No self-respecting scientist concluded that either a natural origin or a lab leak were the definitive cause of the pandemic. This is clear if you actually read scientific literature. It’s why phrases akin to “the most supported hypothesis is X” or “the Y theory is unlikely without more supporting evidence” are used. Both hypotheses were and are still possible explanations.

It’s people who get their scientific info from sources like the Telegraph that keep jumping to conclusions. Or people who don’t understand what a section leader at the NIH does, how research grants work, or what gain of function research is. You know, like yourself.

[+] TrismegistusMx@lemmy.world -66 points 1 year ago (2 children)

Yeah, it was just coincidence that the exact same strain evolved in the wild and transferred to humans in the same place at the same time!

[–] justdoit@lemm.ee 68 points 1 year ago (2 children)

The original grant was to the EcoHealth Alliance, which then subcontracted the Wuhan institute to collect wild samples from bats. In other words, the whole point of the research was to try and catalogue viruses that existed in the wild with pandemic potential.

It’s not coincidence that lab samples there or in other facilities exist that are close in sequence to viruses later identified in humans. That was, in fact, the goddamn point of surveying bat coronaviruses: to identify those with spillover potential. And it’s absolutely possible one of these collected samples was mishandled and leaked from the lab. After all, lab leaked viral outbreaks happen almost every other year, and there were already safety concerns at this particular site published long before the pandemic.

But what you and every other mouthbreathing idiot is trying to say is that Fauci, a director of the NIAID at the time, personally directed gain of function research to engineer new viruses to infect humans and then that virus escaped. Which, speaking as a molecular biologist myself, is laughably backwards.

[+] bandario@lemmy.dbzer0.com -26 points 1 year ago* (last edited 1 year ago) (1 children)

It seems like you've read enough to get halfway there.

You should go back and read the source documents and go over what ecohealth alliance were actually doing, and where they were doing it. The funding proposals were extremely detailed, right down to carrying out gain of function research to aerosolise the corona viruses harvested from bats.

It is almost impossible to immunise bats using droplet transmission and this is the source of the global fuckup.

At some stage during this process, the modified pathogen from very early stages of developing a corona vaccine FOR BATS (the stated goal of the funding request) it somehow got out of one of the labs involved. (Malice or stupidity, we'll never know)

At that stage it would still be fair to call the original escaped variant a VIRUS because it had not yet reached the development stage of being attenuated sufficiently to be called a vaccine, but it was a long way from a wild type variant.

This lines up with early sequencing of the virus that is widely documented. Those with any scientific integrity have acknowledged from day 1 that there were portions of the sequence that can not occur without human intervention.

In short, this was all being done with US funding in labs with woefully inadequate safety protocols.

So long as we are prepared to accept the risk/reward profile of gain of function research being carried out anywhere in the world, the risk of a similar global pandemic will never go away.

[–] justdoit@lemm.ee 37 points 1 year ago* (last edited 1 year ago) (1 children)

Grant Project Number: 2R01AI110964-06

“Aim 1. Characterize the diversity and distribution of high spillover-risk SARSr-CoVs in bats in southern China. We will use phylogeographic and viral discovery curve analyses to target additional bat sample collection and molecular CoV screening to fill in gaps in our previous sampling and fully characterize natural SARSr-CoV diversity in southern China. We will sequence receptor binding domains (spike proteins) to identify viruses with the highest potential for spillover which we will include in our experimental investigations (Aim 3). Aim 2. Community, and clinic-based syndromic, surveillance to capture SARSr-CoV spillover, routes of exposure and potential public health consequences. We will conduct biological-behavioral surveillance in high-risk populations, with known bat contact, in community and clinical settings to 1) identify risk factors for serological and PCR evidence of bat SARSr-CoVs; & 2) assess possible health effects of SARSr-CoVs infection in people. We will analyze bat-CoV serology against human-wildlife contact and exposure data to quantify risk factors and health impacts of SARSr-CoV spillover. Aim 3. In vitro and in vivo characterization of SARSr-CoV spillover risk, coupled with spatial and phylogenetic analyses to identify the regions and viruses of public health concern. We will use S protein sequence data, infectious clone technology, in vitro and in vivo infection experiments and analysis of receptor binding to test the hypothesis that % divergence thresholds in S protein sequences predict spillover potential.”

