The case against the lab leak theory
Every reason why lab leak theories fail and a natural origin of covid is more likely.
(Edit 2/1/24: I debated this topic with Rootclaim. This blog post is a little bit out of date, I presented a more thorough version at the debate, but this is still a good hour long read explaining why covid was not created in a lab)
The lab leak theory has taken a strange ride.
In early 2020, scientists at the NIH e-mailed each other wondering if covid was a lab leak. A few months later, the same scientists wrote a paper announcing that the virus had a natural origin. Then, some news articles described the lab leak theory as a racist conspiracy theory. In 2021, people across the political spectrum started to speak openly about the lab leak theory. By 2022, public opinion had split, with more than half of Americans now believing that covid came from a Chinese lab. There’s a political divide, with most Republicans believing the theory and less Democrats, but some polls find that even a slim majority of Democrats believe the lab leak theory.
This story is strange, because research has gone in the opposite direction — at first, there was a lot of uncertainty about where covid came from. Since 2020, there’s been more work linking the virus to a market in Wuhan. There’s been more research finding closely related bat viruses.
I was personally open to the lab leak theory back in 2020. I was never 100% convinced, but for a while I said the odds were 50/50. I changed my mind after I saw more evidence in favor of a natural origin. I also stopped believing the lab leak theory because I noticed how it contradicts itself.
Watch a short clip from Robert Redfield, explaining why he thinks Covid leaked from a lab in September:
That sounds interesting. But, over in the Wall Street Journal you’ve got this story saying it happened in November:
So, when do they think the virus leaked? In September or November? It’s not just a time lag for people to get sick — the lab leak claim is that some database went offline on September 12th. Healthy young scientists aren’t going to get covid and then go to the hospital 2 months later. It also doesn’t make sense that the first known covid cases would show up at a Wuhan market fully 3 months later, in early December — covid is highly contagious, if it had leaked in September, it would already be around the world by December.
I read all the government reports, and it didn’t get any clearer. The House GOP report on the lab leak theory claims that covid leaked from a lab in September 2019, then spread around the world in October through the Wuhan military games. The US senate GOP report disagrees and says that covid started sometime between October and November. Neither of those reports have any information on those “3 sick researchers”. Meanwhile, Biden’s intelligence report couldn’t decide if covid is a lab leak or not. These theories can’t all be true — if covid started in September and spread all around the world by October, then it doesn’t even matter if Wuhan lab employees got sick in November.
If you do a little digging, the “3 sick researchers” narrative breaks down further. That Wall Street Journal article was written by the same journalist who first announced that “Iraq has Weapons of Mass Destruction”. The anonymous government sources he quoted turn out to just be members of Trump’s state department.
The lab leak theory is politicized, but even outside of the government reports, it’s not any clearer. We have theories pointing at anywhere from August to December. Some give vague reasons, others point at specific things — one story says it leaked from the lab in October, because of “cell phone records” or “roadblocks outside the lab”.
Lab leak theories also don’t agree on how the virus was made. They don’t agree which natural virus the lab started with. Some theories say covid is a bat virus with a furin cleavage site added, or it’s a chimera combining bat and pangolin viruses, or it was created synthetically by stitching together multiple segments of RNA, or it was created by serial passaging in ferrets, or by serial passaging in transgenic mice, or by serial passaging in cells, or it has HIV genes inserted, or it was developed as a self-spreading vaccine against other coronaviruses, or that Moderna patented the virus 3 years before the pandemic. There’s also a theory that it was a natural virus harvested in a mineshaft back in 2012, in which case it doesn’t need gain of function research, because it was already 50% fatal. There’s even a theory that it was made in a US lab and released in China.
Some of these theories are more fringe than others, but there is no single popular lab leak theory. Not in the US government. Not in the DRASTIC group. None of the lab leak theories agree on the most basic of details, like which month the pandemic started. They don’t even agree on which lab the virus leaked from: various theories blame 3 different labs in Wuhan — some blame the Wuhan institute of virology, Wuhan CDC, others the Wuhan Institute of Biological Products. There are 2 campuses of the WIV, and the theory has no idea which one it leaked from.
Even if you’re a lab leak supporter, you have to accept that most of the individual theories must be wrong. Only one story can actually be true. You still need to go through the evidence to figure out which one is.
This article shows which lab leak theories we can reject, which ones are still possible, and argues that a natural spillover from animals is more likely than any lab leak theory.
While the lab leak theories struggle to agree on where, when, and how the virus started, the natural origin theory has tracked it down to one most likely shop in a Wuhan market, has a clear timeline, and has a guess for which animal started the pandemic.
In 2020, it was fair to say that the lab leak theory was suppressed. Facebook had rules against discussing it. That’s partially because some of the 2020 theories said Covid is a Chinese bioweapon, and some of them were funded by Steve Bannon.
Today, there’s not much censorship. There’s a lot of mainstream coverage of lab leak theories on TV, in the news, in podcasts. The theory has been discussed in liberal newspapers like the New York Times and the New Yorker. It’s all over conservative news. Authors have written best selling books about it. There have been government investigations and congressional hearings. The lab leak theory is about as mainstream as you can get.
Despite all this, some lab leak supporters still claim they are censored, silenced, or even faced with threats of violence. One newcomer to the lab leak field, Andrew Huff, says that the government tried to stop him from publishing his book by shining laser pointers into his windows and flying “mosquito sized drones” inside his house to spy on him. While I’m not sure whether or not mosquito sized drones exist, I do wonder why the US government can’t just use those to fly around the Wuhan lab and gather information, so that the congressional reports could agree on details.
This article is a long read, but I’ve divided it into sections that can be read separately. The first half starts by looking at where and when covid started, the second discusses genetic features of the virus, like the furin cleavage site. Near the end, I discuss leaked evidence like Fauci’s e-mails and the DEFUSE grant.
It’s long because it takes more effort to debunk a conspiracy theory than to create one. It took only one podcast to make me think the lab leak theory was possible, but it took months of research to understand why it’s not.
Conspiracy theories are popular because they make you feel smart, they make you feel like you’re learning some hidden truth. Reading the debunking of a conspiracy theory can be unpleasant. If you’ve invested a lot of time in the theory, it can make you feel frustrated, like you’re not smart.
How does that saying go?
“It’s easier to fool someone than to convince them they’ve been fooled”
Perhaps it’s best to not get too emotionally invested and just think of the question of how covid started as a puzzle, and to enjoy finding more pieces to it. No one has all the pieces. This article may contain some pieces you’ve missed.
What are the odds that a new virus would show up in Wuhan?
The earliest known Covid cases were at a market in Wuhan that sold wild animals like raccoon dogs and civets.
The 2003 SARS epidemic also started in markets that sold raccoon dogs and civets.
I remember listening to lab leak podcasts that said that Wuhan is an unlikely place for a pandemic to start, because “the bats live 1,000 miles away in Yunnan province”.
It turns out that’s misleading — the 2003 SARS pandemic started just as far away from Yunnan, in Guangdong:
The 2003 SARS virus also showed up on Hubei farms, so we know for sure that natural viruses can get from Yunnan to Hubei.
The bats that carry SARS viruses are found all over China and Southeast Asia, it’s only the density that’s highest in Yunnan and Laos:
The human population density is lower in Yunnan, so there are less people for a virus to jump to. If we map the overlap between human and bat populations, Yunnan doesn’t stand out anymore:
We also know that some of the animals sold at the Wuhan market came directly from Yunnan. For instance, bamboo rats sold at the market were from Yunnan, and other animals may have been as well:
Those Yunnan farms are near where we’ve found some of the bat viruses that are most similar to Covid:
But the virus doesn’t necessarily have to come from Yunnan. It could also have started in Hubei province. Hubei has caves and it has bats.
It also has civet farms very close to caves. Before the outbreak, there were 631 wildlife farms with 1.1 million animals in Hubei.
SARS family viruses are naturally found near Wuhan. A 2005 study found coronaviruses related to SARS in bats, in Hubei province. Another study from that year found SARS viruses in masked palm civets, on a farm in Hubei province.
A virus could get to Wuhan from a Hubei bat to a Hubei farm to a Wuhan market. Or it could get there from a Yunnan bat to a Yunnan farm to a Wuhan market via the wildlife trade.
We don’t know yet, which of those scenarios happened, but there’s no need to think that only researchers could bring a virus to Wuhan.
What are the odds that a natural virus would show up in the middle of Wuhan, as opposed to some other city in China? For a first guess, let’s say that 11 million people live in Wuhan, out of 1.4 billion people in China. If you said the odds were even for anyone in China to randomly get infected, the odds that person lives in Wuhan are 0.8%, or 1 in 130.
That’s a low end estimate. The actual odds are higher. A pandemic is more likely to start in a big city, where it can spread. Covid started in Wuhan, the 9th largest city in China. SARS started in Foshan, the 14th largest.
Excluding rural China, the odds of a pandemic in Wuhan are more like 1.6%. A pandemic is also unlikely to start in northern China, where there are less bats and less wildlife markets. That excludes another half of the people. So it’s more like 3.2%.
Other factors, like Wuhan’s large size, central location in China’s railway network, and Hubei’s unsafe farming practices could maybe bring the odds higher, perhaps to 10%.
We know that bat viruses can jump directly into people. A study in Yunnan province found 3 percent of villagers had antibodies to SARS-like bat viruses. One paper estimates that 70,000 people across Asia get infected with a SARS-like bat virus every year, but typically those cases don’t transmit onwards to start a pandemic.
