Closest known relatives of virus behind Covid-19 found in Laos
nature.com
nature.com
"Regarding the spike, we identied a breakpoint at the beginning of the SARS-CoV-2 RBD, resulting in a downstream fragment composed of the RBD, the furin cleavage site, and ending in the N-terminal region of S2. Despite the absence of the furin site in these novel bat sarbecoviruses, phylogenetic reconstruction of this fragment, key for the virus tropism and host spectrum, revealed that Laotian R. malayanus BANAL-52, R. pusillus BANAL-103, and R. marshalli BANAL-236 coronaviruses are the closest ancestors of SARS-CoV-2 known to date."
Basically, the human furin cleavage site that allows for human cell infection is lacking in these newly discovered viruses. Speculation that the site was introduced into a progenitor bat coronavirus deliberately as part of gain-of-function research is still valid, i.e. the question remains open.
“The main problems that the Institute of Virology has is that the outbreak occurred in close proximity to that Institute. That Institute has in essence the best collection of virologists in the world that have gone out and sought out, and isolated, and sampled bat species throughout Southeast Asia. So they have a very large collection of viruses in their laboratory. And so it’s — you know — proximity is a problem. It’s a problem.” - Ralph Baric
(https://nymag.com/intelligencer/article/coronavirus-lab-esca...)
The timeline of HIV pandemic has been established decades after pandemic started. This will take time.
I'd assume that virus originating anywhere in SEA region would be detected in China first. Just like many other viruses originating in America continent would be first detected in USA.
And assuming the chinese haven't destroyed the relevant Wuhan lab samples. That's what I would do in their place. Better never know than take the risk that a technician leak such sensitive information.
Afaik, there was zero additional clarity around those after USSR dissolved, so don't hold your breath.
What's weird is that nobody talks about WHY Shi Zheng-Li/"Bat Woman" was digging around random caves in Yunnan.
She was sent to investigate a lethal outbreak with CFR of 50%.
"Lethal Pneumonia Cases in Mojiang Miners (2012)" https://www.frontiersin.org/articles/10.3389/fpubh.2021.7021...
https://www.scientificamerican.com/article/bat-cave-solves-m...
https://journals.plos.org/plospathogens/article?id=10.1371/j...
https://algulf.net/2021/06/09/2019-video-shows-wuhan-scienti...
She is an expert on SARS-like viruses, and her research focus is on the threat of zoonotic spillover from bats. One would expect her to be involved in the investigation of an apparent zoonotic spillover from bats that causes SARS-like symptoms. Hell, it would be weird if she wasn't part of the investigation.
The weird part is how hushed up it is. Nobody talks about the 2012 outbreak, even though it was supposedly a very similar virus, and they already talked about the Yunnan caves.
Just can't talk about the outbreak? Why?
Wuhan Center for Disease Control and Prevention is a 5 minute walk from the wet market. And went through the disruption of a move just before COVID broke out.
See https://nypost.com/2021/08/13/who-scientist-eyes-on-wuhan-la... for more.
Still closer than Southeast Asia, though.
>Do all people only travel on one subway line each and never change trains?
It's not what all people do that matters when trying to find the origin of a highly contagious virus. It only takes one person going from point A to point B to cause a pandemic.
[1] https://drasticresearch.org/2021/09/21/the-defuse-project-do...
If a lab did in fact accidentally leak the virus, what more can we gain at this point? Isn’t the cat out of the bag? We all agree that gain of function research is a bad idea. What’s so interesting about this beside some rather bland historical footnote?
I guess for other people who don't care about those things it will be a footnote.
I suppose that would in and of itself be quite a story, but my question was why would this accidental release through a lab, so far an unsubstantiated and not necessarily conspiracy linked event, be so important that one would state things like “someone else” funded a program that didn’t receive funding?
I wonder how much is this due to this noble pursuit of truth and the scientific process, and how much is due to having an axe to grind and desperately seeking any scapegoat to be sacrificed in the altar of self-righteousness.
Even your justification reeks of "you're with us or against us" mob mentality.
Who is "we" here? Fear of GoFR is similar to the fear of nuclear power - there are obvious risks, but people don't think about the benefits.
You should explore this comparison more deeply.
How many people has nuclear power killed in the past 20 years? How many people has SARS-CoV-2 killed in the past two?
We have to prevent such mistakes in the future, and if this was an accidental leak due to carelessness then there is reparations to be paid.
This is similar to how after the titanic we identified why it sank, and why after it sank so many people died.
But it's the first piece of concrete evidence that people were in fact doing what has been claimed.
Also remember that there are two virus labs in Wuhan. One is WIV, but the other is across the street from the wet-market (as I understand it).
The virus was already looking suspiciously engineered, in ways that you wouldn't expect from natural evolution. It appeared right next to a lab doing virus work. Now there's a document saying they wanted to engineer a CoV in the exact same way that SARS-CoV-2 appears to have been changed. The question is not "did they get funding to do the work" at this point but rather "who funded it" (assuming it needed explicit funding in the end and wasn't simply creamed off another project).
