XBB.1.16.1 with S:Y453F 3 seqs from USA airport surveillance (California, Atlanta)

[FedeGueli]

I spotted a couple of american airport surveillance samples with S:Y453F belonging to XBB.1.16.1

We never saw S:Y453F spreading in a fast lineage or pushing a lineage to rapid growth.

But i prefer to propose and monitor it.

Defining mutations:
XBB.1.16.1 >> T29410C, S:Y453F (A22920T)

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1970c_6ec5c0.json?label=id:node_7703085

Gisaid query : C11750T, C11956T, A22920T (thx @josetteshoenma)

Sequences:

USA/GA-GBW-H10-010-4814/2023|EPI_ISL_17308511|2023-03-17
USA/CA-GBW-H10-011-2874/2023|EPI_ISL_17308536|2023-03-19

[ryhisner]

These are both pooled samples, so I kind of doubt if they are really XBB.1.16.1 with Y453F. I think it's more likely that some XBB.1 with Y453F got mixed in with some XBB.1.16.1.

Annoyingly, Ginkgo Bioworks often uploads pooled samples to GISAID with no clear indication that they are not normal samples. You have to look pretty far down the GISAID entry to discover that they are pooled samples.

[FedeGueli]

Thx @ryhisner i didnt get they were the same samples you talked about some days ago

[FedeGueli]

Third sequence of this one same day of one of the first two. And this time it is from Hong Kong traveller.
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_24eb5_b52660.json

This makes this much more real than initially thought. cc @ryhisner (Also all the 3 samples have. a silent nuc mutation in common, it would be weird if unreal

[FedeGueli]

Closing this no new sample came from airports or India.

[FedeGueli]

Designated FU.4