the path to r0 << 1
Jan. 12th, 2022 08:27 pm![[personal profile]](https://www.dreamwidth.org/img/silk/identity/user.png){kind=small}
solarbirdThis is an insurance statistics type of calculation, not an epidemiologist type of calculation. All my original science has been genetics and computer science, not virology or epidemiology, and I'm not a source for either here. This is accounting maths, not biology. But given that... it's still a path to r0<<1.
All data Washington State. All projections based on Washington State numbers. All data is specifically 12-and-over Washington State residents - including population numbers - because under that age is restricted in funny ways and harder to get. For 11-and-unders, I'm going to pretend that you're going to get a similar path, or worse.
But for the purposes of these calculations, by worse, I mean faster.
All of this assumes bad cases in terms of additional vaccination and mitigation measures, intentionally pessimistic assumptions that will be basically correct for Republicans in particular, due to the party's current status as literally pro-plague, but less so for everyone else.
Finally, none of this should be taken as endorsement of what I'm laying out. This is not how we should be doing this, and I mean it, it's really not. Even with omicron, there was no reason any of this had to be this bad, and no reason we had to get where we are. And this path's downside includes the greatest possibility of generating a new and worse strain of mutations.
But now that we are here, we are here, and this is what I think is reasonably enough likely to happen that I'm willing to put it in a post.
In other words, if I had to put down money, this is how I'd put down the money.
Let's go.
73.9% of 12-and-overs have full doses of vaccine out of a population of a 6,529,327.
That leaves 1,704,154 12-and-overs partially or unvaccinated, 1,253,630 of which have no vaccination resistance at all (80.8% have partial vaccination, leaving 19.2%), 450,524 who have partial vaccination and some resistance.
In very crude terms - who am I kidding, this is brutally crude terms - partial vaccination gets you around 40% resistance. Probably lower now with omicron, certainly lower with time, but some (possibly most) of those are recent and will get their second shots. But let's not assume that, and let's call it 30%.
70% of 450,524 gets you 315,367 cases, given everyone fully exposed again.
Full vaccination plus time still gets you around 70% resistance to omicron. Booster takes that higher to a bit above 90%, and we'll round down. Booster uptake here is pretty good amongst those already vaccinated, and some percentage of people have already had COVID and also been vaccinated, which in the right order improves ongoing resistance further. So let's call it 80% resistance. It's kind of a shot in the dark, but it's probably not too wrong.
20% of 5,275,697 gets you 1,055,139 cases.
Of the unvaccinated, with a 100% infection rate, you get 1,704,154 projectable cases.
That's a total of 3,074,660 bad-scenario/bad-behaviour cases moving forward from now.
But.
That leaves out prior cases in and of themselves - as opposed to resistance gained by them, which we have included. We need to include both.
There have been 1,009,187 total cases (all ages) by positive antigen test or better, many (most?) PCR confirmed. This is most certainly a substantial undercount, given 70% asymptomatic, an old number but the estimates I've had. Omicron really does produce a less severe disease overall, from the data I've seen, so it's possible that percentage goes up, not down - but I'll keep it as per historical.
There are 10,203 deaths, also most likely an undercount, from what I've heard by a factor of 1.4. So it's call it 14,284 deaths, and that's far enough below the really... really two-digit accuracy of this wild guestimation festival that I'll set them aside.
Based on the current numbers, about 86% of COVID cases would be 12-and-up. (I can't get that broken up separately from the state dashboard. I imagine there's a way to get it more exactly, but I haven't dug enough to find it.)
86% of 1,009,187 is 867,900 cases in the 12-and-up population.
867,900/.3 gives you 2,893,000 total cases, or 2,025,100 undetected cases. Maybe.
Some of these cases are definitely re-infections, particularly amongst the unvaccinated, which would reduce the number of people, vs. the number of cases. That would lengthen the timeline I'm about to - finally! - describe. But because I have no solid knowledge of those percentages here, I'm leaving that aside.
(I remind you: I said, this is crude.)
