COVID Transmissions for 1-10-2022
Deltacron: is it real?
Greetings from an undisclosed location in my apartment. Welcome to COVID Transmissions.
It has been 755 days since the first documented human case of COVID-19. In 755, Trisong Detsen became emperor of Tibet. Trisong Detsen played a pivotal role in the introduction of Buddhism to Tibet.
Today we’ll discuss a supposed new variant, and I have some thoughts about some comments from the CDC director this weekend.
Also, we’ll talk about a concerning surge in pediatric cases in the US.
Bolded terms are linked to the running newsletter glossary.
Keep COVID Transmissions growing by sharing it! Share the newsletter, not the virus. I rely on you to help spread good information, which you can do with this button:
Now, let’s talk COVID.
Deltacron
There were news stories over the weekend about a hybrid Delta-Omicron variant apparently detected in a laboratory in Cyprus. Cypriot researchers, led by Dr. Leonidis Kostrikis, claim that this virus appears to be the result of a recombination event between the Delta and Omicron variants, and called it “Deltacron.” The Cypriot health ministry has apparently said that this is not a variant of concern, and according to the discoverers, only 25 cases have been identified.
This one is a developing story, but virologist Tom Peacock—who was one of the first to alert people to the seriousness of Omicron’s changes—has suggested on Twitter that this looks like a sequencing artifact. In other words, he thinks it is not real and the result of sample contamination:
This is technically complicated, but basically what Dr. Peacock is saying here is that the insertion of Omicron sequence corresponds exactly to the segment of Omicron that PCR-based virus identification will amplify. Otherwise, the sequencing result looks entirely like Delta. The odds of this being the result of random recombination seem really low. I mean really, what are the chances that a recombination between two viruses, a process that happens at random, would select the same specific part of the Omicron variant that happens to be between two specific PCR primers used around the world for identifying SARS-CoV-2?
They’re low. They’re really low chances. Dr. Peacock does seem to have the right end of this.
However, Dr. Kostrikis has said, apparently in an email to Bloomberg, that it is not contamination. His claim is that the result has been verified in sequencing in multiple labs in multiple countries. That can be read here: https://www.livemint.com/news/world/cypriot-scientist-says-deltacron-covid-variant-isn-t-error-11641771855319.html
I honestly think it is more likely for this sequencing result to have come from an artifact, even in multiple labs, than for it to have emerged at random.
This contamination could have originated anywhere, not even in the labs necessarily. It’s possible for perfectly competent researchers to experience these kinds of things, and the nature of this particular error is, as I understand from Dr. Peacock’s writings on the subject, one that is more likely to emerge when a Delta variant virus is being sequenced.
Ultimately, I think it’s unlikely for this particular “deltacron” variant to be a real thing. There may be Delta-Omicron recombination events in the future, but right now, this one doesn’t seem like it’s a genuine isolation of that.
Maybe my opinion will change when data become available.
CDC Director takes heat for comments dismissive of individuals with comorbidities
This is one of the rarer moments where I will get both philosophical and political, because the world of COVID-19 has gotten into a political mess that contradicts my philosophical sensibilities as a person in the healthcare industry.
A small firestorm erupted over the weekend when Dr. Rochelle Walensky, the CDC director, made some comments on Good Morning America. There’s video in this tweet (along with some editorial comments from the person who tweeted it):
I want to start by saying that I think Dr. Walensky’s comments here were terrible communication. They were dismissive, imprecise, and also ableist. They implied that as long as the only people who are dying are those with preexisting serious conditions, that’s OK.
It’s not OK.
Public health needs to be about reaching an ideal of providing everyone with the level of healthcare that they want and need, individually, despite resource limitations. That’s what it seeks to balance. Individual health conditions, whatever they are and whatever impacts they have,1 do not diminish a person’s basic right to the healthcare they want to support their wellbeing. To even imply that there are some groups who do not deserve equitable healthcare concern goes against everything I got into this business to do.
COVID-19 has become an emergency for public health specifically because the strain it places on the system makes it impossible to have enough resources to be even acceptably close to that ideal.
While under normal circumstances, people with various comorbidities would be at different risks of serious outcomes with respiratory disease compared with people who do not have those comorbidities, this pre-pandemic status quo is not something we should simply write off as acceptable, and we also shouldn’t put all comorbid conditions into the same big risk evaluation basket.
Right now, the goal should be to end the COVID-19 emergency, which does involve returning to the pre-pandemic status quo, but we cannot pretend that that status quo is where the work of public health can end. It is not “encouraging” that a new respiratory disease will continue to pose a threat to people who have comorbidities of any time. That is added health burden that the public and individual health spaces need to take seriously and work on, both during and after the current emergency.
What am I doing to cope with the pandemic? This:
Reading: A Song For a New Day, by Sarah Pinsker
I write this recognizing that many of the readers of this newsletter have already heard of Sarah Pinsker’s A Song for a New Day, particularly after it won the Nebula Award for Best Novel in 2019.
The book examines a world where live music concerts have been outlawed due to combined threats of terrorism and a deadly pandemic. I want to reiterate that this book was published in 2019.
I wouldn’t, however, say this is a “pandemic novel.” It’s a music novel and a people novel, in my reading of it. Like with the best science fiction, the world that is drawn creates a stage to say something about the nature of the human experience—in this case, what it means to create and perform music, and beyond that, basic human relationships of trust, loyalty, and love.
It took me a while to get to this book because I didn’t think I was ready to read something involving a pandemic. I’m glad I’ve gotten to it now, because it really is excellent.
Reader Tom Quetchenbach shared a resource to find masks for children and also asked a question about mask reusability:
This is another option for a reasonably priced, apparently legit KN95 mask for kids (and adults with smaller faces, too), although they currently show a 2-week lead time: https://bonafidemasks.com/powecom-kn95-sm-respirator-mask-10-masks-per-pack/ (This model is mentioned on Project N95's website but doesn't seem to be currently sold there.)
Are you aware of any guidelines about reuse of surgical/N95/KN95 masks? I've seen some guidelines published, but they all seem to be targeted at healthcare workers, not at the general public. I understand the CDC's official recommendation is "throw it away after wearing it once," but it seems like that's not necessarily a realistic recommendation for everyone when KN95/N95 masks can cost $1+ each and aren't always easy to find in stock, and might only be worn for a few minutes at a time.
I am not an expert on mask engineering, but I do have some thoughts based on what I’ve heard from experts on this:
I have heard that N95 masks are rated to maintain filtration up to when they have absorbed a 200mg load, and that this load is equivalent to wearing them in Shanghai for about 200 days. So I think based on that, we're pretty OK reusing them. Probably the straps on them will break before reaching that point.
Maybe it's best to have 2 of them at least, and let them each lie unused for about 24 hours at a time while the other is in use.
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
I want to point out that it’s very possible to have a “health condition” that the patient feels has no meaningful impact on them and doesn’t require healthcare support. The impact of a health condition is not for any outside person to evaluate, stigmatize, or judge.
I bought and read A Song for a New Day in January of 2020. I don't think I've ever seen something go from speculative to current events that fast.
And while that future obviously had its bad points, I could wish we paid half as much attention to ventilation as they do.
On re-use of KN95: I’ve seen different sources recommend 24, 48, or 72 hours between reusing a mask. Store it in a breathable container e.g. brown paper bag; have 3 or 4 masks and rotate among them daily.