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tags: viruses
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# SARS-CoV-2 news

A collection of worldwide news and resources (mainly from twitter) about SARS-CoV-2 with a focus on emerging variants (and their names) and mutations.

I will try to keep this up-to-date. Please feel free to add information.

__Important and up-to-date ressource__: https://virological.org/

Spike surveillance based on daily updated GISAID data: https://cov.lanl.gov/

[toc]

## Variants summary

[Wikipedia](https://en.wikipedia.org/wiki/Variants_of_SARS-CoV-2)

### UK: VOC 202012/01 (old VUI-202012/01, also B.1.1.7 or 20B/501Y.V1)
* South East of England
* multiple spike mutations such as: N501Y, del69/70, delY144, P681H
* ORF8 truncated with Q27* becoming a stop codon
* also N mutations: D3L, S235F
### SA: 501.V2 (also B.1.351 or 20C/501Y.V2)
* South Africa
* multiple spike mutations such as: N501Y, K417N, E484K, D80A
* N mutation: T205I
* __does not have__ del69/70 in spike like VOC 202012/01
### Nigeria: B.1.207
* [P681H mutation](https://virological.org/t/detection-of-sars-cov-2-p681h-spike-protein-variant-in-nigeria/567), shared in common with VOC-202012/01
* no other mutations shared with VOC-202012/01

## Clades

Based on https://virological.org/t/updated-nextstain-sars-cov-2-clade-naming-strategy/581

At this moment, major clades from 2020 onwards are:

* 20A: basal pandemic lineage bearing S 614G that’s globally distributed
* 20B: derived from 20A bearing N 203K, N204R and ORF14 50N, also globally distributed
* 20C: derived from 20A bearing ORF3a 57H and ORF1a 265I, also globally distributed
* 20D: derived from 20B bearing ORF1a 1246I and ORF1a 3278S, concentrated in South America, southern Europe and South Africa
* 20E: derived from 20A bearing N 220V, ORF10 30L, ORF14 67F and S 222V, concentrated in Europe
* 20F: derived from 20B bearing ORF1a 300F and S 477N, concentrated in Australia
* 20G: derived from 20C bearing ORF1b 1653D, ORF3a 172V, N 67S and N 199L, concentrated in the United States
* 20H/501Y.V2: derived from 20C bearing S 80A, S 215G, S 484K, S 501Y, S 701V, concentrated in South Africa
* 20I/501Y.V1: derived from 20B bearing S 501Y, S 570D, S 681H, ORF8 27*, concentrated in the United Kingdom

## [How the novel coronavirus has evolved](https://graphics.reuters.com/HEALTH-CORONAVIRUS/EVOLUTION/yxmpjqkdzvr/index.html)

> The original strain, detected in the Chinese city of Wuhan in December 2019, is the L strain. The virus then mutated into the S strain at the beginning of 2020. That was followed by V and G strains. Strain G mutated yet further into strains GR, GH and GV. Several other infrequent mutations were collectively grouped together as strain O.

## [CoVariants: SARS-CoV-2 Mutations and Variants of Interest](https://github.com/hodcroftlab/covariants#20aeu1)
A really good overview! below extracted information for the UK and SA variant (from 2021-01-05):

* '20B/501Y.V1' (B.1.1.7) was announced in the South East of England on 14 Dec 2020 ([COG-UK Report](https://www.cogconsortium.uk/news_item/update-on-new-sars-cov-2-variant-and-how-cog-uk-tracks-emerging-mutations/))
* This particular variant is associated with multiple mutations in Spike, including: N501Y, a deletion at 69/70 (as seen in S:N439K & S:Y453F) ([Kemp et al. bioRxiv (21 Dec)](https://www.biorxiv.org/content/10.1101/2020.12.14.422555v3)), Y144 deletion, and P681H (adjacent to the furin cleavage site).
* There is also a notable truncation of ORF8, with Q27* (becomes a stop codon) (deletion of ORF8 was previously associated with reduced clinical severity ([Young et al. Lancet](https://www.thelancet.com/article/S0140-6736(20)31757-8/fulltext))), and mutations in N: N:D3L and S235F.
* '20C/501Y.V2' is found in South Africa and was also announced in December 2020 ([Tegally et al., medRxiv](https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1))
* This variant is associated with multiple mutations in Spike, including: N501Y, K417N, and D80A.
* There is also an N mutation: T205I.
* It __does not have__ the deletion at 69/70.

## [Mutations arising in SARS-CoV-2 spike on sustained human-to-human transmission and human-to-animal passage](https://virological.org/t/mutations-arising-in-sars-cov-2-spike-on-sustained-human-to-human-transmission-and-human-to-animal-passage/578)


## [Naturally occurring indels in multiple coronavirus spikes](https://virological.org/t/naturally-occurring-indels-in-multiple-coronavirus-spikes/560)

## [WHO: Variant analysis of SARS-CoV-2 genomes](https://www.who.int/bulletin/volumes/98/7/20-253591/en/)