We have a projectable 3,074,660 additional cases moving forward, with previous case resistance already factored in, but assuming no undetected cases to date.
And that's not what we have.
3,074,660 - 2,025,100 (estimated undetected) leaves 1,049,560 cases anticipated.
(Yes, possibly more, depending upon reinfection rate of prior cases. But that's data I don't have, so I can't go with it.)
70% of those would historically go undetected, so don't look for that million more in the dashboards. But not being detected isn't really relevant here - what matters is actual cases to come.
(Besides, there'll be a... bad-case 30% reinfection rate amongst the post-omicron unvaccinated if or when delta manages a resurgence, but we'll leave that aside for now. Watch data over the coming weeks in fading hotspots for signs of that.)
So.
1,049,560 cases/12,000 (cases/day) - roughly the last two weeks averaged and frankly too low - leaves you 87 days on this bullet rail of bullshit. Three months.
Mid-April.
1,049,560 cases/15,000 (cases/day) - a little under the last four days averaged - leaves you 70 days. A bit over two months.
Late March.
1,049,560 cases/20,000 (cases/day) - a number we haven't seen yet, but if we spike up - leaves you 52 days. Seven and a half weeks.
Early March.
And whenever it is we get here, be it early March or mid April, all the anti-vaxxers - and, unfortunately, all those who aren't anti-vaccination but who haven't been able to get vaccinated for various good and unfortunate reasons - will have received the shittiest, most dangerous, least effective de facto vaccination available, 70% and falling resistance in exchange for 10% or more with long-term major organ damage, 2-3% with Long Covid, and let's say half a percent dead if the medical system doesn't collapse.
Assuming half the damage of delta.
(Spoiler: the medical system is already near collapse. A lot more people than that will die.)
Funny part is, the worse the anti-vaxxers act, the sharper the case spike. The shaper the case spike, the sooner the case collapse. Not down to zero, but down to actually controllable even with active ongoing active Republican sabotage.
Barring, of course, some kind of New Pandemic/Covid-22 variant that resets the entire clock to zero.
When I said a few posts ago that the heavy-duty phases of this could be over by May, this is what I meant, and basically how I got there.
When I said in comments "and I could mean March," well... all the anti-vaccination/pro-plague people have to do is just keep doubling down on being the massive dicks they've already been and getting omicron once or twice, the sooner, the better. Given their history, I think the odds of that are pretty good.
But if they change their minds (HA!) and start getting vaccinated, en masse, the timeline actually shortens - with less harm to them, and to their collateral damage.
(The way to extend the timeline is to keep not getting vaccinated but at the same time act better to control the plague, adopting masking, and so on. It's a little ironic, in that if they want to keep the plague going to keep the grift going as they have so far, they have to be much less dickish, but not about everything - about specific things in specific ways. I don't think they have the nuance for that. Let's hope they don't prove me wrong.)
And now, here we are.
The light at the end of the tunnel is a train - but it is also, I think, the end of the tunnel.
It's not too late to get vaccinated, and it's not too late to get your booster, and it's not too late to skate over this. Most people can move themselves from the 100% to the 60% to the 10% or even less with varying degrees of ease here.
Get yourself lucky. Get your shots. Dodge the train.
Because if you can, it's looking like after a nasty, nasty winter...
...it might be a pretty good spring in Cascadia.
All data Washington State. All projections based on Washington State numbers. All data is specifically 12-and-over Washington State residents - including population numbers - because under that age is restricted in funny ways and harder to get. For 11-and-unders, I'm going to pretend that you're going to get a similar path, or worse.
But for the purposes of these calculations, by worse, I mean faster.
All of this assumes bad cases in terms of additional vaccination and mitigation measures, intentionally pessimistic assumptions that will be basically correct for Republicans in particular, due to the party's current status as literally pro-plague, but less so for everyone else.
Finally, none of this should be taken as endorsement of what I'm laying out. This is not how we should be doing this, and I mean it, it's really not. Even with omicron, there was no reason any of this had to be this bad, and no reason we had to get where we are. And this path's downside includes the greatest possibility of generating a new and worse strain of mutations.
