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Slack / Private Message Drop, p.373 [SLACK_000587] · slack_pm:msg:03888

Date: 2021-01-10 06:31
Type: chat message · slack
recipient: Kristian G. Andersen, Edward C. Holmes, Andrew Rambaut
speaker: Robert F. Garry
Topics: Natural origin / zoonotic spillover

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I'm gonna break reviewer privacy because it's relevant to share an title of an article I just this minute was asked toreview: "Hypothesis of Potential Evolution of SARS-CoV-2 through Hybridization of SARS-CoV-1 withSaccharomyces cerevisiae and Mycobacterium avium naturally inside an immunocompromised Pangolin" Incredible.

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I'm gonna break reviewer privacy because it's relevant to share an title of an article I just this minute was asked toreview: "Hypothesis of Potential Evolution of SARS-CoV-2 through Hybridization of SARS-CoV-1 withSaccharomyces cerevisiae and Mycobacterium avium naturally inside an immunocompromised Pangolin" Incredible.	quoted / not their view	quoted_external sentence carries quotation marks	asserts

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2021-01-10 06:25 Robert F. Garry open

https://www.medrxiv.org/content/10.1101/2020.12.24.20248834v1.full.pdf Phase change may be too strong a term. SC2 is still SC2. But it is adapting - evolution is indeed a pain in the arse. When you allow a pathogen that came from an animal to spread unchecked in humans like this one (thank you Donald Trump et al), it will find ways to get better at spreading in humans. The plots of Ct values from nasal swabs suggest that the UK variant is a heck of a lot better at replicating in the URT (I'm guessing if you did G614 vs D614 you see something similar maybe not asdramatic). Coupled with what we can infer from the immune escape studies from Bloom lab and Zahradník[@Kristian Andersen above] we can see that the SC2 is getting fitter and more evasive. [shared file(s): image.png]
2021-01-10 06:31 Robert F. Garry

I'm gonna break reviewer privacy because it's relevant to share an title of an article I just this minute was asked toreview: "Hypothesis of Potential Evolution of SARS-CoV-2 through Hybridization of SARS-CoV-1 withSaccharomyces cerevisiae and Mycobacterium avium naturally inside an immunocompromised Pangolin" Incredible.
2021-01-10 06:45 Robert F. Garry open

The next data point that's going to be super critical is IF we start to see vaccine breakthrough with the UK variant. Ithink enough people have been vaccinated in the UK to perhaps start to see a trend.
2021-01-10 07:04 Kristian G. Andersen open

I'm not so sure immune selection isn't showing an appreciable selection pressure - "phase change" might be a little too strong, however, I think it could already be one of the most selective forces. We'll see. Bob - yeah, Doug had higher viral loads too, but much less of a dramatic difference than Nelly. Of course, the plot we're looking at here is Doug vs Nelly - Nelly vs Hugo (Hu-1..) would be even more dramatic.
2021-01-10 07:19 Robert F. Garry open

Indeed -here's one of many Hugo vs Doug (Genome copies not Ct) ~1 log whereas Nelly vs Doug is ~2 Logs on average it seems: [shared file(s): image.png]
2021-01-10 07:21 Robert F. Garry open

This is just the URT (nasal) I think data in the lung not as dramatic if any change at all (need lung data for Nelly, Eeek and Pooh) - worth noting Doug alone is easier to neutralize.

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