We also know that the most likely person to start a pandemic is not a villager, but an animal trader.
3% of villagers living near caves in Yunnan had antibodies. But, after the first SARS epidemic, 13% of animal traders tested had antibodies, and 70% of the traders that worked with civets had antibodies. The most likely person in China to get sick is a trader working with these susceptible animals, or someone who buys those animals.
We know that viruses often jump better when there’s an intermediate host.
The first SARS virus jumped from bats to humans via civets.
The MERS virus jumped from bats to humans via camels.
The Hendra virus jumped from bats to humans via horses.
The Ebola virus jumped from bats to humans via some unknown species, maybe some other primate.
If you had to guess at random, who is the most likely person in China to catch a new SARS-related virus, it would be an animal trader working with some SARS susceptible species. It would be in a big city. And it would be in Southern or Central China, not in the North.
A wet market in a big city is the most likely place in China for a pandemic to start. It’s not that improbable that market would be in Wuhan. The same thing could have also happened in other big cities in the southern half of China. Maybe we’re talking somewhere between a 2% and 10% chance that Wuhan is the particular city that it happens in.
Mixing unfamiliar animals is a known recipe for starting a pandemic. That can even happen in America. There was a Monkeypox outbreak in America, in 2003. An animal seller housed imported African rodents in the same room as prairie dogs, then sold the prairie dogs as pets. The African rodents had Monkeypox, the children who bought the prairie dogs caught the virus. The first victim was a 3 year old.
Covid was first seen in a wet market, in a big city, that was selling wild animals. We have videos from the market and we have pictures:
To disprove the lab leak theory, we want to show that it’s much more likely that the virus started at this market, where the first cases were found, and not at a Wuhan lab. We also want to show that the features of the virus are natural, that there are no clear signs of genetic engineering.
And we want to show that this is by far the best explanation for what happened, that the odds of a lab leak are much lower than the 2% to 10% coincidence that the market and the lab are in the same city.
What are the odds of a lab leak?
The lab leak theory sounds possible, at first, because lab leaks have happened in the past. The first SARS virus came from nature, but it leaked out of 3 different labs studying it. Other viruses, like smallpox, have also leaked out of labs.
Lab leaks are usually easy to spot. You can tell it’s a SARS lab leak because the people infected were researchers and the virus looks identical to the SARS strain they were studying. The Covid pandemic involves a novel virus, though, so you can’t easily say that it was something from a lab.
There’s one pandemic that could be lab caused: a flu pandemic in 1977. Even in that case, the key evidence is that the flu strain was very similar to a flu strain sampled 27 years prior. That’s also not an accidental leak theory — scientists suspect people were intentionally infected in a vaccine trial. But they’re not sure, they’ve never tracked down which lab it was or if this is true.
There haven’t been many lab leaks of novel viruses before. The only case I know of is the Marburg virus. Researchers in Germany imported some primates for an experiment and the animals were infected with an unknown virus. In that case, it was still easy to spot as a lab accident because the researchers were the first people infected.
So, one novel virus in history leaked from a lab, all the rest were natural. Covid would be the first ever pandemic caused by a novel lab virus. But there’s a first time for everything, we should still consider the possibility.
Over the last 15 years or so, researchers have gained the ability to enhance viruses. If an enhanced coronavirus did show up somewhere in the world, Wuhan is one of the possible places. Covid also has some genetic features, like a furin cleavage site, that scientists knew could make a virus more potent. Scientists in Wuhan had discussed adding cleavage sites to similar viruses. So it all sounds possible, at first glance. In 2020, some virologists suspected it was unnatural, for all these reasons.
But the odds are actually a lot lower than you might think.
For one thing, the earliest proven covid cases were not lab researchers, but people working at a wildlife market. That’s a very likely place to find a natural virus, and it wasn’t close to the lab.
Beyond that, the virus is something we’d never seen before. There isn’t any known virus that could be turned into Covid. The particular furin cleavage site used is not a very effective one, or one that scientists have ever put into another virus. And we’ve since done experiments showing that many ways to try to engineer Covid would fail.
The odds that Covid was created through gain of function research are low, because it’s a chained probability. It’s something like:
Odds Covid is a lab leak =
odds the lab had a secret virus to start with *
odds the lab manipulated that virus to look like Covid *
odds that virus leaked *
odds that virus first showed up at a market across town *
odds that they successfully hid the evidence of this
None of these steps are impossible, but the combination makes it unlikely, overall. We’ll go through some of these in the article. (For a longer discussion, here are the odds everyone came up with at the Rootclaim debate)
Historically the odds of a lab accident are maybe 1 in 500, per lab, per year. But you could argue the odds would be higher for the Wuhan lab, if you think it was abnormally unsafe.
The odds that the virus would leak from the lab but show up at the market across town are very low. We’ll see in the next section that the odds are like 1 in 10,000, or possibly even lower than that.
And you have to consider the odds that they even had a secret virus to start with — we’ve uncovered documents showing which viruses the lab had in August 2019 and there’s nothing similar to Covid.
Even though it’s not common for a lab leak to cause a pandemic, it is common for lab leak theories to arise during a pandemic. There were several conspiracy theories blaming labs for the start of HIV.
In fact, some of the same people writing about the HIV conspiracy theories are now writing about the covid lab leak:
There was also a lab leak theory for Ebola, for Monkeypox and for Omicron. There was even a lab leak theory for Lyme disease.
Perhaps it’s just a human desire to explain natural disasters, similar to the way that some people try to blame hurricanes on sin.
The reality is that viruses jump from animals to people all the time. Almost every pandemic in history has been a natural event. This isn’t the first pandemic coronavirus, and it won’t be the last:
Covid did not originate near the Wuhan Institute of Virology
So far, we’ve only guessed at the odds of each hypothesis. To figure out what happened, we need to look at data on where and when Covid started.
The first known covid cases happened at the Huanan Seafood market.
The market is in Wuhan, but it’s not next door to the lab. You can look this up in Google maps, it’s a 30-minute drive between the two:
There’s also a second campus for the Wuhan Institute of Virology, which is even further south.
A paper from June 2022, with Michael Worobey as the lead author, mapped the earliest covid cases in Wuhan:
Each dot is the home address of someone who had covid in December 2019. The orange dots are cases linked to the market, the blue dots are unlinked cases.
People from both groups are clustered around the Huanan market. There aren’t any cases particularly near the Wuhan lab, the closest one is maybe 3 kilometers away.
The authors used some statistical techniques to try to show how well-centered the cases are:
Another way to see this is to map out the cases by date, and show the spread. The first few are near the market. As time goes on, they spread further away from it:
The address data for all these cases come from the 2021 WHO report on the origin of covid.
Worobey’s group also checked this against another data source, location data for people who used a covid-19 assistance app provided by Weibo (a Chinese app that’s sort of like Twitter, with some additional features):
Cases are no longer centered as closely on the market, they move more towards the center of Wuhan’s population. The Wuhan lab is still far from the center.
The Weibo data is from January and February, after the virus has spread around the city more, so it can’t show the origin. Only 3 cases were reported before 2020, and 25 cases before January 18th.
Let’s consider a few theories for why the cases are centered on the market.
- The market is the origin of the pandemic.
- The market is not the origin of the pandemic, but it’s the first superspreading event.
- The data is biased, because China was only looking for cases associated with the market.
- Something else, very near the market, is actually the origin.
- China is lying about the case locations.
The first theory is the simplest one. The first case cluster was found at the market because it started in the market. As we’ll see later, surfaces all over the market tested positive, including those on one specific animal cage.
The second theory says that the virus didn’t originate at the market, and the market was just the first known superspreading location. Perhaps an employee from the Wuhan lab brought it there.
First off, a superspreading event usually means something like: one person brings Covid to a wedding, gives it to 50 other people. What happened at the market was slow spread from one person to another. We can map the cases in the market from week to week:
Still, maybe someone came from outside and started the slow spread?
In that case, why did it spread there? Why not in a train station, a grocery store, a restaurant, or a school?
Worobey’s paper considers this possibility and ranks the number of visitors to various public spaces in Wuhan. The Huanan market is way down the list for most crowded places, it’s not where you’d expect the virus to show up:
There are 1,677 places in Wuhan that are more crowded than the market.
Based on number of visitors, Worobey estimated the odds at only 1 in 10,000 that the market would be the first superspreading event in Wuhan.
Even just mapping out large markets and shopping centers in Wuhan, Huanan market doesn’t stand out. There are dozens of large markets in Wuhan, and many of them are closer to the Wuhan institute of virology:
If I mapped every crowded place in Wuhan that could have been the first cluster of cases, you’d have 1,600 pins on this map, many of them closer to the lab.
Although it didn’t receive a lot of traffic, the market was one of only 4 places in Wuhan that were selling wild animals. Huanan had more shops selling wild animals than the other 3 markets, more than any place in town.
It’s literally the most likely place in Wuhan for a natural virus to emerge, and scientists had previously flagged it as a dangerous place, a likely spot for a pandemic to start.
As we’ll see later, there were 2 early strains of covid, so there may actually have been two jumps from animals to people at the market. Now we’re talking about odds of 1 in 100 million, that the virus leaked from the lab twice and both strains made it to the market but showed up nowhere else in Wuhan.
The odds that this virus made it across town, unseen, once or twice, are both incredibly low. It would be a much wilder coincidence than finding a market and a lab in the same town.
