Covid 7/15: Rates of Change

Cases rose by over 60% in America this week, and we’re seeing large jumps in cases around the world. I am highly suspicious about the jump in the rate of increase, but Delta certainly seems to be the real deal, and this was well above my expectations. 

I worry that recently I’ve lacked sufficient skin in the game. Everyone I personally care about is vaccinated or young enough that they don’t need vaccination, so the real sense of danger is largely gone. The worry is about the reaction to Covid, rather than about Covid itself. But that’s a very real danger, and I have back that sense of ‘oh no, things could go very wrong’ because there’s the danger that we really will blow up our way of life over all this, and go into a permanent dystopia of sorts. That’s what we need to ensure does not happen.

Thus, the bulk of this post is a numbers analysis trying to figure out what we know about Delta’s transmissibility and the effectiveness of vaccines in reducing that transmissibility, using data from a variety of sources. Others are encouraged to continue this analysis and try to get to the bottom of this.

So let’s run the numbers.

The Numbers

Predictions

Prediction from last week: Positivity rate of 3.3% (up 0.4%) and deaths increase by 7%.

Result: Positivity rate of 4.8% (!) and deaths increase by 15%.

Prediction for next week: Positivity rate of 4.7% (down 0.1%) and deaths unchanged.

The null prediction is always an option, here two distinct null predictions with distinct reasoning. For deaths it’s clear that there was a reporting gap as predicted, so I do not think the death rate last week represents things getting worse, but they likely should start to get worse given Delta is deadlier and cases have stopped dropping within the required time window, and it doesn’t seem like last week’s number was too artificially high.

The case number is trickier, as there’s good reasons to think the data is distorted, either by July 4 or otherwise:

That giant spike represents going from an average of 2.6% to an average of 5.0% over two days. That’s not a thing that should happen to seven day averages. If it does, then the next five days things should continue to rise as old data cycles out for new, but that didn’t happen so far. 

Perhaps July 4 was truly a superspreader event in the way that previous holidays were almost always underwhelming, as much as the previous holidays make that seem unlikely. Perhaps it’s a giant delayed data dump that didn’t include negative tests. It is hard to say. What I do know is that either things were worse than this before the jump and the low number wasn’t fully real, or the jump and new number are not fully real – one of these two numbers is misleading.

Thus, we have the standard question when a number seems to clearly overshoot, where it’s unclear where the ‘real’ number is and how fast it’s moving, so it’s unclear where it will end up. In this case, substantial real growth seems almost certain, and I definitely feel like the null prediction here is ‘chickening out’ but I’m not sure which direction to go, although I notice I’m more comfortable predicting a small reversion than an increase, while noting that such a decrease wouldn’t be ‘real.’ Thus I’m choosing a very small decline, with discussion continuing in the cases section and the Delta section, but this data doesn’t make sense. 

Deaths

DateWESTMIDWESTSOUTHNORTHEASTTOTAL
May 27-June 252783811704562991
June 3-June 97208179154312883
Jun 10-Jun 163686119613142254
Jun 17-Jun 235294438312632066
Jun 24-Jun 305504597061861901
Jul 1-Jul 74593296121281528
Jul 8-Jul 145323986891451764

Cases

DateWESTMIDWESTSOUTHNORTHEASTTOTAL
May 20-May 2633,89034,69448,97324,849142,406
May 27-June 231,17220,04433,29314,66099,169
Jun 3-Jun 925,98718,26732,54511,54088,339
Jun 10-Jun 1623,70014,47225,7528,17772,101
Jun 17-Jun 2323,85412,80126,4566,46469,575
Jun 24-Jun 3023,24614,52131,7736,38875,928
Jul 1-Jul 727,41317,46040,0317,06591,969
Jul 8-Jul 1445,33827,54468,12911,368152,379

Cases are up by 66%, and the positive test rate is up by 65%, which implies the number of tests was constant. 

The more I think about this, the less sense it makes. 

If cases were up by anything like 66%, why aren’t we running more tests? Aren’t people testing in large part based on whether they suspect they have Covid, and whether they have symptoms or known exposures, which both should be up a lot? Are we somehow supply constrained on this, despite no observations of difficulty in getting testing done on demand? How do these numbers make any sense?

Thus, I come to the conclusion that the numbers don’t make sense, and don’t belong in the same universe. If cases double test counts should rise a lot, and that not happening is super weird. 

For now, I’m going to mostly ignore the test percentages and act as if the raw positive test counts are more accurate, because if there’s one thing I definitely don’t believe, it’s the reported number of negative tests. That doesn’t make any sense no matter how bad things are. 

One possible way for this to kinda sorta work is that perhaps there are people who get tested in order to show a negative test, whose tests get reported every time, and people who get tested because they want to actually know if they have Covid, who mostly only report when they’re positive. Then, doubling the size of the second group doesn’t change reported test counts much? That’s the best I can come up with.

What should we make of the 66% rise in cases? How much of it might be timeshifted and in what ways? Is this a fully real rise, and should we expect it to continue? If so, what happened?

Discussion of all that will continue in the Delta section, where I attempt to reconcile all the various different data points.

Vaccinations

Given no attempts to halt the course of events, this is a strong result. 

There’s a new warning on J&J shots (WaPo), because there were about 100 detected cases of an autoimmune disorder out of 12.8 million shots. There was one (1) death involved, again out of 12.8 million shots. It will be an interesting control group for the previous experiment where J&J got suspended. If we take a side effect that doesn’t matter, and treat it like it exists but doesn’t matter, does that have an impact? Versus treating it as a huge freaking deal and freaking out everyone and suspending the vaccine, which we are pretty sure had a fairly large impact the last time there was a side effect of magnitude epsilon. 

New paper says that neither ‘give people fact box’ nor ‘explain how mRNA vaccine was developed and that it wasn’t too fast’ impacted vaccine hesitancy. Kudos for publishing the negative result. Why aren’t we seeing a lot more studies like this of various things one might do? 

Then there’s the question of what is happening in Tennessee (news article).

