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Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

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Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#211

Post by yters »

DiogenesKynikos wrote: post #196
yters wrote: post #193

Earlier quoted context omitted.

i dont understand why it would have to jump through a bunch of animals first. cant it go from bat to human? fauci was conducting coronavirus gain of function experiments in wuhan in 2019 trying to go from bat to human, so at least some scientists didn't consider the evolutionary distance to be so great UPDATE: newsweek article on fauci https://www.newsweek.com/dr-fauci-backed-controversial-wuhan...

I can't make heads or tails of what you're saying. Fauci was conducting experiments in Wuhan? Where are you getting this from?

here is the article about fauci endorsing and funding such research

https://www.newsweek.com/dr-fauci-backed-controversial-wuhan...

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#212

Post by at_a_remove »

slim wrote: post #201
koheripbal wrote: post #170

Earlier quoted context omitted.

There are still a lot people spreading the misinformation that hetero sex is as risky as anal sex, because they have some odd agenda to push.

do you mean that vaginal sex is less risky than anal sex? Wikipedia says otherwise https://en.m.wikipedia.org/wiki/HIV/AIDS#Transmission do you have any source for what you believe?

You may wish to try https://en.m.wikipedia.org/wiki/HIV/AIDS#Transmission

Receptive penile-vaginal intercourse* at 0.05–0.30% Receptive anal intercourse* at 0.04–3.0%

Given the error bars ...

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#213

Post by DiogenesKynikos »

yters wrote: post #211
DiogenesKynikos wrote: post #196

Earlier quoted context omitted.

I can't make heads or tails of what you're saying. Fauci was conducting experiments in Wuhan? Where are you getting this from?

here is the article about fauci endorsing and funding such research https://www.newsweek.com/dr-fauci-backed-controversial-wuhan...

Good. This is very important reasearch, as the pandemic has shown.

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#214

Post by yters »

DiogenesKynikos wrote: post #213
yters wrote: post #211

Earlier quoted context omitted.

here is the article about fauci endorsing and funding such research https://www.newsweek.com/dr-fauci-backed-controversial-wuhan...

Good. This is very important reasearch, as the pandemic has shown.

So I'm still not following. You say it is infeasible for a lab to generate sars2, yet it seems Fauci thinks it is feasible enough to fund an attempt.

If I understand your argument, you claim sars2 is too genetically different from the closest public sequences to have been lab engineered. But, what precludes a lab from discovering a virus in the wild that is close to making the jump, and then pushing it the rest of the way? I am not understanding the argument that we have to limit the range of possibility to only the publicly disclosed virus sequences.

For example, if you line up the ace2 site between sars2 and sars, they have a lot of similarity. This author claims the section is essentially copied over, although I don't know if it is statistically significant enough to not just be an accident. https://nerdhaspower.weebly.com/blog/scientific-evidence-and...

So, a "lab origin" theorist could say they isolated a virus in the wild, and copied over the ace2 section from sars, and then ran it through human tissue until it gain enough function to spread effectively in the human population. Is that less or more likely than a coronavirus in the wild mutating enough to make such a lethal jump to humans? Is there any way to put a probability on the two theories?

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#215

Post by DiogenesKynikos »

yters wrote: post #214
DiogenesKynikos wrote: post #213

Earlier quoted context omitted.

Good. This is very important reasearch, as the pandemic has shown.

So I'm still not following. You say it is infeasible for a lab to generate sars2, yet it seems Fauci thinks it is feasible enough to fund an attempt. If I understand your argument, you claim sars2 is too genetically different from the closest public sequences to have been lab engineered. But, what precludes a lab from discovering a virus in the wild that is close to making the jump, and then pushing it the rest of th…

> You say it is infeasible for a lab to generate sars2, yet it seems Fauci thinks it is feasible enough to fund an attempt.

Saying they were trying to generate SARS-CoV-2 in a lab is a very polemical way of saying that they were studying viral transmission in cell culture. They didn't create SARS-CoV-2. They created viruses that are extremely different from SARS-CoV-2.

> But, what precludes a lab from discovering a virus in the wild that is close to making the jump, and then pushing it the rest of the way?

