3 ms·

This article is very light on details. Here’s a better one: “Update on new SARS-CoV-2 variant and how COG-UK tracks emerging mutations” Dec 14, 2020 https://w

by jt2190 6y ago

This article is very light on details. Here’s a better one: “Update on new SARS-CoV-2 variant and how COG-UK tracks emerging mutations” Dec 14, 2020 https://www.cogconsortium.uk/news_item/update-on-new-sars-cov-2-variant-and-how-cog-uk-tracks-emerging-mutations/ https://www.cogconsortium.uk/news_item/update-on-new-sars-co... Edit: Here’s a report: “Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations” Recently a distinct phylogenetic cluster (named lineage B.1.1.7) was detected within the COG-UK surveillance dataset. This cluster has been growing rapidly over the past 4 weeks and since been observed in other UK locations, indicating further spread. Several aspects of this cluster are noteworthy for epidemiological and biological reasons and we report preliminary findings below. In summary: • The B.1.1.7 lineage accounts for an increasing proportion of cases in parts of England. • The number of B.1.1.7 cases, and the number of regions reporting B.1.1.7 infections, are growing. • B.1.1.7 has an unusually large number of genetic changes, particularly in the spike protein. 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 https://virological.org/t/preliminary-genomic-characterisati...

yread 6y ago
> Mutation N501Y is one of six key contact residues within the receptor-binding domain (RBD) and has been identified as increasing binding affinity to human and murine ACE2. > The spike deletion 69-70del has been described in the context of evasion to the human immune response but has also occurred a number of times in association with other RBD changes. > Mutation P681H is immediately adjacent to the furin cleavage site, a known location of biological significance.... > nucleotide changes on this branch are predominantly amino acid-altering (14 non-synonymous mutations and 3 deletions). There are 6 synonymous mutations on the branch. This is suggestive of a process involving adaptive molecular evolution > These include spike position 501, one of the key contact residues in the receptor binding domain (RBD), and experimental data suggests mutation N501Y can increase ACE2 receptor affinity (Starr et al. 2020) and P681H, one of 4 residues comprising the insertion that creates a furin cleavage site between S1 and S2 in spike. The S1/S2 furin cleavage site of SARS-CoV-2 is not found in closely related coronaviruses and has been shown to promote entry into respiratory epithelial cells and transmission in animal models (Hoffmann, Kleine-Weber, and Pöhlmann 2020; Peacock et al. 2020; Zhu et al. 2020). N501Y has been associated with increased infectivity and virulence in a mouse model (Gu et al. 2020). Both N501Y and P681H have been observed independently but not to our knowledge in combination before now. > deletion of two amino acids at sites 69-70 in spike ... arose in the mink-associated outbreak in Denmark on the background of the Y453F RBD mutation This doesn't sound good
- contingencies 6y ago
  So roughly speaking it just acquired the Air 2 mutation from Plague Inc.
  - senectus1 6y ago
    dunno why the downvote.. this is a good conceptualization.

by jt2190 6y ago

yread 6y ago

> Mutation N501Y is one of six key contact residues within the receptor-binding domain (RBD) and has been identified as increasing binding affinity to human and murine ACE2. > The spike deletion 69-70del has been described in the context of evasion to the human immune response but has also occurred a number of times in association with other RBD changes. > Mutation P681H is immediately adjacent to the furin cleavage site, a known location of biological significance.... > nucleotide changes on this branch are predominantly amino acid-altering (14 non-synonymous mutations and 3 deletions). There are 6 synonymous mutations on the branch. This is suggestive of a process involving adaptive molecular evolution > These include spike position 501, one of the key contact residues in the receptor binding domain (RBD), and experimental data suggests mutation N501Y can increase ACE2 receptor affinity (Starr et al. 2020) and P681H, one of 4 residues comprising the insertion that creates a furin cleavage site between S1 and S2 in spike. The S1/S2 furin cleavage site of SARS-CoV-2 is not found in closely related coronaviruses and has been shown to promote entry into respiratory epithelial cells and transmission in animal models (Hoffmann, Kleine-Weber, and Pöhlmann 2020; Peacock et al. 2020; Zhu et al. 2020). N501Y has been associated with increased infectivity and virulence in a mouse model (Gu et al. 2020). Both N501Y and P681H have been observed independently but not to our knowledge in combination before now. > deletion of two amino acids at sites 69-70 in spike ... arose in the mink-associated outbreak in Denmark on the background of the Y453F RBD mutation This doesn't sound good

contingencies 6y ago
So roughly speaking it just acquired the Air 2 mutation from Plague Inc.
- senectus1 6y ago
  dunno why the downvote.. this is a good conceptualization.