Slack / Private Message Drop — page 373

[2021-01-09 11:02:00] [Kristian Andersen] The vaccines are not going to be distributed in time - not by a long shot [2021-01-09 11:03:38] [Kristian Andersen] Here's a very simple analysis illustrating the issue - we're currently Rt ~1 [shared file(s): SEIR.jpg] [2021-01-09 11:04:20] [Kristian Andersen] [this is for San Diego - ~ 1% current frequency]. [2021-01-09 11:09:10] [Robert Garry] Yes - totally - the new variants or if ET is correct strains are coming just like in the UK. And I agree they are going to dominate before the vaccines will even start to have any effect on spread. [2021-01-09 14:55:55] [Eddie Holmes] I'm not sure it's a 'phase change' driven by immune selection. If that were the case wouldn't we see more reinfection than we are seeing? I wonder if its just that there is more diversity because there are more cases than there have ever been. The virus population is growing rapidly. [2021-01-09 15:54:46] [Andrew Rambaut] I agree, Eddie (except possibly for parts of Brazil where infection rates from previous peaks were already high). But it just feels like something is going on. [2021-01-09 15:56:07] [Andrew Rambaut] But there is not one of these mutations that haven't cropped up numerous times before (and that is just the times we saw it in the sequences). I think what is new is the combinations. And as you say, that is just a numbers game. [2021-01-10 06:25:35] [Robert Garry] 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 as dramatic). 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 06:31:19] [Robert Garry] [thread - ID: 2021-01-10 06:31:19] I'm gonna break reviewer privacy because it's relevant to share an title of an article I just this minute was asked to review: "Hypothesis of Potential Evolution of SARS-CoV-2 through Hybridization of SARS-CoV-1 with Saccharomyces cerevisiae and Mycobacterium avium naturally inside an immunocompromised Pangolin" Incredible. [2021-01-10 06:45:02] [Robert Garry] The next data point that's going to be super critical is IF we start to see vaccine breakthrough with the UK variant. I think enough people have been vaccinated in the UK to perhaps start to see a trend.