CM.7.1 (BA.2.3.20+S:F486S+ S:K147E) Saltation Sublineage with S:R403K (12 seqs, Spain, Italy, France - June 23- )

[ryhisner]

Edited by Fede:

Ryan found this one very early and so it proposed basically the spanish branch of this one. Now we know that it is spread to 3 countries (Italy, France and Spain) counts 8 sequences (EPI_ISL_17390375, EPI_ISL_17615444, EPI_ISL_17619326,
EPI_ISL_17677150, EPI_ISL_17719461, EPI_ISL_17719468,
EPI_ISL_17726239, EPI_ISL_17726413) found with the query : G14500T, C26801T,G656A, G22770A
and it shows a great within lineage diversity as shown by the today tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_bd9a_662370.json?c=userOrOld&label=id:node_7104726

Today @corneliusroemer designated the parental lineage CM.7.1 .

So now defining mutations are:

CM.7.1 ( S:K147E) >> Orf1a:L16F (C311T),Orf1b:V345L (G14500T), C26801T >ORf1a:A131T (G656A),S:R403K (G22770A )

I apologizes with @ryhisner for the heavy editing but it is needed to keep proposal up to date to be ready tobe transferred

I will close #103

_ORIGINAL VERY EARLY PROPOSAL BY RYAN HISNER

Description

Sub-lineage of: CM.7
Earliest sequence: 2023-4-24, Italy
Most recent sequence: 2023-4-26, Spain (2)
Countries circulating: Spain (3)
Number of Sequences: 3
GISAID AA Query: Spike_R403K, NSP2_T547I, NSP1_L16F
GISAID Nucleotide Query: T23020C, G22770A, C2445T
Alternative Gisaid query (Fede) : G14500T, C26801T,G656A, G22770A
CovSpectrum Query: Nextcladepangolineage:BA.2.3.20* & [8-of: C311T, G656A, C1284T, T3802C, T5377A, C12754T, C13059T, G14500T, C14809A, T14892A, C16329T, A22001G, G22770A, T23020C, G23426A, C26256T, C26681T, C26801T, C26894T]

Substitutions on top of CM.7:
Spike: K147E, R403K, S:V622I
ORF1a: L16F, A131T, T340I, T4265I (NSP1_L16F, NSP1_A131T, NSP2_T160I, NSP10_T12I)
ORF1b: V345L, R448S, D475E (NSP12_V354L, NSP12, R457S, NSP12_D484E)
Nucleotide: C311T, G656A, C1284T, T3802C, T5377A, C12754T, C13059T, G14500T, C14809A, T14892A, C16329T, A22001G, G22770A, T23020C, G23426A, C26256T, C26681T, C26801T, C26894T

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/CM.7_T23020C_K147E_R403K.json

Evidence
The three sequences from Spain are from separate patients with very different ages. One collected April 24, the other two April 26. There's a sequence from March 22 from Italy that shares S:K147E, S:R403K, ORF1a:A131T, and ORF1b:V345L. The closest ancestor to all of them is from Germany, so it seems this branch has been kicking around Europe quite a bit.

The coverage on one sequence is missing a big chunk of the spike NTD and the April 24 sequence is missing even more—10% of the genome has no coverage.

Genomes

Genomes

EPI_ISL_17615444, EPI_ISL_17619326, EPI_ISL_17620611

[FedeGueli]

No new sequence coming up, likely a good news.

[HynnSpylor]

11 seqs now（updated from Italy/France in these two days）

[FedeGueli]

Thx @HynnSpylor

[FedeGueli]

New sample came from France collect in Mid June. interestingly it has Orf7a:S44L that was mutated to P in the successful late BA.5.11 lineage emerged in SA but spread in Denmark.