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Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (383 seqs, mainly in Canada, 9 countries) #2354

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NkRMnZr opened this issue Oct 31, 2023 · 5 comments
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Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (383 seqs, mainly in Canada, 9 countries) #2354

NkRMnZr opened this issue Oct 31, 2023 · 5 comments

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@NkRMnZr
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NkRMnZr commented Oct 31, 2023

Taken from Branch 35 of Multitask sars-cov-2-variants/lineage-proposals#537

Defining Mutations: EG.5.1.4 > C26111T(ORF3:P240L) > C18555T > T17268C > G22927T(S:L455F)
Query: T17268C, G22927T, C26111T
Earliest seq: 2023-08-08 (EPI_ISL_18132133, Newfoundland and Labrador)
Latest seq: 2023-10-23 (EPI_ISL_18448815, Ontario, Canada)
Sampled Countries: Canada (49: ON/22; NL/15; AB/10; BC/1; NS/1), US (7: CA/2; NY/2; AZ/1; UT/1; VA/1), France (1)

Genomes:

EPI_ISL_18132133, EPI_ISL_18256806, EPI_ISL_18258767, EPI_ISL_18258769-18258770, EPI_ISL_18258773, EPI_ISL_18258778, EPI_ISL_18291996, EPI_ISL_18291998, EPI_ISL_18292017, EPI_ISL_18292020-18292022, EPI_ISL_18292026-18292028, EPI_ISL_18333999, EPI_ISL_18344763, EPI_ISL_18357035, EPI_ISL_18372328, EPI_ISL_18372367, EPI_ISL_18383112, EPI_ISL_18383123-18383124, EPI_ISL_18383697, EPI_ISL_18388693, EPI_ISL_18395288, EPI_ISL_18395414, EPI_ISL_18395581, EPI_ISL_18404467, EPI_ISL_18425010, EPI_ISL_18425420, EPI_ISL_18425431, EPI_ISL_18425847, EPI_ISL_18425967, EPI_ISL_18426727, EPI_ISL_18427300, EPI_ISL_18427492, EPI_ISL_18427494, EPI_ISL_18427496, EPI_ISL_18427507, EPI_ISL_18427602, EPI_ISL_18431345, EPI_ISL_18436820, EPI_ISL_18437028, EPI_ISL_18437176, EPI_ISL_18438632, EPI_ISL_18438777, EPI_ISL_18448237, EPI_ISL_18448584-18448585, EPI_ISL_18448588, EPI_ISL_18448699-18448700, EPI_ISL_18448702, EPI_ISL_18448740, EPI_ISL_18448815

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_17f71_c79a0.json?f_userOrOld=uploaded%20sample&label=id:node_3447785

view from EG.5.1.4 polytomy
sc

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@NkRMnZr NkRMnZr mentioned this issue Oct 31, 2023
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NkRMnZr commented Nov 6, 2023 •
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Tracking updates

11-05, 8 seqs from Canada and USA EPI_ISL_18452545, EPI_ISL_18453118, EPI_ISL_18455921, EPI_ISL_18455976, EPI_ISL_18456021, EPI_ISL_18456210-18456211, EPI_ISL_18458925

11-18, 36 seqs from Canada, France and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_15f1e_a33000.json?f_userOrOld=uploaded%20sample&label=id:node_3547056
image

EPI_ISL_18471702, EPI_ISL_18471756, EPI_ISL_18472097, EPI_ISL_18478099-18478100, EPI_ISL_18492946, EPI_ISL_18492980, EPI_ISL_18493023, EPI_ISL_18493102, EPI_ISL_18502374, EPI_ISL_18504771, EPI_ISL_18505074, EPI_ISL_18505078, EPI_ISL_18505082, EPI_ISL_18505458, EPI_ISL_18507687, EPI_ISL_18510105, EPI_ISL_18512544, EPI_ISL_18512558, EPI_ISL_18512563, EPI_ISL_18512621, EPI_ISL_18512807, EPI_ISL_18512852, EPI_ISL_18512892, EPI_ISL_18512957, EPI_ISL_18512973-18512974, EPI_ISL_18512981, EPI_ISL_18513000, EPI_ISL_18513002, EPI_ISL_18513004, EPI_ISL_18513027, EPI_ISL_18513057, EPI_ISL_18513070, EPI_ISL_18513148, EPI_ISL_18516992

11-25, 22 seqs from Canada, Denmark and USA

EPI_ISL_18523235, EPI_ISL_18523295, EPI_ISL_18523869, EPI_ISL_18523928, EPI_ISL_18527098, EPI_ISL_18533639, EPI_ISL_18534436, EPI_ISL_18537422, EPI_ISL_18537427, EPI_ISL_18538417, EPI_ISL_18538422, EPI_ISL_18538438, EPI_ISL_18538630, EPI_ISL_18538700, EPI_ISL_18538849, EPI_ISL_18538862, EPI_ISL_18538883, EPI_ISL_18538888-18538889, EPI_ISL_18538958, EPI_ISL_18538971, EPI_ISL_18540263

