Another XBB.1.9.1 sublineage with S:H146K and Orf1b:K1383R circulating in United States and other countries(55 seq)

[Over-There-Is]

XBB.1.9.1> C21998A(S:Q146K)> A3069G(Orf1a:D935G)> 5 nuc saltation: A2647G, C11455T, A17615G(Orf1b:K1383R), G27225A, G27870T(Orf7b:E39*) Query: A2647G, A3069G, A17615G(edited) Earliest Sequence: 03-15 Honolulu, Hawaii, US EPI_ISL_17617365 Latest Sequence: 07-12 San Joaquin, California, US EPI_ISL_18317630 Regions Detected: US 49(California 30, Hawaii 8, Minnesota 4, Ohio 3, Utah 2, S. Dakota 1, Virginia 1), Japan 3(Tokyo 2, Kyoto 1), France 2(Hauts de France), Canada 1(BC)

Genome Tree

Sequences:

EPI_ISL_17423639, EPI_ISL_17429327, EPI_ISL_17430704, EPI_ISL_17508607, EPI_ISL_17526647, EPI_ISL_17526975, EPI_ISL_17536098, EPI_ISL_17536100, EPI_ISL_17538163, EPI_ISL_17556426, EPI_ISL_17558662, EPI_ISL_17585485, EPI_ISL_17589834, EPI_ISL_17617365, EPI_ISL_17627380, EPI_ISL_17631972, EPI_ISL_17644269, EPI_ISL_17653477, EPI_ISL_17677355-17677356, EPI_ISL_17688428, EPI_ISL_17690053, EPI_ISL_17694132, EPI_ISL_17734764, EPI_ISL_17738091, EPI_ISL_17743701, EPI_ISL_17778436, EPI_ISL_17789375, EPI_ISL_17798164, EPI_ISL_17798167-17798169, EPI_ISL_17831761, EPI_ISL_17846948, EPI_ISL_17847095, EPI_ISL_17860860, EPI_ISL_17861017, EPI_ISL_17861138, EPI_ISL_17861145, EPI_ISL_17861481, EPI_ISL_17861490, EPI_ISL_17862611, EPI_ISL_17880097, EPI_ISL_17965952, EPI_ISL_17997694, EPI_ISL_17997794, EPI_ISL_17997986, EPI_ISL_17997997, EPI_ISL_18009329, EPI_ISL_18080855, EPI_ISL_18297724, EPI_ISL_18297761, EPI_ISL_18297773, EPI_ISL_18317630

[Over-There-Is]

Minnesota +1

[JosetteSchoenma]

I mentioned this one here. https://github.com/sars-cov-2-variants/lineage-proposals/issues/97#issuecomment-1562339077

I do not think it is growing fast anymore, but designation (after main branches) might be useful to avoid confusion with the other XBB.1.9.1 alike subbranch with ORF1b:K1383R an S:H146K from issue #2016 (FL.2).

Putting the downsampled Usher tree here, to easily see the difference between the 2 sublineages. I believe @ryhisner looked at the ORF7b:E39* from the XBB.1.9.1/USA (light blue) sublineage.

[Over-There-Is]

Hawaii +1

[Over-There-Is]

Although a "new" sequence EPI_ISL_17759706 is found, it has been submitted for more than a month and actually duplicate to EPI_ISL_17508607.

[JosetteSchoenma]

Indeed, @Over-There-Is . It is probably only useful to designate this one, if the FL.2.3 with H146K gets designated. Just to be able to destinguish between the 2 easily.

[Over-There-Is]

One more sequence hCoV-19/USA/CA-NSYMMPHL-NSYM7420/2023|EPI_ISL_17789375|2023-05-24 can be find with query A2647G, A17615G, G27870T, which was uploaded yesterday.

[Over-There-Is]

But that sequence has too many dropouts.

[Over-There-Is]

25/33 of this sublineage is identified as FL.2 and one identified as FL.9 by GISAID.

[Over-There-Is]

4/33 of this sublineage is identified as FL.2.3 by Nextclade, and 3/30 be done so by CovSpectrum.

[FedeGueli]

No recent samples closing this one