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

[NkRMnZr]

### Tracking Lineages with `S:Q613E(C23399G)`
- [ ] [Branch 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
- [ ] [Branch 2](#branch_2) Transferred to 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