Potential BA.2 sublineage with Spike Y248S and N450D (94 sequences, ~25% prevalence in Kuwait)

[c19850727]

Inspired by #806 I'm to propose another BA.2 sublineage with Spike Y248 change.

It is a sub-branch of an undesignated BA.2 branch with Spike N450D and Nuc C16887T, predominantly found in the US.
Georgraphical distrubution of the parental branch BA.2+S:N450D+C16887T according to cov-spectrum (excluding the sub-branch with S:Y248S) is as follows:

Location	Number of sequences
United States	269
Canada	3
United Kingdom	2
Peru	1
Slovakia	1

I'm not sure if this parental branch needs to be designated first, as it seems it's not growing significantly.

Anyway, georgraphical distrubution of the proposed sub-branch BA.2+S:Y248S+S:N450D+C16887T according to GISAID is as follows:

Location	Number of sequences
Kuwait	36
Israel	14
US	8
India	6
UK	5
Indonesia	4
Germany	4
Australia	3
Belgium	2
Iran	2
Brazil	1
Canada	1
Denmark	1
France	1
Netherland	1
Singapore ex-India	1
Singapore ex-France	1

This potential sublineage seems, according to my rudimentary calculation, to be prevalent in Kuwait: It makes up for ~25% of their latest batch of submissions (36 out of 146), or ~29% of their all sequences sampled since May 2022 (36 out of 126).

Description

Sublineage of: BA.2+S:N450D+nuc C16887T
Earliest sequence: 2022/04/13 (Ireland)
Most recent sequence: 2022/06/20 (Israel, Indonesia and Belgium)
Countries circulating: as shown above
Mutations on top of BA.2: ORF1b:P976S, S:Y248S, S:N450D, nuc C16887T

Evidence

Usher tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_21351_bc2160.json?branchLabel=Spike%20mutations&c=gt-nuc_22910,22305&label=nuc%20mutations:A22910G

Relative growth advantage according to cov-spectrum in recent 2 months, based on only 42 genomes (the remaining 52 genomes were just submitted and will likely be included in cov-spectrum in a few more days):

Genomes:

Y248S+N450D.csv

[FedeGueli]

With that growth advantage it seems could be competitive with BA.5 more sequences needed to be sure of that

[c19850727]

103 sequences as of 2022-06-30.

[FedeGueli]

149 sequences as today.

A branch of this is growing too in India defined by:
S:450D + S:248S
then
orf1a:2016I +orf1b:1416V
It reached 28 seqs from 6 less than one week ago.
and this sublineage has been detected in Singapore, Australia, Israel one sequence each that gives me the idea of travel related samples
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_42338_46cdd0.json?branchLabel=aa%20mutations&c=country&label=nuc%20mutations:C6312T

So if @c19850727 agrees with me i ask the combo designation of both as , for example, BA.2.78 and BA.2.78.1

[c19850727]

hi @FedeGueli no problem at all.
And I also tend to believe that this whole sublineage is from outside of Kuwait.
It popped out in Kuwait around 2022-05-14, and one week later emerged in both Iran and Israel, which, given some geopolitical reasons, seems unlikely to be direct exports from Kuwait, but more likely that some third party is involved.

[FedeGueli]

Thank you @c19850727 !

[chrisruis]

Thanks @c19850727 Due to the geographical focus of this clade in Kuwait and Israel, we've added this as lineage BA.2.79 to start on the branch with C16393T (Orf1b:P976S)