The explanation I found was that in Tennessee teenagers can get vaccinated without ‘parental consent’ and this was creating problems. Which does not seem like much of an explanation, as there’s no reason why such consent should be required or even relevant. And certainly does not explain why this applies not only to Covid-19, but to all vaccinations period. Or why they think it makes sense to strip teenagers out of lists for reminder postcards if they’re scheduled for their second shots, but focus on the other vaccines part of this, if you’re considering that this all might have a perfectly logical explanation.

Perhaps we can at least partially salvage this by taking advantage of the ‘natural experiment,’ and observing what happens to vaccination rates. Do the reminder postcards do anything? What about the other things that got suspended? What happens to the vaccine rates for other diseases? If you can’t go with ‘prevent people from getting sick and dying’ you can at least upgrade your world models. 

Genius in France: Incentives Matter!

The second day exceeds the first, so those 2.2 million appointments are likely only the beginning. It’s one thing to pass up a vaccine, it’s another to pass up the ability to participate in many aspects of life. Make no mistake. If implemented, this will work.

If America’s Delta problem gets sufficiently worse that they start bringing restrictions back, and they don’t start requiring proof of vaccination in such situations but instead once again halt life for the rest of us, I call upon all of us to find this completely unacceptable, the same way I find permanent child masking unacceptable. 

In such a scenario, there are two sane choices. You can either let people do what they want, or severely restrict what the unvaccinated can do. Ending life as we know it, presumably indefinitely, shouldn’t be even potentially on the table, nor should we have any tolerance for such proposals. 

Delta Variant

A post entitled Delta Variant: Everything You Wanted to Know does make a real attempt to be exactly what it says on the tin. The graphs are rather cherry-picked to make things look as bad as possible, as are a number of other discussions, but the data is all legitimate. The question of the day is now exactly how bad Delta is and making sure our models of it are right to figure out what is to come. There’s a bunch of superficially contradictory data that must be reconciled, as there usually is. 

Taking stock of those data points is the logical first step.

Israeli Data

Israel offers the scariest data point, suggesting greatly reduced vaccine effectiveness.

I’ve seen the Israeli data presented in slightly different ways but this is basically what they’re reporting there. I’d like to note that the story doesn’t make sense, even on its own.

For previous strains, this is saying that vaccination wasn’t protective against hospitalization, and mostly wasn’t protective against death, once someone was infected (93% reduction vs. 93% reduction), or at least once someone tested positive. We knew even then this wasn’t remotely the case.

Then with Delta we get this gigantic drop to 64% protection against infection, but then protection against hospitalization stays at 93% and protection against death rises? So conditional on infection, this is saying hospitalization protection went from ~0% to 80%? Really?

Even the 79% number seems very very strange when looked at this way alone. 

You could tell a story that justifies it. In that story, vaccine protection works 96% of the time (and there’s measurement errors), and if that happens you’re protected against severe outcomes no matter which variant you face because that wasn’t a close call, but being infected at all is a lower threshold. Before, if you were successfully vaccinated you basically never got infected (in this model), whereas now if you are vaccinated you sometimes do still get infected, but it’s never serious whereas before it never got that far in the first place. Then there’s the 4% of people for whom the vaccine doesn’t work properly, who are still at real risk. Or something like that.

As a sanity check, what happens if we ignore the reports and attempt to back out the answer from the raw data on infection numbers?

That’s not a picture one can easily read, so click the link if you want to examine it.

Reminder:

There are a lot of confounders, but let’s start with the pre-vaccine comparison.

Next, let’s do a pre-Delta comparison, from when the numbers were very low, but people were mostly vaccinated:

Consider this a ‘post-vaccination’ equilibrium. Many of the young aren’t vaccinated, whereas most of the old are, so the ratios change, but almost entirely for the youngest group. Things were mostly level before otherwise, and remain mostly level now, in roughly the same order.  

Now let’s look at the last day they have data for here:

It’s unfortunate we don’t have the July 10 data, but we go with what we have. This still has to represent almost all Delta cases, and gives us apples-to-apples comparisons. What can we infer from these numbers?

Also, how does this reconcile with this graph?

Israel is young, but it’s not that young, and my response to the above graph is more like ‘those sample sizes are all absurdly small because Israel didn’t have Covid that month.’ Still seems difficult to reconcile in the details, but easy in the bigger picture. 

My conclusion is mostly that this is muddled enough that I can’t draw a fixed conclusion. Especially weird is the 60-79 range. One possibility is that the vaccine needs a threshold of effectiveness to prevent infection, and it’s still mostly good enough to hold off Delta, but those with weakened immune systems are in a different situation and they are mostly very old? But the share of vaccinations in such groups is still super high compared to younger groups, and the order of these groups still seems really odd. It would, however, explain how 20-39 could be the lowest major group while 0-19 is the highest, perhaps – The kids in their 20s can still largely get vaccinated, and their immune systems are still strong, so it’s highly effective? Whereas with the 40-59s it’s less effective especially on the high end, and so on. 

We should also look at case counts in Israel. On June 18 they had 1.92 cases per million, right before things started rising, on June 14 it was 65.09, for R0 = 1.97. From previous data, we can presume that when Delta was a very small portion of Israeli cases, the control system adjusted things to something like R0 = 1, so we’ll keep that number in mind.  

UK Data

We can presume that Alpha hasn’t increased its absolute numbers, so at this point UK is almost all Delta. On May 25 there were 35.7 cases per million. On July 14 there were 512.9, On July 4 there were 361, so the two-week R0 = 1.19. From May 25 to July 4 we get R0 = 1.32, despite a bunch of Alpha early on, so the control system has been adjusting, but also we never see a period with an extreme R0 in the UK. In April, they had Alpha and things were stable (R0 ~ 1). For an extreme situation, let’s look at relatively early lift-off of Delta and assume a base of about 30 Alpha that doesn’t count for growth rate, and start when total cases are at double that, or 60, which is June 4. Over the next 10 days things went to 107, so let’s say that this represents Delta going from 30 to 77, before much adjustment has been made, over two cycles. That would give an estimate of R0 ~ 1.60, on the high end of the range for increased base transmissibility. It doesn’t leave that much additional room. One more cycle gets us to 131, which would be R0 ~ 1.31 for Delta alone, so presumably there were adjustments being made already then. 