The first outbreak occurred in Wuhan, but there's no proof that the first cases were in Wuhan. In fact there's genetic evidence indicating there may have been earlier cases 600 miles to the south [0], where the bats are.
[0] https://www.usnews.com/news/best-countries/articles/2020-05-...
The most scary thing about this research is scientists creating a non-zero risk of another zoonotic virus transfer by getting up close and personal with live bats.
The benefits of the research (extremely minor) don't seem to justify the risk. We should just defund not only gain of function research but also trips to remote bat caves that have no particular benefit but a lot of downside risk.
This is off the cuff so I’m not sure.
Chimp DNA is 99% identical to human, for reference.
The genetic code is a redudant code, small difference in the code can still yield the same information. There are 64 triplets, start is one and stop are 2 and there are 20 coded amino acids coded with the rest. So 22 out of 64.
There is a direct similarity and a similarity of information. For redudant code the former is useless. You can have a direct similarity of 30% and a similarity of information of 100%. (Considering a 1:3 redundant code at its worst, DNA performs much better)
There is also a third layer of redundancy, that is still under investigation, where certain sequences of triplets can be permuted and still yield the same result. The order of assembly is redundant for some big projects also, allowing for the code to be permuted in chunks as well.
So we are looking for the similarity of a redundant code that allows for permutations on two scales.
Without considering how the measure of similarity is taken, something being X percent identical means absolute BUNK. It can not be a direct comparison of the code.
SARS COV2 ~ 30000 pairs HIV ~ 10000 pairs Spike ~ 4000 pairs
The SARS COV 2 virus has 3 times the code of HIV. You are also dealing with different sizes.
But one can cut everything between start and stop, translate it to amino acids and permute the result into oblivion. Whatever is left can be compared by a huge variety of measures.
But when working with it, you just sequence your stuff, feed it into the commerical software and click compare.
There's an entire industry that literally harvests tons of bat guano for fertilizer that's shipped around the world and preventative research carried out by a few scientists is where you draw the line?
Bats fill several important ecological niches globally and based on hendra virus outbreaks in Australia alone, it's clear that interacting with them in the wild is inevitable. Pretending they don't exist is only going to leave us unprepared and defenseless.
We know there is a huge downside risk. Dismissing that with non-equivalent whataboutism doesn’t change that. What is the benefit of this research that justifies a non-zero chance of sparking pandemic 2.0?
Most viruses that live in bats get shed through their feces which animals and humans come into contact with quite frequently in the wild (again, just look at hendra outbreaks). Chances are, even more people are exposed to the droppings in industrial settings before the sterilization step. A few scientists handling bats with protective gear is a drop in the bucket to real world exposure and it's hardly whataboutism when it's about research meant to protect the whatabouts.
The Trumpist attacks on China make the most sense as being for the domestic political audience. The Chinese coverup of anything that makes CCP rule seem imperfect is SOP. I mean seriously, that guy in charge is afraid of a talking teddy bear.
It requires one heck of a lot crazy state system to do something that crazy. Not saying that such crazy states don't exist.
We also have no idea where the outbreak started, only where the first hotspot was.
"Lethal Pneumonia Cases in Mojiang Miners (2012)" https://www.frontiersin.org/articles/10.3389/fpubh.2021.7021...
https://www.scientificamerican.com/article/bat-cave-solves-m...
Supposedly that's the closest related virus?
Not really, if they've been coexisting with the virus for a while they could be somewhat immune already. Also, you cannot compare the impact of an outbreak in a rural town in Laos vs. Wuhan with 11 million people and much more international commuters.
Worth to find out if there are places around Laos where level of COVID infections was lower and people may have such immunity ?
Then again, it may very well be the case that Wuhan was not the place of the first transmission to humans, just the one were it first happened on a large enough scale to be noticed and recognized as something new.
I think there's not enough evidence to dismiss any of the transmission routes.
Natural origin is only incompatible with lab-made, but not at all incompatible with lab leak. Lab-made an lab leak are two very different things, yet even scientific papers interpret evidence against one of those as evidence against the other.
It is indeed good that more data is being collected, because the sad fact is that there are currently far too few actual facts and evidence to make any reasonable deduction of what happened and how best to prevent it from happening again.
they could find actual Covid-19 in a population of bats, and I'm going to ask for proof that they didn't plant it there, since its first appearance was outside the Wuhan lab.
"We hypothesize that the direct progenitor of SARS-CoV was produced by recombination within bats and then transmitted to farmed civets or another mammal, which then transmitted the virus to civets by faecal–oral transmission. When the virus-infected civets were transported to Guangdong market, the virus spread in market civets and acquired further mutations before spillover to humans."
For someone to fabricate a plausible natural origin story, they'd have to create a similar series of genetic variants based on ancestral bat strains, intermediates on the way to Sars-CoV-2. So, it'd be very difficult if even possible.
