SARS-CoV-2 variant profiles (public, discontinued)

--- tags: viruses, SARS-CoV-2 --- [TOC] # SARS-CoV-2 variant profiles (public, discontinued) ## This document will not be continued and is moved to a private space (for now), please contact Martin Hoelzer (RKI, MF1) for access --- __Disclaimer__ This is a regularly updated collection of publicly available information on important SARS-CoV-2 lineages, their naming, mutations, and, when possible, some phenotypic information. Colleagues in the UK (mostly from the group of A. Rambaut) maintain an excellent resource to live track the new lineages: https://cov-lineages.org/global_report.html. Nice ressource to check for mutations globally: https://wan-bioinfo.shinyapps.io/GESS/ __This resource is continuously updating and not all information (such as nucleotide positions, phenotypes, ...) are immediately added and might change according to new findings!__ __Please add a comment if you observe some mistakes or if you want to report important findings. We will check the comments and integrate the information.__ --- __HowTo__ Mutations are listed by the location of a mutation, e.g. in the spike protein (S:) - the letter after : indicates the original amino-acid, the number the position in the spike protein, and the last letter, the 'new' amino-acid. * indicates a stop codon and _del_ a deletion. If possible, also the nucleotide position in the genome is listed. For example: * S:N501Y | A23063T * denotes an amino acid change from N to Y in the Spike protein at position 501 due to a nucleotide change at position 23,063 from A to T. --- ## United Kingdom: VOC 202012/01 (old VUI-202012/01, also B.1.1.7 or 20B/501Y.V1) * 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/)) __Important mutations__ * Mainly obtained from [https://cov-lineages.org/global_report_B.1.1.7.html](https://cov-lineages.org/global_report_B.1.1.7.html). * Matching nucleotide positions from [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-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563) | gene | amino acid | nucleotide | comment | | ---- | ---- | ----| ---- | | ORF1ab | T1001I | C3267T | | | ORF1ab | A1708D | C5388A | | | ORF1ab | I2230T | T6954C| | | ORF1ab | S/G/F/3675/3676/3677del | del:11288:9 | _:9_ denotes the nucleotide length of the deletion. A deletion spanning 3 codons. [Also found in the SA B.1.351 and Brazil/Japan B.1.1.248 variant](https://twitter.com/richardneher/status/1348739384191946758/photo/1). Some thoughts from the same tweet: A. Rambaut: "Little is known about ns6 function I think, but it is transmembrane and the deletion is in an external loop." "Orf1 is a popular target in the RT-PCR tests. Would be interesting to see if the oligos annheal on that stretch. Any variant that escapes test detection will gain in fitness." "The deletion makes the largest outside loop of nsp6 shorter (nsp6 induces the double-membrane replication vesicles where the RNA is transcripted)". Also in Brazil P.1 | | S | 69/70del | del:21765:6 | In-frame 6 nt deletion. As also seen in variants [S:N439K](https://github.com/hodcroftlab/covariants#sn439k) & [S:Y453F](https://github.com/hodcroftlab/covariants#sy453f). Recurrent del desrcibed in [Kemp et al 2020](https://www.biorxiv.org/content/10.1101/2020.12.14.422555v3). Also found in [US samples](https://virological.org/t/identification-of-a-novel-sars-cov-2-spike-69-70-deletion-lineage-circulating-in-the-united-states/577). | | S| Y144del | del:21991:3| | S| N501Y | A23063T| Mutation in RBD, needed for binding to ACE2. N501Y was also found in longitudinally-collected samples from an immunocompromised patient ([Choi et al. NEJM](https://www.nejm.org/doi/full/10.1056/NEJMc2031364?query=featured_coronavirus))| | S| A570D | C23271A| | | S| D614G | | | | S| P681H | C23604A| Adjacent to the furin cleavage site. Also found in Nigeria lineage B.1.1.207| | S| T716I | C23709T| | | S| S982A | T24506G| | | S| D1118H | G24914C| | | Orf8| Q27* | C27972T| Becoming a stop codon, thus truncated ORF8. 