Trevor Bedford on Twitter: "All this said, I'm not concerned that these variants will significantly reduce vaccine efficacy in the 2021 rollout. Most circulating SARS-CoV-2 viruses do not have any mutations in the spike receptor binding domain (https://t.co/TZt5BqhSzk). 15/18… https://t.co/5b1bxKTqKW"

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Trevor Bedford‏Verified account @trvrb 19 Dec 2020

First off, we have new studies on antigenic drift in seasonal coronaviruses. Katie Kistler and I have shown abundant adaptive evolution in the spike proteins of viruses OC43 and 229E consistent with antigenic drift (https://bedford.io/papers/kistler-hcov-adaptive-evolution/ …). 5/18pic.twitter.com/dGknZQgsP1

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Trevor Bedford‏Verified account @trvrb 19 Dec 2020

Trevor Bedford Retweeted Bloom Lab

We also now have direct serological evidence of antigenic drift in 229E from @eguia_rachel, @jbloom_lab et al, suggesting that reinfection by seasonal coronaviruses that occurs every ~3 years is in part due to evolution of the virus. 6/18https://twitter.com/jbloom_lab/status/1339939720558563328 …

Trevor Bedford added,

Bloom Lab @jbloom_lab

In new work, we show a human coronavirus evolves to escape neutralization by antibody immunity (https://www.biorxiv.org/content/10.1101/2020.12.17.423313v1 …). Specifically, we studied the historical evolution of the common-cold CoV-229E to learn how #SARSCoV2 might evolve & if we might need to update vaccines. (1/n)

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Trevor Bedford‏Verified account @trvrb 19 Dec 2020

For SARS-CoV-2, we only expect antigenic variants to spread once enough people have been infected to give these variants a transmission advantage gained by the ability to reinfect some portion of individuals immune to the original variant. 7/18

6 replies . 93 retweets 781 likes

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Trevor Bedford‏Verified account @trvrb 19 Dec 2020

At this point, many countries have had perhaps 10% to 20% of their population infected (https://www.medrxiv.org/content/10.1101/2020.12.01.20241539v1 …), and so we expect some weak evolutionary pressure for antigenic drift. 8/18pic.twitter.com/J1VUfRQQSI

6 replies . 79 retweets 708 likes

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Trevor Bedford‏Verified account @trvrb 19 Dec 2020

We've now seen the emergence and spread of several variants that may have some antigenic impact. These variants are generally labeled based on the mutation to the SARS-CoV-2 spike protein. For example N439K has a change from asparagine (N) to lysine (K) at site 439 in spike. 9/18

4 replies . 79 retweets 654 likes

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Trevor Bedford‏Verified account @trvrb 19 Dec 2020

This variant N439K is now present in ~5% of recent viruses from Europe (https://nextstrain.org/ncov/europe?c=gt-S_439&f_region=Europe&transmissions=hide …) and shows evidence of escape from some monoclonal antibodies and decreased reactivity to some convalescent sera (@emcat1, @robertson_lab et al https://www.biorxiv.org/content/10.1101/2020.11.04.355842v1 …). 10/18pic.twitter.com/J5VsLTbu7n

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Trevor Bedford‏Verified account @trvrb 19 Dec 2020

Trevor Bedford Retweeted Dr Zweli Mkhize

Recent announcements have focused on spread of N501Y in the UK (https://twitter.com/CovidGenomicsUK/status/1338580111986204672 …) and independent emergence and spread of N501Y in South Africa (https://twitter.com/DrZweliMkhize/status/1339970259332325383 …). 11/18

Trevor Bedford added,

Dr Zweli MkhizeVerified account @DrZweliMkhize

We have convened this public briefing today to announce that a variant of the SARS-COV-2 Virus- currently termed 501.V2 Variant has been identified by our genomics scientists here in South Africa. #SARSCOV2MediaBriefing

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2 replies . 90 retweets 636 likes

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Trevor Bedford‏Verified account @trvrb 19 Dec 2020

The UK variant in particular has several mutations that are of biological interest and deserves close attention (@arambaut, @pathogenomenick et al https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 …). 12/18

5 replies . 92 retweets 666 likes

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Trevor Bedford‏Verified account @trvrb 19 Dec 2020

Independent emergence and spread of variants is suggestive of natural selection where in addition to N501Y we see for example S477N emerging independently in Europe (https://nextstrain.org/ncov/europe?c=gt-S_222,439,477 …) and in Australia (https://nextstrain.org/ncov/oceania?c=gt-S_222,477 …). 13/18pic.twitter.com/oEPfSWEQyK

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Trevor Bedford‏Verified account @trvrb 19 Dec 2020

@firefoxx66 is maintaining a list of mutations of interest with associated @nextstrain views and relevant publications at https://github.com/emmahodcroft/cluster_scripts/blob/master/README.md …. 14/18

3 replies . 94 retweets 628 likes

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Trevor Bedford‏Verified account @trvrb 19 Dec 2020

All this said, I'm not concerned that these variants will significantly reduce vaccine efficacy in the 2021 rollout. Most circulating SARS-CoV-2 viruses do not have any mutations in the spike receptor binding domain (https://nextstrain.org/ncov/global?c=gt-S_439,477,484,501 …). 15/18pic.twitter.com/NmgHrotaiJ

1:33 pm - 19 Dec 2020

447 Retweets
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18 replies . 447 retweets 1,532 likes

1. permabullshitter‏ @_DJ_DC_ 19 Dec 2020
  Replying to @trvrb
  
  Aren't we about to apply *much* more evolutionary pressure against the spike receptor, and doesn't that make the probability of circulation of a spike mutation variant much more likely than before?
  
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1. Cari Sullivan Riddle‏ @Cjsullriddle 19 Dec 2020
  Replying to @trvrb
  
  Ok-phew! I am thankful for your analysis breakdown (I can interpret maybe 25% of what you are reporting :) Mostly, I am grateful for you and your colleague's dedication to your work as you guide us through this incredibly challenging time.
  
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