Thread by @angie_rasmussen

Two years ago, we demonstrated that the SARS-CoV-2 pandemic likely began at the Huanan Market via zoonosis resulting from the wildlife trade.

Many unanswered questions remained about the animals themselves.

Some answers, out today in @CellCellPress.

cell.com/cell/fulltext/…

First let's get this out of the way:

We did not find an infected animal. We cannot identify an individual infected animal with environmental samples. To do that, we need a sample taken directly from an infected animal. As far as we know, no such samples were ever collected.

This work follows up on our prior research. In this paper, we demonstrated that early human cases cluster around the Huanan market, and the SARS-CoV-2 positive environmental swabs in the market cluster in the section where the animals were sold.

https://x.com/angie_rasmussen/status/1551937826580824070

A companion paper by my colleagues showed that the pandemic resulted from two separate, independent spillovers.

(And despite what you may have heard, this paper was corrected but the conclusions are unchanged. This finding is not "debunked.")

https://x.com/angie_rasmussen/status/1551937832159158272

If you don't want to read the papers:
-Early cases centered around the market (not a lab)
-Environmental swabs that tested positive for SARS-CoV-2 clustered in the corner of the market where animals were sold
-There were 2 lineages of SARS2 that spilled over separately at Huanan

But of course questions remained. Since 2022, when the initial preprint came out and suggested that genetic data from potential host species at the market existed, we were very eager to get a look at these data.

You can tell a lot about a virus by looking at its hosts.

We wanted to know if genetic material from the hosts could confirm that animals really were in the market, and if they were present in samples that were positive for SARS-CoV-2.

When these data were finally shared last year, we set out to investigate this. Here's what we found:

First, yes, we identified animal DNA in SARS-CoV-2 positive samples.

If you're into true crime/forensics, you know that often DNA left at the scene of the crime can give clues about the perpetrator's identity.

Here is the list of suspects based on this evidence:

And here are the sequence reads broken down by stall within the market. Each stall had DNA from different animals, including humans. But some stalls had very little human DNA, suggesting that any virus at that stall might have been from an animal.

As I said before, we can't tell if these animals were infected based on these environmental data. We'd need to test the animals directly for that.

But we can narrow down the list of suspects based on susceptibility. Not all of these animals can be infected with SARS-CoV-2.

Raccoon dogs, red foxes, and mink are all known to be susceptible to SARS-CoV-2 and capable of transmitting it.

Masked palm civets were an intermediate host for SARS1 and are susceptible in vitro based on ACE2 binding.

The other wildlife species' susceptibility are unknown.

We also wondered where these animals came from and investigated that by analyzing their DNA as well for SNVs (individual mutations) that are linked to geographic locations. This is similar to what 23 and Me does to say you are 10% from wherever.

Geographic references were available for raccoon dogs and this revealed that the raccoon dogs at the market were likely not from fur farms in northern China or Russia. Instead, they were more similar to wild RDs found in Hubei province.

This suggests that the raccoon dogs at the Huanan market were from central or southern China, but the geographic reference data is incomplete. We need more data to ascertain this with confidence, as well as more reference data from other susceptible species.

We also looked at other viruses in the market. If these animals were infected with SARS2, they might have other infections as well.

And guess what, we found other viruses! These are animal viruses that likely can't infect humans, so animals with viral infections were present.

Again, we can't tell which animals were infected with these viruses either, but since they are animal viruses, they were probably infecting animals, not people.

And gee, I wonder what host was infected with raccoon dog amdovirus in a stall that's covered with raccoon dog DNA?

Finally, speaking of virus, we also analyzed the virus sequences obtained from these environmental samples to see if it was evolutionarily consistent with our previous estimates of the timing of spillover and sequences associated with early cases.

In fact, it was! The estimates of when the market viruses emerged are indistinguishable from the estimates of when the pandemic began. This supports our prior finding in Pekar et al 2022 regarding the timing of the emergence of both lineage A and lineage B viruses at the market.

So in summary, we show:

The presence of live, susceptible animals at the market, including in stalls that were SARS-CoV-2 positive

Animal viruses at the market

Where some of these animals may be from

Human emergence is estimated at the same time as when the pandemic began

Back to the analogy of a forensic investigation, DNA evidence places a short list of suspects (animals) at the scene of the crime (southwestern corner of Huanan Market) with the murder weapon (SARS2).

We can't definitively identify the murderer, but we know the murder occurred.

This study is not a "smoking gun," but is strongly suggestive that one or more of the species at the market was infected with SARS-CoV-2, and was the source of the 2 spillovers that led to the virus establishing human to human transmission chains and beginning the pandemic.

Again, we do not and cannot provide evidence of an infected animal. We do not claim that.

But these evidence support our prior findings in Worobey and Pekar 2022 and are likewise consistent with a zoonotic origin of the pandemic. They are not consistent with a lab origin.

I gratefully acknowledge the scientists at the Chinese CDC, who generated these data, made them available, and published their own analysis last year. Our analyses and conclusions differ, but they agree that there were susceptible animals at the market.

nature.com/articles/s4158…

I also am deeply grateful to my co-authors for being inspiring, brilliant scientists. The Zoonati are generous collaborators, an invaluable support system, & dear friends after all we've been through. This has been so scientifically rewarding & I'm honored to contribute. TY, ZC!

One more thing: I've chosen to focus on the science, not hot takes, like Clippy here violating embargo to "debunk" our peer-reviewed paper because it doesn't support his favored conspiracy theory.

We tested hypotheses with evidence, without seeking to validate personal biases.

We were concerned solely with the scientific evidence & didn't test the "people who disagree with us are lying & people who agree with us are telling the truth" hypothesis. Clippy is a prolific content producer, so I invite him to write up his own analysis & submit to Cell.

But I suspect that he and his fellow travellers will not rise to the challenge. The lab leak hypothesis has repeatedly failed testing. It is inconsistent with the evidence base and unscientific to suggest that you can substitute leading questions and speculation for actual data.

The fact is that the evidence is only consistent with zoonotic origin. That doesn't change because a thirsty professional keynote speaker who hasn't been relevant since the 90s misrepresents the evidence base & sows doubt in the scientific method to serve his own agenda.