Color me shocked, but that’s the funding proposal and there’s nothing in there even approaching whatever you’re talking about. But hey, maybe you’re referring to the rejected DARPA grant proposal leaked by DRASTIC:

“THE PROPOSAL PLANNED TO INTRODUCE “KEY RBD RESIDUES” INTO LOW RISK STRAINS TO TEST PATHOGENICITY IN HUMAN AIRWAY-CELLS”

Wowie, looks like we have a hit! Rather than reading their spin though, I went and found the REJECTED grant proposal:

“We will sequence spike proteins, reverse engineer them to conduct binding assays, and insert them into bat SARSr-CoV backbones (these use bat-SARSr-CoV backbones, not SARS-CoV, and are exempt from dual-use and gain or function concerns)”

If you’re not aware, these backbones are common lab vectors which aren’t pathogenic themselves, made from different viruses. Their sequences are significantly different than either SARS-CoV or SARS-CoV-2. So, chimeric receptor/backbone pairs are used to assess viral entry into humanized cells more so than virulence. You may disagree with whether or not that’s still too dangerous of a method, but it’s a moot point here because 1. The backbones proposed here are completely different than COVID, so it can’t be the same viral agent and 2. This is a REJECTED PROPOSAL. None of this was actually done and it’s fantasy to pretend it is.

Next claim: aerosolized droplet for vaccines:

“We will complement [broad scale immune boosting with bat interferon] by coupling agonist treatments with SARSr-CoV recombinant spike proteins to boost pre-existing adaptive immune response in adult bats… we will incorporate [recombinant spike proteins] into nano particles or raccoon pox virus vectors for delivery to bats”

They’re not proposing aerosolizing whole droplets with competent SARS-CoV in them you moron, they’re basically saying “hey, you know those nasal sprays we use for the flu every year? Let’s give that to bats”.

Ooh, my favorite. No scientist with integrity says that the genome wasn’t manipulated.

You’re gonna have to tell that to the couple hundred scientists who have been studying this for a while:

“There is no logical reason why an engineered virus would utilize such a suboptimal furin cleavage site, which would entail such an un- usual and needlessly complex feat of genetic engineering. The only previous studies of artificial insertion of a furin cleavage site at the S1/S2 boundary in the SARS-CoV spike protein uti- lized an optimal ‘‘RRSRR’’ sequence in pseudotype systems (Belouzard et al., 2009; Follis et al., 2006). Further, there is no ev- idence of prior research at the WIV involving the artificial insertion of complete furin cleavage sites into coronaviruses.”

There really isn’t any evidence of manipulation at all. The backbone isn’t a standard lab construct. The cleavage site could have arisen from recombination. In the spirit of good science, I would never rule anything out, but the evidence very much supports a natural origin. Lab leak from a sample? Maybe, but that’s different than genetic engineering. For that you need stronger evidence. The strongest bit of evidence we have is the stonewalling from WIV and China, which is certainly suspicious. But, it’s unfortunately incidental and that isn’t good enough to jump to conclusions.

Try actually reading the text of these proposals before reading someone else’s spin on it.

[–] notacat@mander.xyz 13 points 1 year ago (1 children)

I am somehow still surprised at how many of my intelligent, educated healthcare coworkers believe in the purposeful bio weapon theory despite there being no evidence of human-made genetic manipulation. We can analyze whole genomes now, there’s no need to make shit up.

[–] justdoit@lemm.ee 8 points 1 year ago

Yeah, it’s pretty sad. But I have fun digging into the sources for the misinformation, so there’s that.

[+] TrismegistusMx@lemmy.world -32 points 1 year ago (1 children)

If you were secure in your beliefs, you could use logic, science, or evidence.

You use insults. I question, you insult. Who is wrong?

[–] justdoit@lemm.ee 21 points 1 year ago* (last edited 1 year ago) (1 children)

Funny, you haven’t “questioned” anything. You’ve just regurgitated your same tired disproven talking points. Then you act like your viewpoint deserves respect. It doesn’t. No sources, no evidence, no respect.

If you’d like my sources, here you go. Let me know when you find the spot that says “I, Fauci, personally oversaw the development of a virus that looks absurdly natural in origin.”

