Multiple NB.1+S:R346T branches

[xz-keg]

There seems to be multiple branches of NB.1+S:R346T, make a list

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1. Branch 1: NB.1+Orf1a:S771I,A4277V+S:R346T, Query:G22599C,C25671T,C4683T, G2577T, 5 seqs, Liaoning
2. Branch 2, NB.1+Orf1b:D275Y+S:R346T, Query: G22599C,C25671T,C4683T, G14290T,-C884T,-G6358A, 14 seqs, Liaoning, Hubei, Shanxi, Hong Kong, Singapore, with a S:I478T sub-branch: 22599C,C25671T,C4683T, G14290T,-C884T,-G6358A,-22995, 3 seqs

[FedeGueli]

Thx. As you noticed first in the chats, worth remembering that NB.1 got 100% also in Liaoning after Hubei.

[xz-keg]

Thx. As you noticed first in the chats, worth remembering that NB.1 got 100% also in Liaoning after Hubei.

Sichuan is the first. It seems to be dominating everywhere in Chinese mainland.

[xz-keg]

branch 2: +3 Singapore

[HynnSpylor]

Branch 2 +4 in Sichuan, China

[xz-keg]

There is now an S:I478T cycle reversion branch of branch 2, and it mess up with another NB.1.1(I478T)+S:R346T branch on usher(difference is G6358A), creating messy flip-flops.

@FedeGueli @corneliusroemer

@AngieHinrichs, anyway to fix it?

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice80_genome_test_1d3593_454b90.json?label=id:node_5919540