GF.1 (XBB.1.5.24.1) with ORF1b:G814D (nsp12_G823D), ORF1b:Q1546H (nsp14_G22H) (552 seqs, mainly in China, 12 countries)

[NkRMnZr]

Defining Mutations: on top of GF.1 (XBB.1.5.24.1) > A8197G > G15908A (ORF1b:G814D), G18105T(ORF1b:Q1546H) Query: A8197G, G15908A Earliest seq: 2023-03-15 [EPI_ISL_17494031, Jiangsu, China] Latest seq: 2023-06-07 [EPI_ISL_17790291, Singapore] Sampled Countries: China (367, Anhui/61, Beijing/7, Fujian/4, Guangdong/4, Heilongjiang/2, Henan/4, Hubei/10, Jiangsu/119, Jiangxi/11, Qinghai/2, Shanghai/113, Shanxi/1, Sichuan/5, Taiwan/3, Xinjiang/4, Yunnan/17), USA (11, Cali/4, NY/6, Utah/1), Singapore (4), Canada (1, Ontario), Japan (1), South Korea (1)

Genomes:

EPI_ISL_17494031, EPI_ISL_17505628-17505629, EPI_ISL_17505635, EPI_ISL_17505648-17505649, EPI_ISL_17511820, EPI_ISL_17511892, EPI_ISL_17516743, EPI_ISL_17584959-17584960, EPI_ISL_17614989, EPI_ISL_17615012, EPI_ISL_17618432, EPI_ISL_17618482, EPI_ISL_17618501, EPI_ISL_17618641, EPI_ISL_17618659, EPI_ISL_17618667, EPI_ISL_17618719, EPI_ISL_17619023, EPI_ISL_17619119, EPI_ISL_17619127, EPI_ISL_17619161, EPI_ISL_17619185, EPI_ISL_17620292, EPI_ISL_17625285, EPI_ISL_17625540, EPI_ISL_17625589, EPI_ISL_17625652, EPI_ISL_17637385, EPI_ISL_17637387-17637395, EPI_ISL_17637399-17637400, EPI_ISL_17637402-17637405, EPI_ISL_17637412, EPI_ISL_17637420, EPI_ISL_17637440, EPI_ISL_17637446-17637447, EPI_ISL_17637467, EPI_ISL_17637473, EPI_ISL_17637475, EPI_ISL_17637477, EPI_ISL_17645420, EPI_ISL_17645699, EPI_ISL_17645801, EPI_ISL_17646003, EPI_ISL_17652359, EPI_ISL_17652364, EPI_ISL_17669050, EPI_ISL_17669084, EPI_ISL_17669111, EPI_ISL_17669165, EPI_ISL_17672027, EPI_ISL_17678325, EPI_ISL_17678389, EPI_ISL_17683967, EPI_ISL_17684040, EPI_ISL_17684051, EPI_ISL_17684113, EPI_ISL_17684123, EPI_ISL_17684180, EPI_ISL_17684265, EPI_ISL_17684276-17684277, EPI_ISL_17684290-17684295, EPI_ISL_17684335, EPI_ISL_17684449, EPI_ISL_17689267, EPI_ISL_17689269, EPI_ISL_17689271, EPI_ISL_17689275, EPI_ISL_17689292-17689293, EPI_ISL_17689310, EPI_ISL_17689312, EPI_ISL_17689347, EPI_ISL_17689434, EPI_ISL_17696871, EPI_ISL_17696894, EPI_ISL_17696897, EPI_ISL_17696983, EPI_ISL_17697567, EPI_ISL_17697984, EPI_ISL_17698091, EPI_ISL_17698136, EPI_ISL_17698830, EPI_ISL_17703735, EPI_ISL_17703964, EPI_ISL_17703991, EPI_ISL_17714315, EPI_ISL_17714358, EPI_ISL_17714385, EPI_ISL_17714389, EPI_ISL_17714421, EPI_ISL_17714429, EPI_ISL_17723154, EPI_ISL_17724510, EPI_ISL_17724514, EPI_ISL_17724978, EPI_ISL_17724981, EPI_ISL_17725015, EPI_ISL_17725019, EPI_ISL_17725056, EPI_ISL_17725099, EPI_ISL_17725103, EPI_ISL_17725169, EPI_ISL_17725192, EPI_ISL_17725197, EPI_ISL_17725199-17725200, EPI_ISL_17725233, EPI_ISL_17725241, EPI_ISL_17725243, EPI_ISL_17725250-17725251, EPI_ISL_17725259, EPI_ISL_17725288, EPI_ISL_17725295-17725296, EPI_ISL_17725302, EPI_ISL_17725311, EPI_ISL_17725322, EPI_ISL_17725328-17725329, EPI_ISL_17725353, EPI_ISL_17725359, EPI_ISL_17725371, EPI_ISL_17725461, EPI_ISL_17725477, EPI_ISL_17725485, EPI_ISL_17725502, EPI_ISL_17728929, EPI_ISL_17729094, EPI_ISL_17729760-17729761, EPI_ISL_17729765, EPI_ISL_17729769, EPI_ISL_17729775, EPI_ISL_17729787, EPI_ISL_17729791, EPI_ISL_17729966, EPI_ISL_17735956, EPI_ISL_17738979, EPI_ISL_17739687, EPI_ISL_17739715, EPI_ISL_17744592, EPI_ISL_