Covid: Lucky 13

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On the bad news department (I may as well change my handle to Cassandra), this was expected but it is bad.

Here, coupled with Spike structural comparisons, we show that BA.2.12.1 and BA.4/BA.5 exhibit comparable ACE2-binding affinities to BA.2. Importantly, BA.2.12.1 and BA.4/BA.5 display stronger neutralization evasion than BA.2 against the plasma from 3-dose vaccination and, most strikingly, from post-vaccination BA.1 infections. To delineate the underlying antibody evasion mechanism, we determined the escaping mutation profiles2, epitope distribution3 and Omicron neutralization efficacy of 1640 RBD-directed neutralizing antibodies (NAbs), including 614 isolated from BA.1 convalescents. Interestingly, post-vaccination BA.1 infection mainly recalls wildtype-induced humoral memory. The resulting elicited antibodies could neutralize both wildtype and BA.1 and are enriched on non-ACE2-competing epitopes. However, most of these cross-reactive NAbs are heavily escaped by L452Q, L452R and F486V. BA.1 infection can also induce new clones of BA.1-specific antibodies that potently neutralize BA.1; nevertheless, these NAbs are largely escaped by BA.2/BA.4/BA.5 due to D405N and F486V, and react weakly to pre-Omicron variants, exhibiting poor neutralization breadths. As for therapeutic NAbs, Bebtelovimab4 and Cilgavimab5 can effectively neutralize BA.2.12.1 and BA.4/BA.5, while the S371F, D405N and R408S mutations would undermine most broad sarbecovirus NAbs. Together, our results indicate that Omicron may evolve mutations to evade the humoral immunity elicited by BA.1 infection, suggesting that BA.1-derived vaccine boosters may not achieve broad-spectrum protection against new Omicron variants.

It's impossible to chase this virus with vaccines. That puts makes even the "mucosal immunity through vaccines" route a wasted one by now. What advantage could have been gained from vaccines towards an effort at eradication was wasted by letting the virus rip through the population and greatly hastening its mutations into many variants.

Edit: in addition to the other paper about evidence of original antigenic sin now affecting outcomes from covid infections, there are also papers arguing that has been observed due to exposure to other coronaviruses. The common thing? The S2 protein region. Exactly the region used for most vacines.

Here, we show that a key characteristic of fatal coronavirus disease (COVID-19) outcomes is that the immune response to the SARS-CoV-2 spike protein is enriched for antibodies directed against epitopes shared with endemic beta-coronaviruses, and has a lower proportion of antibodies targeting the more protective variable regions of the spike. The magnitude of antibody responses to the SARS-CoV-2 full-length spike protein, its domains and subunits, and the SARS-CoV-2 nucleocapsid also correlated strongly with responses to the endemic beta-coronavirus spike proteins in individuals admitted to intensive care units (ICU) with fatal COVID-19 outcomes, but not in individuals with non-fatal outcomes. This correlation was found to be due to the antibody response directed at the S2 subunit of the SARS-CoV-2 spike protein, which has the highest degree of conservation between the beta-coronavirus spike proteins. Intriguingly, antibody responses to the less cross-reactive SARS-CoV-2 nucleocapsid were not significantly different in individuals who were admitted to ICU with fatal and non-fatal outcomes, suggesting an antibody profile in individuals with fatal outcomes consistent with an original antigenic sin type-response.

If this is indeed happening, then as covid variants multiply and drift further from each other, and as people get reinfected, this is going to be disaster on its own. Even apart from the other disaster of very likely cumulative damage to the immune system. And vaccines can easily become part of the problem instead of any help.
The authors of this paper point out that almost all the vaccines in use produce this very same S2 subunit, and thus "this phenomena should be studied" as new variants drift away from the original vaccines and people who were exposed to those too get infected with different variants. It would be heresy to say more just now...

And that's your mistake buddy. Buying into culture war nonsense.

It has nothing at all to do with culture war. It's an observation about an unfortunate individual trait people have, it's hard to recognize one was mistaken. Especially hard one's livelihood depends of appearing right. Unless you want to flag Keynes as a cultural warrior (he observed exactly this), you can't dismiss this observation like that. Might have been Galbraith mind you, kind of quoting from memory.
 
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The truth is that the vaccination strategy didn't fail due to the new variants as if that was a surprise. It failed because they discounted the known fact that coronaviruses mutate fast. That was incompetence #1: a vaccine was not a way out of this pandemic, could not be.

