The post mentions lack of vaccines as a potential problem for the Congo, among other third world countries, but also says that there seems to be slack in the control systems. Important relevant fact here: in the Congo, ~40% of the population is under 15 years old (compared to ~20% in the US; source is world factbook). 40-50% under 15 seems pretty typical for third world - Aysajan and I were reading through stats on countries with high child hunger last week, and most of them were in that band.
So, the younger population should make third-world countries a lot more robust to COVID by default.
That tweet on Australia might be a little misleading. The vaccination board's official statement as far as I read is that an under 40 year old is more likley to die of an AZ vaccine than covid given the current covid prevalance and death rate in Australia, which is virtually non-existant. They released a pdf to this effect weighting the risks and their plan is to have everyone under 40 vaccinated on pfizer by the end of the year.
Betting that there won't be an outbreak before then is still likley the wrong risk to be taking, but it's less dumb than just saying AZ is more dangerous than covid full stop 😄. Indeed the Prime Minister has drawn the ire of the vacination board by opening up AZ to all ages rather than just over 40ies (apparently older people have half the risk of blood clots and obviously more risk of dying from covid).
If I was in charge of the country I'd do the same, and if I was being the game theory I wanted to see in the world I'd get the AZ now. But living in a city that has no covid and just does a 3 day lockdown until it's gone every time there's community transmission (4 or so times since march 2020 pretty evenly distributed) I'm weighing up whether to wait until either another outbreak or pfizer becomes available in a couple months.
AFAIK the main effect from the PM's policy change seems to be around relaxing indemnity rules for GPs so that they could hand out AZ if they wanted to without getting sued by people who develop the blood clot disorder. Previously this was an issue due to the current ATAGI advice recommending against it.
I thought the PM's statement on this wasn't too crazy - the blood clot risks are objectively still very low and the ATAGI report contemplates the then near-zero covid in Aus as you note. I assume somebody in govt realised that at current and projected vaccine rates it'll be a long time before the country opens up / stops having to lockdown extremely hard every time covid leaks into the community - and then the recent NSW outbreak brought the issue to a head.
Vaccination supply has not been that reliable or consistent so far, and AZ is the only vax currently made locally so I think vaccination regimes that don't involve AZ do risk a longer 'fortress Australia' period.
Abu Dhabi drops the hammer.
Did this include people who got covid, and don't need to be vaccinated? (Because that seems like a bad move. If you don't have lots of vaccines, that seems like a really bad move.)
I suspect that the reason the control was one dose of AZ in the study you mention has to do with medical ethics at this point. The vaccines are so good that it's no longer OK to ask participants not to take any vaccine.
Result: Positivity rate of 2.4% (up 0.6%) and deaths decline by 8%.
Should this be "0.6 percentage points" rather than "0.6%"?
I think we can lay to rest the hypothesis that Australia did better than other countries because it was more sane and has wiser systems for making decisions. Australia did better for other reasons, including being an island, that led to a different equilibrium. Now that we are in the vaccination phase of the pandemic, Australia is utterly failing.
As I noted on the April 15 post,
From Australia, this hypothesis [Australia succeeded because it was using good epistemics to make decisions] was only ever plausible if you looked at high-level outcomes rather than the actual decision-making. We got basically one thing right: pursue local elimination. ... Nationwide, we continue to make expensive and obvious mistakes about handwashing, distancing, quarantine, and appear to be bungling our vaccine rollout.
Zero active cases and zero local transmission covers a multitude of sins. I attribute the result as much to good luck as epistemic skill, and am very glad that COVID is not such a hard problem that we can't afford mistakes.
Unfortunately it turns out that our national vaccine rollout has been comprehensively bungled, including turning down Pfizer when they approached us in July last year. Hopefully voters can correctly attribute responsibility for our latest round of lockdowns to the current federal government.
For all that though, and while the Delta strain spreads considerably faster, my impression is that we still largely have it under control - just at significantly greater cost via track/trace/lockdown rather than vaccinating everyone and moving on. I'm hoping I'll be able to travel next year, now...
If someone wants to run a mirror of Aalla's poll side effect grades might provide for a better result (https://i-base.info/guides/side/how-side-effects-are-graded):
GRADE 1 (Mild)
Transient (goes away after a short time) or mild discomfort; no limitation in activity; no medical intervention/therapy required.GRADE 2 (Moderate)
Your daily activity is affected mild to moderately – some assistance might be needed; no or minimal medical intervention/therapy required.GRADE 3 (Severe)
Your daily activity is markedly reduced – some assistance usually required; medical intervention/therapy required, hospitalisation or hospice care possible.GRADE 4 (Potentially life threatening)
Extreme limitation to daily activity, significant assistance required; significant medical intervention/therapy, hospitalisation or hospice care very likely.
