XBB.2.3.3 with Orf8:E106Q and Orf1a:I4205V (100 seqs) likely at high prevalence recently in Philippines and been caught in airport surveillance of multiple countries very recently.

[FedeGueli]

I was digging a bit in international sequences labelled as travel related with Philippines when i was hit by this tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3e2da_944300.json?f_userOrOld=uploaded%20sample&label=id:node_8742768

It is self evident also at a first glance that Airport surveillance sequences are over-represented And this become clearer searching on Gisaid the related query A12878G,A12878G, C19884T,A22108T that finds 40 samples : 13 of them are selected inputing Airport and 4 more inputing Travel and 1 more inputing From

Interesting if the input is Philippines 5 out of these 18 of the international caught subgroup are found.

Interestingly if i set Philippines as free keyword on Gisaid querying for samples collected after May 1 i found that 3 out of 20 belong to this sublineage.

My guess is that this sublineage is likely one of the driver of the ongoing wave in Philippines or at least in a part of them.

Defining mutations: XBB.2.3.3 >> > C19884T > Orf8:E106Q (G28209C) >Orf1a:I4205V (A12878G NSP9_I65V)

Sequences: 40 ( 33 of them collected after April 15)

EPI_ISL_17229375, EPI_ISL_17229385, EPI_ISL_17445773, EPI_ISL_17467001, EPI_ISL_17481607, EPI_ISL_17547991, EPI_ISL_17561122, EPI_ISL_17562684, EPI_ISL_17595387, EPI_ISL_17595440, EPI_ISL_17595751, EPI_ISL_17605927, EPI_ISL_17618291, EPI_ISL_17619271, EPI_ISL_17626015, EPI_ISL_17626024, EPI_ISL_17626056, EPI_ISL_17639663, EPI_ISL_17645754, EPI_ISL_17646198, EPI_ISL_17646711, EPI_ISL_17646745, EPI_ISL_17646748, EPI_ISL_17646798, EPI_ISL_17646825, EPI_ISL_17646831, EPI_ISL_17652332, EPI_ISL_17656571, EPI_ISL_17656696, EPI_ISL_17663891, EPI_ISL_17669104, EPI_ISL_17676346, EPI_ISL_17680601, EPI_ISL_17683134, EPI_ISL_17686338, EPI_ISL_17689325-17689327, EPI_ISL_17689335, EPI_ISL_17689522

Complete tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3e2da_944300.json?c=country&label=id:node_8742769

Looking at the tree this sublineage clearly splitted in two main branches the first defined by Orf1b:V1110I and the bottom one by a mini saltation the infamous AY.4.2 mutation S:A222V plus N:R319H plus Orf1a:V1915I

[xz-keg]

It would be best if usher and cov-spectrum can display original country for travel-related seqs. There's limited formats so can be automated.

Currently there seems no way other than checking every single seq manually, which is very inconvenient.

[ryhisner]

This has split into two major branches. The ORF1b:V1110I branch (on top in the tree below) seems to be spreading faster, primarily in China. Lots of long branches here, which likely indicates transmission in an under-sampled area (like the Philippines or remote area of China).

There are 86 sequences on GISAID, but close to 10 of those are pooled samples from Gingko Bioworks, who somehow got the US contract to do airport surveillance sequencing despite consistently shoddy sequencing and repeated violation of basic rules (like "don't upload pooled samples to GISAID"). Maybe some politician's brother-in-law runs the company? Ginkgo Bioworks received a $1.1 billion load from the US government for "COVID-19 testing and the production of raw materials for therapies that may help address future pandemics." With >$1 billion in funding, you'd think they could produce adequate sequences. Not so. Their sequences are consistently bad, and they apparently don't care enough to invest in making them better. https://www.reuters.com/article/us-health-coronavirus-loan-ginkgo-idCAKBN2851TA

[FedeGueli]

Thx a lot @ryhisner ! it quite doubled to 79 , Landing in Italy and Switzerland too.

cc @corneliusroemer @InfrPopGen @thomaspeacock for the reason in the Ryan' comment above and in the original post i suggest a rapid review of this one even if it lacks any spike mutation in comparison to parental XBB.2.3.3.

[FedeGueli]

@corneliusroemer already two sublineage of this one discovered indepently and preproposed i think it should deserve a designation even if it has no spike mutations

[FedeGueli]

12 seqs uploaded in the last 2 days total count is 100 now. 2 more sequences caught by international airport surveillance travel related with Philippines (total 8 out of 100), representing 6 out of 54 samples uploaded to Gisaid with any link to Philippines as keyword. i suggest a rapid review @corneliusroemer @InfrPopGen

[InfrPopGen]

Thanks for submitting. We've added lineage GJ.1 with 43 newly designated sequences, and 2 updated. Defining mutation A12878G (ORF1a:I4205V) (following G28209C (ORF8:E106Q)).

[FedeGueli]

Thank you very much fopr your work @InfrPopGen

[HynnSpylor]

Just today New Zealand updated one more seq of the mini-saltation branch (with S:A222V, S:R357T and several non-Spike mutation).

It may be worth further tracking.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2dabe_a07e90.json?c=gt-S_222,357

-addition: 3 South Korean seqs, 1 other New Zealand seq and 1 Italy seq on the mini-saltation branch (without S:R357T) are also updated. Now the saltation branch reaches 25!