Proposal to designate BA.2.38 sublineage with S:69/70Del, S:71F, S:478R circulating in India (249 seqs)with a sublineage with S:1264L (99seqs) with a cluster of interest with S:144del + S:446S+452Q (40 seqs)

[FedeGueli]

@chrisruis @InfrPopGen this goes on from #814

With this issue i want to propose the BA.2.38 sublineage mentioned already in #814.

This sublineage was first spotted by @zach-hensel and monitored since by the team.

Defining mutations:
BA.2.38 (S:417T)+ NUC: C21622T
then
69/70Del + S:71F
then
S:478R

This set of mutations is common to 108 sequences on Usher tree and it has been sampled in 16 countries and 4 continents:

Today @c19850727 highlighted that there is a subset of 16 sequences carrying an additional spike mutation: S:V1264L that already has been exported to Japan, Usa and Canada (1sequence each):

And tonight i found two sequences of this subset with S:1264L carrying two potential mutations of interest : S:144Del (EDITED: , spptted just today 29/7) S:446S and S:452Q beyond Orf1a:A3357G, ORF1a:F1214I and NUC:C18744T

This last small but potentially concerning clade pushed me to re propose this lineage already discussed in #814 with @chrisruis .

Here Covspectrum (where we can see only 58 sequences due to Gisaid delayed data):
https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=S%3A478R%2CS%3A71F&aaMutations1=ORF1a%3A556K%2CN%3AP364L%2CORF1a%3AD930N%2CORF1a%3AP3504L%2CN%3A136&nucMutations1=A11782G%2C12160A&

This lineage doesnt show any growth advantage over BA.5 but i will expect more sequences to be uploaded soon to understand the trend

[FedeGueli]

119 sequences as today

[FedeGueli]

Hi @chrisruis

This is now showing a 51% growth advantage vs BA.5 in India:
https://cov-spectrum.org/explore/India/AllSamples/Past2M/variants?aaMutations=M%3A3N&nucMutations=12160A&aaMutations1=S%3A417T%2CS%3A71F%2CS%3A478R&analysisMode=CompareToBaseline&

cc @AngieHinrichs @corneliusroemer @InfrPopGen

[silcn]

5 more sequences on @FedeGueli's G446S+L452Q branch turned up today from Maharashtra.

[FedeGueli]

thx @silcn ! 137 seqs as today

Cc: @corneliusroemer @chrisruis looking also at diversity it is showing i suggest a fast designation of this one.

[FedeGueli]

Query updated to NextcladePangoLineage:BA.5* as baseline : +28%

https://cov-spectrum.org/explore/India/AllSamples/Past2M/variants?variantQuery=NextCladePangoLineage%3ABA.5*&aaMutations1=S%3A417T%2CS%3A71F%2CS%3A478R&analysisMode=CompareToBaseline&

@corneliusroemer @chrisruis

[FedeGueli]

As described by me in #814
i want to highlight here too that a sublineage of this sublineage defined by S:V1264L reached 48 sequences and it is showing growth advantage versus BA.2.75 baseline in India:
+25% (CIs -23% - +74% )

https://cov-spectrum.org/explore/India/AllSamples/Past2M/variants?variantQuery=NextCladePangoLineage%3ABA.2.75*&aaMutations1=S%3A417T%2CS%3A71F%2CS%3A478R%2CS%3A1264L&analysisMode=CompareToBaseline&

Although very preliminary and not solid CIs the fact that within the same sublineage with S:1264L there is a clade with S:452Q and S:446S suggests to put this variant under monitoring and to designate the wider parental lineage and its sublineage with S:1264L in my view.

@chrisruis @corneliusroemer @InfrPopGen

[FedeGueli]

The cluster of interest within this sublineage carrying beyond S:1264L further two spike mutations (S:452Q +S:446S )
and two further Orf1ab mutations(Orf1a:3357G + Orf1a:1214I)
grew now at 13 sequences and it has been sampled in WA, USA for the first time.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2e875_295340.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:G25352T

I urge very much @chrisruis @InfrPopGen @corneliusroemer to designate the parental lineage as BA.2.38.X starting with 478R or with S:1264L if that mutation could better correspond with the trespassing the BA.2.75 growth rate and then to put under close watch the sub-sublineage with the double RBM mutation 446+452.