I don't know about using these grades specifically for the COVID vaccine. Grade 3--my daily activity was "markedly reduced"--I stayed in bed all day for one day because I felt blah, but there was never a question of whether I needed a medical intervention or hospitalization. I'd had a similar reaction to some flu vaccines before. (Hospice care? Is the linked website written this way because it focuses on HIV/AIDS?)
I would not interpret your case as severe according to this grade. The specification "some assistance usually required" seems like they mean your reaction is so bad you need help eating/washing/using the toilet, which I assume was not the case for you. While -- especially for a young healthy person -- staying in bed all day is a "marked reduction" of activity, there's still quite some room for further worsening before you're at a point where it's life threatening.
While the wording could be more clear, if my interpretation is correct I would agree this is an OK grading to use.
I don't know about using these grades specifically for the COVID vaccine.
This is a bit like saying: "I know that the vaccine is horrible given the general standards, so we should use something else".
Novavax does manage a low amount of grade 3 side effects.
There's another question about whether there are long term side effects that also interesting.
Er, yes, I do think I'm saying that we should use something else besides the linked standard.
Object level: Feeling blah for a day and staying in bed doesn't strike me as "severe" or "horrible". I'm deeply confused by the fact that you seem to be arguing in favor of standards that would say that staying in bed for a day is "horrible" or "severe".
I'm not trained in this area, but just for comparison, "Common Terminology Criteria for Adverse Events v3.0" https://ctep.cancer.gov/protocoldevelopment/electronic_applications/docs/ctcaev3.pdf has a "grade 3/severe" category for most types of adverse effects, and includes hypertension requiring two drugs to treat; hypotension requiring more that 24 hours' treatment; insomnia so bad that it interferes with your ADLs; and a weight gain of 20% or more from baseline. The "fatigue" I experienced would be a 2/moderate at best under their standard (page 11), but more likely a 1 as I had no actual trouble with ADLs.
Meta level: I think you should give serious, possibly overwhelming, consideration to how such data would get reported. Vaccine-hesitant people will hear about the study results through popular media: "30% of recipients reported 'severe' side effects!" and will never see or hear what "severe" means in the study's context. They will assume that "severe" means whatever they think "severe" means. If I were one such person, I would be expecting side effects far worse than I experienced.
Do you find the UK data worrying? Cases up 5x in a month with high vaccination rate. My rough impression is they still haven’t opened up that much. I’m sure the control system will get it under control but I thought high vaccination rates would make that unnecessary.
The UK still has vaccination rates just around 50%, and we can assume that they focused on the elderly first. The control system is first and foremost about preventing hospitals from being swamped and causing politicians to have a bad press day, so with most of the most likely to die off the table, case counts and hospitalization counts will have to be much higher.
Since May, the UK has seen its cases go up ~7x, its hospitalizations go up ~2x, and deaths hover around the same level (maybe they've gone 2x? hard to tell). To have US 2020 Summer Surge levels of death, their death rate would have to go up 13x, and their case rate would presumably have to go up 26x.
Given that Delta looks like it is going exponential in the UK, and it is doubling between 1-2 weeks, it would be at that high case count by August. However, that rate would be multiple times higher than the UK's existing peak.
Is that worrying?
To clarify that 50% figure: According to [official figures](https://coronavirus.data.gov.uk/details/vaccinations) -- see "Vaccination uptake, by report date" -- about 63% of the eligible population in the UK has had two vaccine doses, and about 85% have had two. But it's about 50% of the whole population, including infants and children, and infants and children are not being vaccinated.
So far as I can tell, the UK government's intention is just to let every schoolchild in the UK get COVID-19. At least, there's no serious plan to start vaccinating them any time soon, and in the face of rapidly increasing case numbers in schools I'm hearing much more "... so we have to find a way to let schools send fewer pupils home when cases occur, to keep children in school" than "... so we have to get stricter about sending pupils home when cases occur, to reduce the spread".
It's just as well children seem to be less badly harmed than adults by getting COVID-19. (Though they are certainly not guaranteed no serious harm, and given the enormous numbers of children likely to get it I suspect the absolute number of cases of serious harm will be pretty large.)
Good call out. I don't know how contagious Covid/Delta is with children, but my intuition is that it is less contagious, which means your clarification is good news.
My presumption is that UK has a bunch of AZ vaccinations in its mix that aren't that good at stopping Delta from spreading (but are very good at preventing hospitalization/death) and so it's not as vaccinated as the numbers suggest. But yeah, it's gotta be frustrating since it means UK won't be able to go back to normal for a while unless they can up their vaccination numbers.
What about Israel? R-value is the highest since the first wave despite ~60% vaccinated with afaict mostly mRNA vaccines: OurWolrdInData Link.
