XBB.1.11.1 (S:S486P) Sublineage with S:K478R (87 seq, May 20)

[ryhisner]

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

[HynnSpylor]

Maybe the Usher tree is the reorganization of #31

[FedeGueli]

Maybe the Usher tree is the reorganization of #31

The branch on the top is the saltation proposed in #31 lemm re check what happened.

cc @angiehinrichs Usher seems to have re sorted this tree in the opposite direction could you take a look please?

[FedeGueli]

@corneliusroemer @angiehinrichs could you please take a look at this one? it was proposed before but USher at that time had S:F186S as main node, then with new sequences of this one with S:K478R accumulating fastly now it broaden the lineage making it start from S:K478R and showing just a branch of it with S:F186S.

Once resolved the tree i think it should be proposed.

[AngieHinrichs]

(looking at the 2023-05-18 tree) The saltation branch from #31 has been moved to a separate branch of XBB.1.11.1 starting with ORF1a:V3078I (G9497A) > S:F186S (T22119C); this is just the branch with S:K478R (A22995G) and these seuqences:

Indonesia/JK-NIHRD-W01459/2023|EPI_ISL_17546448|2023-03-31 Indonesia/JK-NIHRD-W01136/2023|EPI_ISL_17551532|2023-03-31 Indonesia/JK-GSILab-1151115/2023|EPI_ISL_17664323|2023-04-19 Indonesia/JK-NIHRD-W01577/2023|EPI_ISL_17518081|2023-04-12 Indonesia/YO-BBTKLPP-C285-S78B3/2023|EPI_ISL_17654916|2023-04-28 Oman/5237649/2023|EPI_ISL_17550381|2023-03-19 SouthKorea/KDCA231306/2023|EPI_ISL_17554737|2023-04-17 Japan/PG-472308/2023|EPI_ISL_17558668|2023-03-31 Malaysia/C19UMB3912/2023|EPI_ISL_17671125|2023-04-12 Malaysia/C19UMB3887/2023|EPI_ISL_17671106|2023-03-30 England/PHEC-YYEU7WM/2023|2023-04-11 England/PHEC-YYEOQSH/2023|2023-03-25 England/QEUH-326EF4B1/2023|OX450101.1|2023-02-28 Australia/VIC83584/2023|EPI_ISL_17656892|2023-04-25 Spain/GA-CHOP-52075926/2023|EPI_ISL_17652467|2023-04-04 Indonesia/JK-CW62-4290/2023|EPI_ISL_17630702|2023-04-03 Indonesia/JK-GS-GSILab-1149437/2023|EPI_ISL_17389725|2023-03-18 Indonesia/JK-GS-GSILab-1149435/2023|EPI_ISL_17389654|2023-03-18 Malaysia/UNIMAS-GHML2130/2023|EPI_ISL_17612373|2023-02-20 Malaysia/UNIMAS-B19277/2023|EPI_ISL_17612344|2023-03-16 Indonesia/JT-Labkes-WGS-23-067/2023|EPI_ISL_17664301|2023-05-01 Indonesia/JK-CW62-3857/2023|EPI_ISL_17012209|2023-02-02 Malaysia/UNIMAS-B19318/2023|EPI_ISL_17612366|2023-04-01

[FedeGueli]

thx @AngieHinrichs ! Now everything makes sense. @ryhisner please go on proposing it in the main page.

[FedeGueli]

87 seqs @ryhisner did you propose this one then??

[ryhisner]

Not yet, @FedeGueli. I'll copy and paste this to the main page today though.

[FedeGueli]

Not yet, @FedeGueli. I'll copy and paste this to the main page today though.

Have you checked the tree?? i think the saltation sublineage is not more present and i proposed it separately

[FedeGueli]

FP.3