Pandemic Revisionism, Part One: COVID-19 Origins

Because people keep getting this very wrong.

Pictured: COVID-19 times. There were many smart things we did during the pandemic, wearing masks outside was not one of them. Photo by Yoav Aziz on Unsplash

I have, for five years, studiously avoided writing anything about the origins of COVID-19. There are a few reasons for this. I’m not really qualified to comment. While I’m an expert on epidemiology who worked on COVID-19 during the pandemic, I’m not a virologist and much of the discussion is about viral RNA. It’s been 15 years since I spent any real time in a lab, so much of the more in-depth virological data is hard for me to properly assess. Not impossible, but hard.

I also genuinely don’t really care what started the pandemic. People are always shocked when they hear this, but to me it doesn’t matter that much. We know that wet markets should be better regulated and that globally laboratories should have strong oversight - these are both true regardless of what precisely caused the pandemic.

But a recent piece in the Guardian irritated me enough that I feel like I have to write about it. And since I’ve been thinking about writing a series on the current revisionist history of the pandemic, this might as well be the first piece. So let’s look at the origins of COVID-19 and why most of the current discourse is wildly off the mark.

Before we start, I should reiterate that I’m not the definitive word on this matter. These are my thoughts and opinions about the likelihood of various options. I’m going to give a numeric rating of certainty just to give you an idea of my personal beliefs, but these numbers are basically meaningless. Also, feel free to change my mind, I’ll leave the comments open.

Let’s go from least to most likely.

Theory 1: China Created COVID-19

My Rating For Possibility: <1/100

The first theory is the one currently accepted by the United States government under the Trump administration as truth. You can find the propaganda site online if you want, I’m not going to link to it.

You’ve all heard some version of this theory. China was doing “dangerous” experiments with bat coronaviruses, called gain-of-function research, and they managed to create SARS-CoV-2 in a lab. Specifically, the Wuhan Institute of Virology (WIV), which is located in the city where COVID-19 first broke out. Then a series of unfortunate events occurred leading to the virus escaping into a nearby wet market in the same city, and snowballing into the pandemic that we all know so well.

We’re going to look at the second half of that claim later, but for now let’s think about the main idea. Is it plausible that China was secretly conducting research that led to COVID-19?

One massive strike against this claim is that it is a conspiracy theory. I’m not saying that to discredit anyone, or to take some moral position - it’s just a fact. The idea that Chinese scientists created a novel virus in Wuhan requires a massive cover-up which would include 1,000s of scientists, public officials, and more across the world. This cover-up would also have to predate the pandemic by many years, not just on the part of Chinese scientists but also US government officials working in the embassy in Wuhan.

In addition, the WIV was quite good about sharing information publicly in the years before COVID-19. They regularly posted the genomes of viral samples online, and they actually had a massive repository of data that anyone could download at one point. So not only must the WIV scientists be conspiring with US officials to hide the origins of the pandemic, anyone who downloaded their data prior to the database going down would have to be in on the conspiracy - or, just as unlikely, the WIV scientists must have been hiding all of the many samples of virus that they were working on before the pandemic happened.

It’s important to understand how hard it would be to design a virus that can cause a pandemic. This is not a month-long undertaking - it would’ve been a massively expensive project taking years or even decades. Even gain-of-function research is notoriously difficult and rarely results in a useful virus that we can actually test. For one thing, we still cannot reliably predict how well a virus survives in the world based on its genes - we can guess, but we’re often wrong. So not only must the Chinese researchers have hidden their work, they must’ve hidden one of the biggest projects in the WIV for the last decade, including countless failed experiments, from everyone including their US colleagues who came and looked at their work.

Even more outlandishly, they must have hidden their success. This is the sort of project that would’ve made careers. Even a single experiment showing some measure of success in this arena - creating a new virus that was genetically very similar to SARS - would’ve been a monumental scientific announcement. Every step along the way would be a top-cited paper. Instead, the researchers kept this all secret for years at a time when there was no real reason to keep anything secret.

No conspiracy is impossible, but the more people that are involved with one the harder it gets to keep it secret. As the old saying goes, "two people can keep a secret if one of them is dead”. It stretches credulity that such a large group of people would have no whistle-blowers at all.