A third theory says that the case search was biased, that China only found covid cases at the market because they only looked there. Here’s lab leak theorist Alina Chan making that claim.
It’s an amusing argument, because Worobey wrote another paper in 2021 to figure out if the case search was biased, before he even started writing the 2022 paper finding that the cases were centered on the market.
The key point of Worobey’s earlier paper is that the connection between the market and the disease was not publicly noticed until December 29th, 2019. Prior to that, it was a few doctors finding pneumonia cases in various hospitals in Wuhan. Several doctors independently noticed that they were seeing abnormal pneumonia cases, many of which were among workers at the market. On December 29th, doctors at a few hospitals compared notes, realized they were all seeing the same thing, and it became publicly known.
Worobey’s strategy was to look at the cases identified before the market connection was known, before there could have been a bias. Prior to that point, about half of the cases found were linked to the market. That makes perfect sense for a market origin, but it’s insanely unlikely to find 50% of market cases in multiple hospitals, had the virus been all over Wuhan.
This wasn’t only true for hospitals near the market. Zhongnan hospital is across the river and very near the Wuhan lab. On December 31st, the hospital VP ordered a search for all pneumonia cases with an unknown cause. They found 2 cases — one worked at the Huanan market, the second had friends who worked at the market, who had visited his home.
You can also just use common sense to think about this question — the retrospective search for patients was done in hospitals, not by going door to door near the market. Most of the patients it found were not linked to the market (blue dots in this next map), and some of them lived very far away:
Why would a biased search find mostly cases unlinked to the market?
How would it find unlinked cases that were nowhere near the market?
And somehow, Alina thinks this biased search would find mostly unlinked cases that were centered on the market?
We can also look for other data sources to confirm whether the cases were centered on the market.
Covid antibody testing was done in April, 2020, in Wuhan and 6 other Chinese provinces. This should be an unbiased search. Antibodies were highest near the Huanan market, lower further from the market, and very low in 6 other provinces:
We also have data on excess mortality, as the epidemic in Wuhan got bad enough that people started dying:
The key part is these 2 weeks. People first started dying on the north side of the river, near the market:
As we’ll see later, there was also an effort to go through hospital records and blood banks, looking for cases before December. It didn’t find any.
There are many reasons to conclude that Alina Chan is wrong here. Let’s suppose, just for the sake of the argument, that she’s right. Suppose that the case search was biased, that covid was all over Wuhan in December, not just near the market. Does that prove that a lab leak is the source?
It would open up the lab leak as a possibility, but it also opens up another possibility — that covid didn’t start in Wuhan and came from somewhere else in China.
The bat viruses related to covid are most common in southern China. Lab leak supporters say that a bat virus starting in Wuhan is unlikely, it’s more likely for one to start elsewhere.
If covid was actually all over Wuhan in December, then you don’t know that it started in Wuhan. It could have also been in some other Chinese city in December or earlier. It could have started in southern China, and come to Wuhan on a train.
Alina Chan’s argument actually makes a natural origin more likely. Now there are a billion people who could have been the first case.
The fourth theory is that something near the market is actually the epicenter. Here’s the neighborhood:
There’s one hospital near the market. There’s a busy train station, one of 3 in Wuhan. And there’s the Wuhan CDC.
If the virus actually started in southern China, the market being close to a train station makes sense. That station handles 60,000 passengers per day and offers service to some big southern cities like Guangzhou.
The Wuhan CDC is not the same as the Wuhan institute of virology. This isn’t a lab that worked on gain-of-function research, it’s a a place that tests people for diseases. Given the proximity, it seems like the Wuhan CDC should get more attention than the WIV, but I rarely see it mentioned in lab leak theories. The WHO report briefly notes that one employee of the Wuhan CDC, “was confirmed SARS-CoV-2 seropositive after infection due to family cluster transmission”.
One complication is that the Wuhan CDC moved to this location on December 2nd, from somewhere further away. That may be after the virus started. There is some remote chance that this location is related to the pandemic, but if it is, you’ve lost all the theories about gain of function research, funding from Tony Fauci, and just about every other detail of the usual conspiracy theories.
The fifth theory is that China lied about all the case location data. This idea is a little bit strange. Some of the data they could not lie about, like the hospitals had reported a connection between covid and the market before any censorship would have started. Actually, China tried to censor these doctors when the news first started to come out. One early whistleblower, doctor Li Wenliang, identified the wet market as ground zero of the epidemic in December. 7 out of 7 of the patients he reported were from the market. China tried to censor him.
Some of the later data could be faked, but if China lied to make the market look like the source, you’d think the lie would at least be consistent. Maybe they would also claim they’d found the host animal. Or, they’d at least stick to the story. The Chinese government now claims that the virus came into China on frozen food, that it was made in a US lab, or that it started in another country. We’ll ignore this theory for now, but talk about it more later. For now, let’s assume that we can actually trust data and analyze it.
The market is the center of the pandemic, in all the data we do have.
Evidence from inside the market points to infected animals
Chinese authorities closed the market on Jan. 1st, 2020 and investigated it.
They took 900+ samples on different surfaces around the market. 73 samples tested positive for covid.
They also sampled ~450 animals, but it wasn’t many live animals. The wild animals on sale appear to have been killed when the market was cleaned out. Testing was done weeks later on frozen animals and a few stray cats.
The samples weren’t all taken at the same time:
The surfaces got tested right away, but animal testing was done weeks or months after the market was shut down.
Here’s a list of the environmental samples that did test positive:
It’s a lot of samples of the floor, the water drains, the sewers. But there are also some positive samples from carts and animal cages, and one inside a freezer.
So, did sick people in the market contaminate the floor? Or did animals contaminate their carts? Or was it a bit of both?
The people who got infected with covid worked all over the market. The west half of the market got infected first, all cases before December 20th were only on the west side of the market. After December 20th, people were infected in both the east and west sides:
Even though there were infected humans on both sides of the market, the east side only had 2 positive samples. The west side had all the rest. And the samples that came back positive were clustered in one corner of the market:
Worobey’s group thinks all the positive samples are in one corner because that’s the corner that sold wild animals, and some of them were infected.
The most suspicious part of this diagram is the shop with 5 positive samples, including a positive sample taken from one of the animal’s cages.
China tried to claim that the market didn’t sell any wild animals. One scientist from Worobey’s group visited the market a few years prior to the pandemic and happened to take a picture of raccoon dogs in a cage, at exactly that location.
It’s a wild story that didn’t even sound real at first. I went as far as translating the signs in his pictures to confirm that it’s the same shop.
The scientist took that picture because raccoon dogs were susceptible to the first SARS virus, back in 2003. They’re a risky animal to sell and eat.
The market sold about 40 of these animals every month, leading up to the pandemic. Raccoon dogs were photographed for sale at the market in December, 2019.
It’s since been found that raccoon dogs can catch and transmit covid. So, that’s one theory for how the pandemic started. This is our culprit:
The specific animal host isn’t for sure — that shop was selling a lot of different animals for people to eat: dogs, raccoon dogs, civets, marmots, hedgehogs, porcupines, bamboo rats, rabbits, weasels, muntjac, and more.
We know for sure that covid can infect some of those animals. Raccoon dogs have been infected in a lab. In 2020, Covid easily spilled over from humans into mink in both Denmark and Spain, so weasels should be highly susceptible. A few other animals here, like the bamboo rats, may be susceptible to covid as well.
Why didn’t the Chinese team find a positive test in raccoon dogs?
As we already saw, they didn’t test the wild animals before cleaning up the market. They tested some frozen samples and some stray cats.
We have a list of the frozen animals tested, and raccoon dogs are not on it. They tested rabbits, snakes, and a few other animals:
The viral spillover happened earlier, at least a month before testing. So the sick animals could also have been sold before the market was cleaned. But you wouldn’t know, either way, with the amount of testing they did.
In January, Chinese authorities shut down farms supplying the market, with about a million animals affected in Hubei. The animals were killed or released into the wild, without testing any of them. In February, they shut farms across China, killings tens of millions of animals.
I want you to revisit the idea that Chinese authorities faked all the evidence to make it point to the market. Did they also fake the evidence within the market? If so, they faked data pointing towards an animal that was already known to be susceptible to SARS and has since been found to be susceptible to covid. Then they admitted that they didn’t promptly test any of the animals. Then they provided a list of the few animals they did test, and admitted that none of the wild animals were on it. And, within a month of closing the market, they started shutting down farms in Hubei province.
It does look like there’s a conspiracy here, but it has nothing to do with the lab leak. It looks like Wuhan authorities just did a quick and careless clean-up of a disease outbreak caused by the wildlife trade.
In 2022, we also learned that China found animal DNA while sampling the market but didn’t share it. In March, 2023, western scientists got a copy of the data and found raccoon dog DNA in that one suspicious shop.
Lab leak theorists aren’t convinced by the data from within the market. They came up with two ideas for why it was wrong.
First, they said it was bias — maybe they only sampled near the animals?
Then, they said the reason is that all the positive samples were in one corner: the public restrooms were near that corner.
Those two theories contradict each other. If the data can’t be trusted because of sampling bias, then that disproves both the “toilets theory” and the infected animals theory.
Can we test those 2 theories? In March 2023, we got the total number of samples, so we can check the percent that are positive. The raccoon dog shop still has an abnormally high ratio, compared to other shops:
So the sampling bias theory should be dead.
The Chinese team also took a few environmental samples from other markets in Wuhan. Of 30 samples, only 1 tested positive. Of 14 samples from warehouses related to the Huanan market, 5 tested positive.
