EG.5.1.1 with ORF3a:D155H and S:S494P, already with spike diveristy of S:R403T, S:S704L etc. (478 seqs, 16 countries)

[NkRMnZr]

Taken from Branch 1 of multitask sars-cov-2-variants/lineage-proposals#648

Defining Mutations: EG.5.1.1 > G25855C(ORF3a:D155H) > T23042C(S:S494P) Query: C6541T, T23042C, G25855C Earliest seq: 2023-07-04 (EPI_ISL_18046800, South Korea) Latest seq: 2023-08-18 (EPI_ISL_18208475, Shanghai, China) Sampled Countries: South Korea (31), China (7: Shanghai/3; Gansu/2; Anhui/1; Henan/1), Israel (1), South Africa (1)

Genomes:

`EPI_ISL_18046800, EPI_ISL_18047579, EPI_ISL_18047616, EPI_ISL_18067477, EPI_ISL_18067703, EPI_ISL_18067843, EPI_ISL_18068488, EPI_ISL_18096876, EPI_ISL_18105782, EPI_ISL_18111600, EPI_ISL_18113582, EPI_ISL_18114674, EPI_ISL_18114826, EPI_ISL_18114912, EPI_ISL_18116437, EPI_ISL_18116466, EPI_ISL_18116549, EPI_ISL_18116640, EPI_ISL_18116815, EPI_ISL_18117127, EPI_ISL_18117318, EPI_ISL_18117416, EPI_ISL_18117444, EPI_ISL_18117550, EPI_ISL_18117652, EPI_ISL_18117880, EPI_ISL_18118004, EPI_ISL_18138008, EPI_ISL_18139779, EPI_ISL_18139815, EPI_ISL_18139893, EPI_ISL_18140132, EPI_ISL_18140336, EPI_ISL_18140544, EPI_ISL_18140567, EPI_ISL_18165816, EPI_ISL_18165845, EPI_ISL_18165967, EPI_ISL_18208326, EPI_ISL_18208475`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1aa71_311810.json?f_userOrOld=uploaded%20sample

[FedeGueli]

47 now Quinqhai and South Korea

[NkRMnZr]

Tracking updates

23-09-08, 16 seqs from Canada, China, France and South Korea

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3f185_c31a00.json?f_userOrOld=uploaded%20sample&label=id:node_6952382  `EPI_ISL_18213354, EPI_ISL_18213358, EPI_ISL_18213718, EPI_ISL_18213965, EPI_ISL_18214081, EPI_ISL_18214214, EPI_ISL_18214374, EPI_ISL_18217175, EPI_ISL_18232621, EPI_ISL_18232729, EPI_ISL_18236903, EPI_ISL_18236948, EPI_ISL_18237006, EPI_ISL_18237464, EPI_ISL_18239465, EPI_ISL_18240590`

09-15, 6 seqs from China, and South Korea

`EPI_ISL_18246319, EPI_ISL_18246343, EPI_ISL_18254210, EPI_ISL_18254233, EPI_ISL_18254912, EPI_ISL_18261453`

09-23, 28 seqs from Canada, China, France, South Korea and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_16375_ee3040.json?f_userOrOld=uploaded%20sample&label=id:node_6959006  `EPI_ISL_18271679, EPI_ISL_18271740, EPI_ISL_18271894, EPI_ISL_18272009, EPI_ISL_18272091, EPI_ISL_18272189, EPI_ISL_18272253, EPI_ISL_18272274, EPI_ISL_18272279, EPI_ISL_18272330, EPI_ISL_18274279, EPI_ISL_18276057, EPI_ISL_18278535, EPI_ISL_18278559, EPI_ISL_18279187, EPI_ISL_18284780, EPI_ISL_18284837, EPI_ISL_18284875, EPI_ISL_18284924, EPI_ISL_18292997, EPI_ISL_18293027, EPI_ISL_18293408, EPI_ISL_18293462, EPI_ISL_18293694, EPI_ISL_18293727, EPI_ISL_18294432, EPI_ISL_18295736, EPI_ISL_18296328`

09-28, 27 seqs from China, Singapore, South Korea, Sweden and USA. A Branch of S:R403T and another one with S:S704L emerged

