EG.5.1.1 with ORF8:A65V and S:L455F (224 seqs, 13 countries) further gained S:A348S (54 seqs, 4 countries)

[NkRMnZr]

Taken from Branch 15 of multitask sars-cov-2-variants/lineage-proposals#537

Defining Mutations: EG.5.1.1 > C28087T(ORF8:A65V) > G22927T(S:L455F) , mostly with further C8982A(ORF1a:T2906N/nsp4_T143N), T19710C, C27213T sub-branch Query: C6541T, G22927T, C28087T, -A4306G, -G4444A, -A6889G, -G8171A, -T8305C, -C10039T, -C19185T, -C25207T OR C8982A, T19710C if only count the major ORF1a:T2906N sub-branch

Defining Mutations for further S:A348S sub-branch: Main proposal > C8982A(ORF1a:T2906N), T19710C, C27213T > G1067T(ORF1a:G268W) > G22604T(S:A348S) Query for further S:A348S sub-branch: G1067T, C8982A, G22604T

Earliest seq: 2023-08-10 (EPI_ISL_18138246, Shanghai) Latest seq: 2023-10-11 (EPI_ISL_18397348, Singapore) Sampled Countries: Singapore (39), China (16: SH/6; SC/3; QH/2; HA; HB; HL; LN; SX), Japan (6), South Korea (5), Belgium (2), Canada (2: AB; ON), Australia (1: NSW), Austria (1), USA (1: AZ)

Genomes:

`EPI_ISL_18138040, EPI_ISL_18138246, EPI_ISL_18208534, EPI_ISL_18213338, EPI_ISL_18243416, EPI_ISL_18284693, EPI_ISL_18284883, EPI_ISL_18284945, EPI_ISL_18285015, EPI_ISL_18285039, EPI_ISL_18289913, EPI_ISL_18292661, EPI_ISL_18312855, EPI_ISL_18313044, EPI_ISL_18313125, EPI_ISL_18313232, EPI_ISL_18320677, EPI_ISL_18320703, EPI_ISL_18324382, EPI_ISL_18324868, EPI_ISL_18346119, EPI_ISL_18354784, EPI_ISL_18354968, EPI_ISL_18354976, EPI_ISL_18355029, EPI_ISL_18361857, EPI_ISL_18361924, EPI_ISL_18361928, EPI_ISL_18361967, EPI_ISL_18362004, EPI_ISL_18362012, EPI_ISL_18362042, EPI_ISL_18362056, EPI_ISL_18362082, EPI_ISL_18372524, EPI_ISL_18376804, EPI_ISL_18376810, EPI_ISL_18376814, EPI_ISL_18376830, EPI_ISL_18376851, EPI_ISL_18376867, EPI_ISL_18376933, EPI_ISL_18379403, EPI_ISL_18382112, EPI_ISL_18382725, EPI_ISL_18384400, EPI_ISL_18385457, EPI_ISL_18385461, EPI_ISL_18397250, EPI_ISL_18397275, EPI_ISL_18397308, EPI_ISL_18397326, EPI_ISL_18397348, EPI_ISL_18397352, EPI_ISL_18397366, EPI_ISL_18397371, EPI_ISL_18397408, EPI_ISL_18397428, EPI_ISL_18397446, EPI_ISL_18397456, EPI_ISL_18397463, EPI_ISL_18397524, EPI_ISL_18397532, EPI_ISL_18397540, EPI_ISL_18397553, EPI_ISL_18397602, EPI_ISL_18397623, EPI_ISL_18402854, EPI_ISL_18406266, EPI_ISL_18408689, EPI_ISL_18409307, EPI_ISL_18411310, EPI_ISL_18411340`

UShER: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_28cd5_2dbad0.json?f_userOrOld=uploaded%20sample&label=id:node_3458668

[FedeGueli]

Being Orf8:A65V a known messy homoplasic mutation we could decide to start it deeper with Orf1a:T2906N cc @corneliusroemer @NkRMnZr

[FedeGueli]

103 now , It is going fast in Singapore.

[NkRMnZr]

Tracking updates:

10-26, 35 seqs from Canada, China, Denmark, Japan, Russia, Singapore, and Slovenia

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_210b4_9d9610.json?f_userOrOld=uploaded%20sample&label=id:node_3469844  `EPI_ISL_18415930, EPI_ISL_18416722, EPI_ISL_18417304, EPI_ISL_18417692, EPI_ISL_18419695, EPI_ISL_18425084, EPI_ISL_18425101, EPI_ISL_18425113, EPI_ISL_18426835, EPI_ISL_18427092, EPI_ISL_18428518, EPI_ISL_18428521, EPI_ISL_18428531, EPI_ISL_18428541, EPI_ISL_18428547-18428548, EPI_ISL_18428550, EPI_ISL_18428565, EPI_ISL_18428577, EPI_ISL_18428583, EPI_ISL_18428627, EPI_ISL_18428629, EPI_ISL_18428686, EPI_ISL_18428689, EPI_ISL_18428704, EPI_ISL_18428709, EPI_ISL_18428719, EPI_ISL_18428739, EPI_ISL_18428753, EPI_ISL_18433181, EPI_ISL_18434927, EPI_ISL_18434937-18434938, EPI_ISL_18434941-18434942`

