BA.5.2 + Orf1b:1050N with S:K444R circulating globally (147 seqs)

FedeGueli commented 2 years ago

Here i want to propose another sublineage of BA.5.2 with S: K444R

Defining mutations: BA.5.2 + 12310A + orf1b:1050N + 27513T +27012T + S:444R

Tree Schermata 2022-09-04 alle 10 12 29 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_a014_3dd820.json?branchLabel=aa%20mutations&c=country&label=nuc%20mutations:A22893G

It is very hard to establish a reliable CovSpectrum query or Gisaid Query for this one cause it starts directly from the politomy of main branch of BA.5.2

I suggest to designate it looking at growth advantage usually conferred by S:K444 mutations and specifically by S:444R (Bf.16)

Countries: Schermata 2022-09-04 alle 10 15 35

Nr of sequences from Usher : 101

Gen Bank list of sequences:

OP166543.1 OP241129.1 OX260796.1 OX237538.1 OX274550.1 OX275355.1 OX275936.1 OX279457.1 OX277428.1 OX236546.1 OX247358.1 OX238850.1 OX277605.1 OX280866.1 OX279098.1

Expand for EPI_ISLs

FedeGueli commented 2 years ago

109 sequences as today: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=Orf1b%3AP85L%2Corf1b%3AN1700S%2CS%3AK444R%2COrf1b%3AT1050N&

FedeGueli commented 2 years ago

There is a clear sublineage of this one linked to Sweden defined by one further Orf1b mutation: Orf1b:N1700S Schermata 2022-09-05 alle 20 50 17 To be sure to generate the right tree of this lineage (the one proposed here) a good tip could be to use the query from Gisaid: NSP13_T127N,Spike_K444R, NSP14_N176S ( which finds Sweden sublineage only) and from those sequences build the Usher tree.

FedeGueli commented 2 years ago

124 sequences as today: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1436b_d00cd0.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:A22893G Schermata 2022-09-10 alle 23 36 55 The Orf1b:N1700S branch of this sublineage reached 44 sequences with some clusters defined by additional spike mutations

@corneliusroemer not super urgent but also looking at the main branch there are some geoclustered sequences with NTD mutations as S:N148T in Uk, one with a RBD mutation S:D427Y in Sweden , one with a FCS mutation S:A688V . I suggest a designation as a whole or starting with the "swedish branch" waiting if some of the other branches show signs of growth advantage ( I personally dont like to jump to Sons/siblings but better than none )

FedeGueli commented 2 years ago

@corneliusroemer this reached 147 sequences: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2a4fc_109970.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:A22893G

corneliusroemer commented 2 years ago

We need to look into whether this could be in fact a homoplasic branch - where Usher pulls all the S:444R together, when in fact the sequence of mutations was the other way round: first the branches, then S:444R.

Way to check: see whether there are branches in the tree without S:444R that have the mutations that come off the S:444R node.

FedeGueli commented 2 years ago

thx @corneliusroemer i will do as soon as possible

corneliusroemer commented 2 years ago

Thanks this does look interesting. If I search for BA.5.2 + ORF1b:1050N and S:444R I get ~400 sequences worldwide and growth advantage over ORF1b:1050N of about 30%/week.

So quite interesting - if it were to acquire something else. It's ~2% in Sweden. So I guess worthy of designation if we can figure out monophyletic branches.

corneliusroemer commented 2 years ago

There's a separate South Korea branch that is not part of this that has ~30 sequences.

Nextclade will not know the difference so miscall it as also this lineage - but I guess no big harm done.

FedeGueli commented 2 years ago

thx Cornelius.

FedeGueli commented 2 years ago

Thanks this does look interesting. If I search for BA.5.2 + ORF1b:1050N and S:444R I get ~400 sequences worldwide and growth advantage over ORF1b:1050N of about 30%/week.

So quite interesting - if it were to acquire something else. It's ~2% in Sweden. So I guess worthy of designation if we can figure out monophyletic branches.

3 sequences from Massachussets with S:R346T edited
oh guys! Now Usher changed its mind and place the whole #1026 as a sublineage if BA.5.2.18. so it is 13 sequences now: Schermata 2022-09-28 alle 00 27 51

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1bfcf_377480.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:A22893G

cov-lineages / pango-designation

BA.5.2 + Orf1b:1050N with S:K444R circulating globally (147 seqs) #1025