However, you are not addressing that there has been zero natural origin evidence, but they've all along been saying it's the likeliest, despite the Wuhan lab, and they've not been considering gain of function even though the US has been funding it in China at that lab.
There could be a lab-leak of a naturally occurring virus, but you're saying experimentally man-made virus.
I agree with you, but I think it's necessary to be precise.
Asking for negative proofs is as silly as it always was
Just to take one example: researchers are finding zoo animals in the US are testing positive for COVID:
https://zooatlanta.org/update-on-zoo-atlanta-gorilla-populat...
https://www.nationalgeographic.com/animals/article/bears-bab...
https://nationalzoo.si.edu/news/update-covid-19-positive-gre...
In other words, now SARS-CoV-2 is being passed from humans back to other animals. Who's to say what direction things went in at this point? Wouldn't bats be even more susceptible than, say, lions?
I assume you could maybe tease some of this out with molecular phylogenetics but who knows at this point.
>The Laos study offers insight into the origins of the pandemic, but there are still missing links, say researchers. For example, the Laos viruses don’t contain the so-called furin cleavage site on the spike protein that further aids the entry of SARS-CoV-2 and other coronaviruses into human cells.
Nobody’s saying that COVID-19 was built atom-by-atom from carbon and hydrogen. We’re saying that virologists inserted the furin cleavage site into an existing coronavirus since that’s what they said they would do in their own leaked grant papers.
100% a bad-faith article, shifting the goalposts and spinning like there’s no tomorrow.
All other viruses from animals were found very soon after an outbreak. It’s been almost 2 years now and the closest they could find is thousands of miles away and kind of sort of similar.
Let’s not look for a zebra when all we have is a horse.
At the very minimum samples would've been brought back to WIV.
Were they manipulated/gain-of-function enhanced since?
I do not have enough back ground in bio to say, but what are the odds they'd just let samples sit and do nothing with them for years in a research lab? is that something they normally do?
"Lethal Pneumonia Cases in Mojiang Miners (2012)" https://www.frontiersin.org/articles/10.3389/fpubh.2021.7021...
Shi Zheng-Li's research, 2017:
https://www.scientificamerican.com/article/bat-cave-solves-m...
It took a long time to find the animal source for HIV and if memory serves, swine flu took some time to be tracked down.
> obvious now it didn’t
I’m open to the lab leak origin as a possibility, but it seems far from obvious either way. The evidence is still pretty circumstantial. It’s worth further investigation, but I don’t think we should rush to a conclusion.
The reason we haven't tracked SARS2 back to a starting animal source, is likely because there isn't one in that it didn't spread directly from an animal to humans without modification (they sampled it from bats, then they modified the virus, from which it was able to more easily infect humans); and if there were one, China aggressively blocked all efforts to discover the origins there (including destroying vital early data about the virus), which is beyond incriminating.
You assertion is still wrong. It took about 4 years to nail down MERS as coming from camels, and the link from bats to camels to people is still fuzzy. There are several hemorrhagic fever causing viruses believed to come from animals, but with. no known source. We still don't know where Ebola comes from.
People have been looking for the animal reservoir for Ebola for decades, and we haven't found it yet.
A lab leak could be the source for COVID-19, but the lack of an animal source so far isn't evidence of that. It's precisely a lack of evidence.
It's not weird at all, as the host of the biggest virology podcast (TWiV) said, "lab leak confirmation would be the biggest scandal in the history of science".
The field of virology would be decimated by the fallout. No wonder almost all the virologists are circling the wagons and are desperate for any shred of evidence pointing away from WIV.
But I think the story is starting to become clear. EcoHealth wanted to do gain of function research. DARPA shut them down. (Can you imagine the story if DARPA hadn't and it came out? US research scientists deliberately release virus in bats to infect all of china?).
EcoHealth also has a partnership w/ WIV in china, which was also doing this type of research (which is notably dual-use - so something the Chinese government might be very interested in doing).
I've been very skeptical on the idea of a human modified virus being at the heart of covid. I think it's still far more likely that this was a escape/mutation of a virus from the Wuhan CDC which is next-door to the wet market.
But this certainly raises the specter that we (as in humanity) may have just created the biggest pandemic in a effort to figure out how to avoid a pandemic.
Isn’t WIV the only BSL-4 lab in that city, and WCDC mostly paperwork/admin?
Of course, this is another question that is unanswered.
It usually takes several years.
Ebola's outbreaks in the 90s/early 00s.
We have had outbreaks near campains labs, where no patient 0 or progenitor viruses were found. But Ebola kills a lot more, compared to Covid, so an Ebola progenitor in a small village would be way easier to find than a SRAS progenitor, yes?
I don't know how Africa was 20 years ago, but i know deep China, I think its even more enclaved than any village in Africa ever will be.
Do you think it's likely that all those Ebola outbreaks where no progenitor viruses were found are also lab-leaks? I mean, campaign labs are a lot less secure, so it is even more likely than covid lab-break, yes?