17744604, EPI_ISL_17744611, EPI_ISL_17744643, EPI_ISL_17744747, EPI_ISL_17744791, EPI_ISL_17744794, EPI_ISL_17765823, EPI_ISL_17765848, EPI_ISL_17765885, EPI_ISL_17765891, EPI_ISL_17765914, EPI_ISL_17765930-17765931, EPI_ISL_17765938, EPI_ISL_17769933, EPI_ISL_17769957, EPI_ISL_17769973, EPI_ISL_17769984, EPI_ISL_17769990, EPI_ISL_17769998, EPI_ISL_17770042, EPI_ISL_17770050, EPI_ISL_17770092, EPI_ISL_17770109, EPI_ISL_17770123, EPI_ISL_17770146, EPI_ISL_17770150, EPI_ISL_17770169, EPI_ISL_17770174, EPI_ISL_17770201, EPI_ISL_17770206, EPI_ISL_17770226-17770227, EPI_ISL_17770231, EPI_ISL_17770244-17770245, EPI_ISL_17770251, EPI_ISL_17770267, EPI_ISL_17770280, EPI_ISL_17770291, EPI_ISL_17770314, EPI_ISL_17770325, EPI_ISL_17770338, EPI_ISL_17770354, EPI_ISL_17770411, EPI_ISL_17774029, EPI_ISL_17775176, EPI_ISL_17775200, EPI_ISL_17775214, EPI_ISL_17775654, EPI_ISL_17778684, EPI_ISL_17778705, EPI_ISL_17778717, EPI_ISL_17778726, EPI_ISL_17778750, EPI_ISL_17779892, EPI_ISL_17780121, EPI_ISL_17783137, EPI_ISL_17784868, EPI_ISL_17784892, EPI_ISL_17785122, EPI_ISL_17785146, EPI_ISL_17785148, EPI_ISL_17785169, EPI_ISL_17785205, EPI_ISL_17785214, EPI_ISL_17785217, EPI_ISL_17785271-17785272, EPI_ISL_17785277, EPI_ISL_17785287, EPI_ISL_17785289, EPI_ISL_17785318, EPI_ISL_17785364, EPI_ISL_17788502, EPI_ISL_17788863, EPI_ISL_17789542, EPI_ISL_17790291, EPI_ISL_17790843, EPI_ISL_17791896, EPI_ISL_17793980, EPI_ISL_17793983-17793985, EPI_ISL_17793987, EPI_ISL_17793989, EPI_ISL_17793991-17793992, EPI_ISL_17793994-17793996, EPI_ISL_17793998-17793999, EPI_ISL_17794001-17794003, EPI_ISL_17794005, EPI_ISL_17794008-17794009, EPI_ISL_17794031-17794033, EPI_ISL_17794035, EPI_ISL_17794037, EPI_ISL_17794041-17794046, EPI_ISL_17794049-17794051, EPI_ISL_17794053, EPI_ISL_17794057, EPI_ISL_17794530, EPI_ISL_17794560, EPI_ISL_17794699-17794700, EPI_ISL_17794727, EPI_ISL_17794752, EPI_ISL_17794845, EPI_ISL_17794852, EPI_ISL_17794857, EPI_ISL_17794884, EPI_ISL_17794981, EPI_ISL_17795016, EPI_ISL_17795022-17795023, EPI_ISL_17795025-17795026, EPI_ISL_17795053, EPI_ISL_17795056-17795058, EPI_ISL_17795062-17795063, EPI_ISL_17795067-17795072, EPI_ISL_17795075, EPI_ISL_17795078-17795079, EPI_ISL_17795081, EPI_ISL_17795083-17795084, EPI_ISL_17795086-17795088, EPI_ISL_17795108, EPI_ISL_17795122, EPI_ISL_17795152-17795153, EPI_ISL_17795172, EPI_ISL_17795179, EPI_ISL_17795190-17795191, EPI_ISL_17795198, EPI_ISL_17795206, EPI_ISL_17795235, EPI_ISL_17795278, EPI_ISL_17795296, EPI_ISL_17795332, EPI_ISL_17795347, EPI_ISL_17795371, EPI_ISL_17795379, EPI_ISL_17795428, EPI_ISL_17795456, EPI_ISL_17795471, EPI_ISL_17795479, EPI_ISL_17795500, EPI_ISL_17795502, EPI_ISL_17795505, EPI_ISL_17795524, EPI_ISL_17795528, EPI_ISL_17795532, EPI_ISL_17795542, EPI_ISL_17795564, EPI_ISL_17795572, EPI_ISL_17795574, EPI_ISL_17795578, EPI_ISL_17795581-17795584, EPI_ISL_17795586-17795587, EPI_ISL_17795600-17795608, EPI_ISL_17795620, EPI_ISL_17795626, EPI_ISL_17795652, EPI_ISL_17795656, EPI_ISL_17795660, EPI_ISL_17795676, EPI_ISL_17795685-17795686, EPI_ISL_17795688, EPI_ISL_17795693, EPI_ISL_17795696, EPI_ISL_17795708, EPI_ISL_17795727-17795728, EPI_ISL_17795743, EPI_ISL_17795746, EPI_ISL_17795768, EPI_ISL_17795777, EPI_ISL_17795779-17795780, EPI_ISL_17795783, EPI_ISL_17795786, EPI_ISL_17795789