12-02, 55 seqs from Canada, France and USA

EPI_ISL_18548461, EPI_ISL_18548575, EPI_ISL_18548728, EPI_ISL_18548776, EPI_ISL_18548856, EPI_ISL_18549045, EPI_ISL_18549100, EPI_ISL_18549150, EPI_ISL_18549212, EPI_ISL_18549232, EPI_ISL_18549238, EPI_ISL_18549252-18549253, EPI_ISL_18549258, EPI_ISL_18549346, EPI_ISL_18549351, EPI_ISL_18549383, EPI_ISL_18549396, EPI_ISL_18549452-18549454, EPI_ISL_18549460, EPI_ISL_18549462, EPI_ISL_18549466-18549467, EPI_ISL_18549470, EPI_ISL_18549479, EPI_ISL_18549560, EPI_ISL_18550350, EPI_ISL_18553441, EPI_ISL_18553708, EPI_ISL_18553721, EPI_ISL_18553875, EPI_ISL_18553937, EPI_ISL_18558973, EPI_ISL_18559382, EPI_ISL_18559386, EPI_ISL_18563876, EPI_ISL_18563913, EPI_ISL_18563943-18563944, EPI_ISL_18563994, EPI_ISL_18564135, EPI_ISL_18564155, EPI_ISL_18564164, EPI_ISL_18564169, EPI_ISL_18564177, EPI_ISL_18564179, EPI_ISL_18564206, EPI_ISL_18564250-18564251, EPI_ISL_18566986-18566987, EPI_ISL_18566990, EPI_ISL_18570010

12-06, 44 seqs from Canada, Spain and USA

EPI_ISL_18576552, EPI_ISL_18580933, EPI_ISL_18581098, EPI_ISL_18581819, EPI_ISL_18581934, EPI_ISL_18581993, EPI_ISL_18582012, EPI_ISL_18582014, EPI_ISL_18582269, EPI_ISL_18582377, EPI_ISL_18582382, EPI_ISL_18582534-18582537, EPI_ISL_18582608, EPI_ISL_18582814, EPI_ISL_18583215, EPI_ISL_18583258, EPI_ISL_18583581, EPI_ISL_18589382, EPI_ISL_18591500, EPI_ISL_18591714, EPI_ISL_18592740, EPI_ISL_18593386, EPI_ISL_18593414, EPI_ISL_18593419, EPI_ISL_18593535, EPI_ISL_18593552, EPI_ISL_18593571, EPI_ISL_18593616, EPI_ISL_18593629, EPI_ISL_18593634, EPI_ISL_18593637-18593638, EPI_ISL_18593642, EPI_ISL_18593655, EPI_ISL_18593667, EPI_ISL_18593716, EPI_ISL_18593722, EPI_ISL_18593735-18593736, EPI_ISL_18593748, EPI_ISL_18593877

12-14, 26 seqs from Canada, Italy, Singapore and USA

EPI_ISL_18602037, EPI_ISL_18603961-18603962, EPI_ISL_18603966-18603967, EPI_ISL_18607227, EPI_ISL_18608927, EPI_ISL_18608934, EPI_ISL_18609126, EPI_ISL_18609930, EPI_ISL_18610312, EPI_ISL_18610344, EPI_ISL_18610377, EPI_ISL_18610760-18610761, EPI_ISL_18610880, EPI_ISL_18611052, EPI_ISL_18611060, EPI_ISL_18611072, EPI_ISL_18611134, EPI_ISL_18611555, EPI_ISL_18614924, EPI_ISL_18615024, EPI_ISL_18615065, EPI_ISL_18615127, EPI_ISL_18615132

