Where did the pandemic begin?

Was it from nature or a lab?

Since the start, this fundamental question has gone unanswered.

Until now.

Out in @ScienceMagazine: SARS-CoV-2 emerged into humans via the live animal trade at the Huanan Seafood Market.https://t.co/hnl9j3E6j6

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

For the last 2.5 years there's been lots of acrimonious debate on the various origin hypotheses: nature or lab leak? Much of it was data-free, conspiratorial speculation.

The only thing everyone could agree on was the need for an independent, evidence-based investigation.

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

And while the evidence base is incomplete, imperfect, & inaccessible, there *is* still evidence. Quite a bit, actually.

So we set out to verify & analyze the evidence that we could access. And the results were clear:

All data points lead back to the Huanan Seafood Market.

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

So we did. After multiple rounds of highly critical review over months, these papers are substantively improved. Although many questions remain, these provide conclusive evidence that SARS-CoV-2 emerged via at least 2 zoonotic spillovers from animals sold at Huanan.

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

That brings me to the evidence itself. How do we know it's from nature and not a lab?

Let's start by looking at a map. These are the earliest cases on record. They cluster around the Huanan market and not the WIV, which is on the other side of the Yangtze River. pic.twitter.com/q0SFOkFLiQ

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

Later, the pattern becomes more diffuse as the virus spread throughout Wuhan. Again, this is consistent with emergence at the market in late November or early December 2019 followed by transmission throughout Wuhan (and eventually the rest of China and the world). pic.twitter.com/R90JIoyqk1

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

This schematic illustrates the significance of these center points. Early cases will not just be *near* the site where the pandemic started, they will be *centered* on it. That central place where this pandemic originated is the Huanan Seafood Market. pic.twitter.com/A1tvr0iH0Q

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

Looking at social media check-ins, we see that compared to other likely locations (including places considered high risk for superspreader events), Huanan got very little traffic and was much, much less likely to be the site of an early SSE than 100s of other places in Wuhan. pic.twitter.com/Mo0sxmiKp3

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

We also know there were multiple animal species that are known to be susceptible to SARS-CoV-2 being sold at Huanan in November and December 2019. That includes raccoon dogs & red foxes, as well as other animals likely to be susceptible like badgers, hares, hedgehogs, & muntjacs. pic.twitter.com/9PK6dGMrGu

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

Sleuthing is very popular in origins research, so we did some of our own to identify the specific stalls where these photos were taken. We also got hold of a report from the China CDC that described environmental samples positive for SARS-CoV-2 & their location in the market. pic.twitter.com/VvthAAGceQ

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

You can't find what you are intentionally not looking for. The market was closed Dec 31 without sampling any relevant species.

So we can't know which animal(s) were intermediate hosts. But the environmental samples point to the animals nonetheless.

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

When we look at the distribution of positive samples in the market, we see that they are overwhelmingly associated with the west side where animals were sold, in the corner where the stalls sold animals.

This is a strong statistical association and it's not a coincidence. pic.twitter.com/aTEaBuG4VG

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

Early on in the pandemic, there were two lineages of SARS-CoV-2, lineage A and lineage B.

We knew that lineage A cases were geographically associated with the market in Wuhan, but we thought all the known market cases were lineage B.

Until this preprint put lineage A there too.

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

Try fitting this into a lab leak scenario:

Worker 1 gets infected with lineage B at WIV and immediately goes straight to the market, only infecting other people once there.

A week later, worker 2 gets infected with lineage A at WIV & also immediately goes straight to Huanan.

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

This is very plausible, because the animals were kept in such close quarters and were part of a common supply chain. One infected animal would spread virus to others, allowing for the divergence of the two lineages prior to zoonotic transmission to humans.

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

And I'm not even done with this thread and already the bad faith takes are rolling in from people with a vested interest in a lab origin, like this below.

Our article makes it 100% clear the pandemic originated at Huanan market. We present the evidence & it passed peer-review. pic.twitter.com/nTwOYwLKbP

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

Like any study, this has limitations. The data is imperfect and incomplete. However, it was adequate to support our conclusions.

We have demonstrated that the pandemic started via zoonotic transmission at Huanan Market. pic.twitter.com/D8YWZOFomO

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

But don't just take my word for it. My fantastic co-author @MichaelWorobey explains this in great detail in his wonderful thread on our work.https://t.co/OiTekF2ZFC

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

But we've answered a big one here: the pandemic began via at least 2 zoonotic spillovers from animals sold at the Huanan market. Not a lab, not a cave, not a dentist's office.

This is not our opinion. This is original evidence-based research that withstood a tough peer review.

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

And with that, I'll thank my wonderful co-authors for the privilege of working with them on this: @MichaelWorobey, @josh__levy, @LrnM9, @acritschristoph, @jepekar, @stgoldst, @MOUGK, @WildCRU_Ox, @MarionKoopmans, @suchard_group, Joel Wertheim, @LemeyLab, @robertson_lab…

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

I'd also very much like to thank my institution @VIDOInterVac @usask for their continued support, as well as @CoVaRR_Net, a @CIHR_IRSC-supported network, for supporting my work. I'm proud to represent some of the best scientific institutions in Canada and the world.

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022

Finally, I'd like to thank both the five peer reviewers and team of editors whose thoughtful criticism and guidance significantly improved this work.

— Dr. Angela Rasmussen (@angie_rasmussen) July 26, 2022