Covid 6/24: The Spanish Prisoner

The last scare is underway. Delta is an increasing share of Covid cases around the world, causing cases in many places to rise. Are enough people vaccinated? How bad are things going to get before we turn the corner one final time? 

The incremental news was not good. Calculations that looked comfortable last week look less comfortable now. I still expect things to mostly be fine, especially in areas with high mRNA vaccination rates.

Also, if you think John McAfee found dead in a Spanish prison. If you think he killed himself I have some computer security software and I'd like to sell you a subscription. Works great.

Let's run the numbers.

The Numbers

Predictions

Prediction from last week: Positivity rate of 1.8% (down 0.1%), deaths fall by 9%.

Result: Positivity rate of 1.8% (down 0.1%), and deaths fall by 9%.

Prediction for next week: Positivity rate of 1.8% (unchanged) and deaths fall by 8%.

Got this week on the nose. With the rise of Delta and the shift in tests from safe to unsafe regions, I no longer expect the positivity rate to continue to decline, and if anything an uptick is more likely than a downtick. For deaths, there’s no reason to think things won’t improve for a few more weeks. 

Deaths

DateWESTMIDWESTSOUTHNORTHEASTTOTALMay 13-May 19592119412778113874May 20-May 2661594812796313473May 27-June 252783811704562991June 3-June 97208179154312883Jun 10-Jun 163686119613142254Jun 17-Jun 235294438312632066

As discussed last week, I’ve shrunk the graph so we can see what’s happening recently, which was otherwise impossible to read. We saw progress this week, but the West’s number last week was indeed ahead of itself, so we saw only modest overall progress and hit the 9% decline target exactly. Things now seem like they’re back on the expected track and the orange New York line is down to 51 deaths last week. 

We should expect to see things continue to improve, but the increasing share of Delta infections does mean the fatality rate should now be rising, given the slow pace of additional vaccinations. 

Cases

DateWESTMIDWESTSOUTHNORTHEASTTOTALMay 6-May 1246,04559,94570,74046,782223,512May 13-May 1939,60145,03063,52934,309182,469May 20-May 2633,89034,69448,97324,849142,406May 27-June 231,17220,04433,29314,66099,169Jun 3-Jun 925,98718,26732,54511,54088,339Jun 10-Jun 1623,70014,47225,7528,17772,101Jun 17-Jun 2323,85412,80126,4566,46469,575

The lack of progress here this week is quite worrisome. Delta is only up to around 35% (the data says 30%, but it’s lagged to start with and three days old to boot, and makes me think the 35% I estimate extrapolating from last week is likely slightly low rather than high), so if that’s enough to get us treading water, there’s going to be trouble in the more vulnerable areas within a few weeks. The question then is, will it be contained the way the Alpha uptick was, or will it become a much more serious problem? Discussion in the Delta Variant section, but it looks much less optimistic than it did last week. 

Vaccinations

Some substantial differences in Bloomberg vs. Washington Post, but same basic story. 

Last few days saw a dramatic drop to a new lower level, which does not bode well. Fully 75% of the last week’s doses were second doses, which also bodes quite poorly. Hopefully both have something to do with reporting or some quirk of the calendar. Juneteenth, our latest holiday, is a plausible culprit on both counts. Until I had to adjust for data distortions I never realized how many different holidays we have in America, and for official purposes this one’s all new. 

 Chances are this is some of it, but that a lot of it is that the recent uptick was not sustainable and we will continue our steady decline as we run out of willing arms in which to put shots. 

If not, we are going to be stuck not that far beyond our current level of 53.6% first doses for a long time, and the August 10 date for going from 66.4% -> 70% among adults will be far too optimistic, and more like the asymptote until something changes.

Here’s a state breakdown:

The correct answer to ‘when will the states listed as November or later get to 70% if nothing changes’ is very clearly never.

People have made their choice. If you didn’t want to get vaccinated back when there were lots of cases, why would you change your mind now, with everyone feeling safe and the country reopening? 

Delta. It’s time.

Delta Variant

I did a bunch of calculations last week to figure out if we could handle the Delta variant. There’s also a much simpler way to view the situation. Delta is the forward-looking pandemic. Anything less dangerous than Delta, including Gamma/P1, will soon be dominated by Delta, so it’s a reasonable approach to ignore the total numbers and look only at the Delta numbers in various places. Essentially, treat the red lines as the pandemic here, not the grey:

The problem with that approach is it requires a good appreciation of the rate of absolute growth of Delta rather than its current level, which is trickier to get right and causes errors to get compounded. Also, such a model would freak out about every variant we’ve ever seen emerge anywhere. It’s still clearly not going to be a comforting answer.