The Wuhan Institute of Virology publishes identifying genetic sequences of the viruses it samples from the wild. SARS-CoV-2 is not among those viruses. The closest virus (RaTG13) that the WIV found before the pandemic was 4% different from SARS-CoV-2. If SARS-CoV-2 were engineered from RaTG13, then the two viruses would be virtually identical throughout most of their genome. The only differences would be those introduced by the researchers. Yet the two viruses have seemingly random differences throughout their genomes - the types of differences you would not get in gain-of-function experiments. A 4% difference corresponds to many years of divergent evolution. The two viruses might have split as far back as the late 1800s.

So it's certain that SARS-CoV-2 is not engineered on the basis of RaTG13. If you want to claim that the WIV secretly found a different virus, then for unknown reasons didn't publish about that virus, and then started doing gain-of-function experiments on it without telling anyone (including their American scientific collaborators), you're just so far out in the realm of evidence-free conspiracy land that it's not worth responding to.

> copied over the ace2 section from sars

The receptor binding domains of SARS-CoV and SARS-COV-2 are very different from one another. The blog you're looking to is nonsense.

Listen to actual experts, like the virologists at This Week in Virology, not bloggers making wild claims.

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#216

Post by yters »

DiogenesKynikos wrote: post #215
yters wrote: post #214

Earlier quoted context omitted.

So I'm still not following. You say it is infeasible for a lab to generate sars2, yet it seems Fauci thinks it is feasible enough to fund an attempt. If I understand your argument, you claim sars2 is too genetically different from the closest public sequences to have been lab engineered. But, what precludes a lab from discovering a virus in the wild that is close to making the jump, and then pushing it the rest of th…

> You say it is infeasible for a lab to generate sars2, yet it seems Fauci thinks it is feasible enough to fund an attempt. Saying they were trying to generate SARS-CoV-2 in a lab is a very polemical way of saying that they were studying viral transmission in cell culture. They didn't create SARS-CoV-2. They created viruses that are extremely different from SARS-CoV-2. > But, what precludes a lab from discovering a v…

thanks, i see what you are saying

regarding the binding sites, clearly they are quite different. but, the similarities seem greater than possible by chance, and i am not sure how that could happen. maybe a variant of sars mutated into sars2?

the sites are at least similar enough that researchers are trying to use sars vaccines to engineer sars2 vaccine

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#217

Post by DiogenesKynikos »

yters wrote: post #216
DiogenesKynikos wrote: post #215

Earlier quoted context omitted.

> You say it is infeasible for a lab to generate sars2, yet it seems Fauci thinks it is feasible enough to fund an attempt. Saying they were trying to generate SARS-CoV-2 in a lab is a very polemical way of saying that they were studying viral transmission in cell culture. They didn't create SARS-CoV-2. They created viruses that are extremely different from SARS-CoV-2. > But, what precludes a lab from discovering a v…

thanks, i see what you are saying regarding the binding sites, clearly they are quite different. but, the similarities seem greater than possible by chance, and i am not sure how that could happen. maybe a variant of sars mutated into sars2? the sites are at least similar enough that researchers are trying to use sars vaccines to engineer sars2 vaccine

What do you mean that they're more similar than is possible by chance?

Instead of reading conspiracy blogs, go read scientific papers. If you don't understand them, then there is really good introductory course material on virology available from several universities.

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#218

Post by yters »

DiogenesKynikos wrote: post #217
yters wrote: post #216

Earlier quoted context omitted.

thanks, i see what you are saying regarding the binding sites, clearly they are quite different. but, the similarities seem greater than possible by chance, and i am not sure how that could happen. maybe a variant of sars mutated into sars2? the sites are at least similar enough that researchers are trying to use sars vaccines to engineer sars2 vaccine

What do you mean that they're more similar than is possible by chance? Instead of reading conspiracy blogs, go read scientific papers. If you don't understand them, then there is really good introductory course material on virology available from several universities.

Looking at the ACE2 alignment from the article, it looks like there are 55 spots where the sequences have different proteins. Of those 55 spots, 7 of them are identical between the bat and sars2. On the other hand, I count 20 matches between sars and sars2.