So, the warehouse supplying the market tested positive but other Wuhan markets (mostly) did not. That sounds compatible with infected animals getting shipped to the Wuhan market. It’s not compatible with covid being everywhere in Wuhan.
How about the toilets theory? Maybe that would explain why some ground samples near the bathrooms were positive, but it doesn’t explain why animal’s carts and cages would be positive.
Some of the positive samples at the market were from water drains. That refers to these grates in front of the shops:
Where were those positive samples located?
Right in front of the raccoon dog shop, and few other places.
The drains got retested a few weeks later:
The raccoon dog shop was still positive, as were two drains downstream of it. Nowhere else in the market was positive.
In March 2023, western scientists got a copy of the DNA data from the market. They found evidence of many animals that China never tested, and found proof that raccoon dogs were in that one shop:
This gives good support to the idea that the positive samples were found where the animals were because the animals were sick, not because the bathrooms were sort of nearby. If the positive samples came from people using the bathrooms, the samples would contain human DNA, not animal DNA. And, again, they’d be on the floor, not on animals carts and cages.
It’s not 100% clear yet if raccoon dogs are the right animal. But the infected raccoon dog theory is plausible and fits the facts we have. Shop 6/29 at the Huanan market is our best guess for where Covid started.
An American reporter living in China, Michael Standaert, did some great investigative reporting during the pandemic. During his research, he uncovered one more interesting fact: 3 sellers at the Wuhan market were fined in May 2019 for selling illegal wildlife. The fined shops were 6/29, 8/25, and 9/37. 2 of those shops are the 2 that later tested positive for covid.
No other sellers at other markets in Wuhan were fined for selling illegal wildlife in 2019. That’s yet another weird coincidence you’d have to explain, if this was actually a lab leak.
Since some animals are susceptible to covid, you could still argue that maybe some person came into the market and the warehouse and infected the animals. That person could have come from the Wuhan lab. But they could also have gotten off a train from Southern China.
That brings us back to the same question we had before. How certain are we that the case search was complete and unbiased? Did any patients get sick before the market outbreak?
When did Covid start? Who was patient zero?
Patient zero refers to the first person in an epidemic. If covid was a lab leak, it would be the person infected in the lab. If it spilled over from an animal, it would be the person that got infected by that animal.
There were 174 confirmed covid cases in Wuhan, in December 2019:
The earliest listed case was December 8th. This man was not connected to the Huanan market.
When I used to think the lab leak theory was possible, I would look at data like this and wonder, “how can it have started at the market, if the first case was unconnected?”
It turned out this was just a recording error. Michael Worobey studied the case and thinks that this man didn’t actually have covid at that time, he had a dental emergency. Then, 8 days later, he got covid in the hospital. Two lab leak theorists independently came to the same conclusion, so both sides of the covid origins debate agree that this guy was not the first case.
The case on December 10th was a shrimp vendor at the market named Wei Guixian.
It’s unlikely that this is really the first case. Most people who catch covid don’t end up in the hospital. There could be 20 mildly ill people for each hospitalized case. Wei Guixian is just the first person who got sick enough to need a doctor. She likely got infected by someone else at the market — she lived very closer to work, did not commute, and did not do much outside work. When asked how she got sick, she said:
“Looking back, Ms. Wei thinks she might have been infected via the toilet she shared with the wild meat sellers and others on the market’s west side.”
In the market origin theory, the actual patient zero is likely one of the people selling wild animals, who either did not get very sick with covid, or did not inform the authorities that they got sick.
To disprove the market origin theory, we would want to find earlier cases that weren’t associated with the market.
The WHO report described 3 earlier cases that could be covid but probably weren’t.
There was an elderly man who got sick on December 1st. He was not connected to the market — he lived nearby, but he was in poor health and rarely left his home. Further investigation suggests he had a minor respiratory illness on December 1st. It probably wasn’t covid, because it responded to antibiotics. He got sick again on December 26th and tested positive for covid. His wife had been to the market and also got covid.
The second case is a woman who got sick with clotting and pneumonia on December 2nd. She tested negative for Covid during a long hospital admission ending in mid-February 2020.
The third case got sick on December 7th. He had a cold, a fever, and chest X-ray changes. He responded to antibiotics. Blood collected in April 2020 showed he had no covid antibodies.
Did anyone get sick before December?
The WHO report searched for earlier cases by combing Wuhan hospital records for people who had pneumonia, fever, influenza-like illness, or acute respiratory distress:
There’s no obvious uptick before December. There is an uptick around December 8th that’s bigger than previous months. There might also be something happening around December 1st, but it’s hard to tell.
That could be covid showing up in undiagnosed cases. Or it could also be winter cold and flu season showing up, at roughly the same time as the first handful of covid cases.
China also tested saved samples from flu patients. None of the early samples tested positive:
A 3rd study tested saved samples, throat swabs from sick people, going back as far as October. They couldn’t find any early positives. The positives they did find (from early 2020) clustered around the market:
We also have data on how many people searched for disease symptoms on Chinese search engine Baidu:
You can often see a large outbreak just from the symptoms people look for. It looks like there might be a sudden increase in coughing people, sometime around December 1st. There’s no big trend before December.
There is an uptick in people with diarrhea, starting around August. That could be relevant, but I suspect it’s unrelated. Covid usually has respiratory symptoms.
The WHO team also reviewed patient records for the last few months and looked for every hospital admission that sounded like it could be covid. They found 92 possible cases between September and December, evenly distributed across time.
None of these are proven covid cases, just respiratory illnesses that sounded similar to covid. None of these people formed clusters, or infected their families. There’s no trend, over time. Covid is an exponential disease that grows fast when it reaches a new city, it doesn’t just hang out for 3 months without growing. The WHO team took blood samples from 67 of those 92 people. All 67 tested negative for covid antibodies. But the testing was done in January 2021, over a year after these people were sick, so there’s no guarantee that they’d still test positive.
The virus probably wasn’t going around Wuhan before December.
We can confirm this from a blood bank study done in Wuhan. One study looked at 40,000 blood donor samples taken between September and December 2019. None of them tested positive for covid antibodies. The virus was not widely circulating around Wuhan in 2019.
It’s also unlikely that the virus started on the outskirts of Wuhan. The WHO report noted that excess mortality first rose inside Wuhan (in the 3rd week of 2020) and didn’t rise outside the city:
The report doesn’t rule out covid starting somewhere else in China and then coming to Wuhan. There was no testing in other cities.
This timing data helps us rule out certain theories.
The US house GOP report claims that covid started with a lab leak in early September. They pick this date because they think the Wuhan lab took some database of viruses offline on September 12th, 2019 (that didn’t actually happen, by the way). The report also says that covid was spread around the world by October.
Both of these things are unlikely — covid is highly contagious. Every time it gets to a new city, it quickly goes from one case to hundreds of cases within a few weeks. It doesn’t make sense for covid to start in September and go all the way until December with no hospitalized cases and no superspreading events.
The same is true in other countries — if they were infected in October, the spread should have been detectable long before large numbers of cases showed up in February or March.
It is possible there were a few cases in Wuhan in November or early December that we don’t know about. But there’s not much proof.
The closest thing we have are two anonymous sources.
There was an article in the South China Morning Post that claimed there were 5 cases in November, with the earliest on November 17th. The article says the source is “government data seen by the South China Morning Post”. Lots of people have linked to this news article, but no one has ever seen that “government data”, since then. The article happens to say that there were 266 early cases. 266 = 174+92, exactly the same number of cases in the WHO report. So, this might be exactly the same data as the WHO report, but the November cases were ruled out just like the early December cases.
Then there’s that famous article in the Wall Street Journal, saying that 3 Wuhan lab employees got sick in November 2019 and needed to go to the hospital. We don’t have any direct access to that information, it cites anonymous US intelligence sources. The US senate report doesn’t even mention any such intelligence information. The house GOP report mentions it, but lists the WSJ article as the source.
This is possible, and fits the timeline of when covid started. But it’s also suspicious. There are no details given. The journalist who wrote the article has a bad history as a government propagandist — he’s the guy that reported that Iraq has Weapons of Mass Destruction.
The hospitalization rate for covid is fairly low, only something like 5%. For 3 people to get severely ill, you’d think that maybe 60 lab employees caught covid. Or, perhaps these 3 got an extremely high dose of the virus, somehow? But then that doesn’t sound like a small, accidental exposure.
A separate version of this story claims that one of the researcher’s wives died from covid, a month later. That’s even less likely, for healthy young researchers.
The “3 sick researchers” story popped up again in 2023, reported by Michael Shellenberger and Matt Taibbi. Their article gave names to the 3 specific sick researchers.
But it’s still a highly questionable source of information — it still comes from “anonymous government sources”. Shellenberger is not a trustworthy journalist — a week earlier, he wrote a story saying the government is hiding 12 alien spacecraft.
A week later, the 3 names were confirmed by the Wall Street Journal, but it still only cited “anonymous government sources”, and the article was again written by that same journalist who reported on Iraq’s WMD’s.
A week after that, the Biden administration declared it had no information on sick researchers at the Wuhan institute.
It looks highly likely that the “3 sick researchers story” was simply invented by people in Trump’s state department.
If these people did get sick, the virus would still have to get from them to the market without spreading anywhere else in Wuhan. It would help to know where they lived and what hospital they were treated in. It would help to know if any of this actually happened at all. Unless US intelligence share their information, I can’t evaluate any of it. The Biden administration seems to say the intelligence doesn’t exist.