The best data source I found last week continues to be the best known source. It shows us up to 30% Delta for data reported as of Monday the 21st. If the estimates from last week are accurate, it should become a majority of infections within a week, and become dominant soon thereafter. Within a month it will effectively be the pandemic’s present, not only its future.

The only questions are, can we handle it? What happens if we can’t?

Last week I approximated 25% Delta, which if we take its reproduction rate seriously is now 32% Delta after an additional 5-day cycle, or 35% now. That change only adds a few percent to R0, so it doesn’t explain the lack of progress last week in case counts. As we’ve seen in the past, weekly numbers can be quirky.

The problem is that last week’s estimate of how fast we were vaccinating was too optimistic. Part of that was a bad estimate, part of that was bad news over the last week, but it looks like a more realistic guess is 0.5% off the population per week rather than 1%. Also, I have to increase my previous guess on the old R0 from 0.84 to more like 0.86 after this week’s numbers.

That would start us out at R0 = 1.13 with a gain each week of only 1% that is plausibly fading, if you ignore immunity from infections and further control systems entirely in all directions, which would take us three months to turn the corner. During that time, Delta would go up by a factor of 6 or so (and all other variants would presumably get mostly wiped out) which would mean we’d peak around double our current case rate. 

Basic sanity checks on these calculations look like they check out, and are at least in the right ballpark. 

That ignores that different regions are different, which likely makes things worse overall. The Northeast essentially ‘wins’ and shrugs things off, while the South could be in serious trouble. Which in turn leads to control systems, including an increased willingness to get vaccinated.

That’s not great. Is it too close for full comfort? Absolutely. But given that this excludes control system reactions and the effects of immunity from infection, both of which work in our favor, and I used a bunch of conservative estimates in various places, it’s a worst-case scenario I can live with. An all-Delta world, even with double or triple current rates, is still better than things used to be even for the unvaccinated, that’s the peak of trouble before things get better again, and the unvaccinated have a choice to change their status. 

The usual suspects are out in force, as one would expect, raising the alarm. On the lighter side, some of them cut more corners than others...

Did you know that you... can... just... put... lines... into... graphs? And label them however you like, with no relation to reality? Don’t wait. Use y = ax + b today!

Seasonality

This is the second year of Covid posts, so when we point to the South and say ‘this is what happens when people refuse to get vaccinated’ perhaps we should remember what the headline was a year ago?

It was 6/18/20: The Virus Goes South, followed by 6/25/20: The Dam Breaks. It looked like the South, plus Arizona, had lost control of the situation entirely. Then two weeks later, things there peaked and started declining again. Once again, I had underestimated the control system. It wouldn’t be my last time.

Exactly one year later, the exact same spots are showing the same pattern, to a lesser extent than last time. It hardly seems fair to ascribe this primarily to vaccination differences, even if the math says that those differences are a very big game. This is not our first rodeo, and I’m not about to repeat the same mistakes that easily. 

This goes both ways. We also shouldn’t get too cocky about things going well in the Northeast in the same way they went well last year, even if we have good reasons to be optimistic this time around.

In Other News

I remember what it was like to have this kind of failure of imagination. I miss those days.

Claim that vaccinated children in Los Angeles will be required to wear masks while at the places they are required to report to for the bulk of their day. On the plus side, if they opt for ‘distance instruction’ they only get ‘scant hours of instruction’ leaving them free to spend the rest of their time learning. 

Also worth noting is that I don’t think this is how math works, on multiple levels? Am I missing something?

Thread on vaccine situation in Taiwan, which is a disaster on multiple levels, and its interaction with the question of reunification with China. Especially after what happened in Hong Kong, I notice I am confused how so many could take such an indifferent attitude towards reunification.

MR once again hammers home that the Moderna dose of 100ug is clearly too big. I continue to think this undersells the case, because 100ug isn’t merely unnecessary overkill, it is likely actively worse than 50ug because the extra size makes the next-day side effects worse, without a meaningful increase in the level of protection.