In addition, the argument put forward that the virus was created in a lab is astonishingly weak. The White House website lays out these points:

1. The virus possesses a biological characteristic that is not found in nature.

2. Data shows that all COVID-19 cases stem from a single introduction into humans. This runs contrary to previous pandemics where there were multiple spillover events.

3. Wuhan is home to China’s foremost SARS research lab, which has a history of conducting gain-of-function research (gene altering and organism supercharging) at inadequate biosafety levels.

4. Wuhan Institute of Virology (WIV) researchers were sick with COVID-like symptoms in the fall of 2019, months before COVID-19 was discovered at the wet market.

5. By nearly all measures of science, if there was evidence of a natural origin it would have already surfaced. But it hasn’t.

The first of these claims is straightforwardly false. The claim is that the furin cleavage site of the COVID-19 virus - an element of SARS-CoV-2 that is critical to its success in infecting people - is not found in nature, and therefore the virus cannot have evolved naturally.

It is true that furin cleavage sites are rare in the family of viruses that SARS-CoV-2 comes from. In particular, in bat coronaviruses that mostly do not infect human cells that are related to SARS-CoV-2 directly, there are no other examples with this specific feature around.

But there are many other coronaviruses that have evolved furin cleavage sites. For example, two of the human coronaviruses that circulate every year causing colds have precisely this feature. Here’s a paper from 2015 describing the potential problems that the furin cleavage site of HCoV-OC43 could have for human neurological cells.

While it’s true that this feature is somewhat unusual, that’s entirely expected. If furin cleavage sites evolved all of the time, we’d be inundated with pandemics. Instead, most bat viruses just infect bats, and never evolve features that could cause them to be dangerous for humans.

The second point from the White House propaganda site is also untrue. The best current evidence indicates that there were almost certainly two or even more introductions into humans at the onset of the pandemic. While this sort of genetic epidemiology is complex, the data shows that there were two distinct lineages of SARS-CoV-2 spreading in November and December 2019, which could only happen if there was more than one introduction into the population at that time.

Point three is entirely speculative. We’ll cover the “biosafety” concerns more in the next section, but even without looking too deeply into the evidence you can’t infer much from this sort of statement.

Point four is astonishingly misleading. COVID-like symptoms encompass almost the entire spectrum of human illness, and therefore it is entirely meaningless to say that there were a few people sick in Wuhan in August-October 2019. It’s a large lab, of course people were sick. The average human adult is estimated to have 3-4 symptomatic colds per year, most of which happen in the colder months. Moreover, there is no evidence whatsoever of a COVID-19 outbreak in the WIV in 2019. The US Director for National Intelligence released a report in 2023 that found that none of the early 2019 supposed COVID-19 cases were actually workers in laboratories, and the only laboratory worker who did get sick in this time period did not have COVID-19 symptoms. In addition, WIV workers who had antibody tests to see if they’d previously had COVID-19 in 2020 tested negative, which is essentially impossible if the outbreak started at the lab. Not only is point four not proof, it is mostly not true.

The final point is simply a matter of opinion. Most of the experienced virologists I know believe that SARS-CoV-2 came from a zoonotic outbreak. The White House prefers to trust the small minority of experts who think differently. That’s not evidence, and so we cannot really appraise it as such.

We’ve now had five years for proponents of the lab leak conspiracy to find literally any evidence that the virus was designed. It should be trivially easy to prove. A single email discussing a new virus very similar to SARS being tested in the Wuhan lab. A viral sample from an old paper that is a genetic predecessor of SARS-CoV-2. Anything. Instead, the entire argument comes down to a series of vague statements about how a group of people in theory could have potentially gone about creating a virus. Even more bizarrely, the entire thing seems to be a right-wing US conspiracy, which is strange because most of the work would’ve been done while Donald Trump was president (2016-2020) and given US officials had a fair bit of oversight into the WIV it’s hard to imagine any secret virus programs would’ve escaped the administration’s notice.

All in all, I am wholly unconvinced by this concept. Any conspiracy theory is pretty unlikely, and there is not a shred of evidence that SARS-CoV-2 could have come from a lab, never mind that it actually did.

Theory 2: A Big Accident

My Rating For Possibility: 5/100

The next theory is a much more realistic but still very improbable series of events. This is not a conspiracy theory, but the idea is still very hard to believe given the evidence we have got so far.