Transmissibility

There’s the question of how much more deadly Delta is than older strains, but I’m mostly going to ignore it because it doesn’t impact the path of the pandemic much. The question is containment versus lack of containment. If Delta is twice as deadly, that’s quite bad, but it’s an isolated question. As commentators have pointed out, the data supporting the increased deadliness is not that solidly grounded. The extra viral loads are suggestive, and the early data does look like it’s more deadly for a given unvaccinated person, but our data remains not great.

The much more key variable is transmissibility of Delta versus Alpha or the original strain. I’ve been using a 120% increase, or 2.2x (220% of original infectiousness) for Delta, and a 1.4x (140% of original) for Alpha, which continues to match estimates I’ve seen. Those all presumably refer to transmissibility among the unvaccinated and ignore the vaccinated population, and I’ve been treating the numbers accordingly. I see no reason to change that methodology, but that means that we need to reconcile our numbers with the case counts that we see. 

An open question is how tight the bounds are on such numbers. If we have a model where things were previously going fine and then you ‘multiply by Delta’ then the bounds are reasonably tight. However, if you think that behaviors are adjusting in real time and seasonality causes ‘random looking’ ebbs and flows naturally, then there’s room for the data to look highly misleading, and my position at this point is if anything is closer to that second view. 

Either way, your model has to make predictions whose math checks out, and that’s a good place to start.

Let’s say we accept that Delta’s ‘multiplier’ is 2.2, versus the old baseline, and Alpha’s is 1.4. Now let’s suppose vaccine effectiveness is reduced from 95% to 65%. What happens? Given current vaccination rates, with an adjustment for children, that’s about another 50% increase in the rate of infections.

That would mean that Alpha to Delta is a full effective +120% increase in the rate of infection, on top of the increase from original to Alpha, or a final factor of around 3.3. Or, alternatively, it would have a ‘base’ R0 of something like 6, with a vaccine that only reduced that for the vaccinated to 2, which would mean that even in fully vaccinated populations this would double every five days under pre-pandemic behaviors. 

Set aside for the moment the question of what we would want to do about that. How does it line up with the data? 

In the UK, where the Delta problem is currently largest and we are confident Delta is essentially the whole pandemic (using Our World In Data as my source), we had 36 cases/100k on May 25, and 494 on July 14, 52 days later, or just over 10 cycles, and R0 ~ 1.28. During April and the first half of May, we saw the number of cases stay roughly constant within a factor of 2, so R0 > 0.9. We could factor in some increase in vaccinations, but if Delta taking over sent R0 from 0.9 to 1.28, that’s only a 42% increase, similar to what we’d expect from Delta taking over from Alpha, minus some existing more infectious strains and some extra vaccinations, give or take behavioral adjustments and seasonality. 

None of this matches the greatly reduced effectiveness hypothesis, unless you presume that behaviors are substantially adjusting during this period, but the shape of the curve isn’t suggestive of that either. 

American Data

In the last week, America has seen a 66% increase in cases. As discussed above, going +10% then +20% then +66% is extreme, and can’t be explained by Delta alone. The share of Delta cases can only rise by about 30% in one week, even under extreme assumptions (e.g. from 35% to 65% or something like that, would be the theoretical limit) so a +46% effect in seven days off a 30% rise would mean Delta was at least twice as transmissible as Alpha. It also means the numbers in previous weeks would have shown a bigger problem, since the displacement of Alpha by Delta has to be gradual – there’s no way there was three times the growth in Delta this week that there was last week, because math.

Overall, though, the number isn’t crazy – if we presume that the control system had already adjusted for our vaccinations and for Alpha. If we take the +66% number seriously, and compare it to the pre-Delta situation, it’s safe to presume that we had previously stabilized under a full-Alpha situation, then +66% in a week represents a 43% rise in transmissibility from Delta versus Alpha minus any extra vaccinations, so 50-60% total, which doesn’t even leave room for the vaccines to lose effectiveness since that’s our estimate range for Delta already among the unvaccinated.

Under such assumptions, we can backchain, and it matches up with the sample data claiming that by percentage there wasn’t much Delta running around in early June, despite Delta now having taken over and now being 85%+:

An alternative calculation would be to look only at Alpha, or to compare Alpha to Delta. We have a percentage for it, so we can back out its growth in absolute numbers. It was something like 60% of cases on June 15 by this graph, and is now down to 5%. Whereas Delta went from roughly 4% to 85%.

From June 15 to July 15 is thirty days. Thirty days allows for six serial intervals. So if all of that is accurate, we get a ratio of 2.5:1, or +150% increased infectiousness, which is even higher than the +120% estimate for the full effects previously measured. We then look at absolute numbers, and see Alpha having an R0 = 0.75 over this period, versus R0 = 2.25 for Delta. Which would mean that both we’ve taken a lot more precautions recently than we did before to get things that low, and also that Delta should be doubling every four days, yet cases over the last week only rose by 66% despite starting off with the majority being Delta.

Thus I don’t believe the chart above is a representative sample – the math doesn’t add up.

One can have a hypothesis that strains crowd each other out in some sense but I don’t think the base rates are high enough for that effect to be big right now. 

Then again, as I’ve been noting, if you take the numbers too seriously (as in, you don’t think there are big hidden factors and random distortions) then none of this adds up.

So where does that leave us? Can we put bounds on things?

Our lower bound should presumably be that Delta is 50% more infectious than Alpha, but that vaccine effectiveness is mostly unchanged. 

Under Israeli conditions, it seems mostly safe to say that Delta is at most twice as infectious as Alpha, but that about twice is possible. This is the scariest data set. 

Under UK conditions, it seems mostly safe to say that Delta is at most 75% more infectious than Alpha, and it would be difficult to get to a doubling.

Under American conditions, it seems mostly safe to say that Delta is going to be less than twice as infectious, given everything we know – the math starts to fold in on itself if we get above 75% or so, in the sense that things need to look much worse than they do. I’d put a soft bound around 75%.

We could also look at any number of other places. Israel and UK are especially picked because they’re well-vaccinated and having trouble. 

