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Lab leak fight casts chill over virology research

nytimes.com

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Re: Lab leak fight casts chill over virology research

#231

Post by lamontcg »

wdr1 wrote: post #202

Or, you know, "Lab Leak of Coronavirus casts chill over virology research". I know it's not definitive it was a lab leak, but many US agencies including, notably, the Department of Energy, say it's likely it was. And when you change the headline to reflect that, it sure does change the message.

The National Intelligence Council of the Office of the Director of National Intelligence found:

> The IC assesses that SARS-CoV-2, the virus that causes COVID-19, probably emerged and infected humans through an initial small-scale exposure that occurred no later than November 2019 with the first known cluster of COVID-19 cases arising in Wuhan, China in December 2019.

And that:

> As of August 2021, we still have not observed genetic signatures in SARS-CoV-2 that would be diagnostic of genetic engineering, according to the IC’s understanding of the virus. Similarly, we have not identified any existing coronavirus strains that could have plausibly served as a backbone if SARS-CoV-2 had been genetically engineered.

Also:

> The WIV previously created chimeras, or combinations, of SARS-like coronaviruses, but this information does not provide insight into whether SARS-CoV-2 was genetically engineered by the WIV.

And:

> Early in the pandemic, the WIV identified that a new virus was responsible for the outbreak in Wuhan. It is therefore assessed that WIV researchers pivoted to COVID-19-related work to address the outbreak and characterize the virus. These activities suggest that WIV personnel were unaware of the existence of SARS-CoV-2 until the outbreak was underway.

And as far as spillover from collected samples in the lab goes:

> They also see the potential that a laboratory worker inadvertently was infected while collecting unknown animal specimens to be less likely than an infection occurring through numerous hunters, farmers, merchants, and others who have frequent, natural contact with animals

https://www.dni.gov/files/ODNI/documents/assessments/Declass...

A prior declassified report found:

> Prior to the pandemic, we assess WIV scientists conducted extensive research on coronaviruses, which included animal sampling and genetic analysis. We continue to have no indication that the WIV’s pre-pandemic research holdings included SARS-CoV-2 or a close progenitor, nor any direct evidence that a specific research-related incident occurred involving WIV personnel before the pandemic that could have caused the COVID pandemic.

https://www.dni.gov/files/ODNI/documents/assessments/Report-...

No idea why DOE continues to think it was a lab leak, other than we can't definitively prove it wasn't and since ChinaBad(tm) we have to assume it was.

Re: Lab leak fight casts chill over virology research

#232

Post by improv »

cbsmith wrote: post #177
improv wrote: post #165

Earlier quoted context omitted.

NIMBYism != People being concerned about their neighbors possessing weapons of mass destruction/super viruses capable of killing them and millions/billions of other people.

No, but it does equal a people being concerned about the effects of making a change while completely ignoring the effects of NOT making a change.

>while completely ignoring the effects of NOT making a change

The completely hypothetical effects of not making a change in just one area of virology research which is highly criticized by many in the scientific community.

It's hilariously absurd to compare people who don't want a dual use bioweapons research facility in their neighborhood to NIMBYism.

Re: Lab leak fight casts chill over virology research

#233

Post by peteradio »

lamontcg wrote: post #230
peteradio wrote: post #229

Earlier quoted context omitted.

DEFUSE proposed insertion of human-specific cleavage sites not serial passage.

RaTG13 differs from SARS-CoV-2 by a lot more than just an FCS

How far away would it be? Would it still take millions and millions of bats or is it now within the realm of possibility to infect humanized mice and get SARS-CoV-2 out the other end?

Re: Lab leak fight casts chill over virology research

#234

Post by keneda7 »

lamontcg wrote: post #231
wdr1 wrote: post #202

Or, you know, "Lab Leak of Coronavirus casts chill over virology research". I know it's not definitive it was a lab leak, but many US agencies including, notably, the Department of Energy, say it's likely it was. And when you change the headline to reflect that, it sure does change the message.

The National Intelligence Council of the Office of the Director of National Intelligence found: > The IC assesses that SARS-CoV-2, the virus that causes COVID-19, probably emerged and infected humans through an initial small-scale exposure that occurred no later than November 2019 with the first known cluster of COVID-19 cases arising in Wuhan, China in December 2019. And that: > As of August 2021, we still have not…

I am assuming the 1 IC element in the link I reference below is the DOE. It claims

"One IC element assesses with moderate confidence that the first human infection with SARS-CoV-2 most likely was the result of a laboratory-associated incident, probably involving experimentation, animal handling, or sampling by the Wuhan Institute of Virology. These analysts give weight to the inherently risky nature of work on coronaviruses."

Based on the quote (if the one IC element is in fact the DOE) is seem they are basing it on the "inherently risky nature of the work on coronaviruses.

I do find it interesting this was given with moderate confidence but the natural occurring is only given low confidence. Any idea how the whole confidence level is determined?

See the second bullet point on key takeaways.

https://www.intelligence.gov/assets/documents/702%20Document...

