XBB.1.41 with ORF1b:A186T (nsp12_A195T) and S:S494P (26 seqs, 6 countries)

[NkRMnZr]

Defining Mutations: XBB.1.41 > G14023A(ORF1b:A186T) > C9724T, T23042C(S:S494P), T28636C
Query: C9724T, T23042C, T28636C
Earliest seq: 2023-05-26 (EPI_ISL_17854037, Oregon, USA)
Latest seq: 2023-06-22 (EPI_ISL_17955591, Texas, USA)
Sampled Countries: South Korea (3), USA (2, Oregon, Texas), Spain (2)

Genomes:

EPI_ISL_17854037, EPI_ISL_17955591, EPI_ISL_17956133, EPI_ISL_17966614, EPI_ISL_17969853, EPI_ISL_17970224, EPI_ISL_17975901

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3da4d_d2b930.json?f_userOrOld=uploaded%20sample&showBranchLabels=all

[NkRMnZr]

By the way, is XBB.1.41 a sub-branch of XBB.1.28? Or is it simply misplaced in UShER?

[FedeGueli]

By the way, is XBB.1.41 a sub-branch of XBB.1.28? Or is it simply misplaced in UShER?

it was discussed at the start, also @AngieHinrichs thought it could have been designated as XBB.1.28 sublineage.

[AngieHinrichs]

Yeah, not enough samples to tell which mutation(s) came first.

[NkRMnZr]

Tracking updates:

07-28, 3 sequence from Iceland, Israel, and USA: EPI_ISL_18012525, EPI_ISL_18044173, EPI_ISL_18045466
08-01, 1 sequence from California
08-05, 3 seqs from USA
08-13, 4 seqs from USA
08-18, 8 seqs from Canada and USA

[NkRMnZr]

08-01: 1 sequence from California, USA: EPI_ISL_18050202

[NkRMnZr]

08-05, 3 seqs from USA: EPI_ISL_18057007, EPI_ISL_18057375, EPI_ISL_18069736

[NkRMnZr]

08-13, 4 seqs from USA: EPI_ISL_18072741, EPI_ISL_18090186, EPI_ISL_18090229, EPI_ISL_18095888

UShER:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_16296_8df060.json?f_userOrOld=uploaded%20sample

[FedeGueli]

Although interesting it shows a disadvantage in the US where it has sampled the most:
https://cov-spectrum.org/explore/United%20States/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=C9724T%2CT23042C%2CT28636C&analysisMode=CompareToBaseline&

[NkRMnZr]

08-18, 8 seqs from Canada and USA:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_27ad9_98800.json?f_userOrOld=uploaded%20sample&label=id:node_7006202

1 from Alberta: EPI_ISL_18103912
1 from New York: EPI_ISL_18104089
1 from California: EPI_ISL_18104117
2 from Florida: EPI_ISL_18104151, EPI_ISL_18104650
1 from Pennsylvania: EPI_ISL_18104316
1 from Indiana: EPI_ISL_18104853
1 from Mississippi: EPI_ISL_18110543

[aviczhl2]

This one is designated XBB.1.41.2

[FedeGueli]

Designated XBB.1.41.2