Now let’s look at vaccination rates. Using Bloomberg’s ‘enough for X people’ metric, Israel is around 60%, the UK is also around 60%, and the USA is at 52.4%. That’s out of the full population, which includes children, so effective vaccination rates are somewhat higher especially for Israel (which has a younger population), and one dose is more than half of two doses, so the USA is effectively closer to 60%, and we can put Israel and the UK closer to 67% in terms of our effective percentage.

Let’s presume that in the base case, vaccinated people are 96% protected in terms of transmission. If we presume that the unvaccinated transmit at a 50% higher rate, but that the effective increase is 100% in Israel, that would give a vaccine effectiveness versus transmission of 67%. If we take the UK and presume 75% increased transmission, that implies vaccine effectiveness versus transmission of 80%. For the USA, a 75% increase in transmission would imply 76% vaccine effectiveness versus transmission. 

It is possible, in theory, that this difference could be that vaccine effectiveness against transmission fades somewhat over time, and the difference here would be that Israel vaccinated earlier than other countries did. 

If things were instead at our lower bound, by assumption, vaccines would remain at 96% effective. 

It’s really hard to put bounds on things given all the factors we can’t account for, including control system adjustments in both directions, seasonality, and so on and so forth. 

These are likely not tight bounds. There are likely a lot of behavioral adjustments involved in all of this. But it’s all very noisy, and I haven’t seen other serious attempts to figure this out. I’m encouraging everyone to take a stab at this from various angles and see what you find. There’s tons of data to work with.

If this reduced effectiveness is near those upper bounds, there is a very large problem. Even fully vaccinated populations wouldn’t be able to fully return to normal if you wanted to avoid Covid outbreaks. You’d either accept that vaccinated people and children often get Covid, and it would be fine, or you’d need to impose restrictions forever, or you’d need to get a new more effective vaccine distributed in the form of booster shots. And that’s if you got close to 100% coverage, which is not going to be happening. 

Thus, the question would become, if Covid is not done with us, can we decide to be done with Covid and that life beckons, or are we actually going to kill our civilization and way of life over this despite having a vaccine that renders Covid mostly harmless? 

In Other News

Fox News has generally not been as anti-vaccine as its customer base likely would have preferred, but some evidence that this may no longer be true. If I have any regular viewers reading this, can you update us? 

Reasonable thread laying out different questions surrounding booster shots, which oddly still leaves out the question of whether shots can be modified to work better versus Delta. I’m confused why there isn’t more discussion about that. My presumption is that modifications wouldn’t help, which is interesting in and of itself and seems worthy of mention if true. 

Deal between Israel and South Korea where Israel gives Pfizer shots now that it couldn’t use and were going to expire, gets future shots in exchange because selling things for money is evil. Post (from MR) points out that Covax’s quest to allocate vaccines equally is going to end up wasting a lot of vaccine, as many places don’t have the means to distribute the shots they’ll get. 

Moderna begins a trial for yearly mRNA shot that would combine vaccines for flu, COVID-19, respiratory viruses RSV and HMPV. It turns out that not only does mRNA allow us to cure a wide variety of diseases, it lets us cure all of them at the same time, because the technology allows the payloads to be delivered together. I’d be a little concerned about short term side-effects similar to the ones with the current Covid vaccine, but my hope is that the problem can mostly be solved by proper dosing. 

This is also an excellent way to give people Covid booster shots without everyone freaking out. If one shot, once a year, can deal with a wide variety of problems, that should work great, so long as the misinformation from anti-vaxxers doesn’t cause too many problems.

New Zealand didn’t secure enough vaccine shots, which is unfortunate, but is taking the AZ -> Pfizer booster path seriously, which is great. 

You don’t often get to pick your allies, such as in the war on school. Or is it the war on children? 

Map of such insanities:

My understanding is this applies even to private schools, although good luck enforcing that. If they’re going to mandate this now, when will it end? Are they planning on keeping things like this forever? Or even going back to the torturous ‘remote learning’ at the drop of a hat

What would it take to free our children? How bad would it have to get? Shall we run the experiment and find out? 

A rant on the quest to establish that the lockdowns were always painless and super effective and that Everybody Knows this. 

And some really are pushing to make the pandemic restrictions permanent. Who would want such a dystopia? (post

People permanently not being able to leave home after 10pm ‘without good reason’ is the kind of thing hack writers put into young adult novels. Or at least, it used to be. Then again, perhaps there’s always been a 10% share of people who shake their fists at ‘kids these days’ and actually want to be the villains in such novels. How much of this is new? 

A quarter of people wanting to close casinos and nightclubs permanently (but again, how much of that has anything to do with Covid?)? A third of people favoring permanent quarantines for international travel? Tracking everyone who enters a restaurant, again, permanently? This is still less than half of people, but a third is a lot of people. 

This is the fight that is coming, even if conditions are good. They hate us for our freedom. You gotta fight for your right to party

One can still party a little too hard, even outdoors. Outdoors is much safer than indoors, but that doesn’t mean one can’t push the envelope too far:

So yes, there’s mass gathering and then there’s mass gathering, might want to not do that second one. Also, ‘cannot be ruled out’ is technically true but I think we could have gone with something a little stronger. A thousand identified cases is not a thousand cases. 

Or, alternatively, instead of protesting for left-wing causes, one can protest against a Communist regime, in which case your protest is dangerous:

Remember, whether or not something spreads Covid depends on whether it is approved of by the proper cultural authorities and Very Serious People. And this is what they think about protesting against authoritarian Communism. 

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55 Responses to Covid 7/15: Rates of Change

  1. Luke says:

    Any thoughts on getting the third shot of the mRNA vaccine? https://www.lesswrong.com/posts/8RYxQrKegKMDGHcvo/for-some-now-may-be-the-time-to-get-your-third-covid-shot

    I’m currently against, unless there’s suddenly a significant immune escape, and the third shot accounts for the new mutations responsible for the said escape.

  2. aviavi says:

    The Netherland’s massive increases in cases seems to be by far the most critical story of the last week:
    https://pbs.twimg.com/media/E6LnVu7X0Aw0-NS?format=jpg&name=4096×4096

  3. Tom W says:

    With all due respect, I think this “variant transmission math” is so difficult because variant transmission doesn’t actually work the way people keep modeling it.