It's the same with influenza. We're doing fine with influenza.
(could be better, but could be a lot worse)

Incompetence #2 was the kind of vaccine supported and peddled, with no others being subsidized or even so much as tolerated (approved for use). Can you explain why western countries only ever approved 3 vaccines? Do you have any scientific explanation to justify "vaccine nationalism"? This is kind of besides the point because real useful vaccine to end this pandemic should have produced reasonably high immunity against caching the infection. And none of the many used across the world did. But it also shows imo evidence of state regulators carrying water for their favorite corporations - delivering captive markets. And if they are willing to junk science for that, won't they just science for approving an ineffective product?
A vaccine is not a way out, but a vaccine that did produce partial immunity could be part of a way out. These presently in sue are not even fit for that.
[...]
Incompetence #3 was the sloppy way in which the vaccination campaign was decided on and implemented, based on just a few corporate-run tests, and this rests on the politicians and the bureaucrats. They chose the "experts" to promote and platform, and to shut down the others. Wanted an easy way out and that was to be vaccines, originally on the promise of ending the pandemic ("you can throw away masks"), known even at the time to be false - "virtuous lies", that tenebrous guy name Fauci called it. Then continued based on "controlling" it - the boosters. In both cases I have said, and it remains blindingly obvious to me: vaccination is being used as an excuse to have people acquiesce with "living (dying) with the virus", avoiding ever having to make an effort to eliminate it. Or dropping such efforts, as it happened in Australia, NZ and more recently Taiwan.

Wait, with #3 you complain about the new fast technologies and accelerated approval, and in #2 you complain that everyone is not fast enough, right :p?
Also you're objectively wrong, it has been 4 for a long time, and in the meantime it's 5, https://www.ema.europa.eu/en/human-...accines-covid-19/covid-19-vaccines-authorised .

In the meanwhile other "miracle cures", this time new medications, also have a dismal track record. First it was remdesivir, resulting in failure and possibly more harm than good for takers. Paxlovid more recently keeps failing in new trials, how is it supposed to act, again? If it did act as an antiviral, if Pfizer's claims were correct, how come it shows no efficacy in these trials? Increasingly it seems it only "worked" on the Pfizer-run trial! How many RCT apart from the Pfizer-ordered one, back Paxlovid as an effective treatment? And whatever happened to molnupiravir? Thankfully that aid to covid mutation seems to have been quietly discarded, but that at one point was peddled by authorities just shows how this whole process has been based on arbitrary decisions taken according to pharma industry lobbying efforts. A testing system where tests are paid for and effectively under the control of the party most interested in declaring it a"success", is broken. And people who attempt to publish how broken it is are blacklisted, cannot get media time. That is incompetence #4 , more properly called corruption, and also applies to the approval of these vaccines.

Also, as above, before you've been calling for more antivirals, and now you're unhappy with the ones you got.
You might as well take on a cardboard sign with "we are all doomed".
Antivirals are notoriously difficult. This is not a surprise to anyone. Can't kill something, if the easiest route is to kill the host. Effective antivirals exist for very little viruses.

It's impossible to chase this virus with vaccines.

As we've been doing with a lot of other bugs. For years already. So much for "impossible" :p.
 
Universal healthcare as pandemic preparedness: The lives and costs that could have been saved during the COVID-19 pandemic

338,000 deaths & US$105.6 billion

Costs of COVID-19 so far that could have been averted by universal health care in the United States.

Significance
The fragmented and inefficient healthcare system in the United States leads to many preventable deaths and unnecessary costs every year. Universal healthcare could have alleviated the mortality caused by a confluence of negative COVID-related factors. Incorporating the demography of the uninsured with age-specific COVID-19 and nonpandemic mortality, we estimated that a single-payer universal healthcare system would have saved 212,000 lives in 2020 alone. We also calculated that US$105.6 billion of medical expenses associated with COVID-19 hospitalization could have been averted by a Medicare for All system.

Abstract
The fragmented and inefficient healthcare system in the United States leads to many preventable deaths and unnecessary costs every year. During a pandemic, the lives saved and economic benefits of a single-payer universal healthcare system relative to the status quo would be even greater. For Americans who are uninsured and underinsured, financial barriers to COVID-19 care delayed diagnosis and exacerbated transmission. Concurrently, deaths beyond COVID-19 accrued from the background rate of uninsurance. Universal healthcare would alleviate the mortality caused by the confluence of these factors. To evaluate the repercussions of incomplete insurance coverage in 2020, we calculated the elevated mortality attributable to the loss of employer-sponsored insurance and to background rates of uninsurance, summing with the increased COVID-19 mortality due to low insurance coverage. Incorporating the demography of the uninsured with age-specific COVID-19 and nonpandemic mortality, we estimated that a single-payer universal healthcare system would have saved about 212,000 lives in 2020 alone. We also calculated that US$105.6 billion of medical expenses associated with COVID-19 hospitalization could have been averted by a single-payer universal healthcare system over the course of the pandemic. These economic benefits are in addition to US$438 billion expected to be saved by single-payer universal healthcare during a nonpandemic year.