There was one Australian scientist working at the Wuhan lab in November 2019. She says she was never sick and didn’t know of anyone else at the lab falling ill. She wrote a paper with one of the 3 researchers named by Michael Shellenberger, so she should know if that person got covid.
During this whole time, the Wuhan scientists seemed to be acting like nothing was wrong. In December, some of the Wuhan scientists travelled to a foreign conference (on Nipah virus) like nothing was wrong:
In January, the Wuhan lab scientists were still acting like life was normal. Here they are, on January 15th, sitting at a restaurant in Wuhan:
That’s a month after the first case at the market, and two weeks after the market got shut down. So, we’re supposed to think they created a deadly virus, 3 of them already went to the hospital, they now know for sure the virus got loose in Wuhan, and now they’re all just going out to dinner without concern?
All the Wuhan lab employees tested negative for covid antibodies. I suppose that would be one of the easiest things for China to lie about, in a lab leak cover-up.
To disprove the market spillover theory, we would need confirmed covid cases before December 10th with no market exposure. There’s very little evidence for that. There’s only that one old news article which doesn’t list its source, and that WSJ article about an anonymous US intelligence source.
There was probably more than one patient zero
We can also use genetics to figure out when covid started and who the first patients were.
Covid mutates a little bit, over time. At the beginning of the pandemic, every covid infection was similar. As more people got infected, the virus had more mutations, and turned into many different strains.
You can take the virus samples from a bunch of patients and put them all into a genetic tree. Here’s what the tree looks like, as of the end of 2022:
Making a tree from early cases helps us say when the virus started. As time goes on, the virus has more and more diversity. But at the very beginning, it should have none. We can graph the diversity over time and follow it back to find where it had none:
That gives a date around December 10th, which lines up really well with the earliest known case.
This should be an unbiased way to find the origin date. If China had somehow hidden earlier cases, or missed a lot of cases outside the market, you’d be able to tell once the virus got outside of China — the cases would then show a big jump in diversity.
This doesn’t prove that the start was exactly December 10th — there would still be a few more patients earlier, that weren’t sampled and didn’t have many mutations.
We can make models to guess when the actual first patient was. Those models give a range, they say it’s probably some time in late November. One model gives this range:
This helps rule out certain theories. Like, some lab leak theories say the pandemic started in September or August. You can intuitively say that covid is too contagious to spread around Wuhan for 3 months before producing its first outbreak at the market. These models confirm that intuition, it’s very unlikely that covid started that early.
These models also help show why the lab leak theory is unlikely. If the first known patient was at the market on December 10th, they got infected around December 3rd, and we think the virus started in late November.
That only gives the virus a week or two to get from the lab to the market, without spreading anywhere else. That’s not impossible, but it’s very unlikely.
A more interesting finding is that the tree of early cases has two separate branches. Everyone belongs to a lineage A or a lineage B.
The two strains are very similar, the RNA only differs by 2 letters at two places. One paper writes:
Lineage B viruses have a “C/T” pattern at these key sites (C8782 and T28144), whereas lineage A viruses have a “T/C” pattern (C8782T and T28144C)
If you make a tree of how all the cases connect to each other, genetically, you see 2 clusters. The market cases are at the root of the lineage B cluster, on the left here. That’s the earliest cluster:
The WHO team was confused when they first saw this diagram, because the earliest (December 8th case) was not at the root of the tree, so some of the scientists thought that maybe the virus could have existed before the market outbreak.
But, as we saw earlier, the December 8th case did not actually get sick on this day, but a week later. DRASTIC also later discovered that the “December 8th” case was mislabelled here, and his genome was actually root lineage B.
Further investigation also found that there are no intermediate cases between lineage A and B, only sequencing errors. So it looks like the virus started twice.
An updated version of the diagram looks like this:
There are two early lineages. The market cases are at the root of lineage B. The 2 earliest known lineage A cases were also found near the market. Genetically, they are at or near the root of the lineage A tree.
In 2020 and 2021, lab leak supporters held out hope that these two lineages could still prove that covid came from a lab. Their theory would be that Lineage A leaked from the lab, made its way across town to the market, turned into Lineage B, and then started spreading from the market.
It wasn’t a terrible theory — Lineage A happens to be 2 mutations closer to the closest known bat viruses, so there’s a reason to think it might have come first.
But the theory also had other problems — if Lineage A started first, at the lab, then you’d expect it to be more widespread than B. You’d expect it to have more mutations, and more genetic diversity. In reality, the opposite is true. B has more cases, more mutations, and more diversity.
Let’s graph it like this:
If A came first, why is it lagging behind B?
One paper in 2021 calculated a 96% chance that lineage B, the strain found at the market, came first.
We can see when each started pretty easily, just by graphing the number of mutations over time. Both start with zero mutations and then gain more as time goes on. B started before A:
The lab leak theory fell apart here as more data came in. Researchers mapped out the locations for the first 2 lineage A cases. The first one lived right by the market, only 2 km away. Here’s a diagram of the location, as compared to 1,000 possible places in Wuhan where they could have lived:
It’s about a 3% chance they’d live so close to the market, compared to some random location.
Then, we found out that the second earliest lineage A case had stayed at a hotel less than 2 km from the market for 5 days before getting sick. Now with both cases so close, it’s more like a 1 in 1,000 coincidence.
Things got even worse for the lab leak theory when we saw the samples taken at the market. 4 of the positive samples from the market were sequenced. 3 were lineage B and 1 was lineage A.
And the lineage A sample was pretty close to the raccoon dog shop where we think the pandemic started.
All of the genetic diversity of the virus can be found within a small corner of the market and then all subsequent cases in the world can be traced back to those early cases.
This is the genetic equivalent of “cases start at the market and radiate outwards”.
The market is the center of the pandemic, geographically and genetically.
Explaining this evidence is easy, for the market origin theory. The virus started out in some animals. Those animals infected 2 different people. Lineage B spilled over first, then A spilled over slightly later.
This is all very hard to explain, if the virus came from the Wuhan lab. Now it’s not just one person that got infected at the lab, made their way to the market, and caused a superspreading event. Now it’s 2 workers who got infected at the lab and both made their way to the Huanan market. Both lab workers infected people and animals at the market. But neither infected lab worker spread the virus anywhere else in Wuhan.
Now, instead of the 1 in 10,000 chance that the market caused the first superspreading location, we’re looking at odds of 1 in 100 million that it caused two superspreading events there and nowhere else.
Is there any way to dismiss this argument, and still defend the lab leak theory?
Perhaps the virus mutated from one lineage to the other, from the first patient to the second patient, and then cases from both patients started spreading. This could happen by chance. Pekar’s simulation says there’s 1 in 30 chance things would happen that way.
Even if it just looks like two origins, by chance mutations, then you still have to explain why it looks like B started before A. You still need to explain why the 2 earliest known lineage A cases were found right next to the market. Add up each of those coincidences and maybe we’re talking 1 in 2 million odds, not 1 in 100 million. Either way, it’s very hard for a lab leak to match the evidence.
When did covid reach other countries?
A final way to check the origin date of covid is to look at when it reached other countries, to make sure that it wasn’t outside of Wuhan before the outbreak at the market.
I decided to separate this out into its own article:
The short summary is that it’s highly unlikely there are any positive samples outside of Wuhan, before December 2019. But the investigation gets a bit tricky because you need to evaluate each study and throw out some that are giving false positives, for a variety of reasons.
Looking at Google search trends around the world can also confirm there weren’t many people getting sick before February 2020. We can use those to see when the first big wave hits each country.
In summary:
All the data we have points to covid starting sometime around late November or early December, at the Huanan market.
There is zero place and time evidence linking covid to the Wuhan lab. It’s in the same city as the lab, and there are a whole lot of lab leak theories, but there’s no evidence linking the two.
A September lab leak of covid is very unlikely. A November lab leak is still possible, but it’s unlikely that the virus got to the market (twice) without showing up anywhere else.
It doesn’t look like the market origin data is biased by sampling.
If you make assumptions that it is biased or that lots of cases were missed, you can maybe open up other possibilities besides the market origin. If you do make these assumptions, you don’t just open up the lab leak theory but also the possibility that covid came to Wuhan on a train from somewhere else in China.
The market origin is by far the most likely. If I were forced to pick between one of the other two theories, I’d pick a natural origin somewhere else in China.
I say that because there are 2 million people coming into Wuhan on trains every month and only a few working on viruses at the lab.
I also say that because the genetic code for the virus looks natural, and there’s no convincing theory for how someone could make it.
What about genetic evidence?
Other lab leak theories claim that the proof lies not in the case data but in the genetic code for the virus.
One problem with the lab leak theory is that we don’t even know which virus the lab would have started with. If you wanted to design a SARS virus to spread in people, you would probably start with SARS and see if you could improve it. But covid is not SARS with a few modifications, it’s only 80% similar to SARS.
Since the pandemic started, we’ve found a few other natural viruses that are closer to covid, but the closest matches are still only 96–97% similar. It would take a thousand mutations to turn one of those viruses into covid. In nature, that would take a few decades.
In a lab, someone can splice 2 viruses together or add a piece of genetic code. But no one is going to randomly swap 1,000 letters spread all throughout covid’s RNA.
There is no known natural virus that you could easily turn into covid. The lab would need a secret virus to start with.