    Somehow the assumption has become that every variant has some sort of “inherent transmission rate” that stays mostly constant across time/place, and the reason new variants keep “taking over” is because they have somehow evolved a higher inherent transmission rate. I can see why people (especially people without a history of studying other viruses) might make this assumption, but it doesn’t really make a lot of sense of you think about it directly.

    Take, for example, everyone’s favorite point of comparison: influenza. Here is a study discussing shift among some of its “variants” over time: https://www.nature.com/articles/s41598-018-38105-1

    The first graph is revealing: over a period of several years, different strains gained and lost, and sometimes gained again, a percentage share of total flu disease per season, and the total seasonal infections rose and fell with them. This is difficult to explain with a model where, say, B/Y amagata (the red strain) is simply more transmissible than any of the others, though there are several individual points on the graph where someone might conclude that!

    I think a better model of variant transmission focuses on the idea that viruses continue to tweak their infection model in an attempt to “surprise” immune systems, and immune systems continue to tweak their threat model to stay up-to-date. So new tweaks emerge regularly (or old ones re-emerge), they replace the existing dominant strains which have taught their tricks to too many people, and the circle of life moves on.

    So what I suspect is “really happening” with Delta is the same thing that happened with the last few terrifying new variants that were going to take over and ruin everything: it figured out some new exploit that manages to target people in a way the old strains didn’t, it’s making big gains among the subset of the population who is most vulnerable to this exploit, and eventually it will make itself obsolete, fade away into the background, and various Extremely Concerned People will be issuing dire warnings about the new Ligma variant.

    • Triskele says:

      Intuitively this seems correct. R for measles is like 10+, and you can get that from just being in a room that someone with measles left an hour earlier. So having a raw R0=6 “and going up” seems kind of pretty high for something that WHO was not even confident declaring airborne until a few months ago.

      • Tom W says:

        Great point! Naive R-multiplication models would also imply that existing diseases, which have been mutating for millennia, should have R numbers in the hundreds by now.

    • TheZvi says:

      That’s mostly quite fair, and on reflection I should have included a ‘this is all a very crude approximation’ disclaimers that were much stronger. However I do think that Delta is not merely exploiting a niche here. The viral loads are *much* higher, and this seems like a generally more fit version of the virus, rather than an exploit. I do agree that it’s likely getting some benefit from the element of surprise, as it were.

      • Tom W says:

        Fair enough! Will be interesting to see how things play out–diseases do in fact sometimes develop higher levels of transmission, though things always adjust to some sort of equilibrium in the long term–but we’re also concerned about the short term!

      • Matty Wacksen says:

        This would sound plausible if I didn’t have an extremely strong sense of déja vu taking back to the British variant and all of the fear around it.

        See e.g. https://cspicenter.org/blog/waronscience/the-british-variant-of-sars-cov-2-and-the-poverty-of-epidemiology/ for a strong criticism of simplistic modelling as applied in France; since France didn’t really vaccinate much you can’t say vaccines are to blame.

        Back with the “British variant”, people were saying all of the things (“higher viral load”, “more transmissible”, “deadlier”) as they are now saying about Delta.

  4. myst_05 says:

    “nor should we have any tolerance for such proposals”

    I’m predicting another big wave of people moving to Red states this winter if we see new lockdowns in Blue states. Personally I was considering it last winter but it seemed like vaccines are just around the corner and living in Washington is nice, so I didn’t actually do it. But if the “new normal” is that Blue states lockdown every winter in spite of vaccines, I think a lot of people would be convinced that moving is the only viable choice.

    • bugsbycarlin says:

      Time for my monthly plug that Austin has been a nice balance. I grew up everywhere (including Austin, Seattle, Germany and England, FWIW), moved back to Austin in late 2019, live in the burbs with a lot of nice outdoor space and parks, and although I never had any love for the politicians of this state, I have been… so, so happy with my choice in light of 2020 and 2021.

      • bugsbycarlin says:

        Other than the heat, which, holy shit. Don’t move to Texas if you don’t like the heat. Even with AC in almost 100% of homes, it’s still a force to be reckoned with.

  5. Basil Marte says:

    My guesses as to what mindset would generate the Tennessee decision: heavily/blindly “social reality”/”narrative” thinking (as I like to call it, LARPistemology), perhaps with a helping of halo/horns effect of mapping everything into a single yay/boo scale.
    – “This covid thing was a one-off and basically has already passed.” (Not necessary but IMO fitting addition: “Thus you are trying to earn gratitude for “protecting” us from …no future risk.”)
    – “My/our children in particular, and family/population in general, are pure and moral; your claim that they are so unclean as to get sick without your protective intervention is an insult.”
    – Possibly overfitting, but add an insistence on parents getting the final say over what kinds of information their children are exposed to.

    • TheZvi says:

      How do you explain the splash damage of all other vaccine information?

      • Basil Marte says:

        General opposition to vaccinations has been surprisingly common for well over a decade, but it had not been actionable in official collective policy (AFAIK individual parents moving their children was most of what physically happened). It seems that something locally shifted the Overton window. Specifically, from another article at the same site, https://eu.tennessean.com/story/news/health/2021/07/12/tennessee-fires-top-vaccine-official-covid-19-shows-new-spread/7928699002/
        “Lawmakers were angry about a letter Fiscus sent to medical providers who administer vaccines explaining the state’s “Mature Minor Doctrine,” a legal mechanism by which they are allowed to vaccinate minors above the age of 14 without consent from their parents.”
        Apparently in the process of firing her, they noticed that were getting away with it, and so they kept going and opportunistically implemented this policy goal of theirs?

      • There is no splash damage when the state is operating at level 3/4 and the median R voter thinks the HPV vaccine turns kids into sluts.

      • wax says:

        The current Republican platform includes reflexive opposition to anything Democrats think is good. For stupid Republicans, if Democrats think something is good, it must be bad, and therefore must be opposed. For Republicans with power, if Democrats are public about thinking something is good, that thing happening might be seen as a victory for Democrats, and stopping it would therefore be seen as a victory for Republicans. That can be a victory in the “we did something good” sense, but it can also just be a victory in the “we’ve demonstrated that we have the power” sense, which is important for conservative parties- projecting an image of strength and reinforcing the fact that they’re at the top of the hierarchy is part of how conservatives maintain power. Either way, Democrats want people to get vaccinated and have been vocal about that, therefore Republicans want to stop people from getting vaccinated.

