November 12, 2022 from Rounding the Earth Newsletter

Over the past few days I've published a discussion with Alex Washburne and Kevin McKernan about the synthetic fingerprint of SARS-CoV-2 that's been viewed over 220,000 times, a discussion with J.J. Couey about infectious clones (and Gain of Purity vs. Gain of Function), and some out-loud thinking about the known capabilities of U.S. biowarfare capabilities.

Then I checked back at Alex Washburne's substack and realized that I'd missed an important article.

Here is the part of the article that caught my attention (with respect to this article series):

Other methods of assembly exist

To say “other methods of assembly exist, so therefore the method proposed was not used for SARS-CoV-2” is like walking up to a murder scene and saying “there are more efficient ways to murder someone, I wouldn’t have chosen this method, so therefore it wasn’t a murder.” At the heart of this critique is an assumption that the method for in vitro genome assembly we study was unlikely or uncommon.

To critically examine this claim, we need to understand whether the particular method of viral assembly we studied was common. Our study conducted a meta-analysis to find all CoV infectious clones from 2000-2019. We searched for all studies containing the terms “coronavirus”, “infectious clone”, and “type IIS”. The proposed other-methods-of-assembly (Golden Gate assembly) also utilizes type IIS restriction enzymes, so such infectious clones would have been found in our analysis.

Our meta-analysis yielded 10 examples of infectious clones:

  1. TGEV (2000)

  2. SARS-CoV-1 Urbani (2003)

  3. SARS-CoV-1 Urbani (2006)

  4. MHV (2008)

  5. SARS-CoV (2008)

  6. A bat SARS-CoV from the same 2008 paper above

  7. HCoV-NL63 (2008)

  8. MERS-CoV (2013)

  9. WIV1 (2016)

  10. PEDV (2018)

Of the 10 examples above, only PEDV and MHV were assembled using golden gate assembly. The other 8 out of 10 CoV infectious clones we found from 2000-2019 were assembled by the method we’ve described. Type II directional cloning was by far the most common method for assembling coronavirus genomes in vitro prior to COVID-19.

Notably, one of these CoVs was even assembled in Wuhan: WIV1 was assembled in the Wuhan Institute of Virology with PI’s Shi Zheng-Li and Peter Daszak. rWIV1 was assembled adding/removing BglI sites with silent mutations (black/white arrows below, respectively), utilizing some pre-existing sites (no arrows), and then proceeding with exactly the method of type II directional cloning we examine in our paper.

Looking past the potentially interesting conversation we can have around whether or not the creation of at least one infectious clone in Wuhan transfers responsibility for violating international bioweapons treaties onto China, we note a significant list of infectious clones published in the literature that can and have been produced in laboratories. If you respect the statistical test as indicative of the result, this is demonstration of the capability of the DoD to have been releasing infectious clones as low grade bioweapons for many years now.

So, how many might have been produced in military laboratories that might never have reached the peer-reviewed journals?

Right.

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https://roundingtheearth.substack.com/p/what-about-the-other-infectious-clones
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