XBB.1.16.11 sublineage with S:K182N (193 seqs in 21 countries)

[HynnSpylor]

Defining mutations: XBB.1.16.11>T25496A (ORF3a:I35K)>C14925T>C26151T>A5553G (ORF1a:K1763R = PLPro_K200R)>C1722T (ORF1a:A486V), A22108C (S:K182N)

GISAID query: A5553G, A22108C, T25496A Earliest seq: 2023-07-24 (Shanghai, China- EPI_ISL_18074407) Most recent seq: 2023-08-22 (SC, US- EPI_ISL_18163113) Countries detected: US (3), UK (3), Bhutan (2), China (1), India (1), Australia (1), Nepal (1)

Usher Tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3bbd0_efea10.json?c=gt-S_182

Notice that the Nepal seq was detected in US International Airport, while Nepal and Bhutan are bordered with India with more contract. Maybe it originated in the north of South Asia subcontinent then spread internationally.

Genomes: EPI_ISL_18074407, EPI_ISL_18093859, EPI_ISL_18120302, EPI_ISL_18124857, EPI_ISL_18124884, EPI_ISL_18135069, EPI_ISL_18142437, EPI_ISL_18145484, EPI_ISL_18161253-18161254, EPI_ISL_18161452, EPI_ISL_18163113

[FedeGueli]

Nice catch very similar to XBB.2.3.3 (182-521) that turned to be the fastest branch of XBB.2.3 , but with 478R.

Note also that Orf1a:K1763R is NSP3_K945R and PLPro_K200R . We should track this one closely. Lets see how many days it takes to double to 25

[FedeGueli]

This seems as fast as FLip lineage propose immediately please.

[FedeGueli]

26 Seqs

[FedeGueli]

40 now. it has slowed down in comparison to HK.3 still in the very high range of lineages without 456/flip 👍 https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=A5553G%2CA22108C%2CT25496A&analysisMode=CompareToBaseline&

please propose it.

[FedeGueli]

74 now No chance to compete :https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=A5553G%2CA22108C%2CT25496A&analysisMode=CompareToBaseline&

[FedeGueli]

This showed up in 4 samples from India (2 with S:T572I) and it is still circulating quite widely, better to track it for a bit more

[xz-keg]

This showed up in 4 samples from India (2 with S:T572I) and it is still circulating quite widely, better to track it for a bit more

The 2 are recombinant of BA.2.86

[FedeGueli]

This showed up in 4 samples from India (2 with S:T572I) and it is still circulating quite widely, better to track it for a bit more

The 2 are recombinant of BA.2.86

dunno think so i think contam is more likely

[FedeGueli]

183. now

[FedeGueli]

192 please propose it.

[FedeGueli]

Not sampled since early Jan, closing it