Thread by @AntGDuarte

@Rossana38510044 @jhouse678 @franciscodeasis @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 1/ Here's some takeaways from Zhou et al's Addendum.

First, some background:

• The authors' earlier version of the Tongguan mine sampling (Ge et al. 2016) says "we conducted a surveillance of coronaviruses in bats in an abandoned mineshaft (...) from 2012–2013."

@Rossana38510044 @jhouse678 @franciscodeasis @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 2/
• The 2016 paper reports a total of 276 bat samples, where the authors detected "150 sequences homologous to alphacoronaviruses" and "two sequences (HiBtCoV/3740-2 and RaBtCoV/4991) homologous to betacoronaviruses"
• Only one of those beta CoVs was said to be SARS-related.

@Rossana38510044 @jhouse678 @franciscodeasis @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 3/
• That SARS-related beta CoV is of course RaBtCoV/4991, which the authors renamed RaTG13 in their Feb. 2020 Nature paper "A pneumonia outbreak associated with a new coronavirus of probable bat origin"
• This is the paper to which they now felt the need to publish an Addendum

@Rossana38510044 @jhouse678 @franciscodeasis @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 4/
• This Addendum confirms that the Tongguan mine sampling was prompted by a cluster of unexplained severe pneumonia in 2012, that killed 3 out of 6 infected mine workers, of suspected viral origin
• Authors also confirm they received & tested blood samples from these patients

@Rossana38510044 @jhouse678 @franciscodeasis @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 5/
• The Addendum says that, besides the previously reported 276 bat samples collected in 2012-2013, a further 1046 samples were collected in 2014-2015
• In these additional samples the authors detected more 134 alpha CoVs, and 7 beta CoVs, that apparently remain unpublished

@Rossana38510044 @jhouse678 @franciscodeasis @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 6/
• While in their first report (Ge et al. 2016), only one of the two reported beta CoVs was said to be SARS-related, the authors now say all 9 beta CoVs found in the Tongguan mine (apparently 2 detected in 2012-2013 samples + 7 detected 2014-2015 samples) are SARS-related.

@Rossana38510044 @jhouse678 @franciscodeasis @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 7/ Some outstanding questions:

• Did the Wuhan Institute of Virology receive other samples from the infected Tongguan mine workers besides the serum samples reported in Zhou et al. Addendum? (Li Xu's Master's thesis reports a thymectomy performed in one of the patients)

@Rossana38510044 @jhouse678 @franciscodeasis @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 8/End
• Are the unreported beta CoVs detected in Tongguan mine samples from 2014-2015 the 78XX group reported in Latinne et al (2020)?
• Is it a coincidence that this group seems closely related to RaTG13 and that a 7896 label shows up in RaTG13 amplicons?

h/t @franciscodeasis

@Rossana38510044 @jhouse678 @franciscodeasis @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen "Recently, we retested the [2012 serum] samples with our validated enzyme-linked immunosorbent assay (ELISA) against (...) SARS-CoV-2 nucleocapsid protein (...) and confirmed that these patients were not infected by SARS-CoV-2."

Is this even immunologically sound @K_G_Andersen?