KP.3.3 and MC.13 branches with S:Q613E

[NkRMnZr]

Tracking Lineages with S:Q613E(C23399G)

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1. Branch 1 KP.3.3 > C1567A(ORF1a:N434K), C7840T, C13647T, G18811A(ORF1b:D1782N), C23399G(S:Q613E), query: C7840T, C23399G, 10 seqs, South Korea, as of Sep27
2. Branch 2Designated MC.13.3 Transferred to MC.13 with S:Q613E (38 seqs, 7 countries) cov-lineages/pango-designation#2793 phylogenetic tree follows: MC.13 > C23399G(S:Q613E), query: C10681T, A13121T, C23399G, 20 seqs, 3 countries, as of Sep 23

Branch 1

Defining Mutations: KP.3.3 > C1567A(ORF1a:N434K), C7840T, C13647T, G18811A(ORF1b:D1782N), C23399G(S:Q613E)
Query: C7840T, C23399G
Earliest seq: 24-07-10 (EPI_ISL_19340504, South Korea)
Latest seq: 24-08-02 (EPI_ISL_19368942, South Korea)
Sampled Countries: South Korea (7)

Genomes:

for lineages.csv commit:

SouthKorea/KDCA293766/2024
SouthKorea/KDCA294088/2024
SouthKorea/KDCA294242/2024
SouthKorea/KDCA294249/2024
SouthKorea/KDCA294368/2024
SouthKorea/KDCA294426/2024
SouthKorea/KDCA294598/2024

epi_isl accessions:
EPI_ISL_19340504, EPI_ISL_19340826, EPI_ISL_19352454, EPI_ISL_19352461, EPI_ISL_19352569, EPI_ISL_19352626, EPI_ISL_19368942

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_40fcb_1e08c0.json?label=id:node_7059740

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Branch 2

Transferred to main repo

Transferred to cov-lineages/pango-designation#2793

Defining Mutations: MC.13 > C23399G(S:Q613E)
Query: C10681T, A13121T, C23399G
Earliest seq: 24-06-13 (EPI_ISL_19265922, Portugal)
Latest seq: 24-08-23 (EPI_ISL_19385724, Brazil)
Sampled Countries: Brazil (5: MS), Spain (1), Portugal (1)

Genomes:

for lineages.csv commit:

Portugal/PT51065/2024
Brazil/MS-FIOCRUZ-FMS306/2024
Brazil/MS-FIOCRUZ-FMS311/2024
Spain/CT-LabRefCat-3669331/2024
Brazil/MS-FIOCRUZ-FMS319/2024
Brazil/MS-FIOCRUZ-FMS333/2024
Brazil/MS-FIOCRUZ-FMS340/2024

epi_isl accessions:
EPI_ISL_19265922, EPI_ISL_19340619, EPI_ISL_19340624, EPI_ISL_19374899, EPI_ISL_19385707, EPI_ISL_19385718, EPI_ISL_19385724

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_899a_27b950.json?label=id:node_7127826

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Trivia:

• Just to track the rare C>G mutation on residue 613, Q613E is much less popolar than famous Q613H, only sampled about 2K times during the whole pandemic.

[FedeGueli]

Thx for the spot on MC.13 too

[NkRMnZr]

the MC.13 branch goes up to 7 seqs (all newly added ones from Brazil)

[FedeGueli]

the MC.13 branch goes up to 7 seqs (all newly added ones from Brazil)

propose it please

[FedeGueli]

the MC.13 branch goes up to 7 seqs (all newly added ones from Brazil)

please propose it

[NkRMnZr]

latest seq from Branch 1 is a mini-saltation

[FedeGueli]

latest seq from Branch 1 is a mini-saltation

did u check for MOV use for that? >> https://movbranchapp.streamlit.app/

[FedeGueli]

Br.2 went to 20 with a BRazilian batch of very recent sequences please propose it

[FedeGueli]

+1 for BR.1

[NkRMnZr]

B2 transferred to cov-lineages/pango-designation#2793 ; B1 seems slowed quite a bit, closing it for now

[FedeGueli]

Designated MC.13.3 via cov-lineages/pango-designation@16205e7#diff-ead4244ff49c81bc758e9f068f5ef42156bd985b9c86de8fa4d6fcd7f2829090R1289