EG.5.1.1 Sublineage with S:L455F (12 seq, 3 provinces, China; July 16)

[ryhisner]

Description
Sub-lineage of: EG.5.1.1 (XBB.1.9.2.5.1.1)
Earliest sequence: 2023-6-20, China, Henan, Puyang — EPI_ISL_17988152
Most recent sequence: 2023-7-5, China, Hubei, Xiangyang — EPI_ISL_17988079
Countries circulating: China (4)
Number of Sequences: 4
GISAID AA Query: Spike_L455F, Spike_F456L, NSP12_D63N, Spike_F486P
GISAID Nucleotide Query: C6541T, G13627A, G22927T, C25572T
CovSpectrum Query: Nextcladepangolineage: EG.5.1.1* & S:L455F
Substitutions on top of EG.5.1.1:
Spike: L455F
Nucleotide: G22927T

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/EG.5.1.1%20+%20L455F.json?c=gt-S_455&label=id:node_5182912

Evidence
Self-explanatory. There's a fourth sequence of EG.5.1.1 with S:L455F, but it appears to be unrelated to the other three. These are all from separate provinces and are separated from one another by at least four nucleotide differences, so this lineage may well be fairly widespread. Too early to tell for sure.

EDIT: Now that I've looked at it more closely, I think the 4th sequence (EPI_ISL_17978556) very likely also belongs in this lineage. It's the lowest-quality sequence of the four, and it's put in a different branch because of an alleged synonymous reversion, T22480C. But there is missing coverage close to 22480, so I think it's most likely an artifact. I've edited the title to reflect this.

Genomes

Genomes

EPI_ISL_17978556, EPI_ISL_17987533, EPI_ISL_17988079, EPI_ISL_17988152

[FedeGueli]

To be proposed once gets 10seqs

[HynnSpylor]

Ah I'm just planning to propose it!
S:L455F+S:F456L "exchange" is popular recently (in XBB.1.5.70). Nowadays EG.5.1* has risen rapidly, and it has the largest proportion in China since mid June. It deserves a further watch.

[HynnSpylor]

one more seq from Sichuan Province, China

[BorisUitham]

There's also an eg.5.1.1 with 455f from shanghai uploaded on 07-18. EPI_ISL_17994488, but it seems to be on another branch than this one, with C11779T

[xz-keg]

Designated HK.3

[FedeGueli]

cov-lineages/pango-designation@39a35ba

[oobb45729]

S:L455F looks very homoplasic within the EG.5.1 tree now. The supposed lineages is defined by a single mutation. I'm not convinced. They might gain S:L455F independently. @corneliusroemer

[ryhisner]

Yeah, you have to look closely to make sure any S:L455F lineages are monophyletic. In this case, I think you have to assume it is until the tree fills out further.

[BorisUitham]

@oobb45729 there are definitely a few convergemt branches (i believe about 6-7 within eg.5*) with 455f: one in eg2, his eg.5.1.1 designated as hk.3, etc. But there are a lot of interesting singlets. Perhaps this should be monitored over these weeks to see if the singlets might still cause further spread.