KP.3.1.4 + S:T29N, S:N477S (R), S:T791P, ORF9b:Q18R, ORF1a:V1143F; ORF1b:T794I, ORF1b:P1675S, ORF1b:T2165M (14 seq, USA, Canada; Oct 3)

[ryhisner]

Description

Sub-lineage of: KP.3.1.4 Earliest sequence: 2024-6-26, USA, North Carolina — EPI_ISL_19216826 Most recent sequence: 2024-7-14, Canada, New Brunswick — EPI_ISL_19284093 Continents circulating: North America (3) Countries circulating: USA (2), Canada (1) Number of Sequences: 3 GISAID Nucleotide Query: G19800A, C19961T, A23933C CovSpectrum Query: Nextcladepangolineage:KP.3.1* & [5-of: G3692T, C15848T, G19800A, C19961T, C21648A, A22992G, A23933C, T27807C, A28336G] Substitutions on top of KP.3.1: Spike: T29N, S477N (Reversion), T791P ORF9b: Q18R ORF1a: V1143F ORF1b: T794I, T2165M

Nucleotide: G3692T, C15848T, G19800A, C19961T, C21648A, A22992G (R), A23933C, T27807C (R), A28336G

USHER Tree Note: This is definitely a misplacement due to the dropout in the North Carolina sequence, which registers as reversions W452L, S455L, and L456F. It ought to be somewhere in the KP.3.1.4 branch instead. https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/KP.3.1_T29N_N477S_T791P.json?c=gt-S_791&gmax=25384&gmin=21563&label=id:node_7030493

Evidence There are several remarkable mutations in this mini-saltation lineage.

• S:T29N – This creates a glycan at N29. Since glycans at N22 (via T22N) and N30 (via ∆S30) have proven highly advantageous, it seems reasonable to suppose that N29 would have a similar effect.

• S:N477S (Reversion) — This is an extremely rare reversion. I can't recall ever seeing it. S477N was a convergent spike mutation even before Omicron.

• S:T791P – S:T791 mutations seem to show up disproportionately in highly mutated sequences. One study found that T791 was the only phosphorylated residue in spike, so there is likely a real functional effect of some sort here.

• T27807C (Reversion) – The number of mutations in this region of ORF7b, many of them synonymous, makes me think they play some significant role in the secondary RNA structure. Once I checked for reverse complement matches to the Octanucleotide Motif, a 3' UTR sequence that is absolutely conserved in all coronaviruses, and this region of ORF7b was one of the top matches. Could be a coincidence though. Hard to say.

Genomes

Genomes

EPI_ISL_19216826, EPI_ISL_19284093, EPI_ISL_19290323

[FedeGueli]

S:N477S (Reversion) — This is an extremely rare reversion. I can't recall ever seeing it. S477N was a convergent spike mutation even before Omicron.

it is also very deleterious according to the new T.Starr calculator:

https://tstarrlab.github.io/SARS-CoV-2-RBD_DMS_Omicron-EG5-FLip-BA286/RBD-heatmaps/

But i have seen it multiple times recently always thought it was not real i ve to check that then

[FedeGueli]

The query is not correct i ve edited it to the right one: G19800A, C19961T, A23933C

[ryhisner]

The query is not correct i ve edited it to the right one: G19800A, C19961T, A23933C

Thanks, I think I forgot to fill that out and so a query from a previous proposal was still sitting there.

[xz-keg]

I believe this is a descendant of KP.3.1.4. (Orf1b:P1675S)

[xz-keg]

Seems not growing.

[Over-There-Is]

11 now

[FedeGueli]

Thx for noticing. could be T29N being better now? we will see

[Over-There-Is]

12, Ohio

[FedeGueli]

12, Ohio

6 regions in US and 2 in Canada it seems interesting

[FedeGueli]

no new seqs closing it

[FedeGueli]

+2 California (recent ) reopening it

[FedeGueli]

dead