Defeating SARS-CoV-2

Treatments and their effectiveness, herd immunity, masks, testing, etc.
jsampson45
Posts: 30
Joined: Tue Oct 20, 2020 1:50 pm

Defeating SARS-CoV-2

Post by jsampson45 »

I would have thought any partially-effective measure against this virus would cause it to evolve to evade that measure. In that case it seems logical to develop and apply many measures simultaneously. It looks as if governments are fixated on vaccines and social measures, ignoring others. Is there any way to stimulate an all-out attack on the virus? For example, a trial of iota-carrageenan started as late as this year and is not scheduled to end until December. There must be other discoveries that have been made but not followed up. Why not?

Splatt
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Joined: Thu Oct 29, 2020 12:46 am

Re: Defeating SARS-CoV-2

Post by Splatt »

We're never going to "defeat" it. Its not going away.
We need to live with it like all the others. It'll evolve, we'll evolve. The endless arms race continues.

Selection pressure is likely already being seen with B.1.1.7 and so on.
Lately E484K and others have evolved independently multiple times globally from unconnected branches.
We're seeing nature in action for the first time. The more the globe becomes partially vaccinated the more we'll see this.

fon
Posts: 1289
Joined: Tue Dec 22, 2020 12:47 pm

Re: Defeating SARS-CoV-2

Post by fon »

jsampson45 wrote: Sat Mar 13, 2021 11:29 am
quote]
Is there any way to stimulate an all-out attack on the virus?
Sadly not, even Bernard Montgomery and his Royal tank regiment would have been stopped in its tracks by the Corona-virus.The Corona virus is more slippery and hard to grapple with than even the Desert Fox, Erwin Rommel, himself.

https://en.wikipedia.org/wiki/Deus_ex_machina

At present all our hopes for a Deus Ex Machina are invested in vaccines , if there is another good compound out there, we'd need to invest heavily in that, but I fear prospects are very poor. Pfizer might be a better bet.

fon
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Joined: Tue Dec 22, 2020 12:47 pm

Re: Defeating SARS-CoV-2

Post by fon »

Splatt wrote: Sat Mar 13, 2021 5:16 pm Lately E484K and others have evolved independently multiple times
globally from unconnected branches.
Yes. Nature is creative mostly when it is prompted to be. If a mutation arises independently multiple times , you can rest assured that it is cheap and easy , effective and sure (from the virus' perspective). As you must know, there will be a strictly finite, and rapidly diminishing number of such changes that would occur matching that profile, which is demonstrated by repeated independent occurrences. I would be very surprised if many protein folding algorithms are not presently plotting the likely course of this molecule on various supercomputers around the globe, such work is critical to developing vaccines to defeat the virus before it even gets started in its newest mantle. Having shown it's possible to develop and deploy vaccines within 12 months, it is almost within the grasp of mankind to outpace nature, but only if we continue to rapidly double our global supercomputer power until we reach break even. Recent advances in computing (namely machine learning and simulated annealing) have brought this much nearer by tremendously short cutting the brute-force approaches of yore.

fon
Posts: 1289
Joined: Tue Dec 22, 2020 12:47 pm

Re: Defeating SARS-CoV-2

Post by fon »

Splatt wrote: Sat Mar 13, 2021 5:16 pm We're never going to "defeat" it. It's not going away.
We need to live with it like all the others. It'll evolve, we'll evolve. The endless arms race continues.
You might be right. It's a safe, traditional PoV, which had much to say for it in times gone by. But it's unambitious. The jury is still out on whether we can outrun it today[p/b]. We'll know in a year. We outran SmallPox recently, and Polio is on the ropes, and even flu has lost some of its potency. But we'll need faster technology to outrun this. As it happens, today, such mighty technology exists,in a primitive but effective form. Protein folding, simulated annealing and AI and othe in-Silico tech is quite likely to overtake this CoronaVirus, I'm sure we have some tricks up our sleeve. We may not defeat it but we can make it cringe and shrink. Defeat is hyperbole, shrink is perhaps achievable, well see.

Splatt
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Joined: Thu Oct 29, 2020 12:46 am

Re: Defeating SARS-CoV-2

Post by Splatt »

fon wrote: Sun Mar 14, 2021 9:31 pm As you must know, there will be a strictly finite, and rapidly diminishing number of such changes that would occur matching that profile, which is demonstrated by repeated independent occurrences.
That simply isn't the case. There are huge possible changes of pairing and folding that can occur. Some of which will have no effect on function but major effects on immune escape.