24-01-13, 135 seqs from Canada, Switzerland, UK and USA

EPI_ISL_18637167, EPI_ISL_18637362, EPI_ISL_18637392, EPI_ISL_18643288, EPI_ISL_18643393, EPI_ISL_18644103, EPI_ISL_18644422, EPI_ISL_18644892, EPI_ISL_18644902, EPI_ISL_18644908, EPI_ISL_18645091-18645092, EPI_ISL_18645097-18645098, EPI_ISL_18645261, EPI_ISL_18645382, EPI_ISL_18645412, EPI_ISL_18645493, EPI_ISL_18645542, EPI_ISL_18645548, EPI_ISL_18645550-18645551, EPI_ISL_18645578-18645579, EPI_ISL_18645581-18645582, EPI_ISL_18645586, EPI_ISL_18645801, EPI_ISL_18645811, EPI_ISL_18645867, EPI_ISL_18645943-18645944, EPI_ISL_18645985, EPI_ISL_18646581, EPI_ISL_18647332, EPI_ISL_18649435, EPI_ISL_18649652, EPI_ISL_18653675, EPI_ISL_18653682, EPI_ISL_18654267-18654268, EPI_ISL_18654417, EPI_ISL_18654555, EPI_ISL_18654926, EPI_ISL_18655457, EPI_ISL_18655902, EPI_ISL_18656038, EPI_ISL_18656499, EPI_ISL_18656800, EPI_ISL_18657243, EPI_ISL_18657264, EPI_ISL_18657468, EPI_ISL_18658240, EPI_ISL_18658292, EPI_ISL_18658626, EPI_ISL_18658772, EPI_ISL_18658871, EPI_ISL_18659300, EPI_ISL_18659318, EPI_ISL_18659422, EPI_ISL_18659601, EPI_ISL_18659632, EPI_ISL_18659645, EPI_ISL_18659649, EPI_ISL_18659664, EPI_ISL_18659667, EPI_ISL_18663312, EPI_ISL_18663319, EPI_ISL_18677443-18677444, EPI_ISL_18677446, EPI_ISL_18677500, EPI_ISL_18677525, EPI_ISL_18677620, EPI_ISL_18677690, EPI_ISL_18677695, EPI_ISL_18677929, EPI_ISL_18686370, EPI_ISL_18688366, EPI_ISL_18695752, EPI_ISL_18696036, EPI_ISL_18696196, EPI_ISL_18696770, EPI_ISL_18696831, EPI_ISL_18696870, EPI_ISL_18696984, EPI_ISL_18697286, EPI_ISL_18697288, EPI_ISL_18697543, EPI_ISL_18699343, EPI_ISL_18707429, EPI_ISL_18707560, EPI_ISL_18708493, EPI_ISL_18708580, EPI_ISL_18708828, EPI_ISL_18710124, EPI_ISL_18710170, EPI_ISL_18711004-18711005, EPI_ISL_18714763, EPI_ISL_18715640, EPI_ISL_18718613, EPI_ISL_18718747, EPI_ISL_18718802, EPI_ISL_18718865, EPI_ISL_18719013, EPI_ISL_18719553, EPI_ISL_18719664, EPI_ISL_18722806, EPI_ISL_18723650, EPI_ISL_18727609, EPI_ISL_18729623, EPI_ISL_18729634, EPI_ISL_18729816, EPI_ISL_18729862, EPI_ISL_18729954, EPI_ISL_18730008, EPI_ISL_18730025, EPI_ISL_18730046, EPI_ISL_18730156, EPI_ISL_18730212, EPI_ISL_18731851, EPI_ISL_18732371, EPI_ISL_18738150, EPI_ISL_18738613, EPI_ISL_18738708, EPI_ISL_18738816, EPI_ISL_18738906, EPI_ISL_18738976, EPI_ISL_18738978, EPI_ISL_18750204, EPI_ISL_18750353, EPI_ISL_18750508, EPI_ISL_18756895, EPI_ISL_18757096

@NkRMnZr NkRMnZr changed the title Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (57 seqs, mainly in Canada, 3 countries) Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (65 seqs, mainly in Canada, 3 countries) Nov 6, 2023
@NkRMnZr NkRMnZr changed the title Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (65 seqs, mainly in Canada, 3 countries) Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (101 seqs, mainly in Canada, 3 countries) Nov 19, 2023
@NkRMnZr NkRMnZr changed the title Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (101 seqs, mainly in Canada, 3 countries) Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (123 seqs, mainly in Canada, 4 countries) Nov 26, 2023
@NkRMnZr NkRMnZr changed the title Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (123 seqs, mainly in Canada, 4 countries) Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (178 seqs, mainly in Canada, 4 countries) Dec 3, 2023
@NkRMnZr NkRMnZr changed the title Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (178 seqs, mainly in Canada, 4 countries) Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (222 seqs, mainly in Canada, 5 countries) Dec 7, 2023
@FedeGueli
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248 now

@NkRMnZr NkRMnZr changed the title Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (222 seqs, mainly in Canada, 5 countries) Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (248 seqs, mainly in Canada, 7 countries) Dec 15, 2023
@NkRMnZr NkRMnZr changed the title Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (248 seqs, mainly in Canada, 7 countries) Another EG.5.1.4 (side-branch of JJ.1) with ORF3:P240L and S:L455F (383 seqs, mainly in Canada, 9 countries) Jan 14, 2024
@FedeGueli
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@krosa1910
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krosa1910 commented Mar 1, 2024 •
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There seems a major stepwise mutation branch here ,defined by G28079T->T508C->G28089C(Orf8:G66R)->G14398A(Orf1ab:V4712M)->C12484T->T14514C->C27567T->G8258T(Orf1ab:V2665F),A11782G

Screenshot 2024-03-01 at 11 38 28 AM **All Sequences** Screenshot 2024-03-01 at 11 44 47 AM **Recent Saltation Branch** Screenshot 2024-03-01 at 11 44 55 AM **Showing Saltation dominates this tree now** Screenshot 2024-03-01 at 11 39 00 AM **How I discovered it and its prevalence in recent samples**

@DailyCovidCases
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Please close this issue

@NkRMnZr NkRMnZr closed this as not planned Won't fix, can't repro, duplicate, stale May 29, 2024
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@FedeGueli @DailyCovidCases @NkRMnZr @krosa1910