1/ THESIS: For unknown reasons, Shi Zhengli (famous "Bat Woman" of the Wuhan Institute of Virology) has obfuscated the connection between SARS-2’s nearest known relative, RaBtCoV/4991 aka RaTG13, and her own research and has elided that she discovered this virus in 2013 while

2/ investigating a still-unexplained outbreak of fatal pneumonias in a bat-infested disused mineshaft located in Mojiang County of Yunnan Province.

3/ SZ identified SARS-2’s nearest known relative as RaTG13 in a February 2020 paper, and uploaded its full genome sequence, which has 96% identity with SARS-2. The only info given in the paper was that the virus was recovered from bats in Yunnan province. https://www.nature.com/articles/s41586-020-2012-7

4/ Almost simultaneously with the publication of SZ's paper introducing RaTG13 as SARS-2's nearest relative, another group pinpointed BtCoV/4991 as a candidate for nearest relative based on more limited available sequence data.
https://ncbi.nlm.nih.gov/pmc/articles/PMC7033720/

5/ In fact, 4991 had originally been described by SZ herself in a 2016 paper describing the recovery of viruses from an abandoned mineshaft in Mojiang County of Yunnan. A 370nt sequence from the RdRp gene SZ uploaded at the time matched RaTG13 exactly.
https://link.springer.com/article/10.1007/s12250-016-3713-9

6/ The equivalence of RaTG13 and 4991 is further supported by the available details on the original source sample that was the basis for the full-genome RaTG13 sequence. https://twitter.com/_coltseavers/status/1259659532583780354?s=20

7/ It is not clear why SZ failed to cite her own 2016 paper or link RaGT13 to 4991 in her paper identifying RaTG13 as SARS-2’s nearest known relative. You would think she might take a bow for having discovered 4991 and having brought it back to Wuhan way back in 2013.

8/ SZ's 2016 paper explains how her team collected samples from the abandoned mineshaft in Mojiang over a period of a year starting in August 2012. It does not mention what motivated the group to focus on this site.

9/ SZ has described various SARS-like CoVs her group has discovered in the bat caves of Yunnan Province in several publications, but 4991 was apparently the only member of this clade found in the Mojiang mineshaft.

10/ A Scientific American profile of SZ mentions she was called out to investigate a mineshaft in Mojiang after an outbreak of fatal pneumonias affecting miners. The temporal & geographical details seem very consistent with the 2016 paper describing 4991.
https://scientificamerican.com/article/how-chinas-bat-woman-hunted-down-viruses-from-sars-to-the-new-coronavirus1/

11/ According to the Scientific American piece, the deaths of the miners in Mojiang were eventually attributed to fungal infections, not viruses. Again, SZ’s 2016 paper does not mention any backstory about being called out to investigate the mineshaft after miner’s deaths.

12/ Aside from the Scientific American article, there are multiple Chinese news reports and journal articles relating to a mysterious outbreak of fatal pneumonias linked to an abandoned mineshaft in Mojiang in the summer of 2012. https://twitter.com/RolandBakerIII/status/1259623784782327810?s=20

13/ The similarity to the incident mentioned in the Scientific American piece suggest they could be one and the same. However, there are a couple of discrepancies. Firstly, per the Scientific American Article, 2 out of 6 miners died, but the other sources mention 3 out 3 dying.

14/ Perhaps more significantly, the other reporting indicates that the true cause of the miner’s deaths was never identified, not that it was discovered to be fungal infection. https://twitter.com/RolandBakerIII/status/1259625285697191936?s=20

15/ Indeed, a 2017 Nature paper describes a novel rat-borne paramyxovirus that another team of virologists (not SZ’s team) identified in the cave while acknowledging that the actual causative agent in the miner’s deaths remains unknown.
https://nature.com/articles/ncomms16060

16/ Is the Mojiang mineshaft fatal pneumonia outbreak described in the Sci Am SZ profile the same as the one that spawned that paramyxovirus paper? Regardless, is it what spurred SZ to discover 4991? And were the deaths really explained by fungus? All questions of interest here.

Addendum to 16/: @_coltseavers pointed out that Shi's 2016 paper mentions that the mineshaft that produced 4991 is the same as the one that produced the paramyxovirus (MojV) => miner deaths stories are presumably same, casts further doubt on fungus story. https://twitter.com/_coltseavers/status/1261413201712828417?s=20

17/ It is prima facie surprising that Shi Zhengli failed to take a bow for having discovered the nearest known relative to SARS-2 and brought it back to her lab in Wuhan back in 2013 when she pinpointed RaTG13 in her 2020 paper.

18/ It is also prima facie surprising that, by accident or design, she obfuscated the identity of RaTG13 with 4991.

19/ If the discovery of 4991 was the result of SZ’s investigation into a (possibly) still-unexplained outbreak of pneumonias, which the evidence seems to suggest, then these apparent obfuscations and the failure to note the backstory to 4991 seem even more remarkable.

20/ Possible motivations for soft-peddling 4991 and perhaps linkage to a mystery 2012 pneumonia outbreak could include: (1) pressure from Chinese authorities to minimize public alarm over a new SARS-like outbreak back in 2012/13;

21/ (2) professional secrecy related to an ongoing effort to put together a major scientific "story" for high-level publication around SZ’s theory of direct bat-to-human transmission of SARS-like coronaviruses;

22/ (3) desire to deflect suspicion that the worldwide COVID-19 pandemic is the result of a biocontainment failure involving SZ’s research at the Wuhan Institute of Virology.

23/ Full credit goes to @luigi_warren - duplicated to threadroll.

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