Soon after the pandemic started, the Wuhan lab disclosed a virus they had previously found, called RATG-13, which was 96% similar to covid. There are more than 1,000 mutations between the two viruses. This is not close enough to turn into covid, but it’s still featured in many lab leak theories.
One theory says that RATG-13 was used to create covid. Another says the Wuhan lab used drugs to mutate it into covid. Or it was passaged through animals to create covid. Another theory holds that RATG-13 is fake, a virus made by the Wuhan lab to throw people off the search. Or it’s real, but they only disclosed half the code and hid the rest, hoping people wouldn’t notice. There’s also a theory that RATG-13 was suspiciously renamed, from another virus in the database called BtCov/4991, to somehow hide where the virus was found.
Most of these theories are strange — if the Wuhan lab had just used RATG-13 to create covid, and was trying to cover that up, why would they disclose RATG-13 at all?
The name RATG-13 stands for Rhinopholus Affinis (the bat it was found in) TongGuan (the place it was found) 2013 (the year it was sampled). It looks like it was renamed to clarify where it came from, yet people instead made a conspiracy theory that it was renamed to hide something.
To believe the lab leak theory, you either have to believe the lab followed some very complicated process to turn RATG-13 into Covid, or you have to believe that the lab had other bat viruses that they never disclosed, and they started by engineering one of those. They could have other viruses, but there’s no proof of it.
We’ve found one unpublished paper from 2018 with access to the Wuhan database, confirming that there were no closer viruses at that time.
There was also one paper published in 2020, which listed all of the SARS family viruses that the WIV had. You’d think that would be useless, because they would obviously censor any secret virus they’d used to create Covid. But the paper was actually submitted for publication in August 2019, before the lab would have had any reason to hide anything. A FOIA request got the original version of the paper, and it still didn’t have any secret viruses.
So, if the lab did have a secret virus, they would have to find it between August 2019 and November 2019, and start all the important experiments in those 4 months.
The numbers on all these papers line up pretty well — the 2018 paper says they have 160 sarbecoviruses. The 2018 DEFUSE grant says they have 180 sarbecoviruses. The paper submitted in 2019 says they have 200 sarbecoviruses.
In all likelihood, the lab just didn’t have a secret virus to start from, and thus the lab did not make SARS-CoV-2.
But we should look through the genetic code anyways, to see if anything looks engineered. We can go through and look for features that seem unnatural or important.
The main feature that lab leak theorists point to is the “furin cleavage site”.
What’s a furin cleavage site?
Explaining cleavage sites is a little bit complicated, but I’ll give it a try.
You’ve seen this picture a thousand times:
Covid is a little ball with spike proteins sticking out.
Each of those spike proteins has 2 functions. First they have to stick to one of your cells via the ACE2 receptor. Then the virus has to fuse to the cell wall and enter inside.
The top half of the spike protein (S1) binds to ACE2. The bottom half (S2) fuses the cells together.
In between S1 and S2, there’s a piece called the furin cleavage site. It reacts to an enzyme inside your body, called furin, which cuts S1 apart from S2. After S1 is cut off, S2 can stick to the cell wall and the virus can enter.
Your body does some of the work for the virus, making its job easier. Viruses with this cleavage site are often more infectious. Covid spreads better and causes worse illness, because of this site. Scientists tried removing it from covid, and the virus spread worse in lung cells.
Adding a cleavage site to a virus can make it more dangerous to people. Scientists know this, and they’ve done some experiments adding a cleavage site to various viruses.
Adding a cleavage site requires adding 12 letters of RNA to the virus.
You can also think of it as 4 amino acids. That’s how RNA works — every 3 letters code for one amino acid. A string of amino acids is a protein. That protein folds up into some shape, in this case, the shape is the spike. And the FCS is just this little loop in the middle of that shape. Furin comes in and cuts there, to break S1 from S2:
Furin cuts proteins everywhere it sees the amino acids RxxR (R is arginine, X is any amino acid). Furin works better if it sees RRxR or RxRR. RRKR works best.
In covid’s case, the amino acids are RRAR.
So, covid has a furin cleavage site. Some people say that this furin cleavage site could only come from a lab.
In fact, there are 7 coronaviruses that infect humans, and 4 of them have furin cleavage sites:
The first 4 of these viruses cause colds. 2 of them have a cleavage site.
The other 3 are more serious viruses. MERS, Middle Eastern Respiratory Syndrome, is a very deadly disease that jumped from camels to humans. It has a cleavage site. SARS jumped from civet cats to humans in 2003. It does not have a cleavage site.
More generally, furin cleavage sites are found in lots of natural coronaviruses:
It’s not weird to find this in a bat virus. But so far, there are no other sarbecoviruses with a furin cleavage site, which leads many people to wonder whether SARS-CoV-2 was engineered.
The closest known bat virus, called RATG-13, has the same amino acids in much of the spike protein, except for those 4 at the cleavage site:
Since these two are so similar, except for the PRRA, many people began to wonder if a lab had inserted that.
There are a few things that are wrong with this idea. First off, the 12 RNA letters that were added don’t line up with the PRRA, they are “out of frame”:
A human designer could do that, but it’s not something they’re likely to do. They would normally plan out the 4 amino acids they want to add and then come up with the code for these.
Next up, we can tell that RATG-13 is not the precursor to covid. The amino acids in this section are the same but the RNA is not:
Every 3 RNA letters make one amino acid. But different combinations of 3 letters can make the same amino acid.
Of the 288 letters on either side of the cleavage site, 19 are different between those 2 viruses. Over time, mutations change the code even when the virus still works the same way. Those two viruses have about 40 years of genetic drift between them.
Still, the cleavage site is interesting. It looks like 12 letters of RNA were added at this one key spot, either by nature or by a lab. At the time that covid was first discovered, we didn’t know of any closely related viruses with a cleavage site, or even a partial cleavage site, so this looked very suspicious.
It raised the attention of virologists like Kristian Andersen and Bob Garry, both of whom originally suspected a lab leak but later changed their minds and believed a natural origin theory.
Over time, other scientists went out looking for more bat viruses to see if any had a cleavage site here, or something close to a cleavage site.
In 2020, they found one that had 3 amino acids (or 9 nucleotides) inserted at this site:
The virus, called RmYN02, was sampled in a survey of Yunnan bat viruses done in 2019. It’s only 93% similar to SARS-COV-2, also not close enough to be the precursor virus to covid. But it shows that natural processes can add RNA here.
After the pandemic started, scientists went searching caves in Southeast Asia, looking for more bat viruses similar to covid. In 2021, they found 3 other bat viruses with additions at this spot:
One of these viruses was found in bats in Thailand. The other two were found in bats in Laos. It might be possible to find even closer viruses in China.
These 4 viruses show that natural processes can add 9 letters to the RNA, at this spot. If 9 is possible, surely 12 is possible.
To convert the cleavage site from one of those viruses to match covid, you’d need to add one amino acid and change one. We’ll see in a minute that this means you’d have to add 3 letters of RNA and change 1.
The P in PRRA is not necessary.
The suspicious insert is PRRA, but that’s not the furin cleavage site. The cleavage site is RRAR, the final R was already in RATG-13 and other bat viruses.
If you started with RATG-13 and designed this virus, why would you even add the P? You could just add RRA, and you’d have a cleavage site. Or you could use a different letter. RRKR is actually the best cleavage site.
I went through all the previous experiments that labs have done, to add a cleavage site. I found:
A 2006 US study inserted RRSRR into the S1-S2 site in a SARS-CoV-1 pseudovirus.
A 2009 US study inserted RRSRR into the S1-S2 and S2’ site in a SARS-CoV-1 pseudovirus.
A 2008 Japanese study inserted KRRKR into S2’ site in a SARS-CoV-1 pseudovirus.
A 2014 Dutch study inserted RRRRR, into S2’ in a mouse hepatitis coronavirus (pseudovirus).
A 2019 Chinese study inserted RRKR into S2’ in a chicken virus (gamma-CoV infectious bronchitis virus).
This shows us a few things: Labs don’t do this very often, and the Wuhan lab has never done this before. When labs do these experiments, they usually use safe pseudoviruses, rather than live viruses that can infect people. Labs also use efficient cleavage sites, like RRKR or RRSRR. None of them used the P or the A.
Labs can use software to evaluate how good any particular cleavage site will be. One good screening tool is the Prop 1.0 model. It gives a value between 0 and 1, where 0.5 is a barely functional cleavage site and 1.0 is the best one.
Here are the scores for a few choices:
RRKR: 0.884
RRAR: 0.782
PRRAR: 0.626
A lab could use anything they want here. They would likely choose something really effective, like RRKR.
Changing that K to A makes the cleavage site worse.
Adding the P at the front makes it even worse.
So, why does covid have PRRAR and not RRKR?
That’s hard to explain, for the lab leak theory.
This is an easy question to answer, for the natural origin theory — look again at the other 4 viruses we recently found with a partially formed cleavage site. They all have the P in that first spot and A in the last spot.
Instead of looking at the amino acids, we can also look at the DNA for these viruses:
Every 3 letters convert to an amino acid. There are 4*4*4 = 64 combinations for each 3 letters. But there are only 20 amino acids. That means there is more than one way to spell out each amino acid.
P can be spelled 4 different ways. It could be CCT, CCC, CCA, or CCG.
The P found in SARS-CoV-2 just happens to use the same spelling as those other 4 natural viruses. That’s easy to explain, from the natural origin. For the lab leak theory, you need one more lucky coincidence.
