COVID Transmissions for 12-21-2020
Good morning! It has been 399 days since the first documented human case of COVID-19. Welcome back from the weekend.
As usual, bolded terms are linked to the running newsletter glossary.
Keep the newsletter growing by sharing it! I love talking about science and explaining important concepts in human health, but I rely on all of you to grow the audience for this:
Now, let’s talk COVID.
A new “strain” in the UK?
Many of you will already have seen news on this so I want to clear it up up front: No, there is not a new strain of SARS-CoV-2 circulating in the UK.
If you’re not sure what I’m talking about, what happened is that the UK government described that they would enter a new national lockdown in light of an outbreak of COVID-19 there, apparently dominated at this time by a new variant of the virus. Authorities in the UK have described this as a “strain” that may be more transmissible. I can tell you right now that there’s no evidence of this, and I don’t even think there’s good hypothetical suggestion of it.
Please note that the word “strain” is being used inappropriately to describe this variant. The word is not used to describe every single changed virus that can be documented, because viruses mutate quite frequently, and a mutation in the genome of a virus is not at all unusual or notable. Most particles of most viruses contain at least one mutation relative to the “canonical” genome. That canonical genome is usually just whatever variant of the virus was sequenced and uploaded first, anyway. With billions of particles floating around inside a single patient, there are going to be many many variants, and not all of them will really impact what the virus actually does.
“Strain” is the word that gets used when a set of changes cause the virus to either (1) become immunologically distinct from other strains or (2) lead to a clear change in the genome that is circulating in a given place.
(1) is a little easier to explain; what I mean is that a new virus strain has emerged if a change in that strain makes it possible to infect and/or cause disease in people who are documented to be immune to other strains.
(2) is a fuzzy definition. Basically, if we find that in a given large geographical area, the circulating virus genomes appear to be of a distinctly different lineage than in other places, that distinct genome will often be labeled as a separate strain. This is especially true if we know that this geographic difference is the result of well-documented changes over time.
In the UK, there is no evidence that (1) has been satisfied and there’s no reason to believe that it has been. The number of changes in this variant also doesn’t satisfy (2), because the number of mutations is pretty small. We should be calling this a “variant” of the virus, and everyone who is not being sensationalist is doing that. Let’s stop using the word strain.
This variant is interesting, though. It contains the D614G amino acid change that has generated headlines in the past, as well as several other changes that may be worthy of further study. However, none of them have any clear impact on the structure or function of the virus. They are just “interesting”; I am sure we will learn more about them soon.
At this time, though, no evidence exists to suggest that they will cause any problems for vaccination or any impacts on transmission. No evidence suggests that this variant is any more deadly or dangerous.
For balanced takes on this variant, please read the following two sources:
British Medical Journal: https://www.bmj.com/content/371/bmj.m4857
GISAID (more technical): https://www.gisaid.org/references/gisaid-in-the-news/uk-reports-new-variant-termed-vui-20201201/
The GISAID article is interesting because it notes that there are almost 25,000 virus sequences from the UK alone in their database, and 6% contain the mutations from the variant of interest. This is hardly a dominant variant, at least by that measure. Though, that could change.
What am I doing to cope with the pandemic? This:
Praying in the snow
It snowed a lot last week, and that has interfered with what my synagogue has been doing lately: holding half of our Saturday morning service outside. We decided to go forward with the outdoor portion of the service anyway, despite the thick pack of snow on the ground, and see how many people might show up anyway.
As it turned out, quite a few people came! Almost as many as in better weather, by my rough estimation. The snow was well-sledded-over, so there were a few slippery moments, but only one person actually fell in the end.
We were snapped by a passing photographer, and I’m kind of hoping those pictures will show up at some point. Afterwards, we had whiskey and cookies in the snow.
I understand that our children’s program, which regularly meets in the park as well, involved some attendees on sleds.
It’s a strange year, but some of the coping has turned out pretty fun.
Reader Carl Fink commented the following on the last issue of the newsletter:
You wrote, "Something interesting to me here is that education employees appear to be about as frequent a source of infections as restaurants and bars. In past issues, I had suggested that I think that indoor dining should have closed before schools in New York. Having seen these data, I now think that perhaps both should have been closed at the same time. Can’t argue with data."
Can I argue with your reasoning? Priorities matter. Schools are *more important* than eating in badwording restaurants, and for that reason could and should be allowed to remain open even when they represent some risk, even when indoor dining is forbidden.
I don’t actually disagree with Carl here. So here’s my reply:
I don't think you're arguing with my reasoning here at all. I've expressed before, and continue to express, that if schools are closed, indoor dining absolutely should be closed as well. The data suggest to me that closing them at the same time might have similar beneficial effects on controlling spread of disease, which is what I'm commenting on here. I'm not a sociologist, economist, or politician. I'll have to leave the value judgments to those folks.
Important to note is that I didn’t say “if restaurants are closed, schools should also be closed.” I haven’t commented on that proposal, intentionally. As a matter of personal opinion, I don’t necessarily agree with that statement, but I am not certain that I can make a quality scientific argument for or against it. I’ll leave it with the politicians.
You might have some questions or comments! Send them in. As several folks have figured out, you can also email me if you have a comment that you don’t want to share with the whole group.
I’ve been contemplating changing the schedule of this newsletter a little bit; perhaps reducing it from daily to 3 times a week. I’m interested in your thoughts; feel free to comment publicly or send them my way privately.
Thank you to those who answered me about this already; I’m taking all of the feedback under consideration.
Join the conversation, and what you say will impact what I talk about in the next issue.
Also, let me know any other thoughts you might have about the newsletter. I’d like to make sure you’re getting what you want out of this.
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.
Always,
JS