Greetings from an undisclosed location in my apartment. Welcome to COVID Transmissions.
It has been 766 days since the first documented human case of COVID-19. In 766, Emperor Constantine V discovered a plot against his rule, and executed the two ringleaders. He had the rest of those involved blinded and exiled.
Since I’ve been somewhat critical of my country’s leadership during the COVID-19 pandemic, I’m pretty glad I didn’t live in the Byzantine Empire.
Today we’ll talk about an article predicting an end to the pandemic, the concept of pooled rapid antigen testing, and the ethics of denying care to the unvaccinated.
Have a nice weekend.
Bolded terms are linked to the running newsletter glossary.
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Now, let’s talk COVID.
IHME head predicts that Omicron will end the pandemic—I say, never bet against a virus
Writing in The Lancet, head of the Institute for Health Metrics and Evaluation Dr. Christopher JL Murray says that the rapid spread of the Omicron variant will mean that society is so populated with protected people that future waves of COVID-19 will result in mild disease akin to annual influenza. The article, such as it is, is here: https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(22)00100-3/fulltext
Dr. Murray may be right; it is possible that every future variant that we experience will be similar enough to the Omicron variant that this will be another influenza-like illness with a seasonal pattern. I will return to that scenario in a moment.
Dr. Murray may also be very, very wrong. His argument centers on the concept that we have some capability of predicting what this virus will do next, and that it will obey the rules that have been set out by our understanding of other seasonal pathogens like influenza virus. The history of COVID-19 public health messaging is littered with wreckage from the damaged reputations of people who have made this same prediction. So far, SARS-CoV-2 has defied us all. I’ve even made some hasty predictions of my own only to be later humbled by this virus.
The fact is, viruses can and will explore every possible option that allows their survival. It’s a common story in virology that nearly as soon as some other field of biology discovers an entirely new piece of machinery in some organism or another, a virologist discovers a virus that exploits that machinery. In fact, sometimes, we’ve discovered entire elements of fundamental biology because someone found a virus that subverts those elements to their will. Viruses, through their power of rapid, diverse replication and mutation, are able to find brute force solutions to take over the most complex systems. We should be very wary of assuming we can outsmart viruses, because they are capable of taking nearly complete control of organisms that humanity only barely understands.
This is not some grand pronouncement without practical implications. Take the Omicron variant, for example. It contains numerous mutations that, right now, we understand at only the barest level. Some we don’t understand at all.
Past variants also, apparently, have capabilities that we understand poorly. The Beta variant, for example, appears to have the ability to infect normal laboratory mice, something that other SARS-CoVs can’t do. In fact it has made the virus more challenging to study, because generally mouse models need to be complicated transgenic mice that are engineered to express human ACE2 receptors. The Beta variant needs no such accommodations, it seems. That research can be read here: https://www.nature.com/articles/s41392-021-00848-1
This mouse storyline is relevant to Omicron as well, because there have been claims—ones I’m not sure I believe—that the Omicron variant actually originated in mice, and some of its adaptations come from experience in that host. I’m not sure what the origin of the Omicron variant actually is, but this possibility is opened up by the fact that the various interesting SARS-CoV-2 variants did not originate as descendants of each other, but rather share a common ancestor from early in the pandemic. That I am quite certain of, and it is meaningful because it implies that there remains a large mutational possibility space for this virus to explore.
Even if Omicron itself is not the product of a sojourn into mice, it is not the first time we have heard a story where the virus entered an animal from humans and came back out into humans, perhaps even with adaptations. In 2020, an outbreak in mink farms that spilled back into humans prompted the country of Denmark to cull 17 million minks: https://www.bbc.com/news/world-europe-54890229
Promiscuity in host range can allow a virus to tolerate variants which are more devastating for one particular host, because it doesn’t matter if, say, the virus runs out of humans. There are other hosts to infect. That is a bit extreme as a scenario, but there are intermediate possibilities. For example, Nipah virus, which launched my PhD, caused its worst known outbreak after a journey through an intermediate pig host and then into humans. The experience in pigs appears to have adapted the virus to be able to be somewhat more able to establish a large outbreak in a human community, for whatever reason. Passage in a new host can do weird things.