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1f28d_55d9d0.json?f_userOrOld=uploaded%20sample&label=id:node_6964970  `EPI_ISL_18303517, EPI_ISL_18307124, EPI_ISL_18309339, EPI_ISL_18312308, EPI_ISL_18312478, EPI_ISL_18312513, EPI_ISL_18312553, EPI_ISL_18312561, EPI_ISL_18312604, EPI_ISL_18312627, EPI_ISL_18312633, EPI_ISL_18312673, EPI_ISL_18312682, EPI_ISL_18312740, EPI_ISL_18312851, EPI_ISL_18312860, EPI_ISL_18312870, EPI_ISL_18312919, EPI_ISL_18312921, EPI_ISL_18312939, EPI_ISL_18312994, EPI_ISL_18313011, EPI_ISL_18313017, EPI_ISL_18313030, EPI_ISL_18313059, EPI_ISL_18320815, EPI_ISL_18320817` Query for `S:R403T` sub-branch: `G22770C, T23042C` Query for `S:S704L` sub-branch: `T877C, C23673T, C27752T`

10-07, 42 seqs from Canada, China, Germany, Japan, S. Korea, Singapore, Sweden, and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3d67a_2aa420.json?f_userOrOld=uploaded%20sample&label=id:node_3433858  `EPI_ISL_18324088, EPI_ISL_18324112, EPI_ISL_18327598, EPI_ISL_18338367, EPI_ISL_18339290, EPI_ISL_18343319, EPI_ISL_18343921, EPI_ISL_18352173, EPI_ISL_18353944, EPI_ISL_18353966, EPI_ISL_18353968, EPI_ISL_18354151, EPI_ISL_18354296, EPI_ISL_18354358, EPI_ISL_18354400, EPI_ISL_18355080, EPI_ISL_18355094, EPI_ISL_18355096, EPI_ISL_18355263, EPI_ISL_18355274, EPI_ISL_18355290, EPI_ISL_18355364, EPI_ISL_18355398, EPI_ISL_18355428, EPI_ISL_18355544, EPI_ISL_18355548, EPI_ISL_18355553, EPI_ISL_18355559, EPI_ISL_18355561, EPI_ISL_18355565, EPI_ISL_18360090, EPI_ISL_18360102, EPI_ISL_18360109-18360111, EPI_ISL_18360114, EPI_ISL_18360133, EPI_ISL_18360144, EPI_ISL_18360148, EPI_ISL_18360152-18360153, EPI_ISL_18360265`

10-14, 23 seqs from Canada, Japan, S. Korea, Singapore,and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_24e3e_abaa50.json?f_userOrOld=uploaded%20sample&label=id:node_3444135  `EPI_ISL_18361902, EPI_ISL_18366270, EPI_ISL_18369564, EPI_ISL_18374510, EPI_ISL_18374512, EPI_ISL_18376694, EPI_ISL_18376738, EPI_ISL_18376772, EPI_ISL_18381247, EPI_ISL_18381859, EPI_ISL_18381861, EPI_ISL_18382060, EPI_ISL_18382099, EPI_ISL_18382141, EPI_ISL_18382176, EPI_ISL_18382268, EPI_ISL_18382656, EPI_ISL_18382729, EPI_ISL_18382754, EPI_ISL_18382884, EPI_ISL_18382955`

10-23, 51 seqs from Canada, China, France, Japan, S. Korea, Singapore, Sweden, and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_23e71_74e130.json?f_userOrOld=uploaded%20sample&label=id:node_3462739  `EPI_ISL_18396677, EPI_ISL_18397231, EPI_ISL_18400033, EPI_ISL_18401775, EPI_ISL_18401879, EPI_ISL_18401884, EPI_ISL_18401912, EPI_ISL_18404952, EPI_ISL_18406108, EPI_ISL_18406159, EPI_ISL_18406215, EPI_ISL_18406222, EPI_ISL_18408792, EPI_ISL_18408794, EPI_ISL_18408934, EPI_ISL_18408936, EPI_ISL_18408938-18408941, EPI_ISL_18408948, EPI_ISL_18408957-18408958, EPI_ISL_18408967, EPI_ISL_18408973, EPI_ISL_18408978, EPI_ISL_18408990-18408991, EPI_ISL_18409002, EPI_ISL_18409010, EPI_ISL_18409014, EPI_ISL_18409030, EPI_ISL_18409058, EPI_ISL_18409087, EPI_ISL_18409114, EPI_ISL_18409123, EPI_ISL_18409162, EPI_ISL_18409170, EPI_ISL_18409341, EPI_ISL_18411054, EPI_ISL_18411098, EPI_ISL_18411138, EPI_ISL_18411162, EPI_ISL_18411262, EPI_ISL_18411278, EPI_ISL_18411299, EPI_ISL_18413066, EPI_ISL_18418065-18418066, EPI_ISL_18419603, EPI_ISL_18426121`

