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denture-daughter.yml
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unique-id: denture-daughter
phe-label: V-20DEC-01
who-label: Alpha
alternate-names:
- VOC202012/01
- UK variant
- Kent variant
- VOC1
belongs-to-lineage:
- PANGO: B.1.1.7
- nextstrain: N501Y.V1
description: This variant became widespread in the UK in the Winter of 2021 and is characterised by increased transmissibility.
information-sources:
- https://www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201
- 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
variants:
- gene: S
one-based-reference-position: 21764
protein: surface glycoprotein
reference-base: ATACATG
type: deletion
variant-base: A
- gene: S
one-based-reference-position: 21990
protein: surface glycoprotein
reference-base: TTTA
type: deletion
variant-base: T
- amino-acid-change: N501Y
codon-change: AAT-TAT
gene: S
one-based-reference-position: 23063
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 501
reference-base: A
type: SNP
variant-base: T
- amino-acid-change: A570D
codon-change: GCT-GAT
gene: S
one-based-reference-position: 23271
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 570
reference-base: C
type: SNP
variant-base: A
- amino-acid-change: P681H
codon-change: CCT-CAT
gene: S
one-based-reference-position: 23604
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 681
reference-base: C
type: SNP
variant-base: A
- amino-acid-change: T716I
codon-change: ACA-ATA
gene: S
one-based-reference-position: 23709
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 716
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: S982A
codon-change: TCA-GCA
gene: S
one-based-reference-position: 24506
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 982
reference-base: T
type: SNP
variant-base: G
- amino-acid-change: D1118H
codon-change: GAC-CAC
gene: S
one-based-reference-position: 24914
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 1118
reference-base: G
type: SNP
variant-base: C
- amino-acid-change: T183I
codon-change: ACT-ATT
gene: ORF1ab
one-based-reference-position: 3267
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 183
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: A890D
codon-change: GCT-GAT
gene: ORF1ab
one-based-reference-position: 5388
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 890
reference-base: C
type: SNP
variant-base: A
- amino-acid-change: I1412T
codon-change: ATA-ACA
gene: ORF1ab
one-based-reference-position: 6954
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 1412
reference-base: T
type: SNP
variant-base: C
- amino-acid-change: Q27*
codon-change: CAA-TAA
gene: ORF8
one-based-reference-position: 27972
predicted-effect: non-synonymous
protein: ORF8 protein
protein-codon-position: 27
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: R52I
codon-change: AGA-ATA
gene: ORF8
one-based-reference-position: 28048
predicted-effect: no-effect
protein: ORF8 protein
protein-codon-position: 52
reference-base: G
type: SNP
variant-base: T
- amino-acid-change: Y73C
codon-change: TAC-TGC
gene: ORF8
one-based-reference-position: 28111
predicted-effect: no-effect
protein: ORF8 protein
protein-codon-position: 73
reference-base: A
type: SNP
variant-base: G
- amino-acid-change: D3L
codon-change: GAT-CTA
gene: N
one-based-reference-position: 28280
predicted-effect: non-synonymous
protein: nucleocapsid phosphoprotein
protein-codon-position: 3
reference-base: GAT
type: MNP
variant-base: CTA
calling-definition:
confirmed:
mutations-required: 13
indels-required: 0
allowed-wildtype: 0
probable:
mutations-required: 5
indels-required: 0
allowed-wildtype: 0
low-qc:
mutations-required: 0
indels-required: 0
allowed-wildtype: 0
acknowledgements:
curators:
- Natalie Groves
- Ulf Schaefer
- Nick Loman