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The UK’s delta surge is collapsing

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Re: The UK’s delta surge is collapsing

#401
post #395
post #76

Earlier quoted context omitted.

> I'd imagine not too long after safe and effective vaccines are authorized for children under 12. Children are at exceptionally low risk from Covid. It's time to stop with fear, uncertainty and doubt, and deal with facts. https://www.nature.com/articles/d41586-021-01897-w In the US, 340 children under 17 have died from Covid. Total. During the same period, 187 have died from the flu, and over 51,000 children have di…

The Louisiana government had a press conference today where doctors from children's hospitals claimed their hospitals are full, especially the ICUs. [0] Even if kids don't die and just get sick enough to take up beds that still puts stress on limited hospital resources that other children need. The CDC data doesn't seem to show an unusual surge in hospitalizations for kids (0-17) [1]. But the LDH data does show a sig…

The governor had his head in his hands as the doctor was speaking and later asked if Louisiana was really the self described “most pro-life state”

Re: The UK’s delta surge is collapsing

#402

Earlier quoted context omitted.

These are very good points. I'd add that herd immunity isn't a clearly defined threshold, either. It's the point at which the effective R in a population is much below 1 you get, exponential decay might take a few months or even a few years to get down to elimination. The current dip in the UK is trending toward the former. But it's further complicated by the fact that levels of immunity in the population will contin…

> But everything we know about existing respiratory viruses (and indications so far this year) suggest antibodies will wane. Not necessarily the case. Infections with HCoV-229E produces durable immunity and reinfection is due to antigenic drift: https://www.biorxiv.org/content/10.1101/2020.12.17.423313v1 That it at odds with prior studies that found ~12 month reinfections with coronaviruses, but it is with considerab…

Setting up two likely scenarios is a very reasonable way of approaching future development, both scenarios sound likely to me.

We could look at the flu for clues, in that case every year will have one or more variants that are the most prominent.

I'd argue that in the age category with the most infected (10-29 years old) in the UK, that these people are not killing themselves due to their young age.

And the elderly have already gotten the vaccine and are thus up to eight times more likely to not get infected.

Re: The UK’s delta surge is collapsing

#403
post #311
post #232

Earlier quoted context omitted.

There actually is. The evolutionary selection pressure on most coronaviruses exists throughout its infectious stage. So in order to be more infectious for longer the coronavirus would become less symptomatic and so less serious. But with C19 we are aggressively isolating people with symptoms. This focuses evolutionary selection pressure on the initial infectious stage. In order to be more infectious the virus increas…

Are you saying without lockdowns it would have turned in a regular cold by now?

Not lock-downs specifically. Testing and isolating, Maybe, but it would have cost many more lives.

Re: The UK’s delta surge is collapsing

#404
post #360

Earlier quoted context omitted.

Deaths have absolutely plummeted, and correlations have very clearly broken from previous "waves". But in order to extract compliance from the population, there needs to be a call to action, so the goalposts were moved to infections, as opposed to hospitalizations/deaths.

This and similar arguments begin from an assumption of bad faith by scientists. It’s unbecoming. You should care about the number of cases because each case is a potential for a new mutation that could be the one that bypasses vaccines or becomes more deadly or …use your imagination. Nobody cares about controlling you, and if they did they wouldn’t use facts covid they would just use tanks.

> Nobody cares about controlling you, and if they did they wouldn’t use facts covid they would just use tanks.

This is a really great way to cause revolt. Why do you think China retains such an iron grip over information? It’s how you control a large population.

Re: The UK’s delta surge is collapsing

#405
post #365

Earlier quoted context omitted.

Mutations in the genetic replication machinery of the virus. All the world's worst and most untreatable diseases tend to have very fast, but very low quality polymerases. This means they replicate quickly, and generate mutagenic variants quickly. HIV and Ebola have this in common. Delta is already selecting for viral load over vaccine escape - if it keeps getting faster then it could become more dangerous, but it wou…

Interesting, thank you. If I understand correctly, viral load mutations are the current and quickest path to spreading faster, currently. It hasn't selected as fast for vaccine escape, yet, which is not to say it isn't trending in that direction with delta? Or, we're kinda f'd with regular transmissions at the moment, and vaccine escape is a possible accelerant?

The problem is closer to whether the spike protein is near an local maxima for infectivity since it's involved in binding to ACE receptors. Since mutations in COVID seem to conserve the spike protein region, it presently looks quite likely that it can't be changed very much without performing worse. Hence the viral replication optimum: spreading to more individuals makes the virus dominate the population quicker.

Evolution does whatever leads to more of the successful thing existing, so viral loading was a pretty obvious move: the question is whether there's any vaccine-evasion which doesn't compromise that advantageous (Delta suggests yes, but its possible that's as far as it can actually go).

Re: The UK’s delta surge is collapsing

#406

Earlier quoted context omitted.

> We're ALL going to get Delta at some point now, That's by no means certain; even ignoring the possibility of effective countermeasures, a more transmissible variant could displace it (if we’re lucky, it could also be one producing less severe disease, the way it was when Epsilon variant for a while displaced most others in California, before Delta, which is more transmissible than Epsilon, took hold.)

Tangential question: what is the mechanism by which we observe ‘displacement’ of earlier strains? Is it just the exponentially higher transmission factor of the variant that is making it relatively disappear? Or are they somehow also get out-competed directly?

The former: once you have COVID you're immune to it. Unless a strain totally evades the antibody response of recovered individuals (very unlikely), then they're no longer capable of spreading it.

