XBB.1.42 with N:P67L/ORF9b:L64F (70 seqs, mainly in Japan, 5 countries)

[NkRMnZr]

Defining Mutations: XBB.1.42 > C28473T(N:P67L/ORF9b:L64F) Query: A16878T, G23401T, C28473T, -C1812T, -G5720A Earliest seq: 2023-03-31 (EPI_ISL_17502924, Kuala Lumpur, Malaysia) Latest seq: 2023-07-22 (EPI_ISL_18081798, Hyogo, Japan) Sampled Countries: Japan (44), Malaysia (3), Canada (1), New Zealand (1)

Genomes:

`EPI_ISL_17502924, EPI_ISL_17623737, EPI_ISL_17730054, EPI_ISL_17739121, EPI_ISL_17798999, EPI_ISL_17881481, EPI_ISL_17941133, EPI_ISL_17941153, EPI_ISL_17941155, EPI_ISL_17952672, EPI_ISL_17960064, EPI_ISL_17973138, EPI_ISL_17973208, EPI_ISL_17973211, EPI_ISL_17979870, EPI_ISL_17979882, EPI_ISL_17980715, EPI_ISL_17980718-17980719, EPI_ISL_17980779, EPI_ISL_17982190, EPI_ISL_17985828, EPI_ISL_17996469, EPI_ISL_17996535, EPI_ISL_18000629, EPI_ISL_18006665, EPI_ISL_18006700, EPI_ISL_18010308, EPI_ISL_18010357, EPI_ISL_18013000, EPI_ISL_18040399, EPI_ISL_18040790, EPI_ISL_18040834, EPI_ISL_18044077, EPI_ISL_18051706, EPI_ISL_18056112, EPI_ISL_18071624, EPI_ISL_18071646, EPI_ISL_18071735-18071736, EPI_ISL_18073738, EPI_ISL_18081798, EPI_ISL_18081835, EPI_ISL_18081850, EPI_ISL_18081961-18081963, EPI_ISL_18082353, EPI_ISL_18082398`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_86ff_61ea20.json?f_userOrOld=uploaded%20sample

view from XBB.1.42 polytomy

details

[FedeGueli]

XBB.1.42 is likely the fastest not XBB.1.5/9/16/22 or 2.3 lineage so very good to keep it monitored .

This orf9b mutation is predicted to be slighty beneficial:

It seems that the branch spreading in Japan is faster than parental lineage.

[FedeGueli]

Adding a growth advantage tracker: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=A16878T%2CG23401T%2CC28473T%2CA29799T&analysisMode=CompareToBaseline&

[NkRMnZr]

Tracking updates:

08-18, 12 seqs from China, Japan

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_4aee_87da0.json?f_userOrOld=uploaded%20sample&label=id:node_6928847  `EPI_ISL_18097181, EPI_ISL_18097508, EPI_ISL_18097647, EPI_ISL_18097841, EPI_ISL_18097866, EPI_ISL_18100616, EPI_ISL_18109123-18109125, EPI_ISL_18109132, EPI_ISL_18109253`

08-26, 10 seqs from China (with travel history to Japan) and Japan

[NkRMnZr]

08-26, 10 seqs from China (with travel history to Japan) and Japan

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_4a43_a103f0.json?f_userOrOld=uploaded%20sample&label=id:node_6946888

EPI_ISL_18122812-18122813, EPI_ISL_18122824, EPI_ISL_18122828, EPI_ISL_18122832, EPI_ISL_18122834, EPI_ISL_18122846, EPI_ISL_18123174, EPI_ISL_18127223, EPI_ISL_18138029

[FedeGueli]

Please propose it

[NkRMnZr]

Transferred to cov-lineages/pango-designation#2217