      • David W says:

        As usual, when a news story presents ‘facts’ that don’t make any sense, your first hypothesis should be that those facts are incorrect. Doubly so when those are ‘facts’ that have obvious political valence.

        The TN Dept of Health states: “While misinformation has been circulated regarding the status of these resources, parents who need information regarding routine childhood immunizations can find resources here (https://bit.ly/3rbcpn7).” as part of this Twitter thread: https://twitter.com/TNDeptofHealth/status/1415768581082583043

  6. Sebastian H says:

    Newsom has already reversed on the school mandate, presumably because he doesn’t want to get successfully recalled. https://www.cnn.com/2021/07/13/health/california-schools-mask-mandate/index.html

  7. J says:

    Don’t we have explicit data on vaccine breakthrough infections that should shed light on Delta? My impression has been that breakthroughs have been almost entirely confined to immunocompromised old folks in nursing homes.

    Also, I’m trying to assess underreporting on vaccine side effects. A close friend got Moderna and miscarried a seven week embryo shortly thereafter, and is still bleeding three months later (4-6 weeks typical max). I hear rumors of abnormal periods and That Guy claimed unusual spike protein levels in the ovaries, but the internet doesn’t seem to do forums anymore, and everything I try to Google is buried under condescending explainers. I myself had dizziness for weeks starting a week or two after the first dose, and didn’t connect it with the vaccine until researching my friend’s issue. Looked up vaers to report both side effects but they’ve made it pretty imposing and want a ton of identifying information, so I gave up. I’m still in camp vaccine, but the lies upon lies make everything so much worse. Any ideas where to look for useful data that might help inform my friend’s ongoing issues?

    • TheZvi says:

      If we do have such explicit data, it would be great if you (or someone else) could track it down with links and such. I’m not aware of anything sufficiently explicit/direct for that analysis to be a good idea.

      I don’t know a source of useful data that wouldn’t have already be shouting from the rooftops if there was anything to actually find in terms of side effects. Dogs that don’t bark.

      • faul_sname says:

        In the US, HHS maintains a public database of all listed adverse reactions to vaccines called VAERS. You can download a CSV of all reported adverse effects here: https://vaers.hhs.gov/data/datasets.html and then dump in sqlite or whatever to analyze it (note that you probably want to avoid trying to open it in excel, since it’s 285MB zipped, 1.4GB unzipped).

        I looked briefly at that data earlier today to investigate whether reports of fairly significant post-vaccine mortality actually showed up in the data (they did, for certain values of “significant” — about 5,000 reports of death, following a similar age distribution to COVID deaths — 75% of reported vaccine mortality was among those aged 65 or over). I threw a sqlite script in pastebin at https://pastebin.com/TEQ7Hu29 that lets you import all of the VAERS data into a sqlite database which you can then query for whatever you want to.

        It doesn’t help with data that isn’t reported but it should at least help a bit with identifying any trends in data that does exist.

    • Purplehermann says:

      I got delta, am in my 20s, healthy and vaccinated. I know others in the same boat, and vaccinated teachers in schools nearby got it too.

      Make of that what you will

  8. Venture into the Dungeon says:

    As of now, the DEF CON security conference is still on in Vegas, but will enforce masking and ask that everyone show proof of vaccination (but hackers, so assume some folks will flaunt rules purely for sake of flaunting rules). However, Vegas is at ~28/100K cases currently (about 10x my local case rate) and rising.

    From “this is an acceptably low risk, and you should think of it as a single-digit multiple of your normal risk” to “this is an insane act of hubris,” where would you rate the risk of attending DEF CON in person, assuming a) one is two-dose vaccinated with a mRNA vaccine and b) wants to see vaccinated friends the following week who have a (unvaccinated, of course) one-year-old?

    My current hypo is that it is reasonable-but-slightly-higher-risk to do the conference in person, but unreasonable to both do the conference and then see an unvaccinated kiddo within an incubation window (given uncertainty about Delta’s risk to younger folks, even once selection bias is controlled for). What do you think?

    • TheZvi says:

      It’s a multiplier versus your ‘normal’ risk but yes, venture into the dungeon, it’s fine, everyone we care about in the scenario is vaccinated or one year old. I wouldn’t be worried if masks were not being warn. mRNA vaccines mean Covid is not something that should stop life from happening for the vaccinated among the vaccinated (including children that are too young to need it).

    • Error says:

      I’m glad someone brought this up. I expect to have to make the same call with respect to Dragoncon in a couple months. I’m currently leaning towards going, but keeping a wary eye out for new information.

      • TheZvi says:

        A few months is a long time, as you note, but I’d presume you’re going if you’re thinking ahead this far to want to go.

  9. Craken says:

    The polls about Covid restrictions are simply a measurement of the effect of propaganda on various demographics. But, most demographics are powerless, and their opinions on many matters are malleable. Propaganda, corporate responses, government actions tell us what the ruling class intends to do to its subjects. The polls tell the rulers how much trouble they might face from imposing different decisions. Biden’s handlers haven’t been as aggressive on vaccine mandates as Macron because the polls look much less favorable for that in America–so far.

    In Tennessee, an official sent a letter encouraging vaccine providers to remind teenagers that they do not need parental consent for vaccination (the Mature Minor Doctrine). This seems to have set off a chain of events leading to the firing of that official and a pullback on teenager vaccine efforts. I’m sympathetic to this response, though it goes further than I would have. Parents ought to have the right to decide whether their minor children receive the Covid vaccines (since they’re still experimental and there are problems with the VAERS system and teenagers’ mortality risk is extremely low). All of this is in the larger context of outrageous abuses in the American educational system perpetrated by the Leftists in charge and largely against the will of parents (especially propaganda on CRT and transgenderism). But it remains the case that any parent can easily obtain vaccination for any child who is of age in TN. Standard vaccinations for young children are unaffected.