So if there's overall less replicants of one strain then the other, then the population will effectively select for the more infectious one. Actual geography of course is also key here though: if a carrier flies over to an unexposed area with any strain, it's going to take over if the other one doesn't make it there.

Re: The UK’s delta surge is collapsing

#407
post #385

Earlier quoted context omitted.

> But some people can't get vaccinated, and for others who did get vaccinated the vaccine will have no effect How many people are we talking about?

At the moment? At least every person under 12, which is ~15% of the US population (and presumably similar elsewhere in the world).

People under 12 are at such a low Covid risk it’d be more ethical for us to send those vaccines abroad where they can be put to productive use saving lives.

Re: The UK’s delta surge is collapsing

#408
post #365

Earlier quoted context omitted.

Mutations in the genetic replication machinery of the virus. All the world's worst and most untreatable diseases tend to have very fast, but very low quality polymerases. This means they replicate quickly, and generate mutagenic variants quickly. HIV and Ebola have this in common. Delta is already selecting for viral load over vaccine escape - if it keeps getting faster then it could become more dangerous, but it wou…

Interesting, thank you. If I understand correctly, viral load mutations are the current and quickest path to spreading faster, currently. It hasn't selected as fast for vaccine escape, yet, which is not to say it isn't trending in that direction with delta? Or, we're kinda f'd with regular transmissions at the moment, and vaccine escape is a possible accelerant?

I don't know or haven't seen any evidence that polymerase mutations are responsible for the increased R0 of Delta, although it's certainly possible.

What we do know is that the Spike protein is essential for COVID cellular binding.

We also know that spike has mutated between 'vanilla' COVID of 18 months ago and what all vaccines target, and Delta. This makes sense, because the spike (or S) protein wasn't optimised for binding to Human ACE2 receptors; over time mutations in S (ie with Delta) have lead to increases in binding affinity with ACE2, the result being that Delta is more likely to infect a cell with the same viral load as 'Vanilla'. This would be a perfectly acceptable reason for the uptick in viral loads in Delta and infectivity and hence R0.

We are lucky/the vaccine researchers are smart in that S is quite antigenic (that is, triggers a good immune response, although in a 'natural' infection people will produce antibodies to many parts of the COVID virus), and because the selection pressures driving improvements in ACE2 binding affinity of S have not lead to such a great conformational change that antibody responses are useless (ie antibody-antigen affinity is decreased in Delta, but still effective), our vaccines against the earlier S protein are still effective.

Because of the way evolution generally works, pressures driving S evolution tend to end in a local minima (or maxima, depending on your way of looking at it - i tend to think in terms of conformational entropy so hence Xornot and my use of different terms for the same concept) - or as I mentioned earlier, 'Climbing mount improbable', a term coined by Dawkins in the book of the same name.

It is because it is very hard to get out of these local minima that the human body is full of such oddities, such as an eye that is designed with the nerves in front of the photoreceptors, resulting in a blind spot - it's easier to adapt around the minima to reach a new optimum then it is to reinvent the eye with the nerve in the position that would be logical from a functionality standpoint)

Therefore, it is very very unlikely that the S protein, or the virus, will be able to mutate to a S protein that is so radically different that it escapes antibody-antigen affinity from the vaccines we have today - the S protein would basically have to be completely redesigned, which is really unlikely to occur by the gradual process of evolution. Ie the chances of shaking the RNA coding for S into a new functional protein that works and is a completely new, novel shape, is infinitesimal.

So - basically, total vaccine escape is really really unlikely. Like, number of grains of sand on earth unlikely, if not more so. But polymerase mutations could increase the rate at which the grains of sand are sifted.

It is not something that I personally would lose much sleep over - we don't have any evidence from nature that I am aware of (ie flu virus etc) of highly conserved/selected proteins all of a sudden spitting out a completely new model - basically new diseases that we worry about come from species shifting (ie... let's just say SARS to avoid a debate about COVID origins)

Re: The UK’s delta surge is collapsing

#409
post #223

UK citizen here. I just don't think this "collapse" is the case. My gut feel is that everyone has stopped doing lateral flow tests and reporting those tests: noone wants to be isolating now the summer holidays have started, and many people are now ignoring track and trace because they're scared of the possible "pingdemic". I know many people who have stopped scanning in to venues. I reckon many suspect they may have…

It really makes me wonder why the authorities don’t do proper randomized surveys? It is obvious that the testing numbers will go up and down as the population goes scared and then goes don’t care.

UK Citizen here, my parents have been part of the ONS random survey for about 18 months now, every 2 (or so) they have a visit at their doorstep from the ONS who test both of them, they let them know the results via the NHS app and they get £25 of vouchers for each visit.... They have to be honest about who they have been in contact with, where they have been (E.g. supermarket) and if they wore a mask...

This data goes into modelling for how the government should make decisions about easing lockdowns etc. The UK has some of the best genomic sequencing in the world which is why we are able to identify variants so quickly.

It's just a shame it took the government 1 year to get ready and lied to us in the meantime.

Re: The UK’s delta surge is collapsing

#410

Earlier quoted context omitted.

It really makes me wonder why the authorities don’t do proper randomized surveys? It is obvious that the testing numbers will go up and down as the population goes scared and then goes don’t care.

UK Citizen here, my parents have been part of the ONS random survey for about 18 months now, every 2 (or so) they have a visit at their doorstep from the ONS who test both of them, they let them know the results via the NHS app and they get £25 of vouchers for each visit.... They have to be honest about who they have been in contact with, where they have been (E.g. supermarket) and if they wore a mask... This data go…

*every 2 (or so) weeks.
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