Luckily hospitalizations/deaths also appear to be not strongly affected.
One piece of evidence against this: almost all the uptick in the UK is in folks under 40. Under 40s have a much lower vaccination rate due to the age-dependent rollout, but because of the blood clot scare under 40s have preferentially gotten Pfizer. Over 40s meanwhile have a very high vaccination rate but it's mostly AstraZeneca. Their case rate is flat.
Source
Those lines aren't flat, they're just hard to read on that scale. I made my own based on the heatmap of case rates for england (there doesn't seem to be a whole-UK heatmap).
I've seen graphs on /r/CoronavirusUK showing AZ and Pfizer roughly equal in count, and Moderna a tiny sliver. Couldn't find any of those on demand, though. (I thought the data was available somewhere in the adverse effects reports, but I can't find those now either.)
An interesting paper on design choices in the mRNA vaccine sequences; mostly UTRs and codon choice. In summary, pretty good but could have been better.
https://www.mdpi.com/2076-393X/9/7/734/pdf
There's a surprising amount of cut and paste from the human α-globin UTRs.
A good way of framing what Zeynep and I both point out about the question of the origins of Covid-19: What matters is how such an event could have occurred, rather than the way it actually did occur.
I expect more from you. Pretending that it didn't matter that they lied to us is bad.
Both questions matter. A virus that doublicates in a lab is under very different evolutionary pressures as a virus that doublicates out in nature.
A virus in a lab can doublicate easily while having feature that allow it to spread indoors but not outdoors. We had a lot of bad lockdown policy that treated people meeting outdoors the same way as treating people who meet indoors.
In the beginning of the pandemic when we assumed a natural origin we assumed that mutants would likely be less lethal. We could have made prediction that prepared us better if we would have already known that it was a lab leak.
We would have been better prepared for heart and brain damage when we would have known it's a lab leak as there's evolutionary pressure to avoid heart/brain damage for a respiratory virus that's out in nature because it's more likely to kill the host while there's no such evolutionary pressure for a virus that's just in the lab and doublicates in human lung tissue.
This mostly seems wrong to me.
I don't remember anyone saying anything like "we should assume this virus can spread as easily outdoors as indoors, because evolution would make sure that a respiratory virus can do that". (It probably can't; I'm pretty sure all respiratory viruses spread more readily indoors.)
I can't think of any reason to think that mutant versions of a naturally-occurring zoonotic virus would be less lethal than mutant versions of an otherwise similar virus produced in a lab.
There is no evolutionary pressure discouraging viruses from producing the degree of heart and brain damage (or any other ill effects) SARS-CoV-2 appears to produce in humans. You only get evolutionary pressure of that sort when the virus starts killing its host before it has a good chance to spread. Deaths from SARS-CoV-2 almost always happen well after the usual period of infectivity.
Further, not all lab-leak scenarios even have SARS-CoV-2 being a lab-engineered virus. Another possibility is that it's a bat coronavirus that they were studying at the WIV and it got into humans by infecting some of their researchers. In that case, it would be much like any other zoonosis and its having escaped from a lab would tell us nothing useful about it.
It certainly does matter whether we have been lied to about the origins of COVID-19. (Note: Since it has not, in fact, been conclusively established that it did start with a lab leak, you should have written "whether they lied to us" rather than "that they lied to us", but I do not expect you to agree.) But I think Zvi is right that it matters mostly for political reasons -- it's important to know what sort of lies we are being told -- and not because it makes a big difference to how we should (1) try to protect ourselves from COVID-19 or (2) deal with virus research, going forward.
I can't think of any reason to think that mutant versions of a naturally-occurring zoonotic virus would be less lethal than mutant versions of an otherwise similar virus produced in a lab.
In nature a virus benefits from the host being mobile and walking around to be near other animals of the same species. This produces evolutionary pressure to not do things that make the host less mobile and thus less likely to get into contact with other animals.
In the lab where animals live in cages and infection is independent from the ability to be mobile such pressures don't exist and thus evolution optimizes differently.
I don't remember anyone saying anything like "we should assume this virus can spread as easily outdoors as indoors, because evolution would make sure that a respiratory virus can do that". (
The argument is rather: We expect this virus to behave similarly to the flu or SARS as far as transmission outdoors is concerned.
Many people do wear masks outside. They don't do that because any studies show that wearing masks outside is useful for reducing catching COVID-19. Before the first BLM demonstration (where many people were still unmasked) last year we expected that the kind of meeting outdoors would produce a significant amount of infections. We didn't find a significant amount of infections.
Airbone transmission is more likely in a world with a lab leak and a lab leak is more likely with airbone transmission. The WHO is still in denail about airbone transmission and the CDC was for a long time.
