Thread by @Ayjchan

Read the 2nd Yan et al. report. It was frustrating... each statement requires fact-checking to the point where, instead of pointing out the errors, it may be better for someone to write an independent article discussing the circumstantial evidence pointing to lab origins.

The overarching message of Yan's 2nd report is that there has been unscientific behavior surrounding the reporting of SARS2-like CoVs. Based on this, they speculate that these genomes are coordinated fakes to make SARS2 look natural.

Again the report is littered with errors, but I do wonder why there hasn't been international impetus to investigate the source of these SARS2-like viruses. Why not go to the Yunnan mine to look for more RaTG13s? Why not investigate the miners - what actually happened in 2012?

Why not investigate the March 2019 GD pangolins to see where these animals contracted their virus from?Maybe 99% of the answer is politics. There's just no way for an independent team to waltz into China right now and investigate SARS2 origins unobstructed.

I'm glad Yan is shining the spotlight on these research integrity issues. But I worry that framing the verifiable misdirection surrounding RaTG13/pangolins within a specious article may actually hurt the legitimacy of research integrity inquiries regarding SARS2-like viruses.

I was particularly surprised by Yan's interpretation of the medical thesis & PhD thesis that describe the 2012 SARS-like cases in Yunnan miners. Yan suggests that both theses contradict each other and did not reach an agreement on whether the miners suffered from SARS. However...

If you read the actual theses, the medical thesis concludes, based on expert consultations, that the severe pneumonia in the 6 miners was caused by a SARS-like CoV from Rhinolophus bats.

Although the PhD thesis described the miner cases as unsolved, the bat pathogen research described in the chapter was clearly motivated by these pneumonia cases, with a specific focus on the finding that 4 of the patients were tested and found positive for SARS IgG antibodies.

Re: "severe discrepancies" between the 2 theses, I think the number of patients sampled and the type of antibody tests are actually not in disagreement with each other. The 2 theses were written years apart. More tests were run in the follow-up on the miners.

To get a clearer picture of what samples were taken and what the test results were for SARS antibodies, shouldn't journalists be reaching out to the supervisors and authors of the theses, and the consultants mentioned in the theses, to get their version of the story?

Back to report, Yan et al. claim because a cover-up was "orchestrated by the CCP".. "the unleashing of the virus must be a planned execution rather than an accident". I disagree. Just because something is accidental, doesn't mean it has no consequences & will be admitted openly.

Example: hit-and-runs. Just because these are mostly accidental and not premeditated, doesn't mean the driver doesn't panic and try to escape the consequences.

I'm not saying SARS2 has lab origins, only that lab origins should be investigated alongside natural origins - a POV that 1 pro-natural origins expert also espouses, and indeed will be investigated by the Lancet's team led by a long-time WIV collaborator. telegraph.co.uk/global-health/…

In this regard, I think Yan goes too far by asserting that SARS2 is an "unrestricted bioweapon" - this actually hurts her credibility and the credibility of other scientists asking for an objective investigation of lab origins.

I urge a shift away from bioweapons speculation back onto solid ground: the research integrity concerns surrounding some of the closest viruses to SARS2.

These are discussed in Yan's report, but completely overshadowed by claims about SARS2 being an "unrestricted bioweapon".

One of my takeaways from researching SARS2 origins is that the scientific community has been struggling with a research integrity crisis, now made more obvious by the pandemic. Scientists & journals seem to have forgotten what to do when there are research integrity failures.

I go to town on research misconduct in this thread - what it is and how bad actors are enabled when misconduct is not addressed appropriately and in a timely manner.

https://twitter.com/Ayjchan/status/1309591751578001413

We - scientists, journals, sci comm - need to have a discussion about what to do when research integrity failures are discovered in a paper. On the one extreme, e.g. Yan et al., they discard and frame all SARS2-like viruses as fabricated because of these integrity issues...

On the other extreme, scientists are trying to pick out parts that they can verify and hopefully still use, e.g. raw data, from papers suffering from integrity issues - as opposed to urging that these papers be retracted or release full details on sample processing etc.

Somewhere in between, I think that a paper doesn't need to be 100% fraudulent to be deserving of retraction. If intentional misconduct is revealed, the paper should be retracted. If scientists want to keep citing misconduct papers or data, they should clarify in each citation...

... that they are aware that the paper/data in question suffers from research integrity issues, but they have chosen to use the data anyway in the trust/belief that it was not impacted by the misconduct.