HV.1.8*+S:P681R (Originally HV.1.8* as the largest branch of HV.1*+S:T208M)

[krosa1910]

Gisaid Search:C23604G,C22185T,C14195T
Earliest Sequence: EPI_ISL_18465456 US, CO 2023-09-14
Latest Sequence:
EPI_ISL_18663603 Canada 2023-12-10
Geo Spread 85 total , mostly in US, spread to Canada, UK, Greece, Netherlands, Spain, Switzerland
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_3ac33_fe82a0.json?f_userOrOld=uploaded%20sample

(Updated)
Branch with S:P681R
Gisaid Search: C22185T,C14195T,C23604G
Earliest Sequence: EPI_ISL_18465456 CO, US, 2023-09-14
Latest Seqeunce:
EPI_ISL_18892537 Canada, 2024-01-26
pretty wide geographic spread with possible significance in Ecuador.
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_2884d_4c66d0.json?f_userOrOld=uploaded%20sample&label=id:node_1036260

[krosa1910]

This is introduced by the issue 957, or HV.1* Spike Diversity Collection issue in the other sector.

[FedeGueli]

This is introduced by the issue 957, or HV.1* Spike Diversity Collection issue in the other sector.

https://mail.google.com/mail/u/0/?tab=rm&ogbl#inbox/FMfcgzGtxdbRJPLhhksWrjNmhgGHQKTg

[FedeGueli]

92 samples 7 countries

[corneliusroemer]

You somehow got a somewhat misleading subtree from Usher - not all 208M have 681R:

Above is what I get when I make an Usher tree.

I'll designate the 208M.

[krosa1910]

I have changed this issue to make it more meaningful after the S:T208M branch is designated.
Sub-branch 1: S:P681R (convergent to JN.1* of course)
Gisaid Search: C5835T,C1093T,C22185T,C14195T,C23604G
Earliest Sequence: EPI_ISL_18465456 CO, US, 2023-09-14
Latest Sequence: EPI_ISL_18797757 Ecuador 2024-01-10
Geographic Distribution: 7 Canada, 1 Czech, 4 Ecuador, 1 England, 2 Netherlands, 3 Spain, 1 Switzeland, Rest US
Sub-branch 1.1: S:P681R+S:M153I
Gisaid Search: C5835T,C1093T,C22185T,G22021T
Earliest Sequence: EPI_ISL_18497763 CA, US, 2023-10-24
Latest Sequence: EPI_ISL_18779959 CA, US, 2023-12-28
Geographic Distribution: 16 CA, US 4 UT, US
Sub-branch 2: S:R452W+S:E554Q
Gisaid Search:
Earliest Sequence: EPI_ISL_18407513 MN, US, 2023-10-03
Latest Sequence: EPI_ISL_18807668 CO,US, 2023-12-24
Geographic Distribution: 10 MN, 1 CO (latest spread)
Usher for the total Tree:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_ad24_205e30.json?f_userOrOld=uploaded%20sample&label=id:node_1030207

[FedeGueli]

I have changed this issue to make it more meaningful after the S:T208M branch is designated. Sub-branch 1: S:P681R (convergent to JN.1* of course) Gisaid Search: C5835T,C1093T,C22185T,C14195T,C23604G Earliest Sequence: EPI_ISL_18465456 CO, US, 2023-09-14 Latest Sequence: EPI_ISL_18797757 Ecuador 2024-01-10 Geographic Distribution: 7 Canada, 1 Czech, 4 Ecuador, 1 England, 2 Netherlands, 3 Spain, 1 Switzeland, Rest US Sub-branch 1.1: S:P681R+S:M153I Gisaid Search: C5835T,C1093T,C22185T,G22021T Earliest Sequence: EPI_ISL_18497763 CA, US, 2023-10-24 Latest Sequence: EPI_ISL_18779959 CA, US, 2023-12-28 Geographic Distribution: 16 CA, US 4 UT, US Sub-branch 2: S:R452W+S:E554Q Gisaid Search: Earliest Sequence: EPI_ISL_18407513 MN, US, 2023-10-03 Latest Sequence: EPI_ISL_18807668 CO,US, 2023-12-24 Geographic Distribution: 10 MN, 1 CO (latest spread) Usher for the total Tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_ad24_205e30.json?f_userOrOld=uploaded%20sample&label=id:node_1030207

Please put this in the main proposal first leaving in the bottom part the original proposal seaprated by a ************

[FedeGueli]

Branch 1 query: C22185T,C14195T,C23604G
Branch 2 query: C1302T, C6310T,G23222C,

[krosa1910]

Branch 2 is relatively dormant, but I think branch 1 now reaches like 150 and is proposable so I would change this proposal.

[krosa1910]

No submission for a while, I will give it another week?