Using a uniform distribution over the 20 proteins, and saying the probability of two proteins matching is 1/20, then the binomial probability of getting 7 or more matches out of 55 is 0.02, whereas the probability of getting 20 or more matches is less than 0.000001.

I can see 0.02 being achieved by chance, but 0.000001 seems pretty unlikely to happen by accident. So, there is some sort of non accidental relationship between sars and sars2. Maybe 1) sars2 is descended from sars, or maybe 2) it is lab engineered.

If the bat coronavirus is likely the more proximate ancestor to sars2 than sars, then #1 seems unlikely, which makes #2 the more plausible hypothesis.

Also, to return to your argument about restricting our 'lab origin' hypothesis to known viruses, it seems that if WIV found a very effective bat coronavirus, and intend to create a bioweapon from it, this is exactly the situation when they would not share the sequence. I do not understand why you think people creating a bioweapon would want to share their materials with the world.

You may also find this other article by the same author interesting, pointing out the evidence strongly points to RaTG13 being faked. https://nerdhaspower.weebly.com/ratg13-is-fake.html

There is also this interesting tweet from Jonathan Jacobs that the sample data for RaTG13 does not match the assembled genome. https://twitter.com/bioinformer/status/1252813532850081792

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#219

Post by DiogenesKynikos »

yters wrote: post #218
DiogenesKynikos wrote: post #217

Earlier quoted context omitted.

What do you mean that they're more similar than is possible by chance? Instead of reading conspiracy blogs, go read scientific papers. If you don't understand them, then there is really good introductory course material on virology available from several universities.

Looking at the ACE2 alignment from the article, it looks like there are 55 spots where the sequences have different proteins. Of those 55 spots, 7 of them are identical between the bat and sars2. On the other hand, I count 20 matches between sars and sars2. Using a uniform distribution over the 20 proteins, and saying the probability of two proteins matching is 1/20, then the binomial probability of getting 7 or more…

> So, there is some sort of non accidental relationship between sars and sars2.

Yeah, they're both betacoronaviruses. You've just discovered something called "common descent." Charles Darwin published about it in 1859.

I'm sorry, but this is getting comical. You really have to step back and learn some basics about biology before you go on this dive into conspiracy theories.

Re: Oldest 'nearly complete' HIV genome found in forgotten tissue sample from 1966

#220

Post by yters »

DiogenesKynikos wrote: post #219
yters wrote: post #218

Earlier quoted context omitted.

Looking at the ACE2 alignment from the article, it looks like there are 55 spots where the sequences have different proteins. Of those 55 spots, 7 of them are identical between the bat and sars2. On the other hand, I count 20 matches between sars and sars2. Using a uniform distribution over the 20 proteins, and saying the probability of two proteins matching is 1/20, then the binomial probability of getting 7 or more…

> So, there is some sort of non accidental relationship between sars and sars2. Yeah, they're both betacoronaviruses. You've just discovered something called "common descent." Charles Darwin published about it in 1859. I'm sorry, but this is getting comical. You really have to step back and learn some basics about biology before you go on this dive into conspiracy theories.

Hmm, still not following. Why would the fact both are betacoronaviruses entail ace2 is conserved? Is human binding ace2 a common feature of betacoronaviruses? Are you arguing that sars is the more recent ancestor than ratg13?

I blasted sars2 against sars and against ratg13. 88% coverage for the first and 99% for the second, so ratg13 seems to be a much more recent ancestor.

- sars2 v. sars: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=D7WE9PB...

- sars2 v. ratg13: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=D7WGNJG...

Why would ace2 be much better preserved between sars2 and sars than between sars2 and ratg13?

Apologies for being dense :) As you notice, I'm pretty new to bioinformatics. Just trying to understand what your argument is.

UPDATE: Sorry, I see a mistake I've been making that is confusing. I should be referring to Bat_CoV_ZC45 and Bat_CoV_ZXC21, not ratg13. ratg13 is the one that also has a close match to ace2, but the author claims is a forgery. The bat coronaviruses also seem to be more evolutionarily close to sars2 than sars, and they don't have the ace2 binding sites.

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