We’ve also learned that P is not the only amino acid that works here, or the best one. In fact, some changes here make covid more infectious. This is actually what created the alpha and delta strains:
Evolution found this wasn’t optimal, and it gradually improved it. The original virus used PRRAR. The Alpha variant HRRAR, the Delta variant was RRRAR. Each of these changes made covid’s infectivity go up.
Why is the cleavage site spelled CGGCGG?
We can usually trust Robert Redfield to give the dumbest take on every lab leak issue. In this video, he claims that Covid was made with “human codons”, not “bat codons”. Watch until about 2:22:00:
So, a lot of that is actually just gibberish. If you’ve been following along so far, you know that’s not what a furin cleavage site does. But he’s also making a claim here that the virus uses “human codons”, not “bat codons”.
The cleavage site used the amino acids PRRAR.
The DNA letters are CCT CGG CGG GCA CGT.
Two of the R’s are both spelled CGG. Lab leak theorists, like Redfield, think this is suspicious.
There’s more than one way to spell out each amino acid.
The amino acid R (arginine) can be CGT, CGC, CGA, CGG, AGA, or AGG.
Some people claim that CGG is an abnormal way to spell R, either because it’s rare, or because “nature selects against that spelling”.
About 3% of arginines in Covid are spelled CGG. It’s similarly low for other viruses — it’s about 5% in SARS and 5% in the human coronavirus OC43.
CGG is seen about 20% of the time in human genes. It’s also seen about 20% of the time in bat genes.
This isn’t about humans vs. bats, it’s about viruses vs hosts. The immune system recognizes C and G pairs in viral RNA, so these are selected against, in both human viruses and bat viruses.
CGG is not the default choice for experimenters, either, that’s just a part of the lab leak myth.
We can tell it’s a myth because it has grown, over time. For instance, in his 2020 lab leak article, Yuri Deigin wrote a whole section on “codon usage”, where he carefully compared Covid with RATG13, SARS, and several other viruses. Despite all that work, he never noticed the double CGG.
Yuri instead wrote:
If the double CGG is important, he certainly couldn’t find it.
It appears that Yuri first learned about it from some random guy on Twitter, in May 2020.
I went through all the previous furin cleavage site insertion experiments to try to see what they prefer. Many don’t list their codon choice, but I found one that used a cleavage site of RRRRR. Here are the codons they used:
AGA′CGC′CGA′AGG′CGT
That’s right: they had 5 different choices to make for R and they used every single choice except CGG!
Various other experiments have used any of the 6 spellings, with no obvious preference.
Lab leak theories often claim that experimenters prefer to use a double CGG. I couldn’t actually find a single experiment which used a double CGG.
Experimenters know that the immune system selects against these CG pairs, so they would have no preference for a double CGG.
The Wuhan lab never added furin cleavage sites to viruses, that we know of, so there’s no way to know which codons they might have chosen. The closest thing I’ve seen is this Yuri Deigin claim:
• Shi Zhengli published one paper with Shibo Jiang in 2020.
• Shibo Jiang works at a different lab, but he did an experiment in 2013, where he added a furin cleavage site to some DNA
• One of the three R’s he added was CGG, the other 2 were AGG and CGC.
• The experiment had something to do with bacteria, not coronaviruses, and it was done in Guangzhou, not Wuhan.
• But, Shibo Jiang and Shi Zhengli are authors on a different paper together, after the pandemic starts.
• Therefore, Yuri concludes, Shi Zhengli was probably putting CGG into coronaviruses, left and right.
It’s a far stretch to go from that to calling this the smoking gun. Some lab leak theorists don’t even think the double CGG thing holds up at all. Alina Chan says the CGG CGG “hypothesis seems damning at first” but, “once you think about it, it falls apart”.
CGGCGG can be found naturally in some other bat viruses, though not at a cleavage site.
There’s also a feline coronavirus that uses PRRAR for cleavage and spells RR as CGGCGA. That’s one mutation away from the double CGG.
We can also just line this up with the other 4 similar bat viruses:
What would it take, to change that site to match covid? You’d need to add 3 letters and change 1 — add the letters CG in the first gap. Add a G in the second gap. Change one A to a G.
These viruses are constantly mutating and recombining with each other. Changing 4 letters is not wildly unlikely.
If the CGG CGG was unnatural, or nature selected against it, you would think that it would mutate into some other spelling of RR, over time.
You can change only one letter of CGG in 4 different ways and still get R. It could change to CGA, CGT, CGC, or AGG.
We’ve now had millions of covid cases. Of those sequenced, CGG CGG is still found in 99.85% of them. It’s not mutating away from that. For some reason, this spelling works best.
One experiment tried changing the CGG CGG to a different spelling: AGG AGG. The researchers found something interesting — the virus wasn’t as effective without the CGG. Evolution favors the CGG here for a subtle reason (it has to do with protein folding). So, even if the natural virus started out with something else, it might evolve into CGG in this spot, over time, because that works best. That might ultimately turn out to be the scientific explanation here.
What about the DEFUSE grant proposal?
A whistleblower uncovered research planning to put cleavage sites in bat viruses. The Ecohealth alliance proposed something called the DEFUSE project, to study viruses potentially emerging from bats.
The grant proposal is from 2018. It outlines the risk that some SARS-like coronavirus will eventually spill over into people, and it proposes all kinds of mad science to stop that from happening.
They plan to come up with drugs that boost bats’ immune systems and then spray these drugs inside bat caves.
They also propose genetic engineering, to add furin cleavage sites to viruses.
On page 35 of the DEFUSE grant proposal, they write:
“We will analyze all SARSr-CoV S gene sequences for appropriately proteolytic cleavage sites in S2 and for the presence of potential furin cleavage sites. SARSr-CoV S with mismatches in proteolytic cleavage sites can be activated by exogenous trypsin or cathepsin L. Where clear mismatches occur, we will introduce appropriate human-specific cleavage sites and evaluate growth potential in Vero cells and HAE cultures. In SARS-CoV we will ablate several of these sites based on pseudotyped particle studies and evaluate the impact of select SARSr-CoV S changes on virus replication and pathogenesis.”
Is this the smoking gun, showing that scientists made SARS-CoV-2?
Not really. First off, the grant was rejected.
Second, the work adding furin cleavage sites was supposed to be done in the US, at a university in North Carolina.
Third, they talk about doing the work in three known bat viruses that are closely related to SARS but not closely related to covid. The viruses they create should have one of these 3 backbones, and that would be easy to see.
Fourth, it looks like they were talking about adding a cleavage site at S2', a different location as the S1/S2 site found in Covid.
Fifth, they talk about growing the viruses in Vero cells. Vero cells are a line of monkey kidney cells, used in many lab experiments for growing viruses or testing drugs.
After Covid was discovered, researchers tried growing it in Vero cells. They found an important feature — it loses the furin cleavage site.
For it to come from the DEFUSE experiment, you have to assume that the work secretly moved to the Wuhan lab after the grant was rejected. That they had undisclosed bat viruses that they added a furin cleavage site to. That they cultured those viruses in some other kind of cells, maybe HAE (human airway epithelial) cells. Or that they did it in live animals.
It is possible that happened, but it’s all conjecture. There’s no proof that any of that happened.
What about serial passaging in animals?
Some theories say that covid was created by serial passaging in ferrets, or mice, or transgenic mice with human ACE2 receptors.
Early strains of covid could not infect wild mice. Scientists have since mouse made a mouse adapted strain to do covid experiments. When they did this, it caused a mutation in the spike protein, called N501Y. Because covid didn’t already have that mutation, it probably wasn’t created in those mice. Transgenic mice should not have that particular mutation, though.
It probably wasn’t created in ferrets. We’ve also passaged the virus through ferrets in lab experiments, it gains another mutation, called N501T, and sometimes one called Y453F.
When the virus spilled over into mink on farms, it frequently gained the mutations N501T, Y453F, and F486L.
When an experiment infected raccoon dogs with the virus, it did not mutate.
Is SARS-CoV-2 a chimera?
In 2015, scientists in North Carolina made a virus by combining SARS and another bat virus:
Using the SARS-CoV reverse genetics system, we generated and characterized a chimeric virus expressing the spike of bat coronavirus SHC014 in a mouse-adapted SARS-CoV backbone. The results indicate that viruses encoding the SHC014 spike in a wild-type backbone can efficiently use … the SARS receptor human angiotensin converting enzyme II (ACE2), replicate efficiently in primary human airway cells and achieve in vitro titers equivalent to epidemic strains of SARS-CoV.
This shows that scientists can combine viruses to make them dangerous to humans. They did the experiment to show that SARS like viruses were likely to naturally spill over to humans in the future.
The experiment also shows that you need a backbone virus to start with and a “reverse genetics system” built around that virus. No one knows of a backbone that could make SARS-CoV-2 and previous experiments worked with a known reverse genetics system, like the one for SARS.
In 2020, lab leak theorists decided that SARS-CoV-2 must also be a chimera created in the lab. One piece of evidence came from related pangolin viruses. If you compare SARS-CoV-2 to the closely related bat virus RATG-13, you find that it’s more than 90% similar across most of the genome. But the similarity drops down to 70% for one narrow segment, the receptor binding domain (RBD):
A pangolin coronavirus called MP789 showed a closer match across that narrow portion of the genome. Many people speculated that covid had gained some genes from pangolin viruses, either naturally or in a lab. Yuri Deigin wrote that:
CoV2 is an obvious chimera (though not nesessarily a lab-made one), which is based on the ancestral bat strain RaTG13, in which the receptor binding motif (RBM) in its spike protein is replaced by the RBM from a pangolin strain
The speculation of many lab leak theorists was that scientists had taken RATG-13 and altered the RBD so that it would bind better with human cells.