But now that we are here, we are here, and this is what I think is reasonably enough likely to happen that I'm willing to put it in a post.
In other words, if I had to put down money, this is how I'd put down the money.
Let's go.
73.9% of 12-and-overs have full doses of vaccine out of a population of a 6,529,327.
That leaves 1,704,154 12-and-overs partially or unvaccinated, 1,253,630 of which have no vaccination resistance at all (80.8% have partial vaccination, leaving 19.2%), 450,524 who have partial vaccination and some resistance.
In very crude terms - who am I kidding, this is brutally crude terms - partial vaccination gets you around 40% resistance. Probably lower now with omicron, certainly lower with time, but some (possibly most) of those are recent and will get their second shots. But let's not assume that, and let's call it 30%.
70% of 450,524 gets you 315,367 cases, given everyone fully exposed again.
Full vaccination plus time still gets you around 70% resistance to omicron. Booster takes that higher to a bit above 90%, and we'll round down. Booster uptake here is pretty good amongst those already vaccinated, and some percentage of people have already had COVID and also been vaccinated, which in the right order improves ongoing resistance further. So let's call it 80% resistance. It's kind of a shot in the dark, but it's probably not too wrong.
20% of 5,275,697 gets you 1,055,139 cases.
Of the unvaccinated, with a 100% infection rate, you get 1,704,154 projectable cases.
That's a total of 3,074,660 bad-scenario/bad-behaviour cases moving forward from now.
But.
That leaves out prior cases in and of themselves - as opposed to resistance gained by them, which we have included. We need to include both.
There have been 1,009,187 total cases (all ages) by positive antigen test or better, many (most?) PCR confirmed. This is most certainly a substantial undercount, given 70% asymptomatic, an old number but the estimates I've had. Omicron really does produce a less severe disease overall, from the data I've seen, so it's possible that percentage goes up, not down - but I'll keep it as per historical.
There are 10,203 deaths, also most likely an undercount, from what I've heard by a factor of 1.4. So it's call it 14,284 deaths, and that's far enough below the really... really two-digit accuracy of this wild guestimation festival that I'll set them aside.
Based on the current numbers, about 86% of COVID cases would be 12-and-up. (I can't get that broken up separately from the state dashboard. I imagine there's a way to get it more exactly, but I haven't dug enough to find it.)
86% of 1,009,187 is 867,900 cases in the 12-and-up population.
867,900/.3 gives you 2,893,000 total cases, or 2,025,100 undetected cases. Maybe.
Some of these cases are definitely re-infections, particularly amongst the unvaccinated, which would reduce the number of people, vs. the number of cases. That would lengthen the timeline I'm about to - finally! - describe. But because I have no solid knowledge of those percentages here, I'm leaving that aside.
(I remind you: I said, this is crude.)
We have a projectable 3,074,660 additional cases moving forward, with previous case resistance already factored in, but assuming no undetected cases to date.
And that's not what we have.
3,074,660 - 2,025,100 (estimated undetected) leaves 1,049,560 cases anticipated.
(Yes, possibly more, depending upon reinfection rate of prior cases. But that's data I don't have, so I can't go with it.)
70% of those would historically go undetected, so don't look for that million more in the dashboards. But not being detected isn't really relevant here - what matters is actual cases to come.
(Besides, there'll be a... bad-case 30% reinfection rate amongst the post-omicron unvaccinated if or when delta manages a resurgence, but we'll leave that aside for now. Watch data over the coming weeks in fading hotspots for signs of that.)
So.
1,049,560 cases/12,000 (cases/day) - roughly the last two weeks averaged and frankly too low - leaves you 87 days on this bullet rail of bullshit. Three months.
Mid-April.
1,049,560 cases/15,000 (cases/day) - a little under the last four days averaged - leaves you 70 days. A bit over two months.
Late March.
1,049,560 cases/20,000 (cases/day) - a number we haven't seen yet, but if we spike up - leaves you 52 days. Seven and a half weeks.