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)) | | Orf8| R52I | G28048T| | | Orf8| Y73C | A28111G| | | N| D3L | 28280 GAT->CTA| | | N| S235F | C28977T| | * does __not have__ the E484K mutation like known for SA B.1.351 and Brazil B.1.1.28 (B.1.1.248) and the Japan variants, detected from Brazilian travelers __Phenotype__ * ~50% higher transmissibility TODO LINK LITERATURE --- ## South Africa: 501.V2 (also B.1.351 or 20C/501Y.V2) * South Africa, announced in December 2020 ([Tegally et al., medRxiv](https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1)) __Important mutations__ * Mainly from [https://cov-lineages.org/global_report_B.1.351.html](https://cov-lineages.org/global_report_B.1.351.html). Details in [Tegally _et al._ 2020](https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1.full.pdf) . | gene | amino acid | nucleotide | comment | | ---- | ---- | ----| ---- | | ORF1ab | S/G/F/3675/3676/3677del | del:11288:9 | [Also found in the UK B.1.1.7 and Brazil/Japan B.1.1.248 variant](https://twitter.com/richardneher/status/1348739384191946758/photo/1). See B.1.1.7 for details about this 3 codon deletion. Also found in Brazil P.1 | | S| L18F | | | | S| D80A | | | | S| D215G | | | | S| R246I | | | | S| K417N | | RBD | | S| E484K | | RBD. [Reinfection in Brasil](https://virological.org/t/spike-e484k-mutation-in-the-first-sars-cov-2-reinfection-case-confirmed-in-brazil-2020/584) also haboring S:E484K. Classical SARS-CoV-2 reinfection case with the emerging Brazilian lineage B.1.1.28(E484K) | | S| N501Y| | RBD| | S| D614G | | | | S| A701V| | | | E| P71L| | | | N| T205I| | | | orf1a| K1655N| || * __does not have S:69/70del in spike like UK VOC 202012/01!__ * [Scientists noted](https://www.who.int/docs/default-source/blue-print/who-com-statement_new-variant_rev1.pdf) that the variant contains several mutations that allow it to attach more easily to human cells because of the following three mutations in the receptor-binding domain (RBD) in the spike glycoprotein of the virus: N501Y, K417N, and E484K . __Phenotype__ * --- ## Nigeria: B.1.1.207 * first detected in August 2020 [see](https://virological.org/t/detection-of-sars-cov-2-p681h-spike-protein-variant-in-nigeria/567) * two SARS-CoV-2 sequences that share one non-synonymous SNP in the spike protein in common with B.1.1.7, but none of the other unique lineage-defining mutations of B.1.1.7 * [B.1.1.207](https://cov-lineages.org/lineages/lineage_B.1.1.207.html) split from [South Africa lineage B.1.1.53](https://cov-lineages.org/lineages/lineage_B.1.1.53.html) __Important mutations__ | gene | amino acid | nucleotide | comment | | ---- | ---- | ----| ---- | | S| P681H| C23604A| [https://virological.org/t/detection-of-sars-cov-2-p681h-spike-protein-variant-in-nigeria/567](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 __Phenotype__ * implications for transmission and virulence [are unclear](https://virological.org/t/detection-of-sars-cov-2-p681h-spike-protein-variant-in-nigeria/567) --- ## Japan/Tokyo: B.1.1.28(K417N/E484K/N501Y) (four travelers from northern Brazil) * belongs to the B.1.1.248 strain, separated from B.1.1.28 (Brazil) * labeled __B.1.1.28(K417N/E484K/N501Y)__ according to a [post from 2021-01-11](https://virological.org/t/phylogenetic-relationship-of-sars-cov-2-sequences-from-amazonas-with-emerging-brazilian-variants-harboring-mutations-e484k-and-n501y-in-the-spike-protein/585) * [detected in four travelers from Brazil’s Amazonas state](https://www.japantimes.co.jp/news/2021/01/11/national/science-health/new-coronavirus-variant-japan/) * the