Paper Writeup
 
Incompetence #2 was the kind of vaccine supported and peddled, with no others being subsidized or even so much as tolerated (approved for use). Can you explain why western countries only ever approved 3 vaccines? Do you have any scientific explanation to justify "vaccine nationalism"?

Inaccurate. There are currently 5 approved for use in the UK (Pfizer, Moderna, Oxford/AZ, J&J, Novavax) and that's the case for most European countries, including yours.

Your complaint implies there are others that should be introduced, but are not approved solely for political reasons. This doesn't really hold up in reality. Ignoring minor reformulations of the approved vaccines, the other available options are Sinovac, Sinopharm, CanSino, Sputnik and Covaxin. The last of those is still in phase 3 trials in the US.

Sure, politics around China and Russia aren't going to help the others get approved, but given they all gave substantially inferior results to those that were, it's an entirely rational scientific stance to avoid these as well. (Except maybe Sputnik, but remember it's also a valid scientific stance to be suspicious of results in regimes where politicians have that much involvement and influence over the scientists). Sinovac was struggling to even get to 50% efficacy before the virus had time to adapt.

A testing system where tests are paid for and effectively under the control of the party most interested in declaring it a"success", is broken. And people who attempt to publish how broken it is are blacklisted, cannot get media time. That is incompetence #4 , more properly called corruption, and also applies to the approval of these vaccines.

With clinical trials being the most expensive bit of drug development, pharma companies would be very happy to have all the testing paid for by someone else. Who did you have in mind?

Your link here doesn't really seem to hold up that "blacklisting" is going on. It's a vaguely entertaining spat to look through, but it mostly amounts to Paul Thacker sulking that Facebook fact checkers stuck a "health warning" on his piece. Not even removed it - just a "dodgy - this is being used to mislead" warning. Bit of a stretch to argue that's being silenced. The piece in the BMJ is still up there, and rather more important than how much it's being passed around on Facebook.

He rather ties himself in knots trying to argue that his article didn't actually claim to call into question the results of the clinical trials when the piece is literally titled "Covid-19: Researcher blows the whistle on data integrity issues in Pfizer's vaccine trial. (Data integrity issues is science-speak for "their data is a load of made-up crap").

Whether you accept his splitting of hairs here or not, he's rather missing the point. Once his piece was latched onto and passed around as the latest tidbit for the antivaxxer misinformation crowd, it needed that fact checker's warning. The point of the warning was that it was being used to mislead, not what the article itself actually said.

Sadly that's not as paradoxical as it ought to be. Something I have noticed with monotonous regularity is the misinformation crowd posting links to pieces which don't support, or even flat out contradict the stance they are taking. Since most people don't even read the linked material, let alone stop to think about it, you get end up with articles being waved around as "evidence" for a stance they directly contradict. So yes, that can result in a situation where a piece that's reasonable in itself still needs a warning because of what is being done with it.
 
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On the bad news department (I may as well change my handle to Cassandra), this was expected but it is bad.



It's impossible to chase this virus with vaccines. That puts makes even the "mucosal immunity through vaccines" route a wasted one by now. What advantage could have been gained from vaccines towards an effort at eradication was wasted by letting the virus rip through the population and greatly hastening its mutations into many variants.

Edit: in addition to the other paper about evidence of original antigenic sin now affecting outcomes from covid infections, there are also papers arguing that has been observed due to exposure to other coronaviruses. The common thing? The S2 protein region. Exactly the region used for most vacines.



If this is indeed happening, then as covid variants multiply and drift further from each other, and as people get reinfected, this is going to be disaster on its own. Even apart from the other disaster of very likely cumulative damage to the immune system. And vaccines can easily become part of the problem instead of any help.
The authors of this paper point out that almost all the vaccines in use produce this very same S2 subunit, and thus "this phenomena should be studied" as new variants drift away from the original vaccines and people who were exposed to those too get infected with different variants. It would be heresy to say more just now...



It has nothing at all to do with culture war. It's an observation about an unfortunate individual trait people have, it's hard to recognize one was mistaken. Especially hard one's livelihood depends of appearing right. Unless you want to flag Keynes as a cultural warrior (he observed exactly this), you can't dismiss this observation like that. Might have been Galbraith mind you, kind of quoting from memory.
I think this is the critical figure from that paper:



There certainly is some drop in protection with the later variants, but it is not at all saying they are useless or it would be better to be unvaccinated. The smallest effect is seen in the vaccinated only group, the drop is much greater in the infected groups (b and c).
 
We've very much flown over the thread limit. Will there be any protest if I start a new one?
 
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