BA.2.9 sublineage with ORF9b:P51L (40% in Poland, common around Europe, 6k seq)

[corneliusroemer]

Another prominent amino acid mutation in BA.2.9 seems to be ORF9b:P51L which is particularly wide spread in Poland where it makes up around half of all BA.2

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=ORF9b%3AP51L&pangoLineage=BA.2*&aaMutations1=ORF9b%3AP51L&pangoLineage1=BA.2*

[chrisruis]

Thanks @corneliusroemer As outlined here, new Pango lineages need to be associated with both an evolutionary event and an epidemiological event. These epidemiological events can include movement of the virus into a new geographical region, rapid and sustained growth in frequency compared to other co-circulating lineages, a jump into a novel host species and acquisition of a set of mutations of particular biological interest. Pango lineages therefore track more than just amino acid mutations

This is the UShER tree for this clade coloured by country:

There doesn't seem to be a clear epidemiological event associated with this clade. As it's widespread elsewhere, the high frequency in Poland isn't sufficient to constitute an epidemiological event in this case. We therefore haven't designated this at this point

[FedeGueli]

I noticed that there are three sequences from Peru' too :

EPI_ISL_11815638
EPI_ISL_11897939
EPI_ISL_11627925

It would be interesting to know from @Wen1953 if they are from random sampling or from airport surveillance: in the case they are from random surveillance it would be of great relevance.
In one only week (12) we have seen (8) sequences of this sublineage popping up in Brazil, Curacao, Costa Rica, Bonaire suggesting its spread in the Central/Southern America area where it reached 3,2% as share of total sequences in South America.

In the last month it has been over 1% of sequences in three continents ( Europe, North America, South America) and 0,80% in Asia.
This lineage is circulating in four continents,
and even if after week 13 it doesn't seem to have been sampled in new countries ( last one: Slovenia), has to be noticed that 20 out of 27 countries, which have sampled this lineage earlier in week 9, still had sequences of it sampled in week 14 and 15 , suggesting ongoing transmission rather than further importations.

cc @corneliusroemer @chrisruis please take a 3rd look at this one.

https://cov-spectrum.org/explore/South%20America/AllSamples/from=2022-03-20&to=2022-04-22/variants?aaMutations=Orf9b%3A51L&pangoLineage=BA.2*&aaMutations1=Orf9b%3A51L&pangoLineage1=BA.2.9*&

[OrsonMM]

Hi. @FedeGueli

We can check metadata related to genomes. They are from random surveillance but EPI_ISL_11627925 and EPI_ISL_11897939 correspond to the same patient. and the cases are probably from the same family from Lima.
BA.2 in Peru is recent growing respect to BA.1 and BA.1.1.

[FedeGueli]

Thank you very much @OrsonMM !
@chrisruis could this new update meet the designation criteria of an introduction (and circulation) in a new geographical area?

[FedeGueli]

This sublineage reached more than 12k sequences