After the pandemic started, scientists went looking for other bat viruses and found several that had a closer match to the RBD. Here are two bat viruses that have an RBD more than 90% similar to SARS-CoV-2:
One of the viruses was found in Laos, the other in Yunnan province, China.
The virus found in China had only “five amino acid differences between its receptor-binding domain sequence and that of the earliest sequences of SARS-CoV-2”. It should bind well to human ACE2, without any modification.
In summary:
Labs have never disclosed any virus that could easily be turned into SARS-CoV-2.
The furin cleavage site is not one typically used for research. It looks more natural than engineered, because of the out of frame PRRAR.
SARS-CoV-2 wasn’t made in Vero cells.
It wasn’t made in ferrets.
It could possibly have been made in HAE cells or by passaging in some other animal.
There’s no need to make a chimera, because some bat viruses already bind well to human cells.
The genetic evidence points more towards a natural virus than an engineered one.
What about the Wuhan lab’s database that went offline?
It’s widely noted that some WIV database of viruses went offline on September 12th. The US house GOP report uses this as proof that the virus leaked from the lab in September.
First off, it’s highly unlikely that Covid started in September. If this happened months before a lab accident, it’s hard to say they’re connected. Is the idea that they took down some database because they planned to leak a virus?
Second, it’s not clear that the database did go offline in September. One source shows that database wasn’t reliably accessible before June 2019, access was unreliable before September, it was hard to access after September, access was unreliable again a few months later, and then it finally disappeared in February:
A better explanation might just be the lab didn’t have a good sys admin. Another would be this monitoring site isn’t accurate, and the whole September 12th conspiracy theory was made from bad information. The database really is offline now, but it looks like that maybe happened in February, after the lab leak theory was already becoming popular.
Third, it’s worth looking at the timing of other things that happened at the lab. From Vanity Fair:
On September 11, 2019, the CCP’s №15 Inspection Patrol Group arrived at the Beijing headquarters of the WIV’s parent organization, the Chinese Academy of Sciences (CAS), to conduct a two-month political inspection. The inspection was part of a larger routine sweep of 37 state organizations. According to the inspection team’s leader, its purpose was to sniff out any “violations of political discipline, party organizational discipline, [financial] ethics discipline, discipline with regard to the masses, work discipline, and discipline in one’s personal life.” They were also on the lookout for instances of insufficient loyalty to the CCP’s mission.
That would be pretty stupid if the WIV leaked a deadly virus one day after a big, important communist party inspection started.
It would also be almost as stupid if they leaked the virus in November, right after the two month inspection ended.
But, I don’t know, maybe the WIV scientists were relieved that the bureaucrats were finally gone and they said, “we can finally get back to leaking that pandemic we’ve always wanted to”.
What about Fauci’s e-mails?
Freedom of Information Act requests have uncovered some of the e-mails sent between Dr Fauci and other scientists, early in the pandemic.
They discussed the possibility that SARS-CoV-2 was an engineered virus. This is sometimes presented as Fauci and others conspiring to hide the lab leak.
One article says the e-mails point to “panic, lies, and a possible cover-up”.
But if you read the e-mails, the story looks different. You can read all of the messages here.
It sounds like Kristian Anderson called Fauci and said he was worried that covid wasn’t a natural virus. Fauci responded that they should investigate and then possibly notify the FBI if covid is unnatural:
A bunch of scientists then got together and discussed. It was theorized that this is the meeting where they conspired to hide a lab leak.
There’s no recording of the meeting, but one scientist (Ron Fouchier) took notes.
His writing is highly technical, you can probably skip this if you want. But, if you want to know what was discussed, it gives a pretty good idea. It was a discussion of features of the virus and whether or not they looked natural. They didn’t get together to talk about hiding some known gain of function research project:
They went back and forth for a week after that, discussed further steps, discussions to have, papers to write.
The scientists did debate what they should say publicly. For instance, Marion Koopmans wrote:
They discussed the lab leak theory, decided it was probably wrong, and wrote a paper about it. They didn’t announce that because they thought that conspiracy theorists would run wild with the idea. Which is exactly what happened when the e-mails came to light.
It sounds like they debated different theories, settled on the idea that the virus probably jumped from bats to humans via some unknown host.
And that’s still the most likely thing that happened.
Is any lab leak theory still possible?
Sure. You can come up with lots of things that are possible.
But they all need to explain why the virus emerged at the market, with 2 strains, and infected both people and animals there.
Like, if someone from the Wuhan lab made a new virus, infected animals with it, and then sold them to the Huanan market, that would explain it.
Or if the lab found naturally infected animals in the wild and sold them to the market, that would also explain it.
I’ve seen this theory once on Twitter. I’m pretty sure it’s false, especially since the whistleblower they name still has a job.
I’m just throwing it in to be 100% transparent — it is possible to make a story where the virus came from the lab, started spreading at the market, and looks completely the same as a natural virus spreading at the market.
Even that theory struggles a bit, because it doesn’t explain how the warehouses supplying the market got infected.
I can also imagine some highly improbable things. It’s possible an infected bat escaped from the Wuhan lab and flew across town to the market and infected the animals there. Seems pretty unlikely, why didn’t it fly anywhere else in Wuhan?
Or, an infected animal escaped the lab and walked across town to the market, and infected the animals there and nowhere else. That’s even more absurd.
Or, two lab employees caught lineage A and lineage B at the Wuhan institute of virology a few weeks apart. Both made it across town to the market, both infected people and animals there, but neither transmitted the virus to anyone else in town.
Or, the virus was actually made in a secret US lab and delivered to the market in Wuhan to frame the Chinese. And the US maybe did this twice, a few weeks apart. And then they totally failed to control covid in their own country and let a million people die.
Or, it’s possible that China somehow faked all the data, from case records to blood testing to searches on Baidu and Weibo. But, it’s a really weird theory — despite all that effort, why did they frame a market for selling the same animals that were susceptible to SARS? And then they immediately took steps to shut down the wildlife trade in those animals. And then they moved on to denying that the market was the source and blamed frozen food from other countries.
All of these things are possible, but none of them are likely.
It’s much more likely that sick animals infected people at the market.
So, why do people keep talking about the lab leak theory?
If you find it entertaining to read about the lab leak, people will write about it. If enough people find it entertaining, there will be a lot of articles.
People who write about the lab leak theory sell books, get featured on podcasts, and get interviewed by reporters.
I titled this article “the case against the lab leak theory” when it could have been “the case for a zoonotic origin of SARS-CoV-2”. The former will get a lot more traffic.
The lab leak is simply more interesting, to many people. It’s a more entertaining theory because it has actors. We want every story to have a hero or a villain.
Who would you rather blame for the pandemic? This guy:
Or this guy?
You can blame the Chinese government for this pandemic. They increased the odds this would happen by allowing a dangerous wildlife trade. They didn’t learn the right lessons after SARS.
In the United States, China is scarcely seen as the villain anymore. Fauci is.
While lab leak theorists sold a few books, the best selling book about the pandemic was called “The Real Anthony Fauci”, which made it to #16 on Amazon’s best selling books of 2021.
For some people on the political right, there’s now a folk theory where Fauci funded gain of function research to create the virus. Then Fauci conspired to hide how it was made when people noticed. He went on to call for devastating lockdowns. Fauci first said that masks don’t work and then made people wear them. Then he pushed a vaccine that supposedly “killed a hundred thousand people” (it didn’t). These people think that we didn’t need masks or lockdowns or vaccines because the virus is actually just a harmless cold. But it’s also a gain of function Chinese bioweapon.
Sure, none of these stories make sense if you put them all together. But they all work to pick up on people’s resentments. The last 3 years of the pandemic were frustrating for everyone. It helps to have someone to blame. Conspiracy theorists play to that. Politicians can, too.
Politicizing the lab leak doesn’t even make that much sense. Gain of function research was temporarily banned under the Obama administration. It resumed in 2017, under the Trump administration. Trump never fired Fauci. If Fauci was somehow to blame for the pandemic, Trump failed to stop any of it.
One journalist did actually ask Trump about this. He dodged the question and told the journalist how great his covid response was. Likewise, if the covid vaccines really were deadly, they were rushed out and approved under Trump’s watch.
Ron DeSantis might have an advantage over Trump in the 2024 election. He can weaponize this all better than Trump can. He called for Fauci to be fired. He hosted some kind of “vaccine truth commission”.
The truth is, Fauci is not to blame for covid. In all likelihood, the Wuhan lab isn’t either.
But we won’t hear the end of lab leak theories, either way. They’re entertaining. Like all conspiracy theories, they give the listener the satisfaction of believing some hidden truth. And they’re a good way to weaponize people’s frustration about the pandemic.
If anything, it probably helps China that people keep talking about the lab leak theory. Most scientists know a lab leak is unlikely, but half of the public thinks it happened. The scientists end up arguing with the public in western countries. The Chinese government can make up their own theories, either claiming that the virus was made in a US lab or that it came into the country on frozen seafood. Meanwhile, few people talk about making the wildlife trade safer.
Two new coronaviruses came out of China in the past 20 years from trafficking similar animals.
Have the right changes been made? Or will this happen again in 20 years?