new variant has 12 mutations, one of which is also present in the variants found in the U.K. and South Africa (N501Y) * [share some of the mutations in common with those of concern for increased infectivity](https://www.niid.go.jp/niid/ja/diseases/ka/corona-virus/2019-ncov/10107-covid19-33.html). * In Brazil, there are reports of reinfection cases with mutant strains showing the E484K mutation of the B.1.1.248 strain (2021/01/06), but they are not the same as the new mutant strain according to [NIID](https://www.niid.go.jp/niid/ja/diseases/ka/corona-virus/2019-ncov/10107-covid19-33.html) * [B.1.1.248 previously part of Brazilian B.1.1.28](https://cov-lineages.org/lineages/lineage_B.1.1.248.html) __Important mutations__ * information obtained from [NIID](https://www.niid.go.jp/niid/ja/diseases/ka/corona-virus/2019-ncov/10107-covid19-33.html) and this [Figure](https://www.niid.go.jp/niid/images/epi/corona/covid19-33-fig.png) * __belongs to the B.1.1.248 strain__ and has 12 mutations in the spike protein, the NIID said | gene | amino acid | nucleotide | comment | | ---- | ---- | ----| ---- | | ORF1ab | S/G/F/3675/3676/3677del | del:11288:9 | [Also found in the UK B.1.1.7 and SA B.1.351 variant](https://twitter.com/richardneher/status/1348739384191946758/photo/1). See B.1.1.7 for details about this 3 codon deletion. Also found in Brazil P.1 | | S| L18F | | | | S| T20N| | | | S| P26S| | | | S| D138Y| | | | S| R190S| | | | S| K417T| | like in SA B.1.351 but K417T instead of K417N according to this [NIID figure](https://www.niid.go.jp/niid/images/epi/corona/covid19-33-fig.png) | | S| E484K | | RBD. Like in SA B.1.351 and Brasil B.1.1.28 ([re-infection causing](https://virological.org/t/spike-e484k-mutation-in-the-first-sars-cov-2-reinfection-case-confirmed-in-brazil-2020/584)) | | S| N501Y| | RBD. Like in UK B.1.1.7 and SA B.1.351 variant| | S| D614G | | | | S| H655Y| | | | S| T1027I| | | | S| V1176F| | | __Phenotype__ * no clear evidence of the mutated viruses being associated with more severe disease outcomes --- ## Brazil: B.1.1.28 * [B.1.1.28 brasilian lineage](https://cov-lineages.org/lineages/lineage_B.1.1.28.html) * [Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil, 2020](https://virological.org/t/spike-e484k-mutation-in-the-first-sars-cov-2-reinfection-case-confirmed-in-brazil-2020/584) __Important mutations__ | gene | amino acid | nucleotide | comment | | ---- | ---- | ----| ---- | | S| E484K| | Also known in South Africa B.1.351 and Japan B.1.1.248-like strain. [Region that a number of antibodies seem to recognize](https://blogs.sciencemag.org/pipeline/archives/2020/12/22/the-new-mutations)| * [no N501Y in the Brazil base lineage B.1.1.28](https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586) but now found in the Brazil P.1 __Phenotype__ * caused re-infection: "Whole-genome sequencing revealed that the two infections were caused, respectively, by the two most prevalent SARS-CoV-2 Brazilian lineages B.1.1.33 (primo-infection) and B.1.1.28 (reinfection)." --- ## Brazil, Manaus: P.1 * [2021-01-12, Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings](https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586) * new lineage, named P.1 (descendent of Brazil [B.1.1.28](https://cov-lineages.org/lineages/lineage_B.1.1.28.html)) * from Manaus, northern Brazil, Amazonas * unique constellation of lineage defining mutations, including several mutations of known biological importance such as E484K, K417T, and N501Y * the same found in the Brazil travelers that were sequenced in Japan * P.1 lineage carries 17 unique amino acid changes, 3 deletions, and 4 synonymous mutations, and one 4nt insertion > The set of mutations/deletions shared between P.1, B.1.1.7, and