Note: Since it has not, in fact, been conclusively established that it did start with a lab leak, you should have written "whether they lied to us" rather than "that they lied to us", but I do not expect you to agree.)
There are two issues here:
(1) Whether or not it actually was a lab leak is independent from people lying expect for Shi and a few other Chinese that actually know for certain whether it was a lab leak.
(2) This sounds like a weird post-truth idea where what's true depends on whether other people believe something to be conclusively established and what is currently acceptable in the overton window.
I'm using words that are in line with my own estimation of what's true. That has been at p=0.99 days ago. Interestingly, as I'm exposed to new information the new information always points towards it being more likely. Yesterday, for example I learned that the WIV did gain-of-function experiments in a biosafety 2 lab and not as I assumed only in their biosafety 4 lab (which was central evidence to got Ian Lipkin who co-wrote one of the initial papers that presumed it had to be natural to change his position). I don't think it's hard to come to that conclusion based on the available evidence.
In nature a virus benefits from the host being mobile [...]
Yes, that's a reason why maybe lab-engineered viruses might be more lethal than naturally occurring ones. But that's not what you said. You said that if SARS-CoV-2 originated naturally then we would be right to expect that any mutant versions of it would be less lethal, whereas if it was lab-engineered then we shouldn't have that expectation. That is what I don't see any justification for.
In fact, to whatever extent your argument here is right, we should expect lab-engineered viruses to have more reduction in lethality when they mutate, because that would be where the evolutionary pressures for less lethality that you mention would start to come in.
(My understanding -- which is entirely second-hand so I am not suggesting anyone should trust it much -- is that in fact the idea that mutations tend to make pathogens less lethal over time is mostly false, at least for things like SARS-CoV-2 that usually don't kill their hosts and almost never kill them really quickly. So I wouldn't, in fact, expect much difference between natural and lab-engineered viruses either in lethality or in change in lethality over time. Unless of course the lab-engineering was specifically aiming to make them more or less lethal; so far as I know there's no good reason to believe that that was done in the case of SARS-CoV-2 if it did originate in a lab.)
The argument is rather: We expect this virus to behave similarly to the flu or SARS as far as transmission outdoors is concerned.
I think it was reasonable to expect it to be somewhat like SARS because the virus itself is very like the SARS virus. So far as I can tell, there's no particular reason why thinking the virus was lab-engineered rather than zoonotic would change that.
Before the first BLM demonstration [...] we expected that the kind of meeting outdoors would produce a significant amount of infections.
My recollection is that (1) that was not universally expected and (2) at least some people argued -- I forget whether it was before or after it transpired that there wasn't a big increase in infections -- that the effects of BLM demonstrations might be counterbalanced by other people staying home because they didn't want to get caught up in demonstrations, rioting, crowds, etc.
I think "airborne transmission is more likely in a world with a lab leak" isn't at all clear (assuming that it means that lab-engineered viruses are more likely to be able to spread that way), but I do agree that a lab leak is more likely if airborne transmission is possible, which means that Pr(airborne transmission | lab leak) > Pr(airborne transmission), a point that hadn't occurred to me before you pointed it out. I don't know enough about the mechanisms of actual lab leaks to have a good idea of how much bigger the probability becomes on conditionalizing on lab leak.
Whether or not it actually was a lab leak is independent from people lying except for Shi and a few other Chinese that actually know for certain
Surely that's false. E.g., whether there actually was a leak surely isn't independent of whether Daszak genuinely thought it hugely unlikely that there was a leak. (Because both correlate with how much work WIV was doing with SARS-CoV-2-like viruses, and with how good WIV's safety practices were.)
But let's return for a moment to the actual context. Zvi said that the origins of COVID-19 don't matter much, and you said oh yes they do, because it matters that they lied to us. Your statement is actually responsive to Zvi's only in so far as what they allegedly lied to us about is the origins of COVID-19 (as opposed to, say, how confident any particular scientist was at any particular point about how likely it is that it originated with a lab leak). Lies about that are absolutely not independent of whether or not it actually was a lab leak.
This sounds like a weird post-truth idea [...]
Obviously I wasn't saying (and don't believe) the silly thing you accuse me of saying. I do, however, believe the following two quite different things. (1) It has, in fact, not been conclusively established that "they lied to us" about the origin of COVID-19. (One reason for this, though not the most important, is that it's entirely unclear who "they" are. Let's have more precision and less political sloganizing here.) (2) While what's true doesn't depend at all on (though it correlates with) what other people around you find credible, what it's reasonable to state flatly as if it's common knowledge does depend on that. In the present case, accusing Zvi of "pretending it doesn't matter that they lied to us" presupposes that Zvi agrees, or at least that he would agree if he were reasonable, that "they lied to us"; I don't think either of those things is reasonable to presuppose.
