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A (possible) solution to Covid-19

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Re: A (possible) solution to Covid-19

#351
post #342

Earlier quoted context omitted.

Could a strain like this be created with genetic modification? If you just need to delete a bit of it that doesn't sound too difficult. But I know nothing about this subject, so that's probably why...

We don't know exactly what each bit does, so we don't know what to delete.

IIRC, it’s only about 30Kb of information, and the vast majority of that is shared with similar viruses in the same family.

Assuming there’s a reliable way to remove segments of the genome (I’m not a biologist, so I’m not sure if that’s practical), it doesn’t appear to be an impossible problem to solve.

Re: A (possible) solution to Covid-19

#352
> Aren’t most people who have mild/asymptomatic cases infected with a dangerous strain?

> Yes. Almost all (>99.9%) of people who are infected (and have a mild case) are infected with a dangerous strain of the virus, they just happen to have an immune system that can control the virus well. With COVID-19 a mild case does not mean you are infected with an attenuated strain – for most people with a mild case if they happen to infect a person with preexisting conditions or who is old, that person will be at a high risk of dying. A mild case does not equal a harmless strain.

Even if the weak-strain hypothesis holds water (which remains to be seen), the proposal is predicated on something that's physically impossible to do. Test large numbers of people. Hundreds of millions or even billions.

Then, given those tests, find the weak strains.

That's also the minimum needed to "re-open" the country.

If we could test 20-30% of the population, we'd be in great shape. But we can't and may not ever be able to.

Even if you can test that many, you've got to prove that the weak strain is harmless. Then you've got to figure out how to administer doses safely.

So the solution must work within those parameters. And the only practical option is a vaccine.

> The major risk is the virus we think is safe is not 100% safe. While we can use community spread of the identified strain to estimate how safe it will be (i.e. if it has infected 1000 people and none have got seriously ill then we should have a pretty good idea that it is safe), but our knowledge will be incomplete. We can of course spend the next few years testing and trialling, but if we do this by the time any strain is shown to be 99.999% safe (not even the polio vaccine is 100% safe) we will have all got COVID-19 and the world’s economy will be a smoking ruin.

This guy is absolutely bonkers, or pulling a Swift.

He's proposing the (forced?) infection of a large portion of the population with a live virus that has been through none of the safety protocols established over many decades of catastrophic failures.

This is not how drug testing works. This is not how public health works. This is not how you assess safety. This is not ethical.

This is tech bro medicine at its absolute worst.

Re: A (possible) solution to Covid-19

#353

"We have a choice of taking some small risk now, or face the certainty of a much worse problem later. Time to accept some risk and do something." Agreed 100%. What about simply letting the people who young and healthy or immune go about their lives? Letting the young and healthy get sick and then become immune is essentially using an attenuated human instead of an attenuated virus. Same outcome though. This would bot…

This was the UK government's plan until they realised just how many people would die as a result.

Re: A (possible) solution to Covid-19

#354
post #68

Earlier quoted context omitted.

Sort of a weird ask, but as a real, no shit, virologist, what do you think about changing your messaging to make content more accessible to lazy readers? I have some half baked ideas about tradeoffs in infection rate and fatality, but I'm worse than a layman, I'm a layman with an opinion. I'd sorta thought a virus could be real lethal(like ebola) ore real infectious(like a cold) but it's kinda hard to be both at the…

Viruses don’t really care about thing like death rate, they just care about how effectively they are spread from person to person (viruses don’t really care about anything, but I am describing how they appear to act if they had a mind). In general the less deadly viruses spread better as dead people are not able to spread the virus around as well as living people. The general trend is for viruses to become less deadl…

Spread rate would also need to stay in a certain range for a virus to stick around. Spread too fast and there won't be a second wave. The herd immunity effect gives this system some self-balancing properties, but there's surely a tipping point where even that won't help a speeding virus to survive.

Re: A (possible) solution to Covid-19

#355
post #249

Pooling could be used to more rapidly test the asymptomatic population: https://github.com/EFavDB/pooling

Even better than pooling is griding [0]. 0. https://twitter.com/rwade300/status/1247340350076628992

If B2 and D4 are positive, then in the marginals B,D,2,4 will show positive, but you don't know which of B2, B4, D2, D4 are positive.

