BA.2.75* diversity to watch and designate as soon as phylogeny is clear

[corneliusroemer]

There is quite a lot of relevant Spike diversity in BA.2.75* that we should try to get designated as soon as the phylogeny is clear.

I'm opening this issue to have one place to coordinate these and tick them off as we progress.

The following are known spike mutations of interest that have occurred multiple times in multiple countries in BA.2.75*

• S:574V - Designated as BA.2.75.1 in BA.2.75 sublineage with S:D574V (97+ seq as of 02.08.22; 7 countries) #856
• S:346T on top of BA.2.75: BA.2.75.3 sublineage with S:R346T (35seq, 20xIndia/5xSingapore, also Israel, Belgium, US, as of 2022-08-21) #918
• S:346T on top of BA.2.75.1: Proposal for a Sublineage of BA.2.75.1 with S:R346T [~50 seq on Aug 20, 6x non-India] #944 BA.2.75 sublineage with S:R346T, S:F486S, S:D1199N (17 seq. India, Chile, England, Singapore, Spain, Germany, South Korea, Australia, USA. 2022-08-19) #963
• S:356T BA.2.75 lineage with S:356T [43 seq, 2022-08-19, mostly India with 2x Israel/Singapore, 1x Japan/Germany/Denmark/Australia] #947
• S:452R Potential BA.2.75 sublineage with S:L452R in India, Japan and Austria [40 sequences] #935
• S:486S (occurs at least sometimes together with S:346T) BA.2.75.3 sublineage with S:F486S, ORF1a:Q1198K (23 seq. India, Singapure, Australia, Israel, Belgium, USA. 21.08.22) #957 BA.2.75.3 sublineage with S:R346T (35seq, 20xIndia/5xSingapore, also Israel, Belgium, US, as of 2022-08-21) #918 BA.2.75 sublineage with S:R346T, S:F486S, S:D1199N (17 seq. India, Chile, England, Singapore, Spain, Germany, South Korea, Australia, USA. 2022-08-19) #963
• S:490S (occurs at least sometimes together with S:346T and/or S:486S) BA.2.75.3 sublineage with S:R346T (35seq, 20xIndia/5xSingapore, also Israel, Belgium, US, as of 2022-08-21) #918
• S:519Q
• S:677H
• S:E583D in BA.2.75.1 in Denmark (89seq)
• S:S939F in BA.2.75.1 in Austria, Australia, India (7 seq)

I'll try to link existing issues that discuss the above mutations above. These mutations may have already occurred multiple times independently and/or in a correlated fashion so it's not too easy to sort this out all at one unfortunately.

[FedeGueli]

Thx @corneliusroemer great work i think when epi-conditions change quickly this kind of multiple issues are very useful.
My suggestion is to wait a bit before start designating fast sublineages unless they corresponds to branches starting directly from the politomy. Soon we will see which are the successful branches and where (and if) they are geo located

[agamedilab]

@corneliusroemer many thanks! Maybe #963 could be added to the list? All the best!

[alurqu]

I built an UShER tree based around a few BA.2.75+ORF1a:3959A GenBank samples. UShER put that into 2 different branches from BA.2.75. But just in case others may find it helpful in finding BA.2.75 sublineages, here's the link to the interactive tree: https://nextstrain.org/fetch/github.com/alurqu/pango-designation-support-alurqu/raw/main/subtreeAuspice1_BA.2.75_20220818.json?c=gt-S_574&label=nuc%20mutations:C4586T,A22001G. I've set the initial coloring to highlight the BA.2.75.1 S:D574V mutation.

Of course, as more data comes in the UShER tree may evolve and shift. Please note that I did include the date in the file name, so I plan for this tree should remain as a record of the UShER tree produced today. As the tree evolves with new data, it may be appropriate to post a new version of the tree.

Edit: Corrected grammar.

[corneliusroemer]

We've figured BA.2.75 out now, so this can be closed.