Early March.
And whenever it is we get here, be it early March or mid April, all the anti-vaxxers - and, unfortunately, all those who aren't anti-vaccination but who haven't been able to get vaccinated for various good and unfortunate reasons - will have received the shittiest, most dangerous, least effective de facto vaccination available, 70% and falling resistance in exchange for 10% or more with long-term major organ damage, 2-3% with Long Covid, and let's say half a percent dead if the medical system doesn't collapse.
Assuming half the damage of delta.
(Spoiler: the medical system is already near collapse. A lot more people than that will die.)
Funny part is, the worse the anti-vaxxers act, the sharper the case spike. The shaper the case spike, the sooner the case collapse. Not down to zero, but down to actually controllable even with active ongoing active Republican sabotage.
Barring, of course, some kind of New Pandemic/Covid-22 variant that resets the entire clock to zero.
When I said a few posts ago that the heavy-duty phases of this could be over by May, this is what I meant, and basically how I got there.
When I said in comments "and I could mean March," well... all the anti-vaccination/pro-plague people have to do is just keep doubling down on being the massive dicks they've already been and getting omicron once or twice, the sooner, the better. Given their history, I think the odds of that are pretty good.
But if they change their minds (HA!) and start getting vaccinated, en masse, the timeline actually shortens - with less harm to them, and to their collateral damage.
(The way to extend the timeline is to keep not getting vaccinated but at the same time act better to control the plague, adopting masking, and so on. It's a little ironic, in that if they want to keep the plague going to keep the grift going as they have so far, they have to be much less dickish, but not about everything - about specific things in specific ways. I don't think they have the nuance for that. Let's hope they don't prove me wrong.)
And now, here we are.
The light at the end of the tunnel is a train - but it is also, I think, the end of the tunnel.
It's not too late to get vaccinated, and it's not too late to get your booster, and it's not too late to skate over this. Most people can move themselves from the 100% to the 60% to the 10% or even less with varying degrees of ease here.
Get yourself lucky. Get your shots. Dodge the train.
Because if you can, it's looking like after a nasty, nasty winter...
...it might be a pretty good spring in Cascadia.
Building Back Better
Date: 2022-01-13 01:48 pm (UTC)So, will Omicron drown out deadly variants promoted by attenuating vaccine efficacy, or will the mix of the vaccinated and the un-vaccinated provide both the mutations and the semi-vaccinated hosts needed by hyper-infectious specialist mutants to spread with minimal competition? Who knows?
Re: Building Back Better
Date: 2022-01-13 11:09 pm (UTC)The vaccines combined with the fading antibody count characteristic of Covid also mean we're selecting for fast replication. Educated T-cells can make new antibodies once the virus gets into you, but it takes a couple of days to bring a batch of antibodies to maturity. Delta and Omicron were able to crowd out other strains partly because they both replicate *fast*, flooding the body with virus to create the breakthrough infection. Then when the new antibodies are ready, the immune system turns the tide, resulting in the 'four to five days of symptoms, then improving' pattern that distinguishes vaccinated cases from the 'keeps getting worse, body flooded with virus and histamines' that can happen in unvaccinated cases.
Re: Why did you subject-line this "Building Back Better"?
Date: 2022-01-13 11:44 pm (UTC)All vaccines are "leaky" by this definition, keep that in mind.
Social distancing and face masks selects for stickier virions that can achieve colonization and propagation with fewer virions getting from one host to the next. For example: Omicron.
That's not really how omicron transmission works, though, from what I've read. Omicron is more effective at transmission mostly because it produces dramatically more copies of itself in the throat, increasing its population in exhaled breath by a similar number. This _might_ also make it more effective at initial infection in the throat, too, but I haven't seen any numbers showing that.
(Obviously, I do not know everything. But the people I know studying this aren't bringing up the latter, but are very much bringing up the former. It also makes the number of opportunities to contract up, by again producing so much more viral particles in exhalations.)
A side effect of this mutation is that it reproduces less effectively in the lungs, which is probably why it's less impactful overall. Coronaviruses are like Tinkerbell in that they are too small to do more than a few things.