Surely that's false. E.g., whether there actually was a leak surely isn't independent of whether Daszak genuinely thought it hugely unlikely that there was a leak.
In a world where there's a lab leak it's more likely that an expert like Daszak believes that there's a lab leak. We however have information such as him hiding his role as the organizer of the paper that declared that there's a consensus and everything besides that should be seen as a conspiracy theory. Why would someone engage in deceptive behavior like that when they have nothing to hide?
Lying is about saying things one believes to be untrue. Whether something is a lie doesn't depend on it actually true or false. I do believe that lies about the state of the evidence where told to get Facebook/Twitter to censor content early in February 2020. When it comes to "they" and lied it's hard to have a completely list, but Fauci, Farrar, Tedros and Daszak would be a good start as central players for February 2020.
I also see actions of Christopher Ashley Ford to stop the state department from building a Bayesian model of the chances of a lab leak and a natural origin because it would "open a can of worm" as purposefully misleading the public (and lying is the naive word for that).
(I also think that the Chinese constantly lie but that's less interesting)
While what's true doesn't depend at all on (though it correlates with) what other people around you find credible, what it's reasonable to state flatly as if it's common knowledge does depend on that.
I do believe that it's good to flately state the truth and not bend words according to what's in the overton window. It feels like there's some virus going around where infected people suddenly care a lot more about being within the overton window and I don't like it on LessWrong.
I feel like I should begin by pointing out that the discussion is now entirely about one parenthetical side-remark I made, and that you've apparently given up defending all the arguments you made in support of the claim that if SARS-CoV-2 had been thought to be a lab release rather than a zoonosis from early on, it would have changed how we tried to fight it for the better. (I think it's good that you've given up defending them, because I think they're all completely wrong.)
Anyway. Once again, the point is not that I think no one ever lied about anything related to the lab-leak hypothesis. (That would be really surprising. There is always evidence for anything, whether it's actually true or actually false, and if you point at a group of people and say "maybe you guys were responsible for killing millions of people and doing trillions of dollars of economic damage" you should expect that some of them, and some other people who don't want them to look bad, will be less than forthcoming about any evidence supporting your claim. Whether there's any truth to the claim or not.)
The point is that you accused Zvi of "pretending that it didn't matter that they lied to us", and that's not a reasonable accusation unless (1) Zvi actually believes that "they lied to us" or at the very least (2) it's so obvious that "they lied to us" that if Zvi doesn't believe it then it can only be because he's deceiving himself -- where "they lied to us" means something for which it plausibly would matter if "they lied to us". It's not at all clear to me that either #1 or #2 is true.
Also: I think you are misunderstanding the structure of Zvi's argument, because so far as I can see no matter what you take "they lied to us" to mean, and no matter how strong the evidence is that that's so, Zvi is not in fact claiming that it doesn't matter at all in any way whether "they lied to us", he's claiming only that the main conclusions from "COVID-19 started from a lab leak" and "there's a 10% chance that COVID-19 started from a lab leak" and "COVID-19 was zoonotic, but lab safety was poor enough that it could have started from a lab leak" are pretty much identical: any of these means that the virus lab wasn't being nearly careful enough, and any of them means that gain-of-function research is looking like a very poor cost-benefit tradeoff. Whether (say) Anthony Fauci is an honest person whose public statements can be trusted is much less important than those things. (For that matter, I'm pretty sure Zvi is already firmly in the "Anthony Fauci's public statements cannot be trusted" camp, after what he said about masks early on, so learning that "they lied to us" on this score wouldn't much change his opinion about that.) So (I claim) he was never making the statement you objected to.
Suppose everything you claim about lab leaks and cover-ups is correct. What follows, and how is it actionable? 0. We conclude that the lab-leak hypothesis is at least credible. (This is indeed important, but this part is already widely credited, and it doesn't at all depend on your claims about lies and cover-ups. And Zvi already acknowledges this bit; see previous paragraph.) 1. We conclude that Anthony Fauci is not perfectly honest with the public, when he thinks that misleading the public would do more good than harm. We already had good reason to think that, after the business with masks. You might say "so he should lose his job" but (a) I don't think it's very common for people in his sort of job to lose it for behaving in a way that suits the establishment and (b) I see no reason to think that anyone else in his position would behave differently. 2. We suspect ... something? ... about Tedros Adhanom. (Your post about this mentions that Fauci, Farrar et al talked about contacting him, maybe about things related to the lab-leak hypothesis, and then says that the WHO was going to work with social media companies to "counter misinformation". It seems like you want to suggest that Adhanom was in on the conspiracy to suppress the lab-leak hypothesis and that he put pressure on social media companies to do likewise, but the evidence seems awfully thin.) 3. We conclude that Jeremy Farrar (of whom I had never heard before), like Fauci, is willing to mislead the public for their own good. I can't think of any way in which I could actually use that information. (Note: I say "for their own good" because I don't see any obvious way in which Farrar personally would be harmed if the lab leak hypothesis became generally accepted. Fauci's situation might be a bit different, though the alleged connections seem pretty weak to me.) 4. We conclude that various other individual scientists (Daszak, Andersen) are willing to bend the truth to avoid looking bad. I can't think of any way in which I could actually use that information. 5. We conclude that sometimes consensus can be engineered. I'm pretty sure we already knew that.
