Monday, August 24, 2020

On The Long March to Covid-19 Herd Immunity...

... "sorry, but just a few percent more"

August 24, 2020

edits/adds 8/26, 31

There are two ways Covid-19 will leave a place, even temporarily - the exit it came in by (China and New Zealand have done this well, battling it down to effective zero, not that stays right there on its own) - and the exit that runs through us, the "herd" - we live with it up-close and even invite infection until we achieve an overall balance of natural immunity. This is the approach favored by experts and others who favor freedom, are long on distrust of authorities, and/or don't grasp just how harmful this virus can be. 

Some serious work went into this study, for example, to conclude from "unfolding epidemics" and careful application of mathematical formulas, "our inferences result in herd immunity thresholds around 10-20%" as Dr. Eli David quotes it, noting as usual how the utopia of Sweden is believed to have proven it. 

The basic idea of how "herd immunity" works - normally, and as I gather - is after the virus hits more brick walls of immunity more than open paths, and that dynamic has a little time to play out. At the start, with everyone susceptible (perhaps with some exceptions), and assuming a reproduction rate R between 2 and 3, which it often is (it varies with all kinds of details) - as they say you infect 2-3 people, who each infect 2-3 on average, and so on. At the HI threshold, you most likely infect no one, because a solid majority of those you bump into are immune (be it exposed, vaccinated, or maybe cross-immune from something else). I can see how under some circumstances and with some contagions, the slowed rate required might come about with less than 50% immunity, but as we'll see, that doesn't seem to be the case with this virus. 

Whatever the exact level, the one that works is where it too few places left to go. Less infected, less susceptible, and more immune between them is the formula. It still allows for some transmision, but probably just to one person who has the same issue, passing it to maybe one person or no one, who (if one) in turn passes it to maybe one or zero, and again as needed until it's just zero. At this point, cases will resolve faster than new ones are made, and eventually a last case will recover without infecting anyone. And ideally something like 25-35% of the populace was able to avoid being infected.

There might be some validity to the new science suggesting it can be done with as little as 10-20% infected, 80-90% not infected. All such plans seem to involve some special shielding of "the vulnerable" (hopefully defined well, and hopefully the shielding ... you know, happens), and maybe some other special tricks about mixing up immunological homogeneity, and getting the pace right to avoid flooding the ICUs again. But we'll need more than some validity, some calculations, some ifs and maybes we likely can't guarantee. 

We don't want to expose a solid majority of people to this. And the herd immunity promoters insist we probably won't have to. Increasingly, it seems, people are agreeing these 10-20% figures seem credible. But we'll need evidence it might work out this way before we agree to toss that many under the bus, we want a clear-eyed view of what's ahead, how many more will have to get off the bus to get us more traction of a slope that's steeper and muddier than was calculated.

They provide evidence - just look at Sweden, usually as some other Herd Immunity supporter understood it to be back in April, all safe and sound at the edge of herd-vana with 15-30 infected. Sweden's policy planners had bragged of high infection around 30%, low mortality rates considering, and impending herd immunity almost from the start - adoring fans never double-checked or followed up. They just kept repeating the urban legend of the amazing Swedish success story. But the continuing data is clear they haven't reached herd immunity - that's measured in LESS INFECTIONS, not in less-fatal ones. many still hold out hope they'll achieve it after hitting 20% infected, which may finally be close, but it seems the Swedish herd has lost its enthusiasm for the project. And good thing - they might have only reached 20-30% of the infections they'd need.


Another example: Nicholas Lewis back on May 10 favored a level between two models giving 7% and 24% - pointing to Sweden as an emergent example thought close to that level. It was soon shown 7.3% didn't do it. They may be close to 24 by now, and we'll see. 

Maybe they need to reconsider some variables and re-do the calculations - maybe it's 30-33% we need - keep going - more fatal 3rd wave brings it to 37% and it only slows when they make it slow, yet again, to ask the pandemic managers what gives?  Okay, carrying the one and re-checking some factors - sorry, it might actually take a near majority - 44-48% FOR SURE guys, now keep that economy moving full tilt, and keep that virus moving, not so slow but not too fast. ICUs need to keep up. A few months later they hit 52% and AGAIN it's not slowing on its own. As they wait for the next math fix, they might notice thousands more have died, covid confirmed. Thousands more unusual mystery deaths have also piled up, and cardiovascular and pulmonary ailments and deaths have risen to puzzling levels. Even the dumbest populace would refuse the march by this point, happy enough to have never found that tipping point, only wishing they'd never been fooled into trying. Some things are best left undiscovered.