the B.1.351 lineages appear to have arisen entirely independently. __Important mutations__ | gene | amino acid | nucleotide | comment | | ---- | ---- | ----| ---- | | ORF1ab | S/G/F/3675/3676/3677del | del:11288:9 | [Also found in the UK B.1.1.7 and SA B.1.351 variant](https://twitter.com/richardneher/status/1348739384191946758/photo/1). See B.1.1.7 for details about this 3 codon deletion| | S| L18F | | also in SA B.1.351 and in B.1.1.28 detected in Japan from Brazil travelers | | S| T20N| |also in B.1.1.28 detected in Japan from Brazil travelers | | S| P26S| | also in B.1.1.28 detected in Japan from Brazil travelers| | S| D138Y| | also in B.1.1.28 detected in Japan from Brazil travelers| | S| R190S| | also in B.1.1.28 detected in Japan from Brazil travelers| | S| K417T | | RBD. Like in SA B.1.351 but K417T instead of K417N. K417T also in Brazil travelers detected in Japan (makes sense bc/ they arrived from northern Brazil. | | S| E484K| | RBD. Also known in South Africa B.1.351 and Brazil travelers arrived in Japan (B.1.1.248-like) strain. [Region that a number of antibodies seem to recognize](https://blogs.sciencemag.org/pipeline/archives/2020/12/22/the-new-mutations)| | S| N501Y| | RBD. Like in UK B.1.1.7 and SA B.1.351 variant| | S| H655Y| | also in B.1.1.28 detected in Japan from Brazil travelers| | S| T1027I| | also in B.1.1.28 detected in Japan from Brazil travelers| | Orf8| E92K | | | | Orf8| | insertion28269-28273| not in frame? 4nt | | N | P80R | | | __Phenotype__ * --- ## Italy predecessor to B.1.1.7 "UK" variant * based on from Eric Topol [tweet](https://twitter.com/EricTopol/status/1349140550188888064) > A predecessor to the B.1.1.7 "UK" variant was seen in Italy in August in a 59-year-old man with persistent covid infection and accelerated viral evolution * see [Fiorentini _et al._ 2021 (The Lancet Infect Disease)](https://doi.org/10.1016/S1473-3099(21)00007-4) > It is worth noting that the N501T substitution was detected in both MB61-Nov and MB61-Aug SARS-CoV-2 isolates, highlighting that a mutation at the critical amino acid residue 501 was already present in Italy in August, 2020 > spike N501T variants emerged in early August (95% highest posterior density early July to end of August) in northern Italy (appendix), and therefore that SARS-CoV-2 strains harbouring a substitution at position 501 might have circulated unnoticed even before the end of September, 2020 __Important mutations__ | gene | amino acid | nucleotide | comment | | ---- | ---- | ----| ---- | | S| N501T| | RBD. Not __Y__ like in UK B.1.1.7 and SA B.1.351 variant but same position. | | S| Q493K | | RBD. "Differently from B.1.1.7, the MB61 variants showed a second mutation ... that, together with N501T, might alter the binding affinity of the spike protein to the ACE2 receptor | __Phenotype__ * --- ## NEW VARIANT TEMPLATE * __Mutations__ | gene | amino acid | nucleotide | comment | | ---- | ---- | ----| ---- | | | | | | __Phenotype__ * --- # 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 --- # Additional literature * [https://en.wikipedia.org/wiki/Variants_of_SARS-CoV-2](https://en.wikipedia.org/wiki/Variants_of_SARS-CoV-2) * [https://virological.org/](https://virological.org/) * Important and up-to-date ressource, early and updated blog posts * [https://github.com/hodcroftlab/covariants#20aeu1](https://github.com/hodcroftlab/covariants#20aeu1) * CoVariants: SARS-CoV-2 Mutations and Variants of Interest * really good overvie including protein 3d structures and information about phaenotypes, a lot of information above is extracted from here * [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) ![](https://i.imgur.com/Sr5NpdD.jpg) * [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/) ![](https://i.imgur.com/j0xsPvl.jpg)