KP.3.1.4 plus S:G184A (66, 6 countries including China and Hong Kong) with a S:S31F sublineage (38)

[FedeGueli]

The S:181-187 area is a known area for moderate improvements, here i found a small KP.3.1.4 branch with S:G184A , i got convinced to propose it when seeing a recent GBW sequence from China. Out of 9 Chinese GBW samples in June we have 3 XDV.1 but the DeFLirt army is advancing with KP.2.3 , LB.1.3 and one undesignated KP.1.1.1 deflirt . This one is the only KP.3 representative from China sampled in American airports in June.

Defining mutations KP.3.1.4 >> N:Q241H (A28996T) > Orf1b: I1468V(A17869G) > Orf1a:P1497S (C4754T), C6968T > Orf1a:T3488I (C10728T), S:G184A (G22113C)>> A6328G > Orf1b:S1003G (A16474G ) > S:S31F (C21654T) Query: G22113C ,C10728T Query for S:S31F branch spotted by @josetteshoenma in #1576 first and then by @aviczhl2 : C18490T, A16474G, C21654T or A16474G, C21654T,A6328G Samples: 63 , 37 with 31F Countries: Scotland, Spain, US, China ( via GBW) Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1dda7_f77220.json?label=id:node_7007122

IDs: EPI_ISL_19165014, EPI_ISL_19185635, EPI_ISL_19198395, EPI_ISL_19208350, EPI_ISL_19213878, EPI_ISL_19213882, EPI_ISL_19215092, EPI_ISL_19229664, EPI_ISL_19253164, EPI_ISL_19253172, EPI_ISL_19253181, EPI_ISL_19253196, EPI_ISL_19253238, EPI_ISL_19253246, EPI_ISL_19253251, EPI_ISL_19253367, EPI_ISL_19253500, EPI_ISL_19253656, EPI_ISL_19253756, EPI_ISL_19253791-19253792, EPI_ISL_19253794, EPI_ISL_19253861, EPI_ISL_19253886, EPI_ISL_19269753, EPI_ISL_19269755-19269756, EPI_ISL_19269765, EPI_ISL_19269881, EPI_ISL_19269885, EPI_ISL_19269991-19269992, EPI_ISL_19270001-19270005, EPI_ISL_19270013, EPI_ISL_19270025, EPI_ISL_19270074, EPI_ISL_19270171, EPI_ISL_19272401, EPI_ISL_19272405, EPI_ISL_19272432, EPI_ISL_19272509, EPI_ISL_19272512-19272513, EPI_ISL_19272536, EPI_ISL_19272557, EPI_ISL_19273675, EPI_ISL_19273683, EPI_ISL_19275840, EPI_ISL_19276646, EPI_ISL_19276648, EPI_ISL_19276653, EPI_ISL_19276662, EPI_ISL_19276666-19276668, EPI_ISL_19276739, EPI_ISL_19279822, EPI_ISL_19279959, EPI_ISL_19280144

[FedeGueli]

big upload from Scotland triplicated this from 8 to 24

[aviczhl2]

There is an S:S31F sub-branch emerging from this.

[FedeGueli]

two more samples from UK found by GBW surveillance both with S:S31F , this could be something different from a cluster

[FedeGueli]

63 now with a GBW sample from France new country while the S:S31F went to 37 it seems really fast. even if it seems a scottish cluster the international exports don't bode well with something just limited to a cluster.

cc @corneliusroemer @angiehinrichs @thomasppeacock

[ryhisner]

ORF1b:S1003G (NSP13_S80G) is somewhat homoplasic and is one of the few ORF1b mutations that shows up in a decent number of chronic-infection sequences.

. N:Q241H, an A->T nuc mutation is pretty interesting as well. It's a very rare mutation—fewer than 300 sequences ever prior to this lineage according to CovSpectrum. It's in the middle of the Q-rich region of N, which is adjacent to a key region for the binding of N with NSP3 (specifically, the Ubl1 domain of NSP3).

The PDB structure only shows one half of the full dimer formation. There are 10 structures that vary, illustrating the flexibility of the various regions of N and Ubl1. Below I've picked two of those structures at random and highlighted N:Q241. It's near where N and Ubl1 bind, but it's also in a fairly flexible region and therefore it's location varies quite a bit in the different structures.

PDB 7KPU

Ubl1 is blue and N in red

All of this is from the fantastic paper, "The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a." https://www.science.org/doi/10.1126/sciadv.abm4034

[FedeGueli]

One new sample of this one has been sampled by GBW coming from Hong Kong China: Interestingly it has S:F377L and a reversion T15756T : T15756A was one of the defining of JN.1

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice4_genome_test_4eef1_4a85f0.json?c=gt-nuc_15756&gmax=16756&gmin=14756&label=id:node_7031967

[FedeGueli]

Only 2 out of 296 in the today batch from Scotland.

[FedeGueli]

it was a cluster closing it.