HV.1 with S:R452W, ORF1a:T4083M (61 seqs - 7 countries - March 19)

[ryhisner]

Making this one very short as I have to run, and I'm not sure if it's significant in any case. If it grows, I'll fill in the details. The 5 sequences come from near-opposite ends of North America. The two other S:R452W sequences that cluster with it on the Usher tree are most likely unrelated.

Query: C5835T, C12513T, A18492G, C22916T

Usher Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/HV.1_R452W.json?c=gt-nuc_12513&label=id:node_11054571

Genomes: EPI_ISL_18368684, EPI_ISL_18368708, EPI_ISL_18368715, EPI_ISL_18452865, EPI_ISL_18453010

[FedeGueli]

+1 Greece

[FedeGueli]

Slow closing it

[xz-keg]

18 seqs now

[FedeGueli]

thx @aviczhl2 reopend it cause still ongoing in December,.

[xz-keg]

Seems that this is not the real HV.1.10, and S:452W is very very convergent in HV.1

Reopen this.

This is a summary of HV.1+S:452W, as can be seem this one is not the HV.1.10. There seems to be at least 30 separate branches of HV.1+S:452W.
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_ff5a_9e2190.json?f_userOrOld=uploaded%20sample&label=id:node_3577511

@ryhisner @FedeGueli @corneliusroemer

[FedeGueli]

What a mess there were just two lineages and a few of sequences at the time of designation. I ve checked at that time the sequences used to designate and some of them belonged to this one. cc @corneliusroemer @AngieHinrichs important.

At this point maybe more useful to open a multiple lineages issue. for HV.1 and S:l452W inclusing this one, the HV.1.10 and the NZL proposed one plus other branches with more than 3 seqs

[FedeGueli]

What a mess there were just two lineages and a few of sequences at the time of designation. I ve checked at that time the sequences used to designate and some of them belonged to this one. cc @corneliusroemer @AngieHinrichs important.

At this point maybe more useful to open a multiple lineages issue. for HV.1 and S:l452W inclusing this one, the HV.1.10 and the NZL proposed one plus other branches with more than 3 seqs

scratch my words i was confusing it with 450D , but still @corneliusroemer @AngieHinrichs could you take a look

[FedeGueli]

Seems that this is not the real HV.1.10, and S:452W is very very convergent in HV.1

Reopen this.

This is a summary of HV.1+S:452W, as can be seem this one is not the HV.1.10. There seems to be at least 30 separate branches of HV.1+S:452W. https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_ff5a_9e2190.json?f_userOrOld=uploaded%20sample&label=id:node_3577511

@ryhisner @FedeGueli @corneliusroemer

I managed to look into it : HV.1.10 is not this one and has around 100 Seqs , best query i found is : C15720T,C29784T,C22916T

[FedeGueli]

In january a few of the highly homoplasic HV.1 + 452W are still circualting:
1)HV.1.10
2) the lineage proposed here
3) a lineage stemming out of from the politomy
4) one small lineage found by C22916T,C7788T,T3306A : with Orf1a:E377G, Orf1a:M1014K, Orf1a:A2508V
5) one lineage that Usher shows having a intermediate step with C22916A and then A22916T so likely just a flip flop

@corneliusroemer if you want to take a look: (tree cut with just samples from January , but there are 50+ branches with 452W in HV.1)
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_67132_82d7e0.json?f_userOrOld=uploaded%20sample

[FedeGueli]

57 one sample from February

[FedeGueli]

still a couple of recent new samples lets keep it open for a while more

[FedeGueli]

no seuence in March closing it