Large sublineage of BA.2 with Orf3a:H78Y (10000+ Sequences) circulating in Europe and globally

[FedeGueli]

As noted first by @shay671 long ago and recently by @bitbyte2015 in #390 and re highlighted today by Josette Shoenmakers and by Staten Serum Institute in their report: "Ugentlige tendenser: covid-19 og andre luftvejsinfektioner Uge 6 | 2022" at Pag.21

There is a clear large subclade of BA.2 defined by Orf3a:H78Y circulating in Europe. It represents around 4% of all sequences of the last three weeks in Europe and 3,5% globally.

Number of sequences: 10598 List of Sequences: contributors (4).csv First sequence: 49/2021 Denmark Country circulating: Denmark ( 9000+ seqs) Sweden (500+ seqs) It has been sequenced in 4 continents: Europe, Asia, Oceania, North America,Central&South America

In comparison to BA.2 baseline [Its relative growth advantage is estimated in 6%(CI:5%-7%](https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?pangoLineage=BA.2&aaMutations1=Orf3a%3AH78Y&pangoLineage1=BA.2*&analysisMode=CompareToBaseline) It means a +65% relative growth advantage against BA.1

It is self evident in the Neherlab tree fro denmark

[RajLABN]

orf3a:H78Y is found in several BA.1 and BA.1.1 sequences as well.

omicron w/ orf3H78Y mutation in Denmark -9559 sequences [BA.2 (99.93%); BA.1 (0.05%); BA.1.1 (0.02%)] UK - 385 sequences [ BA.2 (62.08%); BA.1 (24.42%); BA.1.1 (13.51%)] USA - 141 sequences [BA.1 (60.28%); BA.1.1 (31.91%); BA.2 (7.80%)]

[silcn]

Not clear what this mutation does, but it appeared on top of many different Delta lineages and may have had a very slight transmission advantage. This may be why SSI chose to single out this lineage despite the lack of an obvious growth advantage on a BA.2 background (yes, cov-spectrum gives a 5-7% advantage, but its claims of small advantages should be taken with a pinch of salt, recall AY.33 last year).

[corneliusroemer]

This is a sub-lineage of the lineage proposed in #390

So that issue should be resolved first, then this one here, since otherwise we're getting into trouble with renaming.

I think I am still in favour of #390 defining a lineage of its own, because it is very clearly associated with the growth of BA.2 in Denmark and spread from there to neighbouring countries (Sweden, Germany, ...). About 60% of all global BA.2 sequences have nuc:C22792T, however, this is largely because Denmark (and Germany and Sweden) sequence so much and BA.2 is very common there.

This lineage is very uncommon outside of Central/Northern Europe. The ORF3a:78Y mutation appeared within that lineage, but makes up only 25% of the lineage proposed here.

Furthermore, the ORF3a mutation does not seem to provide any further growth advantage. Neither in Denmark, nor globally.

So overall, I think it's better to designate this lineage in #390, not the ORF3a:78Y one here for now.

https://cov-spectrum.org/explore/Denmark/AllSamples/Past6M/variants?nucMutations=C22792T&pangoLineage=BA.2&aaMutations1=ORF3a%3A78Y&nucMutations1=C22792T&pangoLineage1=BA.2&analysisMode=CompareToBaseline

[FedeGueli]

Ok @corneliusroemer thank you! i close this one waiting for when #390 would be resolved. Sorry i hurried up a bit it after seeing growing % in the SSI. Ready to re-open if requested or something new will pop up.

[beansrowning]

FYI, from SSI (https://files.ssi.dk/covid19/tendensrapport/rapport/ugentlige-tendenser-covid19-andre-luftvejs-uge7-2022-5l9s)

[corneliusroemer]

Since #390 won't be designated, it makes sense to designate this one here

Is it clean on the Usher tree @AngieHinrichs @chrisruis?

[chrisruis]

Thanks @FedeGueli We've added this as BA.2.9 in v1.2.140