THE origins of SARS-CoV2

Once again, I am tired and not writing about what I expected. I am sure I will finish this after 2 AM after getting up at 7AM to take my daughter to swim class. I spent a couple of nights working until 3AM this week and have a lot more work to do this weekend. How can anyone possibly balance family, exercise, work, learning, staying up on current events and sleep right now? I do not know the answer. I am just trying my best to not regret not doing more and nothing suffers too much. I am relying on my Oura ring to let me know when I need to take a nap to catch up on sleep.

The topic this week jumped to the forefront of my thinking when I was banned for two months from popular gaming site Resetera. I do not know if it was because I didn’t provide sources for what I posted or if that would not have mattered. I do know that I stand by what I wrote. The more I investigated it and thought about it the more important I determined it was.  

There is an interesting tangent here with the NeoGAF/Resetera split and current political conversations. I recently read The Righteous Mind and it has implications there. I am currently reading through Wait Buy Why/Tim Urbans’ epic articles on “The Story of Us” and there are implications there as well. The combination of those two sources with the gaming community split is really interesting. I hope to come back to it later.

For now I will focus on the “conspiracy theory” that got me banned. First a small side-note from an audiobook chapter I heard on my nightly walk tonight. Do these quotes from a world-renowned epidemiologist sound relevant to today?

“In this case, I’m certain that the wrong conclusions from CDC officials … resulted in many more … becoming seriously ill and even dying.”

“This [recommendations from a US medical professional association] turned out to be exactly the wrong advice.”

“Another lesson I learned from my experience… if you don’t know what you are talking about, then don’t talk, or at least say you don’t know.”

“… my launching pad into the big leagues of epidemiologic investigation and analysis; it made me realize how easily data can be misinterpreted into flawed science and how important it is to get a number of perspectives on board. And it taught me to make sure you ask the right questions, lest you be led to the wrong answers.”

They are from the book Deadliest Enemy originally published in March 2017. They come from a chapter on the initial investigation into a rise of Toxic Shock Syndrome tied to tampons in 1980.

From the beginning of January, I have been significantly ramping up my knowledge of infectious diseases and most specifically SARS-Cov2. I have added ~20 specialists on Twitter over time to my feed. I spend more time than normal scrolling through Twitter to see if there is anything I missed. From July 28-30th one of those Harvard & MIT specialists tweeted out the following across a string of Tweets:

“Seen my favorite TV/news hosts take cheapshots at obvious conspiracy theories like 5G & plandemic, but we need you to start covering plausible nature/lab-scenarios of SARS2 origins in a fair and evidence-based manner. Ask experts to explain their hypothesis+evidence to you.”

"In sum, closest relatives to SARS2:
RaTG13 - very slowly revealed origins tied to miners infected by unknown virus, manifesting SARS-like symptoms in 2012
GD pangolin CoV (with the SARS2 RBD) - data missing and confusion among papers
RmYN02 (natural insertion) - data missing”

“So frustrating for scientists to find that data regarding SARS2 natural origins cannot be accessed.”

Wait what? At first I was confused. I though the scientific evidence said it wasn’t a lab created virus. It turns out I was thinking about it wrong. There is a difference between created in a lab and escaped from a lab. There is also a difference between likely and possible. She was just pointing out that it remained a possibility until a source was identified. There was no evidence disproving it as a possibility. Clearly, I had been missing something. It was not just something. It was a lot of things.

First let’s go back through this specific source. She published a paper in May that has some important things that are relevant here:

“Our observations suggest that by the time SARS-CoV-2 was first detected in late 2019, it was already pre-adapted to human transmission to an extent similar to late epidemic SARS-CoV.”

“The sudden appearance of a highly infectious SARS-CoV-2 presents a major cause for concern that should motivate stronger international efforts to identify the source and prevent near future re-emergence.”

“The lack of definitive evidence to verify or rule out adaptation in an intermediate host species, humans, or a laboratory, means that we need to take precautions against each scenario to prevent re-emergence.”

“It would be curious if no precursors or branches of SARS-CoV-2 evolution are discovered in humans or animals.”

“While these investigations are conducted, it would be safer to more extensively limit human activity that leads to frequent or prolonged contact with wild animals and their habitats.”