The pandemic managers behind that might reflect, as they dangle from light poles, how they could have just learned from the following examples available by now, if not at the time of the rosy predictions of April and May people are still recycling:

(note: antibodies known to lapse over time to some degree, so the actual numbers infected should be somewhat higher than indicated in these cases. )

* Diamond Princess cruise ship: 3,711 passengers and crew - 712 cases (19.2%) - 13 or 14 deaths. Cabin lockdown seems to have halted transmission at under 20%. This has been taken as showing herd immunity, presuming the ventilation system would keep blowing the virus to everyone, yet infections barely rose. But this has no logic - the virus won't refuse to infect a person in one cabin just because 20% of people in other cabins have been infected. The simple answer is that it's not airborne like that, as we already knew. It was the isolation of people that kept it spreading further, and kept it from a good test of how high it can go, except to say it doesn't automatically stop much short of 20% (seriously questioning 10-20% predictions that top out where reality seems to bottom out). 

* May 14, 2020 · "Over 25% of the UK likely to have had COVID-19 already" - probably not, but ...

* "Antibody prevalence in New York City, for example, jumped from 6.9 percent in late March to more than 23 percent in May" CDC round 2 found 23.2%. Jun 30, 2020 · "Around 25% of people in the New York City area have probably been infected with the coronavirus by now." It had slowed down, stayed slow, but never did go away - control measures were serious here, hard to discount as the major cause. But maybe they did happen to hit herd immunity around then? Maybe others would do the same? 

* Aircraft carrier USS Theodore Roosevelt: as of last news on 5 May, at least 1,156 cases out of ~4,500 crew = at least ~25.7%. This doesn't push our envelope very far. Some might quit following here and run off the celebrate the news that Covid19 fizzles out at about 25%.

* New Delhi, India, August 20: "Nearly 30% of residents in India’s capital New Delhi have had the coronavirus, according to a seroprevalence" 29.1%. Was 23.48% on July 10. Maybe it's 25-30% needed then?

* Trousdale Turner Correctional Center, Tennessee: prison capacity: 2,500. Inmates tested: 2,444 (sounds like all of them). Positive: 1,299 (53.15%) + 281 Staff tested, 50 positive. Of course this is a prison, not a populace under lockdown in private homes. It's not a place with millions - like India.

* Pune, India, Aug. 17: "seropresence tests show 51.5% of Puneites have developed antibodies" It can keep going til it hits more than half the populace? That wasn't predicted. That could be a disaster. Did they do that survey right?

* Bergamo, Italy:  "Of 9,965 people in Bergamo who had their blood samples collected between April 23 and June 3, 56.9 percent had antibodies against the virus" Maybe they do something differently in Bergamo - it does seem especially hard-hit, even by the standards of Italy, or of the Lombardy region it's in. Unlike those places in India (as far as we know), a lot died here - some 0.5% of the population, at least. And at leas 57%, likely over 60% before antibody lapse, managed to get infected, with no herd immunity emerging to prevent it.

* Mumbai, India: July 29: "COVID-19 antibodies found in 57% of Mumbai slum residents in limited serosurvey by NITI Aayog, BMC, TIFR" (but just 16% in other areas). Okay, maybe Bergamo's an outlier, and there's something odd with Indians and their susceptibility. If so, too bad - there's a lot of them.

* Guayas/Guayaquil, Ecuador: I didn't find anything to say what level of seroprevalance there was in this very hard-hit area of Ecuador (its temporary capitol after recent troubles). I would guess it's about on par with Bergamo and perhaps worse, considering the enormous excess deaths they suffered just then. There was a study into it I found, said to be complete, but with no findings presented. I'll keep an eye out.

* Life Care center, Kirkland, 120 residents, 25 of them died from a Covid19 outbreak in early March. They didn't stop at 20% infected but at 20% dead.  "A March 18 report from the Centers for Disease Control and Prevention found 129 cases of COVID-19 were associated with Life Care Center of Kirkland. This included at the time 81 residents (67.5%), 34 staffers and 14 visitors." But this is a bit like prison, full of frail people in the worst age-bracket and mostly with prior conditions. As such, they might also be especially susceptible to infection. 

* Federal Corrections Center Lompoc, in California "which houses 1,162 low-security inmates." "Nearly 70% of the inmates at Federal Correctional Institution Lompoc have tested positive, exploding by more than 300 in recent days" to a total of 792.  792/1162 = 68.16% Again, that's a prison. Let's hope it's just old people, northern Italians, poor Indians, maybe Ecuadorians, and prisoners who have these unusually high ability to keep on getting infected.

* May 5: Elayn Hunt Correctional Center in St. Gabriel Louisiana: "155 women without symptoms were tested after 39 became ill" - "192 inmates had tested positive, including 66 who had symptoms"  "according to Department of Correction statistics. The unit has about 195 inmates, though the number fluctuates, Pastorick said Monday." 192/~195 = ~98.5% infected here, or the number had fluctuated higher. 