Re: Lab leak fight casts chill over virology research

#235

Post by cbsmith »

nvm0n2 wrote: post #213
cbsmith wrote: post #196

Earlier quoted context omitted.

> Well we spent over a decade and millions of dollars studying SARS coronaviruses and yet none of that work was of any help in fighting the pandemic. Wow. Just wow. It's statements like this that make me think we should indeed halt all virology research, and really all medical research and development entirely. We deserve what we get.

All government funded work maybe, yeah? It wouldn't make much difference. The consumers of that sort of research are ultimately just pharma companies and they don't use it much because so little replicates to begin with.

You honestly believe that government funded work didn't "make much difference" with dealing with COVID?

Re: Lab leak fight casts chill over virology research

#236

Post by lamontcg »

keneda7 wrote: post #234
lamontcg wrote: post #231

Earlier quoted context omitted.

The National Intelligence Council of the Office of the Director of National Intelligence found: > The IC assesses that SARS-CoV-2, the virus that causes COVID-19, probably emerged and infected humans through an initial small-scale exposure that occurred no later than November 2019 with the first known cluster of COVID-19 cases arising in Wuhan, China in December 2019. And that: > As of August 2021, we still have not…

I am assuming the 1 IC element in the link I reference below is the DOE. It claims "One IC element assesses with moderate confidence that the first human infection with SARS-CoV-2 most likely was the result of a laboratory-associated incident, probably involving experimentation, animal handling, or sampling by the Wuhan Institute of Virology. These analysts give weight to the inherently risky nature of work on corona…

I can't explain that.

The DOE seems to have assigned "moderate" confidence to the idea of a lab leak on the basis of zero concrete evidence. Taking the assessment on the whole it seems obvious to me that the argument from them is weak, but the assessment can't come out and just state that in plain English.

Re: Lab leak fight casts chill over virology research

#237

Post by lamontcg »

peteradio wrote: post #233
lamontcg wrote: post #230

Earlier quoted context omitted.

RaTG13 differs from SARS-CoV-2 by a lot more than just an FCS

How far away would it be? Would it still take millions and millions of bats or is it now within the realm of possibility to infect humanized mice and get SARS-CoV-2 out the other end?

Yes, you're still a thousand mutations away from each other. The FCS is tiny. The mutations are spread all over the entire genome--although the main areas are in spike RBD (which suggests that RaTG13 may not be able to use ACE2 at all). The PRRAR FCS that SARS-CoV-2 uses is also a previously-unknown-to-humans FCS and not one a human scientist would have naively guessed would work.

Re: Lab leak fight casts chill over virology research

#238

Post by tootie »

rurp wrote: post #206
tootie wrote: post #192

Earlier quoted context omitted.

Every pandemic ever has been caused by a natural source. Most pandemics happened before virology was a field. The default assumption from the start was animal source until there's proof it was something else.

>Every pandemic ever has been caused by a natural source. That's an awfully bold claim, unless you have proof that covid-19 occurred naturally. Defaulting to your preferred reality and ignoring the potential risks is not a responsible way to guide research policy.

I'm saying every other pandemic in human (or really non-human) history.

Re: Lab leak fight casts chill over virology research

#239

Post by peteradio »

lamontcg wrote: post #237
peteradio wrote: post #233

Earlier quoted context omitted.

How far away would it be? Would it still take millions and millions of bats or is it now within the realm of possibility to infect humanized mice and get SARS-CoV-2 out the other end?

Yes, you're still a thousand mutations away from each other. The FCS is tiny. The mutations are spread all over the entire genome--although the main areas are in spike RBD (which suggests that RaTG13 may not be able to use ACE2 at all). The PRRAR FCS that SARS-CoV-2 uses is also a previously-unknown-to-humans FCS and not one a human scientist would have naively guessed would work.

Thanks.

Re: Lab leak fight casts chill over virology research

#240

Post by sterlind »

lamontcg wrote: post #228
dhdudbd wrote: post #119

Earlier quoted context omitted.

>96% similar what does this mean

That means they were several decades of evolution in the wild away from each other. It would take passage through billions of organisms to turn RaTG13 into SARS-CoV-2. Which is probably what happened naturally through many, many millions of bats (and whatever intermediate animal) being infected and passing it on. Something that is well outside the scale of serial passage experiments in a lab.

How do you arrive at several decades and billions of organisms? You can't extrapolate the current mutation rate to the spillover event; SARS-CoV-2 was already quite fit at infecting humans and didn't need to change much. In contrast, during spillover events there's heavy selection pressure to adapt to the new host.

There's also the possibility of recombination events, which can instantly cause significant drift. Now consider the case of the Mojiang miners, who contracted and slowly succumbed to viral pneumonia in 2012 after inhaling bat guano. WIV found, like, a dozen beta-coronaviruses in that cave alone (including RaTG13.) The miners could have been exposed to several at once, which recombined and adapted quickly to their new home in human lungs. Again, unlikely to have been SARS-CoV-2, since the pandemic almost certainly would have happened already, but whatever they had was virulent enough to kill half of them.

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