So I'm with Zvi on this: even assuming that all the claims and conjectures and insinuations in that post of yours are correct, the at-all-actionable conclusions from "lab leak and cover-up" and from "no lab leak, no cover-up, but it turns out that research on coronaviruses was being conducted in a way that could have led to a lab leak" are close to identical.
Note that "everyone around me is suddenly more concerned about being within the Overton window" is what being infected oneself by a conspiracy theory feels like from the inside. You could be right, of course. But it's not obvious to me that "almost everyone else on LW falls into the same epistemic hole, while Christian doesn't" is more likely than "Christian falls into an epistemic hole, while almost everyone else on LW doesn't". (It's not as obviously less likely as that formulation may make it sound, of course. A widely prevailing narrative backed by the scientific establishment is likely to have an easier time capturing minds around here than a fringe-looking conspiracy-looking theory, conditional on the two having similar amounts of actual truth to them.)
The case numbers this week were clearly bad news. The raw count was somewhat bad news, and the positive test percentage increase was very bad news. It would be easy to treat the whole shift as fully ‘real,’ attribute it all to Delta, and panic.
I do not think that is the correct interpretation. What we are seeing matches what we saw a year ago, so a lot of this is a seasonal and regional change that has nothing to do with Delta. It’s also likely that some of the shift in percentages comes from data being wonky rather than the underlying conditions. Not only do we have alternative explanations, the size of the shift doesn’t match the incremental change in the amount of Delta out there, even if (as I suspect) it’s a rather dramatic takeover, with Delta’s share of the pandemic in America rising 25%+ in a single week.
It’s also going to be tempting to attribute seasonal weather effects to the local vaccination rate, since the two are highly correlated. Differences in vaccination rates in different areas matter a lot, but that’s not central to what is happening this week.
Thus I am still expecting some regional outbreaks, and am still not expecting nationwide problems, but one must ask about whether the winter is going to bring trouble the way last winter did. The hopeful answer is that vaccinations will be far enough along by then to not matter, and the second hopeful answer is that even if it’s bad it won’t be anywhere near as bad as last time. The vaccination numbers this week were quite good.
Still, I miss the confidence I had two weeks ago. Let’s run the numbers.
The Numbers
Predictions
Prediction from last week: Positivity rate of 1.8% (unchanged) and deaths fall by 8%.
Result: Positivity rate of 2.4% (up 0.6%) and deaths decline by 8%.
The case numbers reflect a <10% jump in cases, yet we have a 30% jump in positivity rate. This suggests some combination of a decline in testing and quirky data. I’m no longer confident that the positivity rate is the best measure of the state of the pandemic in America, and am relying on case counts more. A lot of that is no longer fearing that case counts are being manipulated the way they clearly were some of last year, or worries about testing supplies.
Prediction for next week: Positivity rate of 2.7% (up 0.3%) and deaths decline by 5%.
I expect a lot of this effect to be seasonality rather than Delta, but cases likely will rise for a bit. Deaths should still be declining somewhat.
Deaths
This is exactly on track as an average, and I’ve come to accept that week to week numbers in regions bounce around. If anything, it’s surprising that the death numbers nationwide have been so steady when there’s clearly a lot of data collection timing issues and random fluctuations going on. Deaths lag by several weeks, so the bad news from the last few weeks hasn’t had an impact yet, nor has Delta’s increased lethality mattered much yet, but it’s likely that will stop soon, and we won’t get much lower than this for a while.
Cases
I found a new site this week that offers a great view of the data, so here’s the week over week changes by state:
It’s hard to read here, so consider clicking through to see it there. Those are dramatic increases in southern states, and the map makes it very clear that these differences are not primarily about how many people each state has vaccinated so far. The big difference is north versus south, and it looks a lot like this map:
Things have been record-breakingly hot in many places recently, especially the Pacific Northwest, but that only happened in the past few days and it was sufficiently dramatic (both record breaking and >100F) behavioral patterns likely went straight to ‘don’t go outside at all for any reason’ rather than a bunch of meetings indoors.
Also worth remembering this from last year, which tells a very similar story so far.
