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The new South African Strain has the identical N501Y mutation in the Spike protein as in seen recently in the UK and in Brazil. It also confers the ability to infect BALB/c mice. Not this is a different substitution than the earlier reported N501T mutation identified in mink.
Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy https://science.sciencemag.org/content/369/6511/1603
The mutation they are reporting N501Y has been studied in depth. We have been using it to test vaccines in mine. It is the same strain found in the UK and Brazil. But we'll have to get more data on the strain. https://www.cogconsortium.uk/news_item/update-on-new-sars-cov-2-variant-and-how-cog-uk-tracks-emerging-mutations/
Interestingly this appears to be convergent evolution i.e. the South African N501Y mutation (yellow) appeared independently of the UK N501Y mutation which is associated with a 69/70 deletion)
https://nextstrain.org/groups/neherlab/ncov/S.N501?c=gt-S_501,69&r=country
https://nextstrain.org/groups/neherlab/ncov/S.N501?c=gt-S_501,69&r=country
WATCH LIVE | New variant of Covid-19 'may be spreading faster' - Karim https://www.youtube.com/watch?time_continue=4&v=xmFrOBUmX5g&feature=emb_logo
This press release indicated one mutation increases ACE2 binding and two others cause reduced efficacy of some antibodies but they give no specifics so we'll have to hold on for that.
http://nicd.ac.za/the-emergence-of-a-mutated-sars-cov-2-lineage-in-south-africa/?utm_content=buffer80bd3&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer
http://nicd.ac.za/the-emergence-of-a-mutated-sars-cov-2-lineage-in-south-africa/?utm_content=buffer80bd3&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer
http://nicd.ac.za/the-emergence-of-a-mutated-sars-cov-2-lineage-in-south-africa/?utm_content=buffer80bd3&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer
This slide from the press conference states that N501Y is responsible for greater ACE2 binding which is correct but as discussed in the UK link above we don't know if this has clinical significance yet:
Difficult to say if this is a real effect from the new strain or just an artifact of more and better testing.
The new strain spread from Nelson Mandela Bay
Could this be a super spreader event? https://twitter.com/RichardPopperw1/status/1340043156725911554
The new strain is now more than 90% of cases. So it could simply be more transmissible. Possibly these data could end up bolstering the claim that N501Y is causing greater transmission in the UK as well. But we'll have to wait and evaluate this further.
South Africa: The cumulative number of #COVID19 cases stands at 901,538 with 8725 new cases identified since the last report. https://twitter.com/COVID_19_ZA/status/1340005980722122753
This is end of the school year in South Africa just before summer. And there are a lot of parties going on like the “Ballito Rage” festival. So we have to question if this could be a super spreader event. Hard to say. https://www.theguardian.com/world/2020/dec/14/student-parties-south-africa-covid-second-wave
This is a cool 3D visualization of N501 in a spike trimer: https://github.com/emmahodcroft/cluster_scripts/blob/master/README.md#sn501
Currently BMJ reports that we can't say if the N501Y variant causes faster spreads or if it more dangerous. It is unlike to cause issues with the current vaccine.
BMJ: Covid-19: New coronavirus variant is identified in UK https://www.bmj.com/content/371/bmj.m4857
BMJ: Covid-19: New coronavirus variant is identified in UK https://www.bmj.com/content/371/bmj.m4857
If you looks at different strains that become dominant in different countries some of them are due to new virulent mutations but others are just do to social superspreading events and founder events:
