Closest known relatives of virus behind Covid-19 found in Laos

https://www.nature.com/articles/d41586-021-02596-2

by MKais • 5 years ago

85 85 5 years ago

sega_sai2• 5 years ago

It is good there is more data being collected, so we can discuss actual facts with evidence, as opposed to pure speculations 'I believe it is a lab leak' vs 'I believe it is natural'.

labster2• 5 years ago

It could easily be a natural virus that was collected, but leaked from a the lab that studied it. To me, it makes sense to look at biohazard lab safety procedures if there was even a chance the lab was a factor in its spread. It’s possible to make mistakes while following best practices, or that those practices themselves need improved. It’s sad that it’s become a blame game of who caused the pandemic, when what we really need is an impartial account to prevent the next pandemic.

exporectomy• 5 years ago

A blame game is only sad if it was a true accident. If both the US and China were actually trying to develop such a virus and one of them accidentally released it, neither will be able to tolerate transparency because it would lead to international blame and desire for revenge.

peter422• 5 years ago

If it was a natural virus it is way, way more likely that it would have infected locals (farming bat guano for instance) than it would be discovered by a researcher, then brought back to Wuhan, then leaked there.

We also have no idea where the outbreak started, only where the first hotspot was.

poorjohnmacafee• 5 years ago

The lab's published research program, the lab's funding, the almost exact proximity of the outbreak, the lab's and CCP's actions since October 2019, the whistleblowers, the analysis of the virus's genome, does not add up to "pure speculation". We may never know 100% conclusively, but juries never do either.

sega_sai2• 5 years ago

That is your opinion. From my point of view, what I have seen is consistent with both natural and lab leak hypothesis. One can argue how much indirect indications tilt the scales one way or another (from my point of view not much), but at least in my book the original question is still open. That's why I think more data is good.

roelschroeven2• 5 years ago

Even without all the speculation the 'I believe it is a lab leak' vs 'I believe it is natural' debate is severely misguided.

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.

dqv2• 5 years ago

Exactly. I have been a strong proponent of considering all possibilities of origin. It's exciting that we're getting closer. Someone elsewhere in the thread that 95% identical is a very close match.[0]

[0] https://news.ycombinator.com/item?id=28657113

danw1979• 5 years ago

The study also doesn’t clarify how a progenitor of the virus could have travelled to Wuhan, in central China, where the first known cases of COVID-19 were identified — or whether the virus hitched a ride on an intermediate animal.

“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...)

lubos• 5 years ago

They could have been infected by locals in regions they've been travelling to. Many possibilities. Why do we have to speculate? Let's just wait for more data.

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.

cm2187• 5 years ago

We may have to wait for the fall of chinese communism to know what happened though, like for Katyn. Might take a few decades.

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.

inter_netuser7• 5 years ago

Remember that bat cave in Yunnan (specifically Mojiang) which supposedly had also similar viruses? Right on the border of Laos.

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...

kortex• 5 years ago

I'm still surprised very few sources are talking about the third possible origin - WIV scientist(s) contracted COVID19 when doing research in/near bat caves with insufficient PPE. You see researchers wearing what look like surgical masks, which is likely insufficient. And this is post-Covid Chinese media, so it's probably sugar coated. I remember reading a translated article (sadly can't find it at the moment) which reported lab techs in Yunnan working in terrible conditions, getting bat urine and blood on them trying to catch bats, with barely adequate masks and goggles.

https://algulf.net/2021/06/09/2019-video-shows-wuhan-scienti...

jml7c5• 5 years ago

What's weird is that nobody talks about WHY Shi Zheng-Li/"Bat Woman" was digging around random caves in Yunnan.

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.

btilly2• 5 years ago

There are actually 2 virology institutions in Wuhan. WIV is fairly far from the neighborhood where things got going.

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.

moralestapia2• 5 years ago

WIV is fairly far from the neighborhood where things got going.

Still closer than Southeast Asia, though.

ravel-bar-foo• 5 years ago

WIV, the seafood market, and the airport are all on the same subway line. The topology of disease spread in cities is only approximated by physical distance.

Jerry2• 5 years ago

Just a day ago or so, DRASTIC released [1] DARPA funding proposals for Coronavirus research project from 2018. They were released by a whistleblower. They basically outline how to create COVID-19. Incidentally, DARPA refused to fund it because it's GoF research but someone else did fund it. It's a fascinating read.

[1] https://drasticresearch.org/2021/09/21/the-defuse-project-do...

chana_masala• 5 years ago

"Someone" else...

alex_young2• 5 years ago

Pretending that everything you state is true (a seemingly unsubstantiated conclusion), why does it matter?

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?

InTheArena3• 5 years ago

There is no proof that anyone else funded it yet.

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).

mikem170• 5 years ago

The main problems that the Institute of Virology has is that the outbreak occurred in close proximity to that Institute.

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-...

farmerstan• 5 years ago

It’s weird how people are trying so hard to convince others that the virus came from nature sources when it’s obvious now it didn’t. The amount of propaganda is really scary.

