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slinky-antennae.yml
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unique-id: slinky-antennae
phe-label: V-21JAN-02
who-label: Gamma
alternate-names:
- VOC202101/02
- Brazil 2
belongs-to-lineage:
- PANGO: P.1
description: This variant was first identified in Japan in travellers from Brazil and is associated with Manaus in the Amazonas region assoicated with a severe second wave of COVID-19
information-sources:
- https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586
- https://cov-lineages.org/global_report_P.1.html
variants:
- codon-change: GAT-GAC
gene: ORF1ab
one-based-reference-position: 733
predicted-effect: synonymous
protein: nsp1
protein-codon-position: 156
reference-base: T
type: SNP
variant-base: C
- codon-change: GAC-GAT
gene: ORF1ab
one-based-reference-position: 2749
predicted-effect: synonymous
protein: nsp3
protein-codon-position: 10
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: S370L
codon-change: TCA-TTA
gene: ORF1ab
one-based-reference-position: 3828
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 370
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: K977Q
codon-change: AAA-CAA
gene: ORF1ab
one-based-reference-position: 5648
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 977
reference-base: A
type: SNP
variant-base: C
- gene: ORF1ab
one-based-reference-position: 11287
protein: nsp6
reference-base: GTCTGGTTTT
type: deletion
variant-base: G
- codon-change: TAC-TAT
gene: ORF1ab
one-based-reference-position: 12778
predicted-effect: synonymous
protein: nsp9
protein-codon-position: 31
reference-base: C
type: SNP
variant-base: T
- codon-change: GAC-GAT
gene: ORF1ab
one-based-reference-position: 13860
predicted-effect: synonymous
protein: nsp12
protein-codon-position: 140
reference-base: C
snp-codon-position: 3
type: SNP
variant-base: T
- amino-acid-change: T20N
codon-change: ACC-AAC
gene: S
one-based-reference-position: 21621
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 20
reference-base: C
type: SNP
variant-base: A
- amino-acid-change: P26S
codon-change: CCT-TCT
gene: S
one-based-reference-position: 21638
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 26
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: K417T
codon-change: AAG-ACG
gene: S
one-based-reference-position: 22812
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 417
reference-base: A
type: SNP
variant-base: C
- amino-acid-change: E484K
codon-change: GAA-AAA
gene: S
one-based-reference-position: 23012
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 484
reference-base: G
type: SNP
variant-base: A
- 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: T1027I
codon-change: ACT-ATT
gene: S
one-based-reference-position: 24642
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 1027
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: E92K
codon-change: GAA-AAA
gene: ORF8
one-based-reference-position: 28167
predicted-effect: non-synonymous
protein: ORF8 protein
protein-codon-position: 92
reference-base: G
type: SNP
variant-base: A
- gene: .
one-based-reference-position: 28262
protein: .
reference-base: G
type: insertion
variant-base: GAACA
predicted-effect: no-effect
- amino-acid-change: P80R
codon-change: CCA-CGA
gene: N
one-based-reference-position: 28512
predicted-effect: non-synonymous
protein: nucleocapsid phosphoprotein
protein-codon-position: 80
reference-base: C
type: SNP
variant-base: G
calling-definition:
confirmed:
mutations-required: 14
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