually detecting growth in our own sequencing efforts? Are our estimates of the % share of cases due to Omicron showing growth in that variant, or are they just improving in estimation quality because we’re sequencing more?
I don’t think we can know for certain right now. I could be wrong—maybe sequencing has expanded more than I realize more quickly than I imagined possible—but if my sense of this is correct, I don’t think we can tell the difference between actual growth vs surveillance growth right now.
What am I doing to cope with the pandemic? This:
Rapid tests for my trip
As mentioned last issue, I am on my way to Worldcon this week. Part of my safety procedure for the con is to use a rapid test every day. This is the best way to keep the community safe. Vaccination is the best way to keep myself safe, though I’ll also be wearing an N95 mask3 during my trip for better protection.
Getting rapid tests is much harder in the US than in other countries, and it is frankly embarrassing. Here’s what I was able to get:
My first attempts to get these were failures. The only reason I found these at all was that an employee at a store I went to a few days ago told me when their next shipment was likely to come in. When I arrived back at the store, the employees thought they didn’t have any tests, and it was only by chance that one person who know they had gotten tests overheard the conversation and helped me out.
They didn’t want to sell me more than 2 boxes; they were only willing to do so because I told them I was also buying tests for my wife, so they let me get 4. Thankfully that is enough for both of us to test every day of the convention because she will not be attending for the full duration.
Originally they didn’t even want to sell me enough tests for a complete workweek of 5 days. Think about that. These tests are best used every day, by everyone. We’re nowhere near that.
What’s more, this stack cost almost $100. I can probably seek insurance reimbursement, but frankly I’m not sure it’s worth my time. This is a stack of 8 tests. In the UK, you can order 7 tests each day, which will be delivered to your home, as long as you’re over 11 years old and meet certain other criteria. UK readers, by the way, if you don’t know about it already, here’s the link to do that: https://www.gov.uk/order-coronavirus-rapid-lateral-flow-tests
The US doesn’t have a national health service like the UK, so I don’t expect testing here to ever be free, but it sure as hell should be a lot cheaper. At $100 for 8 tests, it would cost me approximately $250 to test every day of going to an office for a month, were that something I was required to do. At the minimum wage of $7.25, that is approximately 35 hours of work (and that’s not even deducting taxes). Nearly a full week of work just to be able to afford testing to safely go to that job. That’s not acceptable.
These tests should be $1 each, maximum. Stores should have more of them than they know what to do with. This is not just an ideal scenario, this is an essential disease control mechanism so that we can eventually take off our masks and live at least a little bit like we used to.
Reader Sam and I had a couple of conversations on the last issue, on different topics. The first was on vaccines and Long COVID. Here is that exchange, starting with Sam’s comment:
There are now a small handful of studies on vaccination's effect (or lack thereof) on long COVID. Unfortunately, some find either no effect (see: https://www.medrxiv.org/content/10.1101/2021.10.26.21265508v1.full.pdf) or a much more modest one (see: https://www.researchsquare.com/article/rs-1062160/v1). A number of commentators have expressed skepticism that billing codes would adequately capture the phenomenon either way.
In any case, if we're going to "live with" SARS-CoV-2, then we desperately need to figure out how to prevent it from leading to debilitating conditions in large numbers of people.
My reply, referring to why I shared the large study showing a protective effect of vaccination against long COVID in the first place:
Yeah--one of the reasons I have not commented extensively on this topic before is that the research studies were conflicting and all of similarly small size. The inclusion of 240,000 SARS-CoV-2-confirmed patients in this analysis gives me some feeling that it will be authoritative--though I do still emphasize the not-yet-reviewed caveat that applies to it and many of the studies on this topic.
Next up was a conversation about vaccine efficacy and durability against the Omicron variant:
Re: vaccine efficacy vs. Omicron, the concern I've seen expressed is that the immune response will prove to be not very durable. Peter Hotez has been in full-on panic mode given this prospect over the past couple of days. Too early to know for sure, of course, but it would seem to accord with the results seen in this study: https://www.medrxiv.org/content/10.1101/2021.12.07.21267432v1
I’d seen this study before, but I think its results are not too different from things I have shared already—the study has small numbers of patients and only looks at neutralization of virus using serum collected from vaccinated patients, rather than vaccine effectiveness directly in the real world. Studies of all designs on this topic are still very small and it is still very early days. Thus my reply to Sam:
While it's certainly too early to tell, you make a good point about the possibilities. I have a feeling that we are going to need to design and deploy an Omicron-specific booster shot eventually. Maybe sooner than eventually.
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.
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No corrections since last issue.
See you all next time. And don’t forget to share the newsletter if you liked it.
Always,
JS
Normally I would not refer to an entire religion as a political entity, but in the politics of the time, this is the most accurate way to describe the situation. It was a very different time, when religious and political identities were much more closely tied together.
Technically there were some other vaccinations before this; they were largely of unapproved or untested vaccines in Russia and China. I don’t feel it’s appropriate to count those as a milestone, considering the scientific and ethical breaches involved.
Carl Fink noted in a comment that there are other mask options like the KF94 or the KN95 that are easier to source than a proper N95; I happen to have some N95s, so that’s what I’m using. But if I didn’t, I would try to get one of those. Barring that, I would use a surgical mask. If I couldn’t get a proper surgical mask, I would use a triple-layer cloth mask.
Hi John,
Would you be available to speak to a group regarding Covid? I am a member of the Ethical Culture Society in Teaneck, NJ & we are looking for someone to speak to our group about rapid testing and other relevant Covid issues. We are looking for someone for Jan. 9th at 12:30 on zoom or in person.