Paper documents loss of grey matter in the brain after getting Covid-19, including for those who were not hospitalized - hospitalization did not seem to impact the magnitude of this effect. You do not want to get Covid-19. Given the timing this does not provide information on vaccinated people who then still got infected, nor does it differentiate between severity levels beyond whether someone was hospitalized. I do not have a good sense of what size impact one should expect from the effect observed here - it’s easy for this type of thing to be quite impactful, and also easy for it to sound scary while not having much impact at all.

Small study finds 39% risk of Covid-19 spread between roommates in hospitals. I didn’t get a chance to form an unanchored prior on this number but it seems well within the range of numbers I would have expected.

Mask wearing study with very large data sets finds that everyone wearing masks most or all of the time in public places leads to a 25% reduction in the rate of reproduction (R0). That is being interpreted as ‘masks work’ but I would caution both that the error bars on this are gigantic in both directions, and that this effect is actually smaller than I would have guessed, if it is indeed contrasting mostly wearing masks to never wearing masks. They couldn’t find any effect of mask mandates on rates of mask wearing, which is a methodological problem rather than a real observation of causal reality. Mask mandates absolutely change the rate of mask wearing, and the lifting of mandates has clearly reduced mask wearing in ways I have observed with my own eyes. I do think it’s fair to take results like this and update towards mandates having less impact than one would otherwise think, especially local mandates in a world where masks were being adopted generally anyway, and to put more of the ‘work’ involved on private reactions. The mistake would be either to translate the ‘masks work’ here as ‘mask mandates work,’ which they definitely did not find, or to translate the ‘mask mandates not found to increase mask wearing’ here as evidence that they don’t increase mask wearing. Two easy to make and opposite mistakes.

Someone Really Ought To (Somehow) Do a (Better) Study

Marginal Revolution highlights a NYT piece on the CDC and how broken it is, calls it one of the best pieces of the year. Giving the secondary link as a compromise with my NYT ban, as the content here is being represented by a credible source as unusually impressive and important.

A study on shelter in place orders and their impact on excess mortality. My conclusion is that the decision on when to issue such an order, and the counterfactual situation if orders weren’t issued (both in terms of people’s actions, and in the medium-term path of the pandemic), are sufficiently hopelessly confounded that this doesn’t provide much if any insight into what is happening here. 

Another study finds that lockdowns kill children, especially in developing areas, ‘potentially’ 1.76 child deaths per pandemic death averted in the least developed areas. As usual, they use an SIR model, which is a very poor way of creating a realistic counterfactual path of the pandemic in the absence of lockdowns, so I don’t take these results all that seriously beyond the headline fact that there’s very large downsides to locking down that are even larger in undeveloped areas. That part seems very true, and worth appreciating.  

Not Covid

Lying with statistics, CNN reversed x-axis edition:

John McAfee found dead in a Spanish prison while awaiting extradition to the United States. 

That ‘could have’ is doing a refreshingly large amount of work, but, I mean, no:

Everything we know about John McAfee, including getting a tattoo years in advance to indicate he didn’t kill himself in case he was found in exactly this situation, strongly indicates he didn’t kill himself. 

That’s a pretty strong move. If you did that and people still think you killed yourself that has to be a rolling-in-your-grave-thinking-literally-what-the-f***-did-you-want-from-me moment. Or it would be, if John was the type to care what other people think enough to bother rolling.

Still, while I find it unlikely, the ‘could have’ technically stands! Cause I gotta think: If McAfee explicitly set the stage to make us all think he was whacked by the government and would never kill himself, then killed himself anyway, would that be both a totally baller move and totally in character? Absolutely. And I’d have to put on a hat, so I could tip it.

In gaming news, while working on Emergents, I’ve had the chance to explore Roguebook, the new rogue deckbuilder from a team that includes Richard Garfield (the creator of Magic: The Gathering). Richard is awesome and takes lots of big swings, and this is effectively a spiritual sequel to Slay the Spire, which is so good it is the game I recommend to most people when they ask me what they should be playing, so I was hoping for greatness. What I got instead was... a solid game that does not swing for the fences and I don’t think is as good as Slay the Spire, but which offers enough new twists on the formula to be well worth playing if you’re up for another experience in the same style. I tentatively have it in Tier 3, a game worth playing if you like the genre.

The game I’m enjoying the most recently is a little thing called Slipways, a chill puzzle/strategy 3X game that’s definitely worth checking out. Not yet sure if it’s quite Tier 1 (Must Play), but definitely at least Tier 2 (Worth It). 

Finally, did you know that supplies are sufficiently backed up that I’ve been warned that if I want to order nice furniture for our new apartment in NYC, it might not get here until January?