My point here is that we should not expect SARS-CoV-2 to play by predictable rules where it evolves exclusively based on the immune pressures applied to it by humans. We should not assume that Omicron will be the last major threat that it can present to us. I’d be delighted if it were, but I am not going to make you promises that I don’t think I can uphold.
Imagine, though, that Dr. Murray is correct, and Omicron variant epidemics are the shape of things to come. He notes in his piece that the current trajectory of deaths from the Omicron wave in the US is comparable to the number of deaths (52,000) in the worst influenza season of the last decade. While this makes a big assumption that the IHME’s death models are accurate—Omicron deaths have not yet peaked, since death is a lagging indicator—let’s assume for a minute that it’s correct.
Should we be reassured about the prospect of a future where every year or two, we experience a death toll from SARS-CoV-2 that is comparable to the worst influenza season in 10 years? This will, of course, be in addition to the seasonal influenza epidemic that we will experience each year. Instead of just flu deaths to worry about, Murray’s prediction says we will now have SARS-CoV-2 causing the death toll of of a bad flu season, plus whatever the actual flu season that year does. This logic does not make me feel better. Previously we had one pathogen that might cause 52,000 deaths. Now we have two? That sounds like 104,000 deaths to me.
I’m sure it’s not that simple, but more threats definitely means more problems. I don’t feel comfortable taking the attitude that this is somehow a good situation.
Really, though, the message I have for you is this: it ain’t over til it’s over, and I’m not going to call an early end to the pandemic when we’ve only just seen a peak in the most recent variant.
Don’t use the same nasal swab on multiple people
Writing in The Atlantic, Rachel Gutman tells us about a truly disturbing and gross practice—families using the same nasal swab to use a single rapid testing kit on multiple people: https://www.theatlantic.com/health/archive/2022/01/sharing-rapid-tests/621318/
Gutman interviews some experts here who tell you why this is a bad idea, but let me summarize:
Pooled PCR testing can be done in laboratories because the scientists there mix a batch of ingredients that is appropriate to testing multiple samples, and PCR is very sensitive
Antigen tests that you use at home are optimized to test a single sample, and using multiple samples on the same or different swabs could cause false negatives
You could also infect each other—and not just with COVID—by sharing swabs; it’s gross
While I could rail against this practice some more, I want to say that this is obviously an outgrowth of the ridiculous cost and absurd scarcity of these rapid tests in the United States. People would not be doing this if these tests, which use technology that has existed for decades, cost what they really ought to cost—at most $2—and were readily available.
We need better test availability! I can’t believe I still have to say this 2 years in.
Ed Yong on the bioethics of denying care to the unvaccinated
Also in The Atlantic, incredible science writer Ed Yong describes the huge ethical problems with the emotionally appealing argument that those who choose not to be vaccinated should be denied care for COVID-19: https://www.theatlantic.com/health/archive/2022/01/unvaccinated-medical-care-hospitals-omicron/621299/
You should really read the entire piece. It is excellent.
That said, here is my take: healthcare is a human right. Treating people who have an infectious disease benefits us all; particularly if they are treated in a hospital that has infection control practices in place. If we begin to deny care on the basis of some kind of moral purity test, I think it sets a terrible precedent that could reverberate very poorly through society.
That said, triage is a completely different story. If you have one hospital bed, and two patients who you think could be saved, but are certain to die without care, and the only difference between them is vaccination status? Well, the vaccinated patient is more likely to live if you give them treatment. In that situation, I think the choice is obvious and ethical. However, this is a very specific and artificial scenario. In most cases, this choice isn’t being made—because very few vaccinated patients are ending up in the hospital at deaths door, in comparison to unvaccinated patients.
What am I doing to cope with the pandemic? This:
Getting by
This has been a tough week. The pandemic is hard to deal with. Please, take care of yourselves and be kind to each other.
