New BA.5.2+Orf1b:1050N sublineage with 27012T + S:346T (157 sequences)

[FedeGueli]

There is a sublineage budding off from BA.5.2 + orf1a:1050N +27012T with S:346T that shows some well defined diversity
48 sequences 14 countries (among them Czechia 5 seqs) 4 continents

Usher tree link:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_2280e_d86a00.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:G22599C

CovSpectrum: https://cov-spectrum.org/explore/World/AllSamples/Past2M/variants?%5D%28https%3A%2F%2Fcov-spectrum.org%2Fexplore%2FWorld%2FAllSamples%2FPast3M%2Fvariants%3FaaMutations=S%3AR346T%2Corf1b%3A1050N&%29=&variantQuery=NextCladePangoLineage%3ABA.5.2+%26+S%3AR346T++%26++13136A+%26+27012T+&aaMutations1=S%3AR346T%2COrf3a%3AR68G&nucMutations1=C26681T&variantQuery1=NextCladePangoLineage%3ABA.5.2+%26+S%3AR346T+&
Sequences:
contributors (1).csv

Originally posted by @FedeGueli in #865 (comment)

Edited: i dont think that any growth advantage can be reliable here cause every country seems to have its own well defined branch

[FedeGueli]

CC @AngieHinrichs i was looking at he usher tree of this sublineage: in the global subsampled tree
(https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_115a2_6bf4b0.json?branchLabel=nuc%20mutations&c=pango_lineage_usher&label=nuc%20mutations:T76A,T78G,A11537G,G22599C)

There it is divided in 3 branches:

While the "italian branch with two mutations at the start of Orf1a is a bit suspicious and i would take it out of the discussion:
(https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice3_genome_115a2_6bf4a0.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:T78G)

the other one defined by:BA.5.2+Or1a:1050N+C27513T+C27012T +13624T+Orf1a:I4291V+S:346T
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_115a2_6bf4a0.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:C13264T

i dont think it is well supported to be distinct ( it is due only to the presence of France/OCC-GENBIO-C41GN1920046/2022|EPI_ISL_13986108|2022-07-11).

[AngieHinrichs]

the other one defined by:BA.5.2+Or1a:1050N+C27513T+C27012T +13624T+Orf1a:I4291V+S:346T
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_115a2_6bf4a0.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:C13264T

i dont think it is well supported to be distinct ( it is due only to the presence of France/OCC-GENBIO-C41GN1920046/2022|EPI_ISL_13986108|2022-07-11).

That little cluster with C13264T also has A13136G/ORF1a:I4291V -- see subtree 2:

So although OCC-GENBIO-C41GN1920046 is the only sequence that has C13264T before G22599C/S:R346T, there are ~1000 BA.5.2 sequences that have C16616A/Orf1b:1050N, C27513T, C27012T and A13136G (like that little cluster) but not G22599C/S:R346T (and C13264T).

[FedeGueli]

Ok thank you very much @AngieHinrichs so this one is different from.the proposed here, and it emerged independently from the C16616A/Orf1b:1050N, C27513T, C27012T and A13136G branch of BA.5.2.

So i'll.monitor separately and i will take that in account for covspectrum queries. Thx vm very precious help!

[FedeGueli]

63 seqs as today and 15 countries
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_26cd3_eeb6b0.json?branchLabel=aa%20mutations&c=gt-nuc_27012&label=nuc%20mutations:G22599C

[FedeGueli]

103 seqs as today

Growth advantage versus parental Orf1b:1050N in Usa:
https://cov-spectrum.org/explore/United%20States/AllSamples/Past3M/variants?variantQuery=NextCladePangoLineage%3ABA.5.2*+%26++orf1b%3A1050N++&variantQuery1=NextCladePangoLineage%3ABA.5.2+%26+S%3AR346T+%26+Orf1b%3A1050N+%26+27012T++%26+13136A+&analysisMode=CompareToBaseline&

@InfrPopGen @corneliusroemer

[FedeGueli]

136 sequences as today: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=NextCladePangoLineage%3ABA.5.2+%26+S%3AR346T+%26+Orf1b%3A1050N+%26+27012T++%26+13136A+&variantQuery1=NextCladePangoLineage%3ABA.5.2*+%26++orf1b%3A1050N++&

[FedeGueli]

157 on Usher it is growing vey fast i think a designation could help in tracking this one. @InfrPopGen @corneliusroemer

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_e5d6_244230.json?branchLabel=aa%20mutations&label=nuc%20mutations:G22599C

[FedeGueli]

CC @shay671 there is a new sublineage of this with NSP14_V14L(orf1b:V1538L) spreading in Israel that now counts 19 sequences on Gisaid (Spike_R346T,NSP14_v14L,NSP13_T127N,) all very recent.
20 displayed on Usher and 7 on Covspectrum:

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=S%3AR346T+%26+orf1b%3A1050N+%26+27012T+%26+13136A%26+orf1b%3AV1538L&variantQuery1=NextCladePangoLineage%3ABA.5.2*+%26+orf1b%3A1050N&

It seems to have a large advantage over the fastest BA.5 (orf1b:1050N)

https://cov-spectrum.org/explore/Israel/AllSamples/Past2M/variants?variantQuery=NextCladePangoLineage%3ABA.5.2*+%26+orf1b%3A1050N&variantQuery1=S%3AR346T+%26+orf1b%3A1050N+%26+27012T+%26+13136A%26+orf1b%3AV1538L&analysisMode=CompareToBaseline&