The idea is that COVID-19 first broke out in Wuhan, where the WIV is located. However, the type of bat that COVID-19 comes from - horseshoe bats - don’t really live in or around Wuhan. WIV, on the other hand, collects samples of viruses from all across China. Therefore, COVID-19 could have come about by a WIV researcher collecting a sample of the disease, bringing it home to Wuhan, and then accidentally leaking it to the general population.

There are some things that are quite well explained by this theory. It is indeed a big coincidence that the pandemic started in the same city in China that houses one of the foremost labs looking into coronavirus research. It doesn’t require a conspiracy theory, just a few stuff-ups and a researcher or two who destroyed their samples before they could be tested by the authorities.

In addition, we know that this sort of outbreak has happened before. There has never been a lab leak of a human-created virus, but there have been plenty of leaks of naturally-sourced viruses into humans. The 1977 Russian influenza outbreak, for example, was genetically identical to an earlier strain of flu from the 50s. There have been several cases where researchers studying SARS caught the disease and even spread it to others.

The main issue with this theory is that it is actually really hard to get infected with a virus while working in a lab. The biggest challenge with working on pathogens is generally keeping them alive. I had a friend in university who lost 6 months of his PhD because one outlet for water in their lab had the wrong piping installed and it kept contaminating his pathogen samples and killing them.

It’s also rare that people work on viruses in a way that allows for easy transmission. Most viral samples are stored in an inactivated form - this usually means some form of chemical to kill and preserve the virus - which means that you can’t really catch them working in a lab unless you are breeding the virus to study it further. Again, there is no evidence that this was happening at WIV at any point in time.

In addition, this theory cannot explain multiple introductions of the disease. You’d need two separate occasions where researchers who were culturing the live virus somehow inoculated themselves at different times with different strains of the same disease. It happens - it happened with SARS - but it’s quite uncommon.

There’s also the matter of the biosafety of the WIV. Much has been made of cables between the US State Department and the Wuhan consulate in 2017 which were reported as showing serious issues with the WIV and their conduct. But when these cables were acquired through a freedom of information act by US Right To Know, they show nothing of the sort. If anything, the State Department thought in 2017 that the WIV was doing appropriate work in a reasonable way.

This theory also doesn’t fit with the epidemiology of the initial cases of COVID-19. This brings us to the early pandemic, and the first place where I am qualified to have an opinion as an epidemiologist who did investigations into COVID-19 outbreaks during the pandemic. It also brings us to the most likely explanation of COVID-19 origins by far.

Theory 3: Zoonosis

My Rating For Possibility: 95/100

Zoonosis is the process of a disease spreading from an animal source to humans. It’s a natural process that is behind many of our infectious diseases, including everything from rabies to influenza. It happens all the time. Unlike lab leaks, which only happen once or twice a decade despite the millions of researchers working with live viruses all across the world, zoonotic outbreaks occur hundreds if not thousands of times a year.

We also know that there are regular human outbreaks of bat-related viruses. A 2018 paper from China found that of 218 people who lived near major bat caves, 6 had antibodies to viruses similar in structure to the original SARS. That means that there were regular outbreaks of completely novel viruses happening in China of viruses similar to SARS - and therefore COVID-19 - long before the pandemic.

There is also abundant evidence that zoonosis is a likely explanation for how COVID-19 came about. The initial outbreak happened at the Huanan market in Wuhan, which had previously been reported to have conditions that were dangerous for viral transmission. The market housed many species that regularly act as intermediaries for the bat to human transmission pipeline. It would be a huge coincidence for the virus to break out in an animal trading market and it not be related at all to zoonotic events.

The market was also clearly a source of many infections. Samples taken from early in the pandemic show multiple positive tests within the market, including the stalls where animals such as raccoon dogs - which are one of the most likely culprits for starting the pandemic in the first place - were kept.

There are some arguments about where exactly the first outbreaks were in Wuhan in November/December 2019. Personally, as an expert in the topic area, I find the evidence convincing that the very first major outbreak was the Huanan market. This does not make it certain, but it is a strong point that I believe makes the zoonotic origin more likely.