Re: A (possible) solution to Covid-19

#356

Earlier quoted context omitted.

No it is not. There is still safety data, it has just been done by nature and not by jabbing people in the arm with some experimental vaccine.

No, the safety data is not well controlled in this case. There are lots of ways to administer a vaccine, it doesn't have to be injection. Look up the history of vaccination. Starting in the late 18th Century, people used to do this exact thing for early vaccinations: they found a naturally occurring, less pathogenic strain (for instance, cowpox[1] in the days of smallpox), and intentionally exposed people. This is ex…

Safety data can be gained from epidemiology studies. There is more than one way to work out if a treatment is safe and effective.

Re: A (possible) solution to Covid-19

#357
post #275

Earlier quoted context omitted.

Serious question: are we not? People are sequencing these things like crazy (c.f. the nextstrain.org data). Epidemiologists are working like mad to come up with data on severity in regions all over the globe. Virologists everywhere are dropping what they're doing otherwise to work on covid. It sorta strains reason to argue that none of these people thought of looking for an attenuated strain. Isn't the simpler truth…

The sequencing is not the important thing here, but the search for strains with gene deletions and contact tracing everyone in the area to find more cases to prove the strain is attenuated. As far as I know nobody is doing this.

You’re fairly hard to get in contact with directly. Would you mind sending me an email? I don’t think I’ll be a your “middle hop”, but I’ll try. My email is lyndsy@.com

My username here is my real name, and I should be easy to find. It’s also my username on Twitter, Keybase, and most other popular platforms.

Re: A (possible) solution to Covid-19

#358

This entire article is a waste of time from the beginning. The “two strain” theory was debunked the very next day as bad science. http://virological.org/t/response-to-on-the-origin-and-conti... I can’t believe that a month later, this bad science is still being circulated, by a purported PhD and former professor.

I'm confused, the paper that's being debunked in your link: https://academic.oup.com/nsr/advance-article/doi/10.1093/nsr... Is not the same paper he's pointing to as having found a milder strain: https://www.medrxiv.org/content/10.1101/2020.03.10.20033944v... What am I missing? Are they both based on a flawed understanding?

Not exactly, but the rebuttal includes:

"As of 2nd March 2020, there are 111 nonsynonymous mutations that have been identified in the outbreak, these have been catalogued here in the CoV-GLUE resource 504 and can be visualised in Figure 1. At current, there is no evidence that any of these 111 mutations have any significance in a functional context of within-host infections or transmission rates."

The premise that there is an "asymptomatic strain" is still theoretically possible but unsubstantiated, despite ongoing investigation.

> "I can’t believe that a month later, this bad science is still being circulated, by a purported PhD and former professor. "

That strikes me as a bit harsh, given that the posted article doesn't actually rely on two-strain to make its case, just the idea of functional variants possibly being out there somewhere. MacLean's rebuttal didn't definitely exclude the possibility that there's some functional variants out there somewhere, we just don't know, haven't seen it in anything we've catalogued so far.

Science is often about calibration. I wouldn't say a search for functional variants is completely worthless. That's why researchers continue to look at variants. On the other hand, completely agree it's overselling to pitch this as a silver bullet for the whole crisis though. Research can be important even when it doesn't solve for everything.

Re: A (possible) solution to Covid-19

#359

This entire article is a waste of time from the beginning. The “two strain” theory was debunked the very next day as bad science. http://virological.org/t/response-to-on-the-origin-and-conti... I can’t believe that a month later, this bad science is still being circulated, by a purported PhD and former professor.

The articles author doesn't claim there are two strains. He claims there are many mutations. The link shared by the parent notes, "As of 2nd March 2020, there are 111 nonsynonymous mutations that have been identified in the outbreak". This seems to agree with the original article.

The article seems to work within the current findings of many mutations and different mutations have varying degrees of impact on people.

Re: A (possible) solution to Covid-19

#360

This entire article is a waste of time from the beginning. The “two strain” theory was debunked the very next day as bad science. http://virological.org/t/response-to-on-the-origin-and-conti... I can’t believe that a month later, this bad science is still being circulated, by a purported PhD and former professor.

I can’t believe you think I am arguing for the “two strain” theory. My proposal has absolutely zero to do with two strains.
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