Proposed north american sublineage of B.1.617.2 with S:V289I , Orf1ab E1633D E1633D and N:G18V

[FedeGueli]

Proposal of a sublineage of Delta with: Orf1ab: E1633D, N:G18V , S:V289I 18000 sequences mainly in USA it reached 6% in Florida and it was circulating in the caribbean area https://outbreak.info/situation-reports?pango=B.1.617.2&muts=S%3AV289I&loc=USA&loc=USA_US-CA&selected=Worldwide&overlay=false

It seems to have now a trasmission disadvantage (2-3%) on the other circulating strains according to: https://cov-spectrum.ethz.ch/explore/United%20States/AllSamples/AllTimes/variants/json=%7B%22variant%22%3A%7B%22name%22%3A%22B.1.617.2%22%2C%22mutations%22%3A[%22S%3A289I%22]%7D%2C%22matchPercentage%22%3A1%7D

But it deserves to be designated to monitor diversity in Delta and it could help to avoid misassignements

https://nextstrain.org/ncov/gisaid/global?branchLabel=aa&c=gt-S_289&d=tree,entropy,frequencies&f_region=North%20America&p=full&tl=pango_lineage

[corneliusroemer]

I support this proposal.

It's clearly related to single outbreak in US, centered on Florida where it reached 15% in June 2021.

Overall in the US it reached 4% and is now still at 2%. It's not really got big anywhere else in the world.

Here are frequency plots from covSPECTRUM and a link: https://cov-spectrum.ethz.ch/explore/United%20States/AllSamples/Past6M/variants/json=%7B%22variant%22%3A%7B%22name%22%3A%22B.1.617.2*%22%2C%22mutations%22%3A[%22S%3A222V%22%2C%22S%3A289I%22]%7D%2C%22matchPercentage%22%3A1%7D

This is what a US-focused tree looks like within 21I, the cluster is nice and distinct:

https://nextstrain.org/groups/neherlab/ncov/north-america?branchLabel=spike_mutations&c=gt-S_289&label=clade:21I%20%28Delta%29&tl=S1_mutations

Here's a country count including first observation, it's 19k in US and never more than 100 in any other country.

Country | Total Variant Sequences | First seq. found at | Last seq. found at |   -- | -- | -- | -- | -- Argentina | 13 | 2021-29 | 2021-35 |   Austria | 2 | 2021-28 | 2021-28 |   Belgium | 1 | 2021-32 | 2021-32 |   Brazil | 5 | 2021-30 | 2021-37 |   Bulgaria | 2 | 2021-29 | 2021-29 |   Canada | 14 | 2021-29 | 2021-35 |   Chile | 4 | 2021-31 | 2021-33 |   Colombia | 2 | 2021-31 | 2021-34 |   Costa Rica | 1 | 2021-32 | 2021-32 |   Croatia | 3 | 2021-32 | 2021-32 |   Denmark | 5 | 2021-31 | 2021-34 |   France | 1 | 2021-33 | 2021-33 |   Germany | 13 | 2021-29 | 2021-40 |   Iceland | 12 | 2021-30 | 2021-33 |   Israel | 3 | 2021-26 | 2021-31 |   Italy | 3 | 2021-34 | 2021-40 |   Japan | 7 | 2021-30 | 2021-36 |   Mexico | 13 | 2021-29 | 2021-38 |   Netherlands | 13 | 2021-28 | 2021-38 |   Peru | 5 | 2021-32 | 2021-36 |   Poland | 5 | 2021-34 | 2021-36 |   Portugal | 4 | 2021-32 | 2021-39 |   South Africa | 1 | 2021-31 | 2021-31 |   South Korea | 1 | 2021-35 | 2021-35 |   Sweden | 3 | 2021-29 | 2021-33 |   Switzerland | 1 | 2021-33 | 2021-33 |   United Kingdom | 60 | 2021-29 | 2021-40 |   United States | 18954 | 2021-17 | 2021-40

[chrisruis]

Thanks @FedeGueli We've added this as AY.47 in v1.2.88 and started the lineage on a branch with C12049T (synonymous) which coincides with the introduction(s) into the USA. AY.47 has 3287 sequence designations