FL.5 (XBB.1.9.1.5) with ORF7b:L25I and S:M177T (84 seqs, 12 countries)

[NkRMnZr]

Transferred from sars-cov-2-variants/lineage-proposals#67

Defining mutations: On top of FL.5 C29358T(N:T362I) > C27828A(ORF7b:L25I) > C2710T > C7039T > T22092C(S:M177T)
Query: T22092C, C27828A
Earliest seq: 2023-02-27 (EPI_ISL_17094227, Singapore)
Latest seq: 2023-05-25 (EPI_ISL_1776205, South Korea)
Sampled in Countries: South Korea (23), Japan (12), USA (10, California/4, Washington/2, Pennsylvania/1, New Jersey/1, Ohio/1, Florida/1), Singapore (3), China (3, Heilongjiang/2, Shanghai/1), Australia (2), Malaysia (1), Canada (1, Ontario), UK (1, England), Indonesia (1)

GISAID Genomes:

EPI_ISL_17094227, EPI_ISL_17388455, EPI_ISL_17416132, EPI_ISL_17495626, EPI_ISL_17539253, EPI_ISL_17540224, EPI_ISL_17552065, EPI_ISL_17552995, EPI_ISL_17554549, EPI_ISL_17561173, EPI_ISL_17563044, EPI_ISL_17563273, EPI_ISL_17585974, EPI_ISL_17590265, EPI_ISL_17604252, EPI_ISL_17605181, EPI_ISL_17619111, EPI_ISL_17621663, EPI_ISL_17629652, EPI_ISL_17629997, EPI_ISL_17631021, EPI_ISL_17631059, EPI_ISL_17631066, EPI_ISL_17637729, EPI_ISL_17646768, EPI_ISL_17648028, EPI_ISL_17651043, EPI_ISL_17653108, EPI_ISL_17662201, EPI_ISL_17672489, EPI_ISL_17678653, EPI_ISL_17688946, EPI_ISL_17690487, EPI_ISL_17691120, EPI_ISL_17691756, EPI_ISL_17694767, EPI_ISL_17717444, EPI_ISL_17721783, EPI_ISL_17723173, EPI_ISL_17723960, EPI_ISL_17728892, EPI_ISL_17729048, EPI_ISL_17730355, EPI_ISL_17730367, EPI_ISL_17730369, EPI_ISL_17730379, EPI_ISL_17730643, EPI_ISL_17730700, EPI_ISL_17730816, EPI_ISL_17739682, EPI_ISL_17739695, EPI_ISL_17761980, EPI_ISL_17762050, EPI_ISL_17762051, EPI_ISL_17762052, EPI_ISL_17762055, EPI_ISL_17774249

GenBank Genomes:

USA/CA-CDPH-500110242/2023|OQ970911.1|2023-04-19, USA/FL-CDC-LC1036184/2023|OQ832929.1|2023-04-03, USA/NY-PRL-230420_81C04/2023|OQ930358.1|2023-04-18, USA/OH-UHTL-3164/2023|OR061356.1|2023-05-13

UShER:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_21de5_17b3f0.json?f_userOrOld=uploaded%20sample

Detailed view:

Overview of proposed lineage on FL.5 polytomy:

Trivia:

• S:M177T is the definition of BN.1.7 and XBB.3.2, also popped up in @FedeGueli 's XBB.1.5 spike mutation tracker XBB.1.5 spike diversity - multiple lineages issue to track easily if any spike mutation appears (and circulates) within XBB.1.5 lineage - Last update 12/03/2023 #1510 , however it doens't seems to make much influence previously, let's see how it does this time on XBB.1.9*.
• Parent branch FL.5 C29358T(N:T362I) > C27828A(ORF7b:L25I) now has at least 345 seqs using gisaid query: G5720A, C11956T, C29358T, C27828A
• A sub-branch with G24842T(S:V1094F) first, then T22092C(S:M177T), involving 3 outliers EPI_ISL_17416132, EPI_ISL_17499428, EPI_ISL_17642618, there could be dropouts that causing the split of branches, and they are not counted.
• EPI_ISL_17669171 now falls under another sub-branch involving C22995G(S:T478R).
• genbank accession OQ970911.1, OQ832929.1, OQ930358.1, OR061356.1 not on GISAID yet but can be found on UShER tree.

[Over-There-Is]

*It is GenBank but not GenBase. GenBank is an American database and GenBase is Chinese.

[NkRMnZr]

Tracking updates:

Update 1: 23-06-15, 5 seqs from 3 countries

3 more from Philippines: EPI_ISL_17796523, EPI_ISL_17796557, EPI_ISL_17796593

1 from NY, USA: EPI_ISL_17783981
1 from South Korea: EPI_ISL_17778905

Update 2: 23-06-16, 9 seqs from 4 countries

6 from Victoria, Australia EPI_ISL_17802495, EPI_ISL_17802521, EPI_ISL_17802655, EPI_ISL_17802795, EPI_ISL_17802907, EPI_ISL_17803110

1 from Japan EPI_ISL_17803922
1 from Sweden EPI_ISL_17804163
1 from South Korea EPI_ISL_17807994

Update 3: 23-06-21, 5 seqs from 2 countries

3 from Philippines: EPI_ISL_17819118, EPI_ISL_17819250, EPI_ISL_17819288

2 from South Korea: EPI_ISL_17816442, EPI_ISL_17816655

UShER tree after 3 updates:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_38c7a_5ba6a0.json?showBranchLabels=all

Update 4: 23-06-26 2 seqs from 2 countries

Ohio, USA: EPI_ISL_17832010

South Korea: EPI_ISL_17835610

Update 5: 23-06-29 5 seqs from 2 countries

1 from NY with travel history to Italy: EPI_ISL_17851578

1 from NY with unspecified intl' travel history: EPI_ISL_17851461
3 from Japan: EPI_ISL_17880553, EPI_ISL_17880602, EPI_ISL_17883179

[FedeGueli]

It is expanding in eastern asia but still i dont see big prevalence of it anywhere, maybe Philippines being already there in April ?