UShER:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_16dd6_a77d90.json?f_userOrOld=uploaded%20sample&showBranchLabels=all

Overview from GF.1 (XBB.1.5.24.1) polytomy

Details

[NkRMnZr]

Tracking updates:

Update 1, 24 additional seqs (23-06-16)

20 From China:

Details:

10 from Anhui: EPI_ISL_17801895, EPI_ISL_17808130, EPI_ISL_17808132, EPI_ISL_17808135, EPI_ISL_17808138, EPI_ISL_17808147, EPI_ISL_17808164, EPI_ISL_17808165, EPI_ISL_17808166, EPI_ISL_17808096 3 from Fujian: EPI_ISL_17801807, EPI_ISL_17801911, EPI_ISL_17801985 2 from Henan: EPI_ISL_17808417, EPI_ISL_17808420 3 from Sichuan: EPI_ISL_17808102, EPI_ISL_17808116, EPI_ISL_17808200 2 from Yunan: EPI_ISL_17808236, EPI_ISL_17808310

2 from Korea: EPI_ISL_17807512, EPI_ISL_17807760 2 from Victoria, Australia: EPI_ISL_17802520, EPI_ISL_17802776

Update 2: 18 Additional seqs (23-06-18)

17 from Shanghai:

Details:

EPI_ISL_17811016, EPI_ISL_17811031, EPI_ISL_17811056, EPI_ISL_17811097, EPI_ISL_17811160, EPI_ISL_17811168, EPI_ISL_17811197, EPI_ISL_17811214, EPI_ISL_17811222, EPI_ISL_17811232, EPI_ISL_17811233, EPI_ISL_17811245, EPI_ISL_17811246, EPI_ISL_17811261, EPI_ISL_17811272, EPI_ISL_17811321, EPI_ISL_17811354

1 from California with travel history to Taiwan: EPI_ISL_17809368 _wondering why sometimes metadata **DOES** work._

Update 3: 12 additional seqs from 2 countries (23-06-21)

4 from China, follows: 1 from Fujian: EPI_ISL_17819890 3 from Henan: EPI_ISL_17816966, EPI_ISL_17816967, EPI_ISL_17817006 1 from Hubei: EPI_ISL_17817039 1 from Ontario, Canada: EPI_ISL_17814685 4 from South Korea: EPI_ISL_17816467, EPI_ISL_17816641, EPI_ISL_17816736, EPI_ISL_17816852 New entries: 1 from Italy: EPI_ISL_17813654 1 from Thailand: EPI_ISL_17816293

Update 4: 7 additional seqs from 3 countries (23-06-23)

3 from Yunnan, China: EPI_ISL_17830353, EPI_ISL_17830374, EPI_ISL_17830392 2 from NSW, Australia: EPI_ISL_17832372, EPI_ISL_17832406 New entry: 2 from Austria: EPI_ISL_17826706, EPI_ISL_17826966

Update 5: 53 additional seqs from 5 countries (26-06-26)

46 from China, follows:

2 from Anhui: EPI_ISL_17837071, EPI_ISL_17836990, EPI_ISL_17850155 2 from Hubei: EPI_ISL_17837027, EPI_ISL_17837029 31 from Shanghai: EPI_ISL_17836452, EPI_ISL_17836467, EPI_ISL_17836479, EPI_ISL_17836518, EPI_ISL_17836524, EPI_ISL_17836526, EPI_ISL_17836541, EPI_ISL_17836560, EPI_ISL_17836562, EPI_ISL_17836566, EPI_ISL_17836635, EPI_ISL_17836690, EPI_ISL_17836697, EPI_ISL_17836734-17836735, EPI_ISL_17836739, EPI_ISL_17836764, EPI_ISL_17836791, EPI_ISL_17836800, EPI_ISL_17836826, EPI_ISL_17836828, EPI_ISL_17836866, EPI_ISL_17836884, EPI_ISL_17836914, EPI_ISL_17836918, EPI_ISL_17836924, EPI_ISL_17836932, EPI_ISL_17836955-17836956, EPI_ISL_17836961, EPI_ISL_17836972 4 from Xinjiang: EPI_ISL_17836228, EPI_ISL_17836272, EPI_ISL_17836346, EPI_ISL_17836354 2 from Fujian EPI_ISL_17850173, EPI_ISL_17850222 2 from Heilongjiang EPI_ISL_17850253, EPI_ISL_17850410 1 from Liaoning EPI_ISL_17850617 1 from Sichuan EPI_ISL_17850755

3 from Singapore: EPI_ISL_17837642-17837644 2 from Korea: EPI_ISL_17835227, EPI_ISL_17835326 1 from Georgia, USA: EPI_ISL_17847349 New Entry: 1 from Spain: EPI_ISL_17837123

Update 6: 13 additional seqs from 5 countries (26-06-29)

7 from the USA:

1 from Georgia: EPI_ISL_17852421 5 from NY: EPI_ISL_17854185, EPI_ISL_17855413, EPI_ISL_17855903, EPI_ISL_17856105, EPI_ISL_17856804 1 from Cali: EPI_ISL_17861551

2 from China:

1 from Anhui: EPI_ISL_17879917 1 from Taiwan: EPI_ISL_17880017

2 from Austria: EPI_ISL_17880930, EPI_ISL_17881028 3 from Japan: EPI_ISL_17882082, EPI_ISL_17883873, EPI_ISL_17884027

Update 7: 13 additional seqs from 4 countries (26-07-01)

1 from NSW, Australia: EPI_ISL_17924300 3 from S. Korea: EPI_ISL_17927884, EPI_ISL_17927954, EPI_ISL_17930501

3 from the USA

1 from NY: EPI_ISL_17937841 1 from Ohio: EPI_ISL_17950900 1 from Cali: EPI_ISL_17951596

6 from China:

2 from Hubei: EPI_ISL_17951222, EPI_ISL_17951233 1 from Anhui: EPI_ISL_17951243 3 from Shanxi: EPI_ISL_17951323, EPI_ISL_17951326, EPI_ISL_17951392

UShER tree after 7 updates

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_5c66_16f4f0.json?f_userOrOld=uploaded%20sample&label=id:node_6997145 

Update 8: 26 additional seqs from 4 countries (26-07-03)

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2d520_408680.json?f_userOrOld=uploaded%20sample 

from China:

19 from Shanghai:

EPI_ISL_17956809-17956810, EPI_ISL_17956868, EPI_ISL_17956923, EPI_ISL_17956938, EPI_ISL_17956943, EPI_ISL_17956958, EPI_ISL_17956975, EPI_ISL_17956986, EPI_ISL_17956990, EPI_ISL_17957005, EPI_ISL_17957028-17957029, EPI_ISL_17957051, EPI_ISL_17957063, EPI_ISL_17957080, EPI_ISL_17957084, EPI_ISL_17957133, EPI_ISL_17957143, EPI_ISL_17957155, EPI_ISL_17957161

1 from Tianjin: EPI_ISL_17956706 1 from Fujian: EPI_ISL_17956761

1 from Illinois, USA: EPI_ISL_17952479 1 from Japan: EPI_ISL_17958715 new entry: 1 from France: EPI_ISL_17958233

[FedeGueli]

Please propose this one it is the main branch of XBB.1.5.24 so nothing of special interesting or different from the parental lineage but still it has a notable 5% of prevalence in Shanghai after June 15

More just look at NSPs you indicated are wrong. Use https://codon2nucleotide.theo.io/ being carefully to distinguish between orf1a and orf1b

So the two mutations in Orf1b are one in RDRP and the other in the proofreading exonuclease so both relevant.

Edited : being curious to see if these two relevant mutations were doing something i have redon my math, this is doubling every 9/10 days it is in the very high ranking of fast lineages. Please propose it.

@memorablea i suggest to add this to your tracking list.

[Memorablea]

Edited : being curious to see if these two relevant mutations were doing something i have redon my math, this is doubling every 9/10 days it is in the very high ranking of fast lineages. Please propose it.

@Memorablea i suggest to add this to your tracking list.

I agree with this, after all, his probability is indeed relatively high, and there is a sequence distribution in China. We will follow it.

[NkRMnZr]

transferred to cov-lineages/pango-designation#2086