11-06, 43 seqs from Canada, China, Japan, S. Korea, and Singapore

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1bafc_894410.json?f_userOrOld=uploaded%20sample&label=id:node_3489495  `EPI_ISL_18435255, EPI_ISL_18435465, EPI_ISL_18438078, EPI_ISL_18444967, EPI_ISL_18444970, EPI_ISL_18444973, EPI_ISL_18444990, EPI_ISL_18445034, EPI_ISL_18445040, EPI_ISL_18445062, EPI_ISL_18445081, EPI_ISL_18445087, EPI_ISL_18445135, EPI_ISL_18445139, EPI_ISL_18445144, EPI_ISL_18447778, EPI_ISL_18448262, EPI_ISL_18448524-18448525, EPI_ISL_18448595, EPI_ISL_18448711, EPI_ISL_18448745, EPI_ISL_18448748-18448749, EPI_ISL_18448754, EPI_ISL_18448757-18448763, EPI_ISL_18454396, EPI_ISL_18460656, EPI_ISL_18460678, EPI_ISL_18460998, EPI_ISL_18461169, EPI_ISL_18464988, EPI_ISL_18465009, EPI_ISL_18465015, EPI_ISL_18465121, EPI_ISL_18465123, EPI_ISL_18465144, EPI_ISL_18465863, EPI_ISL_18466215`

11-08, 40 seqs from Canada, China, Japan, Singapore and Spain

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_adfd_b8bd70.json?f_userOrOld=uploaded%20sample&label=id:node_3489818  `EPI_ISL_18471246, EPI_ISL_18471249, EPI_ISL_18471253-18471260, EPI_ISL_18471338, EPI_ISL_18471526, EPI_ISL_18471545, EPI_ISL_18471723, EPI_ISL_18471755, EPI_ISL_18471758, EPI_ISL_18471761-18471762, EPI_ISL_18471768, EPI_ISL_18472089, EPI_ISL_18472169, EPI_ISL_18472183, EPI_ISL_18472870, EPI_ISL_18473385, EPI_ISL_18473469, EPI_ISL_18473473, EPI_ISL_18473482, EPI_ISL_18473489, EPI_ISL_18473497, EPI_ISL_18473505, EPI_ISL_18473549, EPI_ISL_18473575, EPI_ISL_18473588, EPI_ISL_18473596, EPI_ISL_18473641, EPI_ISL_18473698, EPI_ISL_18475198, EPI_ISL_18475312, EPI_ISL_18475324, EPI_ISL_18475532`

11-18, 31 seqs from Australia, Canada, China, Denmark, Japan, South Korea, Spain

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3be0f_a3fe40.json?f_userOrOld=uploaded%20sample&label=id:node_3484840  `EPI_ISL_18481019, EPI_ISL_18481052, EPI_ISL_18495034, EPI_ISL_18495788, EPI_ISL_18496167, EPI_ISL_18496952, EPI_ISL_18496980, EPI_ISL_18503563, EPI_ISL_18503767, EPI_ISL_18504347, EPI_ISL_18504552, EPI_ISL_18504562, EPI_ISL_18504623, EPI_ISL_18504911, EPI_ISL_18504915, EPI_ISL_18505038, EPI_ISL_18505052, EPI_ISL_18505233, EPI_ISL_18505245, EPI_ISL_18505247, EPI_ISL_18508182, EPI_ISL_18508508, EPI_ISL_18508513, EPI_ISL_18511212, EPI_ISL_18511462, EPI_ISL_18511554, EPI_ISL_18513007, EPI_ISL_18513560, EPI_ISL_18513741, EPI_ISL_18513750, EPI_ISL_18518360`

[NkRMnZr]

The S:A348S/G22604T sub-branch exploded, phylogenetic order follows: Main proposal > C8982A(ORF1a:T2906N), T19710C, C27213T > G1067T(ORF1a:G268W) > G22604T(S:A348S), query: G1067T, C8982A, G22604T

[FedeGueli]

Thx @NkRMnZr good catch on 348S. I noticed two JG.3 in Singapore with S:A348 mutated too, we should monitor if it is nt a possible new pathway fro FLIP to evolve further.

About the growth of this one, it is in some long term care hospice in Canada lets see if it goes well outside that.

[FedeGueli]

India not Singapore.

[FedeGueli]

the 348S branch is doubling in 7 days well below the HK.3 & alike doubling time @corneliusroemer i suggest designation of this one

[FedeGueli]

257 as today subbranch with S:A348S at 63. one of the fastest flip but slower than JG.3

[NkRMnZr]

Designated as three levels: HK.23, HK.23.1 and HK.23.1.1