COVID Transmissions for 1-14-2022
An Omicron peak, and an Omicron-specific vaccine, are both in sight
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. The forecast for New York this weekend is extremely cold, but I am glad I didn’t live in England in 759, where the winter freeze began October 1st and didn’t end until February 26th. That’s a long time in the cold before the invention of HVAC systems.
In COVID-19 today, several places around the world seem to have turned a corner in the Omicron wave, so I’d like to do a brief roundup of things we’ve learned from the experience in these places so far. Also, Pfizer has announced they are working on an Omicron-specific vaccine. So that’s news worth sharing.
Please note that there will be NO issue of COVID Transmissions on Monday, 1-17-2022, in honor of Dr. Martin Luther King, Jr. day in the US. We will return on Wednesday, 1-19 instead.
Bolded terms are linked to the running newsletter glossary.
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Now, let’s talk COVID.
Omicron wave appears to have peaked in many places in the US and the UK
It looks like we have reached a peak in the Omicron variant wave in various places in the US as well as the UK. AP has a story summarizing here: https://apnews.com/article/omicron-wave-britain-us-160ded1ce8d82075057630e11b610358
For Boston in Massachusetts, the first evidence of a peak has come from wastewater surveillance:
Similar indicators are being seen in other cities—drops in case counts, mainly. New York looks to have peaked as well, though it is more cresting than dropping like we see in the Boston wastewater data. It is not easy to say whether that represents just saturation of testing infrastructure or a real change, but I would not be surprised if we see a drop in cases in New York soon too.
This is all matching the timing that I would have guessed for this peak, because ultimately while the Omicron variant has a larger set of susceptible hosts, it spreads through human behavior. Last year, human behavior drove a spike in the US that began around Thanksgiving and then peaked around January 11th, following holiday travel by about two weeks. This is not a big surprise; when susceptible people move around and mix with each other, viral transmission happens.
Omicron has made the case numbers jump up very high, but the same rules apply to it. When it has access to hosts, it will spread. When its access to hosts becomes more limited, it will fall.
I’m not sure if this wave will have a long tail or not—last year’s took until February to really come back down—but we shall see.
In the course of this wave, we’ve learned some important lessons. The Omicron variant was able to cause disease in most people with an unboosted course of vaccination, which is where we got this much larger susceptible population. However, antibodies resulting from vaccination—possibly along with some changes to the virus—made it less likely to cause hospitalization. For unvaccinated people, which unfortunately also includes many children for reasons beyond their control, there were still quite a few hospitalizations. The US saw its highest week so far for child COVID-19 deaths during the course of this surge.
At this point, though, New York data are really showing just how protective vaccination was against hospitalization with COVID-19:
That graph right there is a fantastic topline argument for vaccination. Under normal circumstances, you should want to avoid a hospital stay. What happens to you in the hospital may save your life, but it can often result in damage, both from disease and treatment, that takes a long time to repair. An unexpected hospital visit, not just for COVID-19, is something you want to reduce your risk of.
Here we have a quick and easy intervention that reduces your chances of an unplanned hospital stay for a virus that is not well-known to science. I would take that intervention if it cut my risk by 50%. In fact, in some cancers, after surgery, patients take years of treatment just to get a 20% reduction in their risk of a negative outcome. Here we have a vaccine that, in just two or three doses, cuts the risk of a negative outcome by 90% or more. Incredible.
Of course, avoiding a hospital stay for COVID-19 is even more important than just any unexpected hospital stay, because COVID-19 can cause all sorts of nasty damage. I often hear people concerned about putting the vaccine into their bodies who seem to have no concerns about allowing a virus into themselves that was totally unknown to science before 2019.
A lot of people like that found their way into that blue line in the graph. They could have avoided it. Now, they run the risk of all kinds of terrible things happening—vascular problems, cardiac problems, lung damage, and more—that they could have avoided. None of these problems occur with vaccination.
Since I’ve been hitting this point about hospitals so much, I want to acknowledge that there has been a big debate as to whether people in hospitals are there “for COVID” or just “with COVID.” That is to say, there are people who think many of these hospitalizations are not a big deal because they’re just incidental findings when people are hospitalized for other things.
There are a number of problems with this perspective. First and foremost, if you are in the hospital “with” COVID-19, COVID protocols will apply to you and that will soak up hospital resources that are needed for other patients. COVID-19 will make everything more complicated even if it doesn’t cause a lick of symptoms.
On top of that, COVID-19 can make your other condition(s) worse, ranging from the obvious like exacerbating existing lung issues to the less intuitive like turning well-controlled diabetes into a really unstable situation. “With COVID” is not a healthy situation.
Then there’s the fact that sometimes, COVID-19 presents to care with a nontraditional set of symptoms. Patients maybe did not know what to look for, or didn’t report their symptoms correctly, and show up at the hospital with a situation like the one described in this tweet:
This may be a bit unclear. “Dyspnea” means difficulty breathing, while “bilaterial unprovoked PEs” means a pulmonary embolism (PE), a clot blocking an artery in the lung, that is “unprovoked”—meaning the patient did not have known risk factors for the formation of such clots.
These are both COVID-19 symptoms, yet somehow they were classified as “asymptomatic” with COVID-19 despite these obvious symptoms.
A PE is life-threatening. I think people really discount the importance of lung function. Your lungs take oxygen from the air and put it into your blood. We often take this for granted, because we breathe 8-16 times per minute. Many are actively aware that you can live without food for a few weeks or without water for just a few days. Without oxygenated blood your lifespan will be a few minutes.