The original grant proposal for EcoHealth Alliance: https://reporter.nih.gov/project-details/9819304

Every relevant follow up study produced under that grant proposal:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6171170/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7094983/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6178078/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7097006/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148670/

[+] TrismegistusMx@lemmy.world -28 points 1 year ago (1 children)

I haven't posted any evidence because I've only posted reservations about the narrative. You have chosen to attack me personally and you FINALLY posted several studies that do not say anything about containment, lab procedure, the contents of the lab, or anything else that might assuage my doubts. What they do prove is that gain of function research was being performed on SARS in the area where the pandemic first started. You accuse me of being irrational when you're losing your god damned mind at the very idea that the lab could be the source of the pandemic.

[–] justdoit@lemm.ee 18 points 1 year ago (1 children)

Quite a fast reader, aren’t you?

Please cite the spot in those documents that “prove gain of function research was being performed on SARS in the area the pandemic first started”

[+] TrismegistusMx@lemmy.world -19 points 1 year ago* (last edited 1 year ago) (1 children)

Those documents you posted are ancillary to the actual experimentation. Here's some more details for you.

https://www.documentcloud.org/documents/21055989-understanding-risk-bat-coronavirus-emergence-grant-notice https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006698

But the research on the bat viruses in Wuhan showed that infecting live animals with altered viruses can have unpredictable consequences. A report to NIH on the project’s progress in the year ending in May 2018 described scientists creating new coronaviruses by changing parts of WIV1 and exposing genetically engineered mice to the new chimeric viruses. Research published in 2017 in the journal PLOS Pathogen showed that, in cells in a laboratory, similar chimeric viruses reproduced less effectively than the original. NIH cited that research as one of the reasons the moratorium on gain-of-function research of concern didn’t apply to this experiment. “It was a loss of function, not a gain of function,” the email from NIH explained. (NIH also pointed out that the changes to the chimeric viruses “would not be anticipated to increase virulence or transmissibility in humans.”)

Inside the lungs of the humanized mice, however, the novel viruses appear to have reproduced far more quickly than the original virus that was used to create them, according to a bar graph shown in the documents. The viral load in the lung tissue of the mice was, at certain points, up to 10,000 times higher in the mice infected with the altered viruses than in those infected with WIV1. According to Deatrick, the NIH spokesperson, the difference in the rates of viral reproduction — which were particularly pronounced two and four days after the mice were infected with the virus — didn’t amount to gain of function because, by the end of the experiment, the amount of virus produced by the parent and chimeric strains evened out. “Viral titers were equivalent by the end of the experimental time-course,” Deatrick wrote. The email also said, “NIH supports this type of research to better understand the characteristics of animal viruses that have the potential to spill over to humans and cause widespread disease.”

Scientists The Intercept consulted expressed differing views on whether the increase in viral load could be translated to an increase in transmissibility, which relies on the virus’s ability to replicate. To some, the jump in viral load indicated that the modified RNA virus could replicate far more rapidly than the original in the lungs of the mice, likely leading to increased pathogenicity and spread. Rasmussen, of the Vaccine and Infectious Disease Organization, pointed out that viral load is not identical to reproduction rate, noting: “This shows the chimeric viruses replicated a little faster, but that tells us exactly nothing about transmissibility. Furthermore, WIV1 caught up by the end of the experiment. We see differences in the rate of viral replication all the time, but it is often not directly correlated with pathogenicity.”

Another figure in the documents suggests that at least one of the altered viruses not only enhanced viral reproduction, but also caused the humanized mice to lose more weight than those exposed to the original virus — a measure of the severity of illness.

https://theintercept.com/2021/09/09/covid-origins-gain-of-function-research/

The real question is still, "Why did you immediately jump to personal attacks, infodumping irrelevant studies, and why are you vehemently defending this lab as if you're the one who caused the leak?

[–] justdoit@lemm.ee 12 points 1 year ago* (last edited 1 year ago) (1 children)

Oh boy, so this is where you stumbled. I should have known it would be The Intercept article.

The documents are ancillary, huh? You cited the exact same grant proposal I sent you. So is it ancillary or not?

Here are some really critical points I’m willing to bet you misunderstood:

“We will construct chimeric SARSr-CoVs using WIV1 backbone and the S genes of selected SARSr-CoV strains and assess capacity to infect hACE2, bACE2, and cACE2 Vero cells…”

The WIV1 backbone is NOT the backbone found in SARS-CoV-2. It’s from a completely different human-infectious coronavirus strain. Furthermore, the spike proteins they’re studying would be gathered from bat coronaviruses found in the wild. So, this method is NOT considered GoF research by the NIH nor is it even potentially possible it resulted in the pandemic. They proposed assessing transmissibility by using an already known infectious backbone and an uncharacterized spike protein, not engineering a more deadly virus. WIV1 is already infectious in humans. The spike proteins gathered are the exact same sequences as those already present in the wild. You may still have reservations about this approach, but I’d argue it’s actually safer for studying viruses in this way because you use what’s known as a Bacterial Artificial Chromosome (BAC) to infect the cells rather than live virus. Meaning, no storage, handling, or serial passaging of viral samples is required past the initial isolation and the plaque assessments.