    This fellow wrote a superb thread contextualizing the Cuban situation:

    I learned of the staggeringly bad timing for their currency reform. Cuba seems to have entered its Brezhnevite phase of regime decline, its hold on power made more fragile by communications advances.
    My impression of the uprising is that it will fail to unseat the government unless a significant government faction joins the uprising. Otherwise the lack of internal unity and organization will allow the government to pick it apart.

    What will evolution deliver after Delta? I suppose even higher transmissibility is possible. Under semi-controlled conditions (some masks, distancing, etc) that might be most likely if its contagious period were prolonged from a few days to a few weeks. The mix of vaccinated and unvaccinated people really does increase the risk of effective selection for vaccine escape mutations. And this mix is likely to be present for a long time in very large populations (eg, Africa). If this happens the wisdom of building out much more vaccine capacity would become even more obvious–enough capacity to vaccinate the human population in a few months to minimize the risk of another escape.

    I wonder if the week-to-week predictions are worth the effort given data problems. Maybe it’s more useful to predict major waves. I think Delta will produce a wave similar to last year’s summer wave, only with ~60% fewer deaths.

    • Tom W says:

      That specific poll also was conducted online, and there’s a fairly strong case to be made that people who spend a lot of time online are more likely to support restrictions on offline activities. But you are also correct that public opinion is notoriously easy to manipulate by people in the right positions….

      The TN drama seems like a fairly normal attempt to Own The Libs, and I suspect that it will get as much attention (plenty) and create as much measurable impact (statistically insignificant) as such attempts normally do.

  10. I share your confusion about the matched case rates and positivity rates but don’t believe the numbers are shady—it’s just a failure to explain.

    I suspect that a good portion of the tests are from people at schools and workplaces that have mandatory testing, for which you would expect exactly that pattern. Beyond that, you have people doing discretionary tests on the basis of symptoms. I agree that testing should increase by *some* amount as infection rates go up, unless discretionary testing accounts for almost none of it, which is hard to believe. But… I don’t know what fraction are discretionary, I don’t know what fraction of those are from allergies or common cold symptoms, and honestly I also don’t really know how people behave.

    So, let’s look at a data source where we have actual test counts too: https://www.mass.gov/info-details/covid-19-response-reporting#covid-19-interactive-data-dashboard-

    In Massachusetts, the positivity percent 7 day avg rose 63% from July 6 to 13, but new case count 7 day avg rose 93%. Testing rate stayed steady, and if anything dropped. (There’s data for July 14, but I think there’s a lag on the case data, so I went back a day.)

    Here’s something that could explain it, although I have no particular evidence for this one explanation: An oscillation in the control system, wherein people get overconfident, infection rates rise, but the feeling of safety lags such that testing rates are still dropping. But really, it’s a complex system, and we just don’t have the insight.

  11. On a different point:

    « there’s no way there was three times the growth in Delta this week that there was last week »

    Well, why not? Growth rates change based on people’s behavior. You don’t think that unvaccinated people being idiots at holiday parties can triple the rate of transmission?

  12. Kris says:

    Small correction: that new Moderna trial is for flu strains only for now, the combined vaccine is something they plan to do in the future.

  13. Purplehermann says:

    Israel:
    The spread of delta started from a school student (superspreader), vaccinated teachers spread it between schools. This, in conjunction with very few new cases until delta hit, is why the numbers skew very young. I expect this to change quickly if it hasn’t already

    • Purplehermann says:

      Also, all the kids got tested to go to summer camps. Most adults stopped getting tested, unless they were in contact with a verified covid patient

    • Ariel says:

      I don’t think so. Enough time (1 month) has passed since the start of the epidemic that the age distribution would have “thermalized”, but it is staying stable. The age distribution is also much sharper than it seems – the current epidemic mostly spares the Orthodox Jews & Arabs (either because they have R unvaccinated or unvaccinated->vaccinated infections, but vaccinated->vaccinated infections are rare outside of household infections.

      • Ariel says:

        The blog made a mess of my comment.

        Meant to say: this wave mostly affects non-Orthodox non-Arabs, which are 70% of the population but only 50% of the children, so the ratio of children to adults needs to be bumped by 40% or so. Also, if you look at the statistics, 40-50yo women make 7.4% of all cases this wave (6.3% rest of pandemic) while 20-30yo men make 4.7% of all cases (9.8% rest of pandemic), which combined which anecdotes about vaccinated-to-vaccinated transmission being rare makes it feel like this wave is driven by children and their mothers.

  14. thjread says:

    “My presumption is that modifications [to booster shots] wouldn’t help, which is interesting in and of itself and seems worthy of mention if true.”
    Could you expand on this? My very strong prior is that modifications would help quite a lot. It doesn’t seem to be happening in the near future (except possibly AZ shots modified for Beta…) but I’m assuming that’s for a combination of logistical and psychological reasons, plus the fact that a third (full dose!) booster gives such high antibody levels that you’ll get pretty good protection without modification.

  15. Jonathan Monroe says:

    A tedious piece of epidemiology pedantry, but all your estimates of R0 are actually estimates of R (i.e. the current reproduction number). R0 is the reproduction number in an immunologically naive population. If we use your figure of effective 67% immunity due to vaccination, and 25% immunity among the unvaccinated due to previous infection, then we are at 75% effective immunity, so our best estimate of R0 is four times our estimate of R – i.e. around 5.

    This implies that current precautions are pretty ineffective, because R0 for wild-type COVID before people started taking precautions was just under 4, so R0 for delta without precautions should be between 8 and 9. This is high, but still substantially below measles. and per wikipedia still at the low end of the R0s we see for aerosol-spread viruses.

    Language being descriptive and all, it is possible that public discussion of COVID stats has already changed the standard meaning of R0, which would be unfortunate (because the distinction between R and R0 is valuable).

  16. thechaostician says:

    Another possible way for this to kinda sorta work:
    Most people who get tested do so to show a negative test. Occasionally, it comes back positive because of an asymptomatic infection. Delta has caused a dramatic increase in asymptomatic infections, especially among the vaccinated. The additional positive results are mostly asymptomatic. Test numbers aren’t increasing because the number of additional people who are actually sick is small.

    I don’t have any particular reason to believe this would be true, but it is a possible explanation. If this explanation were true, then we would expect a much smaller increase in hospitalization & deaths than if this explanation were false.