Last year at this time we saw an explosion in cases. This year we are seeing a halt in the decline in cases. That’s not good, but it’s also not a reason to panic. Nor is it reason to attribute the shift entirely to Delta. I am curious why there is so little discussion elsewhere of these obvious patterns this time around, when seasonality has been a talking point in the past.
(Actually, I don’t wonder all that much, because the official Very Serious Person narrative wants to worry as much as possible about Delta, so it would ignore alternative explanations.)
Vaccinations
We picked up an additional 0.8% of the population getting their first dose, and 1.3% of the population got their second dose. The uptick from last week gives hope that we may be in something approaching a short-term steady state, or perhaps talk of Delta has convinced some hesitant people to get the vaccine. That makes sense, since the selfish value of being vaccinated is no longer rapidly approaching zero. It’s becoming increasingly clear that there will be social benefits for some time.
If we can sustain this pace of vaccinations, that is excellent for our ability to close things out. It’s happening in spite of a lot of headwinds. Vaccine misinformation, misrepresentation of information and hesitancy continues to frustrate. There has been quite the abundance of self-inflicted wounds, and giving them attention is always a double-edged sword.
Thus, while I hesitate to give the topic attention and the results could easily be misinterpreted, this seems like useful data:
Looking at the comments, it’s clear that this did not sufficiently disambiguate ‘severe’ and that the category still mostly covered people who got knocked on their ass for two days.
Plus we have to worry about anti-vax people voting combined with the lizardman constant. I’d similarly be unsure whether to say none versus mild for my shots. So this seems consistent with ‘essentially zero side effects other than some people being knocked on one’s ass for a day or two, which occasionally got considered severe.’ It also is clearly inconsistent with the conspiracy theories anti-vax people (and the person everyone needs to stop asking me about) are throwing around.
Hopefully that will be the last I need to say on that matter in any form.
In other good news, mix-and-match vaccines, as one would expect, work quite well, and we finally have a study on that (study).
The control was one shot of AZ for completely insane You Fail Mathematics Forever reasons.
But that’s fine, because we don’t need a control when we’re measuring antibody response, and the whole control group was fetishistic Science(TM) rather than a source of meaningful data.
As an alternative, we have at least one health official in Australia, who happens to be the QLD chief medical officer, talking obvious nonsense:
The idea that AZ poses a greater risk than getting Covid makes zero statistical or mathematical sense, and framing the issue that way indicates that blame avoidance and Sacrifices to the Gods of responsibility are what matters here rather than any attempt to do math on a physical world model.
It would be one thing if they had plenty of mRNA vaccines to use instead. They don’t.
It would be a somewhat different thing if you couldn’t mix and match shots. You can.
That’s all before concerns about population-level effects.
Thus, this should come as no surprise:
I think we can lay to rest the hypothesis that Australia did better than other countries because it was more sane and has wiser systems for making decisions. Australia did better for other reasons, including being an island, that led to a different equilibrium. Now that we are in the vaccination phase of the pandemic, Australia is utterly failing.
Delta Variant
This Nature post provides a perspective of how many are thinking about Delta. As usual, there’s talk about whether the new variant will take over and whether it can be prevented by some magical force, rather than how quickly it will take over and the need to accept that reality, but mostly the reality is being accepted here.
They are worried about Africa:
I continue to not be as worried, because I do not expect that we are approaching the limits of Africa’s control systems. I expect there to be enough slack to absorb Delta without things going critical. I’m not super confident in that, but I do think it’s a solid favorite (~75%).
As estimates of prevalence of Delta go, using this seems like a reasonable method:
Alpha was previously on the rise, so if it declined from 70% to 42%, it’s safe to say that variants that are substantially more infectious than Alpha are replacing both it and the remaining 30% (to the extent that it wasn’t already such variants), so if we think Gamma is mostly similar to Alpha as we did last time, that provides a lower bound for Delta of 40% by mid-June.
Contrast that with last week’s calculation from another source via taking the numbers from Delta directly, which had it at 30%. That’s a reasonably big gap, since here 40% is a lower bound, and if the previous mix included a bunch of stuff less infectious than Alpha we’d expect this to be closer to 45%-50%. And that was two weeks ago, so if it was 40% then it’s presumably more like 70% now. If that math seems quick, keep in mind that we didn’t even break 1% until April.
In other news, look at where that other source is after its last update:
This continues to be consistent with the sequencing data there being accurate but effectively delayed. Note that P.1/Gamma is now declining rapidly as well. Over the last 60 days they have Delta at 11%, but over the last 30 days they have it at 21%, which means it was something like 1% in the previous 30, and 30 days from whatever ‘now’ is in that calculation it implies Delta will be above 80% barring geographic barriers slowing things down.
