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kelp-lesser.yml
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unique-id: kelp-lesser
phe-label: V-21JUL-01
who-label:
alternate-names:
- SIM_B1621
belongs-to-lineage:
- PANGO: B.1.621
- nextstrain:
description: Lineage predominantly in Colombia with several spike mutations,
information-sources:
- https://cov-lineages.org/lineage.html?lineage=B.1.621
- https://github.com/cov-lineages/pango-designation/issues/57
variants:
- gene: S
one-based-reference-position: 21990
protein: surface glycoprotein
reference-base: T
type: insertion
variant-base: TACT
- amino-acid-change: T237A
codon-change: ACA-GCA
gene: ORF1ab
one-based-reference-position: 3428
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 237
reference-base: A
type: SNP
variant-base: G
- amino-acid-change: T720I
codon-change: ACT-ATT
gene: ORF1ab
one-based-reference-position: 4878
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 720
reference-base: C
type: SNP
variant-base: T
- codon-change: AGC-AGT
gene: ORF1ab
one-based-reference-position: 6037
predicted-effect: synonymous
protein: nsp3
protein-codon-position: 1106
reference-base: C
snp-codon-position: 3
type: SNP
variant-base: T
- amino-acid-change: Q160R
codon-change: CAA-CGA
gene: ORF1ab
one-based-reference-position: 11451
predicted-effect: non-synonymous
protein: nsp6
protein-codon-position: 160
reference-base: A
type: SNP
variant-base: G
- codon-change: TCA-TCT
gene: ORF1ab
one-based-reference-position: 13057
predicted-effect: synonymous
protein: nsp10
protein-codon-position: 11
reference-base: A
snp-codon-position: 3
type: SNP
variant-base: T
- codon-change: TTC-TTT
gene: ORF1ab
one-based-reference-position: 20148
predicted-effect: synonymous
protein: nsp15
protein-codon-position: 176
reference-base: C
snp-codon-position: 3
type: SNP
variant-base: T
- amino-acid-change: T95I
codon-change: ACT-ATT
gene: S
one-based-reference-position: 21846
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 95
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: R346K
codon-change: AGA-AAA
gene: S
one-based-reference-position: 22599
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 346
reference-base: G
type: SNP
variant-base: A
- 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: 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
- gene: ORF3a
one-based-reference-position: 26157
protein: ORF3a protein
reference-base: TGTTA
type: deletion
variant-base: T
- gene: .
one-based-reference-position: 26492
protein: .
reference-base: A
type: SNP
variant-base: T
- amino-acid-change: T11K
codon-change: ACA-AAA
gene: ORF8
one-based-reference-position: 27925
predicted-effect: non-synonymous
protein: ORF8 protein
protein-codon-position: 11
reference-base: C
type: SNP
variant-base: A
- amino-acid-change: P38S
codon-change: CCT-TCT
gene: ORF8
one-based-reference-position: 28005
predicted-effect: non-synonymous
protein: ORF8 protein
protein-codon-position: 38
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: T205I
codon-change: ACT-ATT
gene: N
one-based-reference-position: 28887
predicted-effect: non-synonymous
protein: nucleocapsid phosphoprotein
protein-codon-position: 205
reference-base: C
type: SNP
variant-base: T
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
- Aniruddha Pandit