This one is clearly a misclassification of the patient by an overworked healthcare provider who just didn’t really put it together, but if you click through you’ll find a thread of all kinds of things that are probably COVID-19 being characterized as some problem or another happening along “with COVID-19.” This appears to be happening a lot.
So, no, I don’t think any “incidental” finding of COVID-19 is something we can just sweep off the table.
Writer Ed Yong, a really talented science writer who has been continually required reading over the course of the pandemic, recently wrote an article that largely agrees with my opinion on this. What’s better about his article is that he interviewed healthcare workers for it, while I just read what some had to say on Twitter. You should read what he wrote, too:
On the whole though, I think the Omicron variant wave represents a bit of a turning point in our battle with this disease. Yes, the virus has mutated to escape some of the vaccines’ protection against disease, but we really did expect that to happen. What is impressive here is that the critical wall of effectiveness against hospitalization and death has been preserved despite that escape. The most immediate negative impacts are still prevented by the vaccine. That’s incredible.
We’ll still need to learn more about Long COVID symptoms; there just hasn’t been enough time yet. But, I am optimistic.
And, importantly, there is an Omicron-specific vaccine on its way, something that I called for not too long ago in this very newsletter.
Pfizer planning Omicron-specific vaccine by March 2022
Pfizer has announced it is making an Omicron variant-specific vaccine: https://www.cbsnews.com/news/covid-vaccine-pfizer-omicron-variant-march-paxlovid/
This is great news, but I want to start with the negative part of it. We are behaving reactively here. Right now, SARS-CoV-2 has not displayed a clear seasonal emergence pattern that would allow us enough time to make new vaccines against new variants before they have spread across the world. With influenza viruses, we have a nifty surveillance system set up where we can look at what happens in the Southern Hemisphere during their winter, and use isolated viruses from their flu season, which is entirely opposite to ours, to generate a vaccine against the isolates of virus that we expect to see in our own flu season. It’s not a perfect guessing process, but it helps to predict seasonal influenza pretty well, so we can devise vaccines.
We don’t have that with SARS-CoV-2, so we are talking about an Omicron-specific vaccine coming after the Omicron wave has crashed. We can’t get this vaccine out to people before the new variant can get to them. Maybe for future variants we will have some kind of bellwether system that will allow us to make predictions and thus create new vaccines in advance. We don’t have that yet, so we’re behind the game instead of ahead of it.
However, this doesn’t make an Omicron-specific vaccine useless. Far from it, in fact. This vaccine could substantially broaden the quality of our immune responses, and place further restrictions on the severity of disease that a new variant could cause in a vaccinated person.
The Omicron variant has 30 changes in its spike protein, and at least 8 of them are antibody escape mutations that were seen in other unrelated variants. It represents a picture of the diversity that SARS-CoV-2 can evolve to escape the human immune system. If you were vaccinated against the original Wuhan strain (the only option presently to be vaccinated against), an Omicron-specific vaccine could help to expand your immune response diversity to target these well-characterized mutations that have appeared in other variants. It would generate a diversity of immune response that might give you longer-lived defense against SARS-CoV-2 than you had with even your first vaccine. Or at least, I hope it would. I am sure it would provide additional protection for quite some time—whether it is longer-lived really depends on how quickly the virus can find a new solution to evade our immunity.
However, the broader our immune responses are, the more blunted any future encounters with SARS-CoV-2 will be. During my own infection, I experienced what felt like a strong influenza infection—not able to focus, no energy, strong symptoms. If I had a more diverse immune response, I might have experienced all of that more lightly, perhaps like a mild cold.
Whatever variant comes next, if you have neutralizing antibodies that target both the ancestral Wuhan strain as well as the Omicron variant, it will need to evade both sets of antibodies. That puts it under more constraint, and it also probably means less severe symptoms for you.
Getting a new vaccine against immunologically distinct viruses makes sense to me. This is better than just boosting with the same old sequence. While we wait for this thing, I do still think getting a booster dose is a good idea, but when this comes, I think it will provide a benefit that builds on the foundation that the original vaccinations and boosters laid for us.
Eventually, I hope we settle into a pattern where we can keep this disease typically mild and without long-term impacts by administering an updated vaccine very couple of years, or longer. That would be great, and I think would represent real disease control.
We’ll follow this story to see if we’re getting close to that idea becoming reality.
What am I doing to cope with the pandemic? This:
I tried running for the first time after COVID-19 yesterday. I’ll be honest, it wasn’t great. My pace was terrible and my heart rate was higher than it should have been at that pace. But I finished the distance I set out to do and I got the job done. It’ll take me a little while to get back into shape, but that’s worth the wait.
I took a long break from running because, frankly, COVID-19 does a lot of weird stuff to the vascular system, and I really need my vascular system—I mentioned earlier how easy it is to take this for granted. I might have had undiscovered impacts from my illness, and I wanted to let them resolve. What if I had clotting effects that could lead to a PE? What if I had myocarditis and could have had a sudden cardiac event under strain?
So I took a bit of a break from exercising. I’m paying for that a bit now, but I think the trade-off was a wise one to make.
Carl Fink shared some useful notes about high quality masks that I wanted you all to see:
You saw that CDC is considering issuing a guideline recommending high-efficiency respirators? I've been telling people I know to stock up, because supply will dry up just like toilet paper and chicken did in 2020 (which is to say, temporarily).
Folks should be aware, there are lots of counterfeit respirators around, especially KN95 and N95. According to tests by Aaron Collins, you can pretty much count on any KF94 mask out of South Korea--just confirm it was made in SK. Collins publishes his test data:
CDC tips on spotting counterfeit N95s:
There were other comments on the last issue, too, that you might want to go back and check out.
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