You may argue that any viral research which can result in genetic change should be classified unilaterally as GoF, and is too dangerous to be performed, much less at labs we don’t directly regulate. I would disagree on those points, but you’d join a rich debate on the subject which The Intercept article actually points out as well. But the fact remains that none of the above studies were designed to engineer more deadly pathogens for humans, and is ultimately a red herring for the SARS-CoV-2 debate. We know the backbone sequences and they do not match, so you and The Intercept article are barking up the wrong tree.

The same is true for the PLOS study you cited. Same viral backbone, same process. It’s there to assess transmissibility of a naturally occurring virus and try to predict future pandemic potential (of the original SARS-CoV, in their case), not to engineer more effective viruses. Same misunderstanding on its classification as GoF research, too. Even in the Intercept article you cite it talks about the results of other studies as technically “loss of function” in relation to some strains, which is true. But again, all of this is a red herring. SARS-CoV-2 did NOT use the backbone referenced here, and thus this study did not result in a genetically engineered virus that caused the pandemic.

As for citations, I’d point you to this snippet from a review article in Cell:

A near identical nucleotide sequence is found in the spike gene of the bat coro- navirus HKU9-1 (Gallaher, 2020), and both SARS-CoV-2 and HKU9-1 contain short palindromic sequences immediately up- stream of this sequence that are indicative of natural recombina- tion break-points via template switching (Gallaher, 2020). Hence, simple evolutionary mechanisms can readily explain the evolu- tion of an out-of-frame insertion of a furin cleavage site in SARS-CoV-2 (Figure 2).

You keep insisting that I think a lab leak is impossible, when I’ve made it very clear that a lab leak is still a possibility. There were safety concerns at Wuhan long before this whole thing. But a “lab leak” of a stored sample is completely different than “Fauci paid incompetent Chinese labs to engineer deadly pathogens”, and I’ve never seen evidence for the latter. Yet you’ve stated that sentiment here in the comment section, so somehow that unsubstantiated belief lives on. Until our pool of evidence changes, the most likely scenario is a zoonosis from a natural reservoir, or a lab leak from a gathered or cultured sample.

I’m curious why you seem so insistent that the evidence is being hidden and that everyone is silencing you. You come in here with unsubstantiated accusations, and then get angry when people call you out for it. Had you started with sources for your claims, I would have been happy to engage with you on that level. Acting like an ass in any forum isn’t going to get you far. Stop playing the victim.

[–] MossyFeathers@pawb.social 26 points 1 year ago* (last edited 1 year ago) (2 children)

sigh I know you've probably either already made up your mind or you're not arguing in good faith, so I'm not gonna engage any further except to say that it's entirely possible for a virologist to do research on zoonotic viruses. Just because it's a bat virus doesn't mean it stays a bat virus.

Also, there are probably billions if not trillions or quadrillions of individual COVID viruses out there. Each time a new one's made, there's a chance for it to mutate into something else. It's totally possible for a virus to evolve similar features in separate environments. I believe the term, "convergent evolution" applies here, and you can find examples larger than viruses in plants and animals, where even separate species can sometimes evolve the same features independently from one another. Carcinisation is an extreme example of this.

[–] Ropianos@feddit.de 8 points 1 year ago (2 children)

Just so you know, not only them are reading your response. I appreciate your response.

And as someone that isn't working in the field, I have to admit that it is very illogical that they would conduct gain-of-function research on coronaviruses in a country previously hit by a coronavirus outbreak while violating safety standards. Obviously that's hindsight but shouldn't this be very obviously a bad idea? It's not like the existence of a virus like COVID-19/sarscov-2 was completely unexpected.

[–] Silverseren@kbin.social 10 points 1 year ago (1 children)

I mean, you'd do the research where you would be finding the wild zoonotic pathogens you want to study. So the location makes perfect sense.

The biosafety issues are more just a long-standing problem with how science is done in China in general, which is overall bad.