  17. Morgan says:

    Weird things could be happening to the testing rates because rapid at-home testing is now easily available, and those tests are not reported. I wonder if there is a bias where many people test at home and then get a follow up PCR only if the rapid test is positive.

  18. Raven says:

    What do you think of this claim that 30 fully vaccinated people in Louisiana have died of COVID?

    https://www.msn.com/en-us/health/medical/nearly-30-fully-vaccinated-louisiana-residents-have-died-with-covid-19/ar-AALSUBj

    If my math is correct this would be terrifying unless the vast majority of the fully vaccinated have since been exposed to the virus. Which doesn’t seem likely.

    Should we be hoping that there there is a big mistake in this story or is it not actually as bad as I believe?

    • Humphrey Appleby says:

      Why terrifying? Base unvaccinated IFR is about 0.6%. Israel’s data says vaccines are about 97% against death. That means Vaccines reduce the risk by maybe a factor of 30 so that is one in 5000. 30 deaths means 150k exposures (at a level that would cause infection if unvaccinated). That doesn’t sound implausibly high.

      • Raven says:

        Huh. Despite probably hearing that 97% estimate I think I had an impression of higher vaccine effectivness. And fairly shocked that covid exposure levels might be that high – likely a bias that comes from living somewhere that never had a massive outbreak, and seems to have it well under control now.

        Thanks for making me check my assumptions!

      • Humphrey_Appleby says:

        The other thing to watch out for is effects of age stratification in vaccination. e.g. the CDC reports 90% of the over 65 are fully vaccinated, and this is also the group at most risk of death. So given 97% vaccine efficacy against death, the null hypothesis is that about a quarter of deaths from COVID going forward will be in fully vaccinated individuals. And that’s not indicative of vaccine failure, just relative size of the susceptible populations.

    • TheZvi says:

      I don’t see why this is a problem even if it’s fully true and taken at face value? 30 isn’t a very large number in context

  19. llcampos says:

    Hey, new here. :) TheZvi seems to assume that its obvious that children don’t need indoors masking – is there a link presenting the reasoning behind that?

  20. Adam Brown says:

    Catching COVID has negative externalities: I might pass it on, I might overload the ER, or I might incubate a variant. If I wanted to buy an “off-set” for a microcovid’s worth of externalities, (i) how much should I pay, and (ii) who should I pay?

    Let’s say “I” am a median American, and the date is today.

    • Humphrey_Appleby says:

      What are you doing that incurs a `microcovid’ worth of externalities? If you are vaccinated and the answer falls under the umbrella of `living normal life,’ then I’d say the answer to (i) is `zero’ and (ii) is therefore moot.

      Answers would differ if you are unvaccinated and hanging out near vulnerable people, or vaccinated but researching bat coronaviruses.

    • TheZvi says:

      With a control system in place, it’s not clear that passing along Covid has much secondary effect in the long term at this point, so the risk value there is trivial. For the ER/ICU, right now it’s also trivial, since there’s no capacity issue. So basically I’d pay zero.

      Also, not to get into offset theory but ‘who you should pay’ is ‘whoever would do the most good with the money in any capacity’ and that’s up to you.

  21. Humphrey_Appleby says:

    Zvi: I think early on you had some discussion about whether `95% effective’ meant `95% reduction of risk in every interaction’ or `95% chance of 100% protection, 5% chance it didn’t work.’ I would say all the data indicating that effectiveness against death tops out around 97% or so indicates it is closer to the latter. Agreed? In which case, what does the `3% chance it didn’t work’ actually correspond to? Vaccine went bad? (perhaps because of human error at the administration site?) Immunocompromised recipients? Random bad luck? Any insight?

    • TheZvi says:

      Some combination thereof? That’s my best guess. I’m not convinced 97% is the top, but the exact number doesn’t change the theory here.

      Certainly some # of immunocompromised people will still be at risk, so that’s some of it, and certainly sometimes they mess up the administration process. Impossible to have numbers on it though, and your guess is about as good as mine.

    • TheZvi says:

      To the extent this week’s post didn’t already answer that I’ll talk more about it next week. I don’t think all these points are right, but the basic point certainly is – if delta turns out to be sufficiently tough to contain then we won’t contain it, and the key battle will be making sure we don’t destroy too much value in sacrifices to the Gods along the way.

  22. Paulo says:

    I’m quite worried about the matter of standards – how much Covid is acceptable, and how far are we willing to go with restrictions. The Economist’s research is just the tip of the iceberg; add Australia’s multiple lockdowns with surprisingly high popular acceptance (>60%) despite low infection levels, several popular public health figures advising lockdowns against Delta in England, France, Netherlands and Brazil (that I’m aware of) and the whole topic of permanent measures silently entering the Overton Window. I would bet a >75% chance of lockdowns in western europe/Blue states this year and >50% next year. Am I being overly pessimistic?

    Partially related, Brazi is pretty much open, registering 1200 deaths per day (falling down)…. but without significant Delta presence (growing) and a low vaccinated population (41% first dose 15% second dose, also steadly growing). It will be interesting to see (not so interesting from here, though) if deaths will rise, fall or stabilize.

  23. Mark says:

    If delta variant has 1000 times the viral load of previous variants shouldn’t we expect essentially 1000 times the mutation rate?

    Source for the viral load (I think I saw this on your blog but now can’t see where) https://www.dnaindia.com/health/report-delta-variant-infections-can-have-1000-times-higher-viral-load-than-original-covid-19-strain-2899717

    In looking for mutations that spread faster, or spread at the same speed and dodge immunity we seem to be looking for the probability that one mutation (or series of mutations) occurs because if it does there is a significant chance it will thrive and take over. This should scale with the number of times any given virus replicates and I don’t think requiring multiple mutations in series changes this if each intermediate step still has 1000x the viral load in patients.

    Is there a flaw in this reasoning? I would love to be convinced it is wrong or not as important as I am thinking.

  24. Kees Boon says:

    The Dutch festivals weren’t fully open air, there were tents where people sheltered from the rain. The ventilation situation of those tents is being investigated. https://twitter.com/DrEricDing/status/1415278559703220224?s=20

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