That last one might be too high; there might've been more than 195 tested (though it's not likely to be much higher), and the results could include false positives. Any of these might be, I suppose. But AFAIK there's no rule saying infection must stop at the HI level - which cannot be this high. In a prison, maybe it just doesn't slow down the same way it would in a spread-out populace - it can bouncing off the same limited surfaces from prisoner to prisoner until it hits everyone. 

There are a lot of factors and variable going into saying just what level would work for nations and cities that mostly go over my head. I'm happy with that, especially as I see experts SEE EXPERTS USE THEIR EXPERTISE TO predict outcomes far off from the reality. Just from what I've read, followed, and reasoned, I'd say the HI threshold is well above the 50-60% levels found in parts of Italy and India - probably well below the near 100% it can get to - it will vary on the population and just how they go about their business, but the expert views predicting the usual ranges around 60-70% and above always made the most sense, and better predicted the kind of levels emerging, and that we'll be seeing and more of.

One more thing I'll say about the HI level for Covid19: I don't want to see anyone find out what it is by a real-world trial. If it happens by accident somewhere, let's learn from it. But no one should be aiming to make this happen.


8/26: Update: Hard-hit Bergamo enjoyed, on the 22nd, its first day since the start with zero new confirmed cases. They had a few per day before and after, but it's been extremely low, and seems to be about as slow in other regions (perhaps regardless of exposure rates, or independent of any herd immunity). I got curious and dug up some stats from a few sources, all referring to the Bergamo region of Lombardy province, with a population of about 1.12 million. (there's also a Bergamo city of 122,000, which population I once used with deaths in the region to miscalculate 2.5% dead in the city. Rather, it's about 0.5% dead in the city (some 670) and almost as high in the region (was rounded-off to 3,000 dead, later to 6,000 dead - more exact numbers in time). 



10%, 20%, 36%, and 50% estimated exposure marked, using the crude formula of 236.23 cases / 1% infected that gives the result recorded June 3: 57% or more infected, at just 13,465 confirmed cases. It would mean some 46 unconfirmed cases for every confirmed one - inexact, but seroprevalence tests often find ratios similar to that. We can see barely-suppressed acceleration at 10 and 20%, what seems to be control efforts starting to win at what happens to be around 36% infected, and just moderate change from there through loosening controls (after which levels rise a bit faster) to 57% and to August 25, where I use the 15,269 cases to calculate less than 64% infected (noting spread should be slower on average after June 3 than it was before). Anywhere past 50% immune, the rate of spread is bound the affected at least a bit, and it might be a major factor by around 65%. But nowhere in here do we see a significant change in rates of infection - and thus of deaths and bodily damage - caused by mass immunity. This is the same kind of curve we see everywhere else, just more extreme: a deep, widespread outbreak was slow to bring under control, even with unusually strict measures hardly anyone but China can still match. But finally it was brought under control, at great cost of course, and might just remain totally manageable from here, so long as people stay vigilant.

sources:

https://www.ecodibergamo.it/stories/bergamo-citta/coronavirus-in-lombardia-154-positividue-decessi-a-bergamo-27-nuovi-casi_1368519_11/ etc.

https://github.com/pcm-dpc/COVID-19/tree/master/schede-riepilogative/province

http://opendatadpc.maps.arcgis.com/apps/opsdashboard/index.html#/b0c68bce2cce478eaac82fe38d4138b1


Update Aug. 31: this being my antibodies-seroprevalence spot, there will be more of that, and I'll try to note and add it here. Already some updates:

* Pakistan found to have 11% with antibodies. That doesn't say much, but it's a national average. Rates in cities like Karachi and Islamabad must be far higher, but I haven't seen where these are reported. One expert estimates (or knows?) about 40% in Karachi have been infected.

* Ischgl, Austria: 42.4% - Aug. 25 report on a wider study at this Austrian ski town famously hard-hit by infections, if not deaths.

* New York City: 27% average, areas past 50% - An August 19 NYT report cites a city study that found gigher levels of antibodies than previously known. A map shows huge swathes of the city above 35%, and gives 27% as the city-wide average. 

"In one ZIP code in Queens, more than 50 percent of people who had gotten tested were found to have antibodies, a strikingly high rate. But no ZIP code south of 96th Street in Manhattan had a positive rate of more than 20 percent."

"Across the city, more than 27 percent of those tested had positive antibody results. The borough with the highest rate was the Bronx, at 33 percent. Manhattan had the lowest rate, at 19 percent."

High points labeled on the map:

E. Elmhurst 45.7% 

Borough park 46.8% 

Corona (?!) 51.6% 


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