Convergent Evidence, Omicron Edition. Open Thread 26/12/2021
Why I believe many of the worst-case scenarios are now off the table
It's the holiday season for many people! I hope it is joyous and happy for you and yours..
This is the best Omicron update I have yet, but first, a brief announcement.
But if you don’t want to read all the way, here’s the two big items in tl;dr form.
I’m doing a Doctors Without Borders donation drive: I’m matching up to $20K, and others have stepped up so up to $58K in donations is matched! If you’d like to support it, here’s where to contribute: https://events.doctorswithoutborders.org/campaign/zeynepmatch2021
There is convergent evidence that for vaccinated and or/prior infected people—the seropositives—the defenses against severe disease or worse for Omicron are holding up fairly well and that Omicron itself may be causing less severe disease, and is not as good at replicating in a manner that causes the illness to progress to severity and invade the lower respiratory system. (Note! These are two separate mechanisms! The news is encouraging on both fronts!) The first is a lot more firm, the second is emerging evidence, and neither means we can ignore the situation. IT IS STILL SERIOUS. But yes, I believe that more and more of the worst case scenarios are off the table.
Happy holidays! Now the details on both.
A few years ago, I did a donation drive for Doctors Without Borders, supporting their work in Yemen which was facing war, famine and disease at the same time—as it often happens.
I had a hand-me-down 2001 Honda Civic, so I put the money I had saved to replace it as a match for donations. The campaign generated almost $250K, as people stepped up both to increase the match, and to donate.
Well, my Civic made it to 2021! It had other advantages as well, besides being oblivious to new scratches (who could tell!): as a stick-shift, it seemed like it was theft-proof. Here it is back then, in 2016:
It may be that thieves these days can only drive automatics. I never locked it, though when I did put my bike on it, I think its value quadrupled.
Here it is more recently, about to quadruple in value (note the bike rack!):
So this year, I’m doing another campaign. I’m signing my Civic over to a friend’s son, and not replacing it. It still runs, at 200K+ miles. But I am in New York at the moment, and not only do I not need to own a car, trying to park that thing would probably cost more than the car each month.
I’m once again putting the replacement cash towards Doctors Without Borders. I’m thus matching $20K in donations to Doctors Without Borders, this time in support of their work in Yemen and Burundi.
If you want to donate, here’s the link. If you want to add to the match, you can put that in the note field, email me, or direct message me on Twitter. We are now up to $58K in matching donations!
Here’s one Twitter thread about it:
zeynep tufekci @zeynepYemen: Millions of children are at risk of starving. I'm fundraising—matching donations up to $15,000 for @MSF_USA. https://t.co/jQ8P9X6ANq https://t.co/SlMMtK8DO0
And here’s another Twitter thread about why I do these fundraisers—and why I wish we didn’t have to.
Yemen has been suffering from profound hunger, a terrible war, and lack of healthcare for five years now, and now the effects of the pandemic. Only about 1% of the population is vaccinated, and COVID, as terrible as it is, is not the highest challenge they face. The UN Food Program just announced they are cutting food aid to the country—not enough money. Burundi faces similar challenges: the pandemic came at an already fragile moment, adding to their many crises. Doctors Without Borders is one of the organizations that is on the ground in many such places and employs a lot of local staff. Ideally, we would not need these life-vests, the NGO work—ideally, the boat would be built better so it wouldn’t sink. But once people are in the water, the only right thing to do is to respond, even if we work to make such interventions less necessary, in the future.
Onward to Omicron!
So, first: data from Gauteng, South Africa and the United Kingdom and Denmark, and the situation on-the-ground here in New York all add to the same picture. Omicron is wildly good at spreading, and will infect and re-infect many people who are vaccinated or had prior infections, but is not generating a proportional uptick in hospitalizations or death among populations with high combined vaccination rates and prior outbreaks. (The seropositives: people who had prior infections or vaccination!)
Here’s a fantastic thread explaining intrinsic severity is hard to distinguish from “prior immunity”—our immune system reacts better because we have been vaccinated or previously infected.
And here’s the key point, about the multiple causes of severity: intrinsic and contextual.
Roby Bhattacharyya @roby_bhattWow, this thread got more traction than I expected for a wonky summary of a complex (but important) study. For those saying it brushes off milder societal impacts, I thought I'd try once more to clarify why I've been so insistent on unpacking intrinsic severity. meta-🧵 1/9 https://t.co/vWae8DFuw3
If you are immunologically naive—no prior infection or vaccination—Omicron is still likely more severe than many other variants, but maybe not Delta—which is a beast. (And still around!)
For intrinsic severity, though, we have increasing lines of lab studies pointing to similar results: that it may well also be less intrinsically severe compared with other variants.
Gupta Lab @GuptaR_labTMPRSS2 (T2) is higher in the lower airways and so virus goes the second route in those areas. Omicron spike has reduced ability to use the ACE2+T2 route and doesn't respond to higher T2 levels, unlike Delta in the figure. Also, Omicron entry is not blocked by drugs against T2. https://t.co/3NQXwav1Wx
The Sato Lab (Kei Sato) @SystemsVirologyIn sharp contrast, Omicron is less fusogenic (left panel) and its spike is faintly cleaved (right panel). Our data suggest that the efficacy of spike protein cleavage, fusogenicity and pathogenicity are well correlated each other. 3/5 https://t.co/7tetkCjjlD
Once again, none of this means that the ongoing Omicron wave is harmless.
Especially for the elderly or the immunocompromised, the immune defenses may not hold as well (and for them, boosters are essential even more so than everyone else).
Boosters—especially an mRNA booster—can help hold off the breakthroughs, but vaccines remain in short supply. And a small percent of a large number can be a large number, stressing hospitals. AND DELTA IS STILL AROUND—though there are some early signs that Omicron may be displacing it. (Still to see!).
Plus, there are still many, many people around the world who are seronegative, and the high rates of spread of this variant may be a big threat especially in places like that. Less severe than Delta doesn’t mean a cold! If this was the first variant we got back in January 2020 when nobody had prior immunity, it would be much worse than what we faced in that initial wave.
Still, this isn’t the worst case scenario on either counts: there is no substantial severity escape for those who are now seropositive, and it is not as bad as Delta or, yikes, worse, intrinsically.
High-risk people who get infected should clearly be in touch with their doctor quickly: there are treatments now that can help—some are in short supply, unfortunately, thus reserved for high-risk people.
But what about otherwise healthy, immunocompetent people who test positive? Clearly, one does not want to overload emergency rooms, especially if there isn’t much to do in terms of medical interventions.
I have one piece of practical advice in this case, since many such people will now experience a symptomatic breakthrough: a pulse oximeter, measuring the saturation levels of oxygen in your red blood cells, may help you gauge what to do in case you do get sick with symptoms, something that can be unnerving. These are electronic devices that can be had for under $20, and are available in pharmacies, Amazon, etc.
How you feel, subjectively, and what a medical doctor may think of as severe are not necessarily identical. Some of the symptoms are caused by your immune system fighting off the virus. That’s why besides the obvious signs like high fever, the saturation levels of oxygen in your red blood cells is a great indicator. If it falls below 95%, it may be time to seek medical help. If it is getting below 92-90% , it is an emergency, regardless of how you feel subjectively.
To conclude, here it is again: a tax-deductible way to end the year helping people around the world have access to health-care.