MC.13 with S:Q613E (38 seqs, 7 countries)

[NkRMnZr]

Taken from Branch 2 of sars-cov-2-variants/lineage-proposals#1962

Defining Mutations: MC.13 > C23399G(S:Q613E)
Query: C10681T, A13121T, C23399G
Earliest seq: 24-06-13 (EPI_ISL_19265922, Portugal)
Latest seq: 24-09-12 (EPI_ISL_19430296, Mato Grosso do Sul, Brazil)
Sampled Countries: Brazil (18: MS), Spain (1), Portugal (1)

Genomes:

for lineages.csv commit:

Brazil/MS-FIOCRUZ-FMS306/2024
Brazil/MS-FIOCRUZ-FMS311/2024
Brazil/MS-FIOCRUZ-FMS319/2024
Brazil/MS-FIOCRUZ-FMS333/2024
Brazil/MS-FIOCRUZ-FMS340/2024
Brazil/MS-FIOCRUZ-FMS363/2024
Brazil/MS-FIOCRUZ-FMS372/2024
Brazil/MS-FIOCRUZ-FMS377/2024
Brazil/MS-FIOCRUZ-FMS382/2024
Brazil/MS-FIOCRUZ-FMS383/2024
Brazil/MS-FIOCRUZ-FMS385/2024
Brazil/MS-FIOCRUZ-FMS386/2024
Brazil/MS-FIOCRUZ-FMS388/2024
Brazil/MS-FIOCRUZ-FMS390/2024
Brazil/MS-FIOCRUZ-FMS405/2024
Brazil/MS-FIOCRUZ-FMS422/2024
Brazil/MS-FIOCRUZ-FMS438/2024
Brazil/MS-FIOCRUZ-FMS444/2024
Portugal/PT51065/2024
Spain/CT-LabRefCat-3669331/2024

epi_isl accessions:
EPI_ISL_19265922, EPI_ISL_19340619, EPI_ISL_19340624, EPI_ISL_19374899, EPI_ISL_19385707, EPI_ISL_19385718, EPI_ISL_19385724, EPI_ISL_19430235, EPI_ISL_19430242, EPI_ISL_19430245, EPI_ISL_19430249-19430252, EPI_ISL_19430254, EPI_ISL_19430256, EPI_ISL_19430269, EPI_ISL_19430282, EPI_ISL_19430293, EPI_ISL_19430296

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1a213_8dc4d0.json?label=id:node_7224120

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.
• There are 2 seqs placed in other part of the phylo-tree, namely Spain/CT-LabRefCat-3669331/2024|EPI_ISL_19374899|2024-07-26 and Brazil/MS-FIOCRUZ-FMS422/2024|EPI_ISL_19430282|2024-09-06 probably due to low coverage, but these two seqs both have MC.13's definition and S:Q613E so they likely belong to this sub-branch.

[xz-keg]

24 now.
There is a S:R346T sub-branch of this hiding in the artifact S31F branch of KP.3.1.1

Query: C10681T, A13121T, C23399G, G22599C

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice13_genome_test_64fa1_877ac0.json?label=id:node_5654372

[FedeGueli]

24 now. There is a S:R346T sub-branch of this hiding in the artifact S31F branch of KP.3.1.1

Query: C10681T, A13121T, C23399G, G22599C

A better query is : C10681T, A13121T, G22599C, finding 11 samples

[FedeGueli]

@NkRMnZr please add the 346T sub branch to the proposal

[xz-keg]

24 now. There is a S:R346T sub-branch of this hiding in the artifact S31F branch of KP.3.1.1
Query: C10681T, A13121T, C23399G, G22599C

A better query is : C10681T, A13121T, G22599C, finding 11 samples

That includes multiple MC.13+S:R346T branches.

[NkRMnZr]

@NkRMnZr please add the 346T sub branch to the proposal

it's a bit weird, that is splitting on a false kp.3.1.1+S31F branch;
in the newly landing regions, 1 from England does not have R346T; but the one from Rio de Janeiro (1st from Brazil outside of Mato Grosso do Sul) and one from Denmark does have it.

[FedeGueli]

25, Br

[xz-keg]

35, Germany, Singapore

[FedeGueli]

38 Spain Basque country,Denmark

[NkRMnZr]

was waiting for the KP.3.1.1 artifact S31F subtree prune, now it looks like this:

there're now an English sub-branch L441F and a Danish sub-branch R346T to further track