26 March 2022

Plague time

Reproduction causes evolution.  COVID is reproducing in billions of hosts, and as a result keeps evolving.

It's important to know that very small biochemical changes can cause large changes in how transmissible or how lethal a virus is; you get those by luck, but the more reproduction, the more opportunity.  At this point, it feels like it's only a matter of time.

The other thing that's a matter of time is extirpation; we could, in principle, do it in a month.  It would take wanting to do it and being prepared to house and feed everybody for the month everything is shut down, but it could be done.


It's unlikely we're going to see better conventional vaccines.  The two outstanding options are unconventional vaccines -- nasal vaccines, treatment of lung mucous producing cells to produce much more ability to trap viruses, reproducing vaccines etc. -- and novel art such as d-protein wet nano-machinery.  That's going to take time; it's going to take more work because the rate of change in the virus will compel an approach on fundamentals, rather than current dominant virus traits, and that's inherently more difficult.

Possible?  In a functioning post-industrial information economy, sure.

Do we still have that?


Are we going to lose that?

When we lose field agriculture, yes.  

Possibly sooner; Thwaites glacier is probably going to go this decade, which means a lot of coastal sea level rise.  That's going to affect transportation; maybe not enough to stop container shipping as such (tide allowances in ports might be able to handle the initial rise most of the time) but it won't help. (A one metre rise might be enough to cut the trans-Canada and the railroad east of Sackville; Halifax continuing to function as a port will be less relevant in that circumstance.)

If we still have COVID circulating when either field agriculture goes or Thwaites collapses, it's going to stay circulating.

COVID extirpation ought to be a much larger priority, given that we can't stop either the loss of field agriculture or the Thwaites collapse.


Anonymous said...

My hope is that a good nasal-spray vaccine will be approved and available within the next couple years, getting us closer to that dreamed-of ~100% immunity. And I hope also that more buildings will install really good air-quality controls.

Until then, I'm masking. ...It has been a long two years already. -Kathmandu

Graydon said...


My hope is that people will start respiratoring in preference to masking. It doesn't sound like a lot, but the difference between 1% and zero point something percent is a lot in systemic terms. (and it's cheaper!)

Mandatory HEPA air filtration would be a net win even without COVID; with COVID it's a no-brainer.

We don't require vaccines to extirpate the disease; this is in my view fortunate because I don't think more effective vaccines are possible. (Given how BA2 is behaving, effective vaccines might not be possible at all against currently circulating COVID strains.)

Fifteen million people in Ontario; call it 2 kCAD on average to house and feed an individual. That's thirty billion dollars. That's less than the net worth of the Thompson family; you can't argue we couldn't afford it. It's a conscious policy decision that extirpating COVID isn't worth the expense.

Pocketguy said...

There are a handful of other coronaviruses that infect humans. They are mild enough that people think they "caught a cold" and, unless they get very specific tests, the never know or care whether they caught one of those coronaviruses instead of one of the other ~200 viruses that constitute the "common cold".

The most likely path is that the currently popular coronavirus will mutate into a similar state, since it is a similar virus subject to essentially identical selection pressures. The recent Omicron variants are a step in that direction.

So why do you think that extirpating C19 is important?

Zeborah said...

@PocketGuy People keep talking about it being natural for viruses to mutate to become less deadly so that they don't kill their host so they can keep circulating.

This ascribes an awful lot of foresight to a mindless reproductive machine (especially given that humans, who do supposedly have foresight, still can't stop ourselves from destroying the environment that our own survival depends on).

It is true that viruses that survive have not killed their host species. This doesn't mean that viruses never kill their host species, it just means that if the virus does kill its host species it too doesn't survive. This is cold comfort if you're the host species that was killed first! Also, if the virus can survive in multiple species (as C19 can) then it can quite safely kill one host species (say humans) and carry on surviving in plenty of other species.

So. The "common cold" (to call it a single thing for simplicity) isn't mild because it randomly mutated to be mild in order to keep us alive. It's mild because all the human lineages for whom it was severe have, over tens of thousands of years, been eliminated. (Cf what happened every time Europeans rocked up to some society without common colds, flus, measles, etc. I grant common colds aren't as bad as measles but they'll still do a number on a naive immune system and leave the person vulnerable to other infections.) *Humans* are the product of natural selection too.

So C19 *may* mutate into something that's virulent enough to out-compete other strains, but also mild, and also provides immunity to those other strains (otherwise they're not out-competed, they're just tag-teaming).

Or it may mutate into something severe enough to wipe out humanity, and then happily shift into all the dogs, cats, bats, horses, etc we leave behind.

Or it may simply remain endemic, killing hundreds of thousands of humans every year for the foreseeable future, until only humans with lucky genes that make them more resistant to C19 survive to carry on our species' genetic legacy. From a species perspective, yay, humans survive I guess? But there's no guarantee I or my family will be among them, nor is there guarantee that there'll be enough of them to carry on our legacy of civilisation and fundamental agricultural infrastructure.

In all of these scenarios, C19 survives. Which one happens will depend entirely on random mutations.

Pocketguy said...

The other four coronaviruses that infect humans are mutating too. None of them are killing enough people to come anywhere close to destroying civilization or agriculture. Why is extirpating the new one more important than extirpating the other four?