If we estimate that the infections observed now are happening in something like a 65% Delta 30% Alpha/Gamma 5% Other world, with the remaining others largely similar to Alpha, then we’ve absorbed two thirds of the transition from Alpha to Delta, and three quarters of the transition from the old strain to Delta. Going forward, one should expect the share of old strains to be cut in half every ten days or so, and Delta to be almost all infections in most regions by August 1.
Olympics in Japan
The Olympics are here, and Japan is not exactly fully vaccinated, as they’ve been delaying things quite a bit, with Moderna and AZ not even being approved until May 21.
Once again I’m going to come out in favor of doing things that scale, are central to the experience of life and bring lots of people joy, even when they’re not fully ‘safe.’ Any athlete going to the Olympics who wants to be vaccinated, one hopes, has already been vaccinated – if not, it would be trivial to take care of that. Same goes for those who need to be in the Olympic village, it’s not that many people.
What’s crazy is allowing a bunch of spectators who aren’t vaccinated into indoor events, and it looks like there will be 10,000 spectators per event, whether indoors or outdoors.
The idea that something not being ‘the safest way’ means someone is ‘not on board’ continues, and reflects a mindset we need to move past. The safest way to do most everything is to not do it at all, yet things must be done.
One way to think about whether the spectators are providing enough value is to look at the ticket revenue. There are 330 events, so assuming everything sells out, tickets are going to average $121 per full event, many of which are over multiple days. That’s not that much money, so my instinct is they need to charge a lot more at least for indoor events, to justify the health risks involved.
It’s always important to think about base rates…
…where Japan continues to outperform the United States. If Delta wasn’t involved I’d say that this is all basically fine, but it remains to be seen if Japan can handle Delta in its current state, and this could take substantial time ‘off the clock’ for vaccinations to catch up.
The Olympics cost about $12 billion to host and can leave a lasting legacy. If one thinks that the Olympics will be remembered for a long time, I understand taking the full risk, but I still wouldn’t have substantial crowds at indoor events, especially minor ones. Why ask for that kind of trouble?
In Other News
A bunch of people this week mentioned how bad it was that people were making base rate errors, and using ‘some vaccinated people got infected’ as the latest scare tactic in full How to Lie With Statistics mode. Nothing to see here that we didn’t expect.
Thread in praise of the excellent Microcovid project. I disagree with some of the Microcovid calculations but having any plausible calculations at all was the important element here, giving certain types of people a way to both do any of the things ever and not do many of the stupider things. That doesn’t mean the paralysis before that wasn’t a failure mode that requires investigation and correction. The general solution might be ‘if microcovid does not exist it would be necessary to invent it so people have a Schilling estimate to converge on’ and that’s not great but better to know it than not know it.
A good way of framing what Zeynep and I both point out about the question of the origins of Covid-19: What matters is how such an event could have occurred, rather than the way it actually did occur. If the plane could have crashed due to a faulty part, but it turned out something else caused this particular crash, the part is still faulty and we need to fix the root cause of that failure.
If Gain of Function research puts us in danger, that’s enough reason to ban it, whether or not it actually did kill millions of people this particular time around.
Zeynep also points us to this paper about potential lab leaks explicitly warning against exactly the things we frequently do… from 2015.
Abu Dhabi drops the hammer.
No, we can’t know for certain that vaccines provide years-long immunity without waiting those years, but I do think the extrapolation process here is mostly reliable, and a much less misleading statement than the typical ‘provides protection for up to X months’ where X is how many months we’ve had the time to check, which then gets quoted by media as if X is an upper bound rather than a lower bound.
Marginal Revolution previews/reviews the new Michael Lewis book about those preparing for a pandemic, and what they did during the early days of pandemic they’d prepared for. The book, titled The Premonition, if Alex’s summary is accurate, holds the CDC (Delenda Est) in even lower regard than I do, as our heroes who see the pandemic coming are stymied every step of the way, preventing them from having most of their potential impact, while we don’t so much as quarantine or even test those returning from China, let alone take reasonable precautions. As Alex notes, it’s weird to have a (true) story of lone heroes fighting the good fight against the system to stop a global catastrophe, who then completely and utterly lose. A story at least as worth telling as when they win, but definitely hard on the cliche structure.
Paper about long term past effects of pandemics in Sweden over 220 years.
Potential good news in a path towards an all-coronavirus vaccine, I don’t know if it’s meaningful or not but passing it along.
Not Covid
If your goal is to avoid claims that our elections are full of fraud and tabulation errors, and/or you don’t want to ruin ranked choice voting for the rest of us, may I suggest perhaps making more of an effort to not do things like this, as happened in the NYC mayoral election:
Thus, the Evergreen Tweet: I hope we will hear the end of this, but fear that we will not.