It is now three months later and we don’t have anymore answers. In fact it seems like there are more questions. Digging into threads there were a couple of references to a recently translated 2016 research paper on a pneumonia outbreak on miners in 2012. After awhile I ended up here:

“Our supposition as to why there was a time lag between sample collection (in 2012/2013) and the COVID-19 outbreak is that the researchers were awaiting BSL-4 lab construction and certification, which was underway in 2013 but delayed until 2018.

We propose that, when frozen samples derived from the miners were eventually opened in the Wuhan lab they were already highly adapted to humans to an extent possibly not anticipated by the researchers. One small mistake or mechanical breakdown could have led directly to the first human infection in late 2019.”

“In requesting an investigation we are aware that no scientific institution anywhere has made a comparable request. We believe that this failure undermines public trust in a “scientific response” to the pandemic. Instead, the scientific establishment has labeled the lab escape theory a “rumor“, an “unverified theory” and a “conspiracy” when its proper name is a hypothesis.”

Those are some pretty extreme claims, but even if it stopped there I don’t think it qualifies as a conspiracy theory. This small and independent source has been around since 2006. The paper is written by two PhD's. They have been published in prestigious journals and do not have any major corporate sponsors. Their Wikipedia page has no red flags. They had an article in April on their site that had a headline leaning in the other direction (“Did this Virus Come from a Lab? Maybe Not…”). I found a scientific rating site that give them mixed ratings, but the examples they chose was oddly a direct quote easily verified in an FDA published paper. Is it really pseudoscience if the rebuttal includes information that wasn’t in the original paper? If anything that was an FDA fuck up. And even that rating site has them at a “mild” rating on their conspiracy scale.

Nevertheless, extraordinary claims require extraordinary evidence and I went digging for more. The London Times, India Times and Newsweek all picked up on part of the story. From Newsweek who clearly researched the Times article:

“The miners fell ill with symptoms similar to COVID-19, including a fever, cough, sore limbs, and breathing difficulties. Two men died initially. The four who survived men were tested for a raft of infections, but these came back negative.

At the time, doctors sent blood samples from the patients to the Wuhan Institute of Virology, where Shi Zhengli—a scientist dubbed "bat woman" due to her work on coronaviruses in these animals—works.

Four of the men were found to have antibodies for an unknown SARS-like coronavirus. One later died. The coronavirus was not named in the report.”

“However, Jeremy Rossman, honorary senior lecturer in virology at the University of Kent, told Newsweek at the time: "The exact origins of the virus and its jump into humans may never be conclusively proven."
Rossman said Monday: "There are clearly some important and unresolved issues about the origins of COVID-19 and in the absence of transparency it is easy for conspiracy theories to grow. It is important to understand the provenance of the RaTG13/RaBtCoV/4991 strain of virus and its relation to the pneumonia cases in Kunming, as this will help us to better understand the evolution and pathology of SARS-CoV-2.”

This is a big deal. The single fact that there was a potential unknown coronavirus outbreak in 2012 is enough to be a big deal without getting into any theories. How was this not known earlier? Why is it not being discussed more? There are four sources here and a translated 2016 research paper that has been accepted by all of them. That 2016 research paper clearly references viruses. The NIH even has a contemporaneous 2014 account that mentions no known cause. And there is a 2016 paper with Shi’s name on it that details the coronavirus work and makes no mention of the miners but is focused on coronaviruses in the location of the miners.

There is more to this story. The journal Scientific American did an interview with Shi with this claim in it:

“Although the fungus turned out to be the pathogen that had sickened the miners, she says it would have been only a matter of time before they caught the coronaviruses if the mine had not been promptly shut.”

So we have a 2014 source that says unknown. A 2016 source that says virus. And a 2020 source that says they would have got coronavirus, but it was just a fungus?

We also have the fact that the Wall Street Journal (which incidentally was the most broadly trusted source from both political sides in a Wait Buy Why article) published an op-ed on 7/28 that goes even further:

“The alternative explanation, a lab escape, is far more plausible.”

​This is not a conspiracy theory. It is a valid hypothesis with tons of support and big implications. At a minimum the complete dismissal of lab escape potential reflects poorly on the scientific integrity of anyone that considers the evidence and dismisses it as a possibility. You should question any source that does not remain open to the possibility. It is OK to say you don’t know.