Graydon said...


We're losing (at least) field agriculture due to climate change. Plague isn't helping, but is not an immediate cause.

"Coronavirus" is a name from the shape of the virion; it's not a phylogeny thing -- allowing you to predict similar characteristics -- because viruses don't do phylogeny; they do descent, but the "chance of variation" part of Darwinian reproduction doesn't apply.

The narrative that pathogens evolve to be less virulent is wrong. Pathogens evolve because the ones that don't reproduce after random changes don't persist. It's the host organism which evolves to make the pathogen less virulent, and human reproduction is slow enough that everyone now alive will be dead in five generations. In the meantime the virus has gone through many orders of magnitude more generations.

(Nor is the host organism guaranteed to evolve fast enough; the easy example of pathogen-driven extinction is the Easter Chestnut, but there are others; Australia's Christmas Island rats is the first search hit I got.)

So consider smallpox; the earliest examples we have are from a couple centuries BC. From that time until smallpox was eradicated in the 1970s, it didn't get less lethal. (It may well have been getting more lethal toward the end.)

Omicron is the spreadingest disease in human history and the initial UK data have the asymptomatic cases statistically tied (slightly ahead on raw numbers) for damage. (It's also more severe than the wild type.) Think of it as the Uncommon Cold; absent technological intervention, you get it every year, it hurts you every time, eventually you die.

One of the reasons the original SARS alarmed the medical researchers was that they found there were single point mutations that made it a hundred percent lethal in animal models. It's not clear if there's such a mutation in COVID, but it's not at all clear that there isn't. It could certainly be more lethal than it is and there isn't any kind of balance mechanism that says if it's lethal it can't spread; it's just a question of luck. Which is where the inadvisability of allowing uncontrolled spread comes in; all those reproductive events are opportunities to explore the potential space, and if there are enough reproductive events we'll see all the possibilities.

Plus two more things.

We have no idea what the five and ten year mortality rates look like. Long term viral damage is obviously an issue with COVID -- nearly guaranteed brain shrinkage and cellular ageing are strong negative indicators -- but we don't know even as much as we know about MS (where the harmless-as-an-initial-infection Epstein-Barr virus gets reactivated, rarely) about long term COVID.

All previous plagues have happened when the great majority of people were subsistence farmers. That isn't true anymore; we're all dependent on mechanised agriculture which is dependent on supply chains that can't cope with randomly losing significant fractions of the population. (It doesn't have to be dead; incapacitated works.) It doesn't need to infect and kill everyone to be a really bad problem.

Graydon said...


Well said!

JReynolds said...

A friend of mine just came down with COVID today. He's triple-vaxxed. Haven't seen him for months, but we play computer games regularly. He woke up this morning with no sense of smell, with all which that implies regarding COVID in his brain. Otherwise, it just feels like a cold.

I don't think that extirpation is on the table any more. White-tailed deer and other mammals have it, so even if all humans isolated for two weeks and got triple-vaxxed and got boosters when needed, COVID would periodically be jumping back to humans.

I think the only way to deal with it is for us (the collective us) to get our population vaccination rate into the high 90% level, and keep it there. Given the high rate of morons who don't want to do the correct thing, and the lack of will of the government to force the issue, I am not sanguine that this will happen.


Graydon said...

I am sorry to hear about your friend, and I hope he may recover entire.

The choices are extirpation and the Uncommon Cold. The Uncommon Cold isn't plausibly survivable; it looks like it's already going to be worse than the Antonine Plague, and we're not subsistence farmers.

Extirpation more than once, yeah, that's a real possibility of necessity, but having built the mechanism the first time, subsequent extirpation can be smaller and easier and faster.

(I think you're right that the will is not in us, collectively, today. Yet the day may come.)

Anonymous said...

This argument proves too much. Your claim about viral evolution is equally true not just of other SARS-CoV-2 strains, other sarbecoviruses, other coronaviridae, indeed any other widespread viral pathogen, most of which, you will note, have not been eradicated, and many of which cause significant misery and death every year. (And that's not to mention a wide range of *cellular* pathogens from trypanosomes to fungi to archaea to bacteria.) Eradication is certainly one legitimate goal, but you'll note how seldom humanity has managed to do that with any pathogen, and many less costly interventions are available which significantly reduce the disease burden; distributing those as widely as possible is absolutely feasible.

Graydon said...

The reason to go for eradication is that it's still (maybe) possible, and this is not about viral evolution so much as it's about ours. This is a greenfield disease. Any evolutionary response is a differential rate of death, and things are especially fragile right now in terms of how humans live. Economically significant excess death rates are not helping.

(Which is not to say the clean air people don't have a point, or that much more effort should go into eradicating diseases like malaria.)

Also, I would question your accounting; we don't know the five and ten and twenty five year mortality rates. That early-pandemic Lewy Body paper may not have got any followup and I hope that's because no one is finding any such thing in humans, but assuming that the ten year mortality rate isn't a hundred percent still feels a bit rash. So "less costly" is one of those "I'm sure it will be fine" assumptions, and those have not been well-considered so far. This disease has quite literally got worse.