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.

inter_netuser7• 5 years ago

"thousand miles away" in Yunnan (right on the border with Laos) is where the "Bat Woman" was sent to investigate an pneumonia oubreak with case fatality rate of 50% in 2012.

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...

ch4s33• 5 years ago

All other viruses from animals were found very soon after an outbreak.

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.

adventured• 5 years ago

HIV was a very different context and isn't remotely comparable to SARS2. It took many decades for HIV to spread to a consequential base of infected persons, from which it was then able to explode across the globe (due in part to the difference in travel then vs now of course). The reason it took so long to find the animal source, was because it wasn't perceived to be a critically important virus to deal with - it wasn't a priority - in the early decades due to the very low number of cases and related deaths. Depending on which origin theory you believe, it took anywhere from ~20 years to ~60 years, for HIV to go from a small number of cases to being globally threatening. SARS2 did that in a matter of months, so the priority is far different. SARS2 has killed 5+ million people in under two years, it took many decades for HIV/AIDS to do that. The US is still seeing more annualized Covid deaths than the world had total HIV/AIDS deaths annually circa 1990/1991, and that's with 64% of the US population having taken at least one vaccine dose.

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.

htjglhktbrn• 5 years ago

It’s weird how people are trying so hard to convince others that the virus came from nature sources when it’s obvious now it didn’t.

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.

InTheArena3• 5 years ago

And bear in mind, TWIV is also very tightly connected to two of the principles in this story - Beric and Dasak. I say this as a long time listener - but a lot of their basic statements have been incorrect. They still insist that Delta is not more contagious or virulent then alpha. They insisted that masks were not needed at the start of the outbreak, and clearly didn't think it would be a big deal.

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.

tzs• 5 years ago

All other viruses from animals were found very soon after an outbreak.

It usually takes several years.

orwin• 5 years ago

I've had someone who seemed competent in virology/biology explain your point of view to me (it was very convincing), but after doing a bit of research on my side, i have one point i want to discuss:

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?

inter_netuser7• 5 years ago

What’s a campaign lab? Like a vaccination campaign? Those don’t have a live virus afaik?

JetSetWilly2• 5 years ago

To make the discovery, Marc Eloit, a virologist at the Pasteur Institute in Paris and his colleagues in France and Laos, took saliva, faeces and urine samples from 645 bats in caves in northern Laos. In three horseshoe (Rhinolophus) bat species, they found viruses that are each more than 95% identical to SARS-CoV-2, which they named BANAL-52, BANAL-103 and BANAL-236.

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.

ch4s33• 5 years ago

Sampling seems reasonable to me, especially now that we can spin up vaccines so quickly. In this new age of rapid mRNA vaccines it may make a lot of sense to catalog and sequence viruses before they jump the species barrier.

This is off the cuff so I’m not sure.

br-g• 5 years ago

I’m curious to know what 95% identical means in this context. How similar is Covid to HIV, for example?

Chimp DNA is 99% identical to human, for reference.

Enginerrrd• 5 years ago

Excellent question. For viruses, 95% is VERY similar. To give you some calibration, SARS-COV-1 and SARS-COV-2 are like 79% similar.

scantis• 5 years ago

Let me give you the scope of the problem.

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.

akiselev2• 5 years ago

The benefits of the research (extremely minor) don't seem to justify the risk.

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.

JetSetWilly2• 5 years ago

It is not equivalent tho is it? There’s a large difference between actually capturing a bat and extracting its saliva, and obtaining bat guano via an industrial process. We know that covid jumps from humans to cats and dogs simply by being in proximity with them - so actually capturing bats is going to be vastly more risky.

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?

fsckboy4• 5 years ago

with the recent revelation that there was a grant proposal for a "Furan site gain of function experiment" (in the recent past just before Covid-19), and the extreme lengths experts went to stop consideration of the lab leak hypothesis, here's where I stand:

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.

photochemsyn3• 5 years ago

What you would expect to find in a natural zoonotic origin is a series of close ancestor relatives of the pandemic version, some capable of causing mild disease in humans (as with MERS and SARS for example). See this 2013 description for example:

"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.

fsckboy4• 5 years ago

first of all, you're agreeing with me, I said I'd want to see proof, and you're saying what the proof would need to consist of.

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.

8note• 5 years ago

And then somebody else will ask you to prove that the trump administration didn't plant the virus in Wuhan to try and make the chinese government look bad.

Asking for negative proofs is as silly as it always was

derbOac• 5 years ago

Idk. The parent post shouldn't have been voted down imho. The problem is such a long time has elapsed everything is getting murky.

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.

EGreg3• 5 years ago

Also this

https://www.nature.com/articles/d41586-020-03217-0

photochemsyn3• 5 years ago

Very interesting stuff. The article itself doesn't make any claims about the origins of the pandemic, however, that's just the Nature News spin. For example:

"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.

Jorge1o1• 5 years ago

“I am more convinced than ever that SARS-CoV-2 has a natural origin,” agrees Linfa Wang, a virologist at Duke–NUS Medical School in Singapore.
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.

Closest known relatives of virus behind Covid-19 found in Laos

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