BA.2.3 Saltation lineage with several mutations (inc Spike R346T, Y449N, N460K, N481K and Q493L) from Philippines and Australia

[thomasppeacock]

New proposed lineage By Tom Peacock

Description Sub-lineage of: BA.2.3 Earliest Sequence: 2022-09-07 Latest Sequence: 2022-10-3

Countries circulating: Philippines (7 genomes), Australia (2 genomes)

Description: Additional Spike mutations - P9L, Δ69-70, Δ144, V213E, G339N, R346T, Y449N, N460K, N481K, Q493L, K1205N Additional non-Spike mutations - NSP4 – A146V Synonymous mutations - T17901C, A28877T, G28878C

This appears to be yet another BA.2 saltation lineage (second generation BA.2) similar to BA.2.75, BJ.1, etc

Genomes: EPI_ISL_15343178 EPI_ISL_15343197 EPI_ISL_15625844 EPI_ISL_15627678 EPI_ISL_15628269 EPI_ISL_15628276 EPI_ISL_15628277 EPI_ISL_15628290 EPI_ISL_15628301

Evidence:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_384c3_3d2810.json

Proposed lineage name: BA.2.3.x?

[MCB6]

In August, there was EPI_ISL_15625370 with N460K and 144del but without R346T in the same area of Western Visayas. BTW in the admittedly few October samples the new BA.2.3.x jumped to 30% there

[MCB6]

The actual time course:

[cvejris]

This lovely lineage has double nucleotide changes at three Spike AAs. The order of mutations (wt→BA.2→this): 213: V→G→E 339: G→D→N 493: Q→R→L Among all designed BA.2 lineages, 3 DNCs are present only in XBB.1.3

[AngieHinrichs]

With the latest tree these are placed in BA.2.3.21 (BA.2.3 > C21588T/S:P9L).

[AngieHinrichs]

https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~angie/pango-designation-1287.json?c=pango_lineage_usher&label=nuc%20mutations:C21588T

Australia/QLD0x011A1E/2022 and Australia/QLD0x0119E2/2022 are in the tree (in BA.2.3.21); the extra "N:S202C, N:S202T" branches are because the sequences have A28877T and G28878C which are masked after placement in the Omicron branch of the big tree (homoplasic -> tree problems), but they are not masked in the web interface.

[cvejris]

edited: BA.2.3 has given rise to four saltations

[corneliusroemer]

Why do you say it's a minor lineage? It was the major BA.2 in Asia...

[cvejris]

Oops, I forgot to turn off the time limit for last 3 months at CovSpectrum. Thanks for reminding me! Still, the level of saltation in BA.2.3 is impressive

[FedeGueli]

Spike_G339N,Spike_Q493L

[ryhisner]

One of these showed up in USA, Michigan; Collection date September 27 — EPI_ISL_15702572

[aretchless]

@AngieHinrichs - Thanks for putting this lineage into Usher. I just looked at the Usher website to see the sequences mentioned above, and noticed that only the Australian samples were marked as DD.1 (Philippines samples were BA.2.3.21). Is that intended, or does the Usher tree still need to be updated? This is using the larger tree with 12,858,653 genomes that is dated 2022-11-07 ("sarscov2phylo 13-11-20 tree with newer sequences added by UShER")

[AngieHinrichs]

Thanks for pointing that out @aretchless! Yep, I need to move that label back. Should be fixed in the 2022-11-09 tree, which should become available a little after 7pm Pacific time.

[aretchless]

Thanks @AngieHinrichs