Leaky vaccines select for increased virulence as those variants able to aggressively multiply are the most likely to broadcast in sufficient numbers to spread.
Again: all vaccines are leaky.
But putting that aside, I'll say yes: that's possible.
However, it must be contrasted with any form of "let 'er rip" approach, right?
Having previously had COVID is less effective against future re-infection with COVID than any of the mRNA vaccines. (And probably also Johnson and Johnson, but I don't have as good data there.)
This means any evolutionary pressure for anti-resistance-honed COVID is greater from the unvaccinated previous-case population, since they're less resistant to reinfection than vaccinated people are to initial infection.
And they're much less resistant to later re-infection. Vaccinated people who get breakthrough cases have substantially higher immunity to re-infection than either unvaccinated people who have had a previous COVID infection or vaccinated people who have never had COVID. The optimal path for resistance is vaccination, breakthrough case, booster, and I'm not sure the order of those last two parts is strict.
So if you're wanting to assert that "vaccine resistance" is optimising for more virulent strains, you have to accept the absolute fact that "prior case resistance" is the same way, but meaningfully worse.
Not to mention the 20%+ long-term organ damage - hopefully less now with omicron but we just don't know - and the 2-3% or so with Long COVID, all of whom are far more susceptible to not just all kinds of diseases but also early disablement and death now.
Also, we now have an animal reserve of non-optimised-for-these-kinds-of-resistance COVID-19 in the animal population. Particularly with viruses, optimisation for one vector tends to lead to de-optimisation for other vectors, though that's obviously not always true. This means it'll have a great deal of pressure from animal cases as well - ones that may be more effective in other ways. Obviously that adds a lot more complications to the scenario and is well beyond my ability to discuss meaningfully, but it's still there and I felt like mentioning it as I do know enough to know it interacts here in meaningful ways.
"Building Back Better" was a rip on Biden's failed bill and the dangers of an evolving COVID-19
Date: 2022-01-14 01:20 pm (UTC)I was worried that this could be the case, but then on the other hand I've been told (via CBC radio) that after six months post double dose with a mRNA vaccine, immunity fades to 15% efficacy and that a third dose returns immunity to 75% versus Omicron. I decided that counted as a 'leaky vaccine' in my thought experiment. I guessed that polio and chicken pox vaccines would count as sufficiently effective as to not be considered as 'leaky'.
I'm aware that Omicron targets the throat (sore throat is a symptom to watch for) and broadcasts in greater numbers in comparison with earlier successful strains. But when it was first getting described, the omicron strain was notable for aspects of its spike protein that made it easier for it to 'stick' to host membranes, reducing the relative numbers of virions required to score an infection in the disease lottery.
Ah, by 'let 'er rip' you are referring to a laissez faire approach to the pandemic, one without vaccines, or worse. I do not subscribe to that. I am slated to receive a third dose of mRNA in about two weeks from now. I am annoyed that business considerations are depriving billions of people of COVID-19 vaccines, and insult to injury, many are getting our dregs; they are sent nearly expired vaccines and vaccines ineffective against Omicron. Should I abstain from inoculation, it will not remedy vaccine inequity.
This means any evolutionary pressure for anti-resistance-honed COVID is greater from the unvaccinated previous-case population
This is a good point. I do not know what could differentiate the unvaccinated and the vaccinated when it comes to harboring low grade infection and re-transmission of COVID-19 with considerations on evolutionary pressures on COVID-19 populations. Perhaps the resources (target cells) are different in a vaccinated environment, perhaps a patchy distribution of available target cells in an unvaccinated individual vs an even distribution in a vaccinated host? I am at a loss.
As I am particularly fond of whitetail deer, I have a small hope that the discovery that many whitetail deer have been found to have caught COVID-19 will take the thrill out of hunting them. I can also hope that COVID-19 transmission risks will serve as an incentive for cat owners to keep their cats indoors.
Thank you for your reply. Evolution is interesting, as is behavior. ^_^