Its also not just folding. Other factors can be selected for. Delayed onset of symptoms can help it spread as can a longer infectious period and so on.
One admittedly tiny size study in the US suggest B.1.1.7 is potentially more infectious not due to binding affinity but because it shifts the incubation period back a few days which skips some of the isolation rules we have in place.
I would be very surprised if many protein folding algorithms are not presently plotting the likely course of this molecule on various supercomputers around the globe, such work is critical to developing vaccines to defeat the virus before it even gets started in its newest mantle. Having shown it's possible to develop and deploy vaccines within 12 months, it is almost within the grasp of mankind to outpace nature, but only if we continue to rapidly double our global supercomputer power until we reach break even.
Not really. There's a lot more to it than simply folding and the combinations are eye-watering.
mRNA vaccines can get recoded relatively quickly and then mass produced in 2-3 months to start a rollout (which will take months).
AZ is far slower as it needs to be grown in culture.

Realistically thats 6months+ from the detection of a new variant to starting to get the vulnerable people vaccinated yet again.

Several billion people with partial immunity and sporadic and often no genomic sequencing travelling around the globe is a very good system for variant creation.

Meanwhile, when placed under selection pressure, SARs2 has shown it can generate changes in a few weeks. The key deletion in B.1.1.7 evolved spontaneously in an immuno-compromised patient less than 30 days after anti-viral drugs were stopped.

fon
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Joined: Tue Dec 22, 2020 12:47 pm

Re: Defeating SARS-CoV-2

Post by fon »

Splatt wrote: Mon Mar 15, 2021 2:01 pm
Not really. There's a lot more to it than simply folding and the combinations are eye-watering.
mRNA vaccines can get recoded relatively quickly and then mass produced in 2-3 months to start a rollout (which will take months).
They've brought the rate to 1m jabs per day, we can give the whole nation a top up in 10 weeks. But we can increase the rate again, if we needed to. The NHS has turned out to be a very sound system for quickly delivering vaccinations.

https://www.gponline.com/uk-hits-1m-sec ... le/1709129

amanuensis
Posts: 48
Joined: Sun Feb 14, 2021 1:32 pm

Re: Defeating SARS-CoV-2

Post by amanuensis »

I don't know any disease specialists that actually thinks we can 'defeat' covid.

It just isn't that type of virus.

What we can do is protect the vulnerable from the worst of the disease. This would be enough if we did it properly.

Unfortunately, there seems to be a general push to treat this 'like polio or smallpox', which are viruses with different characteristics that could be 'defeated'. This approach is likely to lead to problems (eg, population-wide vaccinations will massively increase selection pressure for the virus to escape the current vaccines).

While it is nice to think that 'technology will save the day', cutting-edge technology is unlikely to do much for us over the next few years wrt 'defeating covid'.

If there is a saviour it will be in new treatments to reduce hospitalisations/fatalities, not in 'defeating covid'.

JohnK
Posts: 63
Joined: Sat Mar 13, 2021 12:47 pm

Re: Defeating SARS-CoV-2

Post by JohnK »

amanuensis wrote: Mon Mar 15, 2021 4:07 pm I don't know any disease specialists that actually thinks we can 'defeat' covid.

It just isn't that type of virus.

What we can do is protect the vulnerable from the worst of the disease. This would be enough if we did it properly.

Unfortunately, there seems to be a general push to treat this 'like polio or smallpox', which are viruses with different characteristics that could be 'defeated'. This approach is likely to lead to problems (eg, population-wide vaccinations will massively increase selection pressure for the virus to escape the current vaccines).

While it is nice to think that 'technology will save the day', cutting-edge technology is unlikely to do much for us over the next few years wrt 'defeating covid'.

If there is a saviour it will be in new treatments to reduce hospitalisations/fatalities, not in 'defeating covid'.
Spot on. Re para 3 - and we could have done, it it was done properly. ‘Lockdown’ was a mad idea, and it still is. After all, it’s entirely possible that lots of us already have ‘defeated’ it, as we do with many viruses; next business.

fon
Posts: 1289
Joined: Tue Dec 22, 2020 12:47 pm

Re: Defeating SARS-CoV-2

Post by fon »

amanuensis wrote: Mon Mar 15, 2021 4:07 pm What we can do is protect the vulnerable from the worst of the disease. This would be enough if we did it properly.
The theory/excuse is that there is no way to do it properly, outside locking down.
Unfortunately, there seems to be a general push to treat this 'like polio or smallpox', which are viruses with different characteristics that could be 'defeated'.
I see no push of that sort. On the contrary, Devi Sridhar threw in her towel, today, see twett below.
it will be in new treatments to reduce hospitalisations/fatalities, not in 'defeating covid'.
I kinda half agree with that, vaccines do the heavy lifting, but where it gets through, better treatment might help there too.Anyway, here's Devi, the fallen Queen of zero covid, throwing in the towel for the umpteenth time:
Screenshot 2021-03-15 at 12.52.12.png
Screenshot 2021-03-15 at 12.52.12.png (35.84 KiB) Viewed 471 times

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