Reader Sam wrote in to share awareness of NIH-funded research that you might be able to participate in:
Re: long COVID, just wanted to draw attention to NIH's ongoing study, RECOVER:
They're seeking volunteers for different cohorts: COVID-recovered with and without long COVID, as well as those never infected.
LHN wrote in about deer transmission:
The wide spread into deer populations does make me wonder a bit about the guidance that outdoor gatherings are generally relatively safe. I don't suppose deer are spending a lot of time at crowded bars and dance parties.
While this also gives me pause, I am reluctant to draw conclusions about humans based on deer, as I say in my reply:
It's important to recognize that the upper airways of many animals are different from those of humans, as is just the overall biology of many of our fellow mammals. As an example, you can use mice to study influenza virus (to an extent), but you can't use them to study transmission. Their upper airways are too different from ours for that to work right. To study influenza virus transmission you have to use guinea pigs or ferrets, which have more similar nasal turbinates to those of humans. Sometimes very subtle differences between species can alter transmission dynamics.
Deer are very social creatures, and at the same time their understanding of basic hygiene, as I understand, leaves a lot to be desired.
It is entirely possible that deer transmit this virus to one another through a fecal-oral route, or from their habit of frequently touching nose-to-nose, or some other undiscovered mechanism.
On the other hand, I have no idea how it's actually happening! And I would very much like to know. There are animal health laboratories where this might actually be studied, so I am wondering if we will see some transmission work conducted using captive deer populations. I do think it's important.
Carl Fink asked about something that’s relevant to our lead story today:
Good to have you back. I know you aren't an epidemiologist, but I'm curious to hear your informal opinion on the idea that Omicron will "involuntarily vaccinate" many, many people who have refused vaccination with the safe, pharmaceutical versions. For one example, I'd expect that South Africa now has immunity equal to the USA because everyone (almost literally) in the country has now been exposed to, and likely infected with, actual active SARS-CoV-2.
Here’s my reply:
I think if the Omicron variant, and its consequent reinfections of many previously-recovered people who had different variants, has taught us anything, it's that immunity generated by infection is a very poor safeguard against future immune-evasion mutants. It does not appear to generate sufficient protection to keep people safe.
Also, to get it, you have to get the very thing you are hoping it will prevent getting, but that's another matter.
Anyway, I don't think it will be a meaningful safeguard against whatever the next escape variant is, because immunity to Delta from a past bout of illness was not a meaningful safeguard against Omicron.
This thread continued with Carl asking for some supporting data; for length reasons I am not including the whole exchange but please do feel free to go to last issue’s comments section if you wish to read it.
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.
Correction: In the emailed version of the last issue, I had an error in the figure legend for the Israeli study of Long COVID. I said that rates of Long COVID symptoms were “lower” in the unvaccinated or single dose-vaccinated than in the double dose-vaccinated or uninfected; this should have read “higher,” as was visible in the graph. I have corrected this in the online edition.
See you all next time. And don’t forget to share the newsletter if you liked it.
Always,
JS
The choice is not just between the vaccinated covid patient or the unvaccinated covid patient. Lately, the choice has been between the unvaccinated covid patient and the cancer patient, or the person living with pain who needs a hernia repair, or some urgent but perhaps not immediately life-threatening surgery. It doesn't seem fair to defer cancer treatment to provide treatment for a condition that could easily have been avoided.
Somewhat related to Carl's question, I was wondering if you had any thoughts on the implications of Delta-Omicron cross-immunity for vaccination. Increasingly, it seems clear that Omicron infection by itself doesn't really yield Delta immunity, just as Delta infection doesn't yield Omicron immunity. But it *does* looks like Omicron infection in *vaccinated* individuals enhances immunity to both Delta and Omicron (see, e.g., https://secureservercdn.net/50.62.198.70/1mx.c5c.myftpupload.com/wp-content/uploads/2022/01/MEDRXIV-2021-268439v2-Sigal.pdf).
My question is: does this imply that an Omicron-specific vaccine might elicit cross-immunity in previously vaccinated people, but not in immunologically naive people? What about unvaccinated people who were infected with an earlier strain, then reinfected with Omicron?