This theory of the origins also doesn’t have any major holes. Multiple introduction events are often - but not always - characteristic of zoonotic outbreaks. You usually have a few different animals sick with the virus before it jumps to humans, which means that you get different lineages of the human disease. This is exactly what we observe with SARS-CoV-2 in the early pandemic. While it’s true that the Huanan market and the WIV are in the same city, they are pretty far apart. The White House propaganda website has a glowing map showing an ominous 7.5 miles between the two, but that’s as the crow flies. The fastest route between the two places takes at least 30 minutes of driving with minimal traffic, and runs more than 12 miles.

It’s hard to explain why two WIV employees, on separate occasions, went all the way across town while infected with an early strain of SARS-CoV-2 and deposited viral RNA around a bunch of live animal stalls. On the other hand, this series of events fits perfectly into the theory that the pandemic started through a zoonotic event.

As the final substantial point of evidence for zoonosis, this series of events is precisely what happened with the almost-identical disease SARS. In the case of SARS, there was an outbreak in a wet market in Shenzhen which was traced back to raccoon dogs and palm civets being sold there. Both of these species were sold in the Huanan market, and epidemiologically there is some evidence that the area the animals were sold is where COVID-19 first started to break out.

But Fauci!

It’s usually at this point in the discussion that people start bringing up the character of the scientists who did all this work. I’ve been told many times on social media that some of the people who identified the epidemiology of early COVID-19 outbreaks are not to be trusted, that all of this data is unserious, and that we should ignore everything produced that shows that zoonosis is a likely explanation for the pandemic. If you look at the White House site, most of the text is just personal attacks on a handful of American scientists, rather than any attempt to prove that the virus came from a lab.

I genuinely do not care either way about any of this. I know none of the people involved, I’ve never worked directly with any virologists - aside from a handful of local Australian people in 2020 and 2021, none of whom had any involvement in this research - and I’m entirely uninterested in whether they are mean or not online. I had never heard Anthony Fauci’s name before 2020, because most of my work was in chronic disease. I have only met two people involved in any of the above research in person, one briefly at a panel and another when they were living in Sydney for a few months.

What I like to focus on is the evidence. And the evidence, to me, is convincing that the pandemic started at the Huanan market in November 2019. There is strong data showing that this was the original source of the COVID-19 outbreak that went on to infect the world. Given the facts as they stand, this makes zoonosis by far the mostly likely explanation.

People also like to argue that China is untrustworthy and therefore we shouldn’t believe anything the government says about pandemic origins. I agree. I’ve even pointed out issues in Chinese COVID-19 data myself in the past.

But the problem is, both explanations for the origins of COVID-19 are terrible for the Chinese government. A lab leak is bad, obviously, but so is a zoonotic event at a wet market. Wet markets are very common in the country, and the Chinese government was aware well before 2019 that they posed a risk of causing pandemics. They had even committed to taking steps to making these markets safer to prevent exactly the sort of outbreak that we saw in the Huanan market.

That’s why official Chinese government sources have spread theories that the virus was created by the USA, or that it was imported from another country in frozen food. Chinese officials aren’t keen on any explanation that makes the government look bad, and zoonosis is almost as problematic as a lab leak in that respect.

We also know, from decades of data prior to the pandemic, that zoonosis is always the most likely explanation. Aside from a handful of lab leaks that were easily traced back to samples held in specific places, every human disease in our history has had a natural origin. There are no smoking guns in the SARS-CoV-2 virus that prove it was created in a lab, and without such a feature there is not a shred of evidence that the virus was designed.

Most arguments about the pandemic’s origins are also just tedious reiteration of the same handful of points. The main argument that the pandemic was human designed is that the WIV is right there, but that’s no more convincing today than it was in 2020. Meanwhile, more and more data has accrued showing that the most likely source of the initial samples of COVID-19 that we have was an animal.

It’s possible that a WIV virologist started the pandemic, but as I’ve said I don’t think it’s very likely. By far the most plausible explanation, given the evidence that we’ve got to date, is that COVID-19 was spread from an animal to humans in November 2019 at the Huanan market in Wuhan. It’s possible that the evidence will change, but that’s my assessment of the facts as they currently stand.

As I said, I’m leaving the comments open. Feel free to try and convince me. That being said, be respectful, I will delete abuse and close the comments if people get too rowdy.