XBB.2.3.14 with ORF1b:T1050I (nsp13_T127I) (92 seqs, 12 countries)

[NkRMnZr]

Defining Mutations: XBB.2.3 > G3259T(ORF1a:Q998H) > C16616T(ORF1b:T1050I) Query: C16616T, G3259T, C23123T Earliest seq: 2023-02-13 [EPI_ISL_17190173, Italy] Latest seq: 2023-06-03 [EPI_ISL_17813120, England] Sampled Countries: France (30, 27/Mainland, Martinique/2, Saint Martin/1), Italy (8), USA (4, all New Jersey), Belgium (3), Canada (3, Ontario/2, Quebec/1), Spain (2, Mainland/1, Canary Islands/1), UK (3, all England), Switzerland (1)

Genomes:

EPI_ISL_17190173, EPI_ISL_17257583, EPI_ISL_17285910, EPI_ISL_17346276, EPI_ISL_17408549, EPI_ISL_17408550, EPI_ISL_17422723, EPI_ISL_17426960, EPI_ISL_17428341, EPI_ISL_17428535, EPI_ISL_17501869, EPI_ISL_17502180, EPI_ISL_17528884, EPI_ISL_17528886, EPI_ISL_17547110, EPI_ISL_17639063, EPI_ISL_17639196, EPI_ISL_17640586, EPI_ISL_17646796, EPI_ISL_17651693, EPI_ISL_17651694, EPI_ISL_17651725, EPI_ISL_17658085, EPI_ISL_17667572, EPI_ISL_17667690, EPI_ISL_17671195, EPI_ISL_17671205, EPI_ISL_17676173, EPI_ISL_17677324, EPI_ISL_17677342, EPI_ISL_17681044, EPI_ISL_17701315, EPI_ISL_17701331, EPI_ISL_17704883, EPI_ISL_17704884, EPI_ISL_17705029, EPI_ISL_17713820, EPI_ISL_17715961, EPI_ISL_17715966, EPI_ISL_17727216, EPI_ISL_17731367, EPI_ISL_17743334, EPI_ISL_17762283, EPI_ISL_17762294, EPI_ISL_17762364, EPI_ISL_17768535, EPI_ISL_17770520, EPI_ISL_17791524, EPI_ISL_17792458, EPI_ISL_17805416, EPI_ISL_17813120, EPI_ISL_17813123, EPI_ISL_17820656, EPI_ISL_17820688

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3261e_3fac10.json?f_userOrOld=uploaded%20sample

overview from XBB.2.3's polytomy

details:

Trivia:

• ORF1b:T1050I(C16616T) is one of the definitions of XBC, one nuc different to BA.5.2's largest undesignated ORF1b:T1050N(C16616A).
• ORF1a:Q998H(G3259T) is one of the largest undesignated branches of XBB.2.3 [query: G3259T, C23123T finds about 160 seqs]
• One of the branch got S:A845V(C24096T), and all the seqs are quite recent. This mutation have about 4k seqs during the whole pandemic, no idea what it does.

[NkRMnZr]

06-26, 3 seqs from 2 countries

1 from Martinique: EPI_ISL_17831347 2 from England: EPI_ISL_17838103, EPI_ISL_17838122

06-29, 5 seqs from 3 countries

1 from Delaware, USA: EPI_ISL_17854078 1 from Florida, USA: EPI_ISL_17855298 1 from Illinois, USA: EPI_ISL_17856608 1 from Austria: EPI_ISL_17881012 1 from England, UK: EPI_ISL_17884484

07-02, 3 seqs from 2 countries

2 from Spain: EPI_ISL_17948471, EPI_ISL_17949057 1 from Belgium: EPI_ISL_17950421

UShER after 3 updates:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_6995_2782a0.json?f_userOrOld=uploaded%20sample&showBranchLabels=all 

07-08, 2 seqs from Israel and UK

1 from Israel: EPI_ISL_17953513 1 from England: EPI_ISL_17964434

09-08, 24 seqs from France, Greece, Ireland, Japan, Spain, UK and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2a456_c3e180.json?f_userOrOld=uploaded%20sample&label=id:node_7395344  `EPI_ISL_17975746, EPI_ISL_18015802, EPI_ISL_18076197, EPI_ISL_18093645, EPI_ISL_18096592, EPI_ISL_18098895, EPI_ISL_18109093, EPI_ISL_18112546, EPI_ISL_18112695, EPI_ISL_18118128, EPI_ISL_18125053, EPI_ISL_18147452, EPI_ISL_18160248, EPI_ISL_18209166, EPI_ISL_18215239, EPI_ISL_18216314, EPI_ISL_18216976, EPI_ISL_18216978, EPI_ISL_18220108, EPI_ISL_18220115, EPI_ISL_18220898, EPI_ISL_18220905, EPI_ISL_18221579, EPI_ISL_18232428, EPI_ISL_18234059`

[FedeGueli]

Slow. lets see next week .