XBB.1.11.1 (S:S486P) Sublineage with S:K478R (87 seq, May 20)—first proposed by @FedeGueli

[ryhisner]

Transferred from pre-Proposal page Issue 66 sars-cov-2-variants/lineage-proposals#66

Note: A sub-branch of this lineage was previously proposed by @FedeGueli, but after a subsequent rearrangement of the Usher tree, I made the following proposal, not realizing it contained within it the branch proposed earlier.

Description
Sub-lineage of: XBB.1.11.1
Earliest sequence: 2023-2-2, Indonesia — EPI_ISL_17012209
Most recent sequence: 2023-5-2, Indonesia — EPI_ISL_17655098
Countries circulating: Indonesia (29), Malaysia (7), England (3) South Korea (1), Australia (1), Spain (1), Japan (1)
Number of Sequences: 43
GISAID Nucleotide Query: C13968A, G16377A, C22995G, T23018C
CovSpectrum Query: Nextcladepangolineage:XBB.1.11.1* & S:K478R
Substitutions on top of XBB.1.11.1:
Spike: K478R
Nucleotide: A22995G

USHER Tree (The tree below excludes several sequences with multiple artifactual reversions, so all the longer branches below consist of real mutations.)
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.11.1_(S486P)_K478R.json?c=gt-S_478&label=id:node_3679455

Evidence
This lineages seems to be most in Indonesia, a country of about 275 million people from which we don't get very many sequences. It is also prominent in Malaysia. The base lineage can't be growing particularly fast or it would be more widespread internationally by now, but there's a great deal of diversity here, including a sizable branch with S:F186S and four additional AA mutations. This branch includes the most recently collected sequence (May 2) and first appeared on March 10 in Indonesia.

Genomes

Genomes

EPI_ISL_17012209, EPI_ISL_17164850, EPI_ISL_17324410, EPI_ISL_17389516, EPI_ISL_17389654, EPI_ISL_17389725, EPI_ISL_17416998, EPI_ISL_17469966, EPI_ISL_17470009, EPI_ISL_17470016-17470017, EPI_ISL_17470030, EPI_ISL_17518081, EPI_ISL_17542013, EPI_ISL_17546410, EPI_ISL_17546448, EPI_ISL_17551332, EPI_ISL_17551361, EPI_ISL_17551494, EPI_ISL_17551532, EPI_ISL_17554737, EPI_ISL_17558668, EPI_ISL_17612344-17612345, EPI_ISL_17612347, EPI_ISL_17612354, EPI_ISL_17612366, EPI_ISL_17612373-17612374, EPI_ISL_17622306, EPI_ISL_17622322, EPI_ISL_17622348, EPI_ISL_17622363, EPI_ISL_17630635, EPI_ISL_17630702, EPI_ISL_17652467, EPI_ISL_17654916, EPI_ISL_17654975, EPI_ISL_17654978, EPI_ISL_17655098, EPI_ISL_17655949, EPI_ISL_17656892, EPI_ISL_17664323

[FedeGueli]

@ryhisner i think now that thing has been resolved with the saltation sublineage being moved to another tree:
(see my pango proposal:
#2012)

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_c6b1_ca5bc0.json?c=gt-S_186,478&label=id:node_6903013

[FedeGueli]

In the same tree your one is the one in the middle coloured for F/R

[ryhisner]

When I run the tree, I still get them both in the same branch, @FedeGueli. Maybe it depends on which sequences you upload together? That's definitely been the case for me before.

I used the nucleotide query above (C13968A, G16377A, C22995G, T23018C) and uploaded all 89 results. Here's what I get:

[FedeGueli]

very weird. try to repeat the op excludimg the saltation maybe now i m off pc i cant.

@AngieHinrichs could you help please?

[FedeGueli]

@ryhisner also.the S:E780A branch was differently placed in mine .

[FedeGueli]

Designated FP.3 from b5e3461

cc @InfrPopGen

[AngieHinrichs]

I haven't verified this, but I think it's possible that matOptimize might sometimes move the branch back and forth from day to day. I can look at specific build dates if you want.