10-28, 18 seqs from Australia, China, South Korea, and Singapore

`EPI_ISL_18428779, EPI_ISL_18435014, EPI_ISL_18435016, EPI_ISL_18435651, EPI_ISL_18435655, EPI_ISL_18435797, EPI_ISL_18438907, EPI_ISL_18439132, EPI_ISL_18439212, EPI_ISL_18439215, EPI_ISL_18439279, EPI_ISL_18439291, EPI_ISL_18439385, EPI_ISL_18439434-18439435, EPI_ISL_18439465, EPI_ISL_18439471, EPI_ISL_18442715`

11-05, 31 seqs from Canada, China, S.Korea and Thailand

`EPI_ISL_18449878, EPI_ISL_18454312, EPI_ISL_18456337, EPI_ISL_18460544, EPI_ISL_18460548, EPI_ISL_18460552, EPI_ISL_18460574, EPI_ISL_18460582, EPI_ISL_18460586, EPI_ISL_18460626, EPI_ISL_18460652, EPI_ISL_18460683, EPI_ISL_18460702, EPI_ISL_18460785, EPI_ISL_18460829, EPI_ISL_18460838, EPI_ISL_18460932, EPI_ISL_18461049, EPI_ISL_18461070, EPI_ISL_18461092, EPI_ISL_18461101, EPI_ISL_18461113, EPI_ISL_18461121, EPI_ISL_18461123, EPI_ISL_18461144, EPI_ISL_18461180, EPI_ISL_18461182, EPI_ISL_18465273, EPI_ISL_18465307, EPI_ISL_18465341, EPI_ISL_18465348`

11-18, 64 seqs from China, Japan, S.Korea, Russia, Singapore, Sweden, and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_32001_a26b00.json?f_userOrOld=uploaded%20sample&label=id:node_3480217  `EPI_ISL_18470748, EPI_ISL_18473466, EPI_ISL_18475265, EPI_ISL_18481135, EPI_ISL_18484311, EPI_ISL_18484335, EPI_ISL_18484386, EPI_ISL_18486936, EPI_ISL_18487445, EPI_ISL_18487815, EPI_ISL_18488820, EPI_ISL_18489007, EPI_ISL_18490063, EPI_ISL_18490069, EPI_ISL_18495658, EPI_ISL_18495944, EPI_ISL_18501969, EPI_ISL_18501991, EPI_ISL_18502032, EPI_ISL_18503519, EPI_ISL_18503523, EPI_ISL_18503543, EPI_ISL_18503548, EPI_ISL_18503556, EPI_ISL_18503580, EPI_ISL_18503610, EPI_ISL_18503622, EPI_ISL_18503781, EPI_ISL_18503785, EPI_ISL_18503798, EPI_ISL_18503839, EPI_ISL_18503894, EPI_ISL_18503903, EPI_ISL_18507987, EPI_ISL_18508500, EPI_ISL_18508512, EPI_ISL_18508526-18508527, EPI_ISL_18511044, EPI_ISL_18511066, EPI_ISL_18511117, EPI_ISL_18511126, EPI_ISL_18511214, EPI_ISL_18511262, EPI_ISL_18511302, EPI_ISL_18511340, EPI_ISL_18511370, EPI_ISL_18511381-18511382, EPI_ISL_18511390-18511391, EPI_ISL_18511398-18511399, EPI_ISL_18511408-18511409, EPI_ISL_18511413, EPI_ISL_18511417-18511418, EPI_ISL_18511427-18511428, EPI_ISL_18511438-18511439, EPI_ISL_18511447, EPI_ISL_18511588`

12-02, 42 seqs from China, S.Korea, UK, and USA

`EPI_ISL_18521534, EPI_ISL_18525068, EPI_ISL_18525568, EPI_ISL_18529276, EPI_ISL_18535363, EPI_ISL_18539060, EPI_ISL_18539271-18539272, EPI_ISL_18539274, EPI_ISL_18539279, EPI_ISL_18539283, EPI_ISL_18539286, EPI_ISL_18539297, EPI_ISL_18539329, EPI_ISL_18539331, EPI_ISL_18539337, EPI_ISL_18539340, EPI_ISL_18539347-18539348, EPI_ISL_18539350, EPI_ISL_18539396, EPI_ISL_18539592, EPI_ISL_18539660, EPI_ISL_18539704, EPI_ISL_18539716, EPI_ISL_18539729, EPI_ISL_18539761, EPI_ISL_18555464, EPI_ISL_18564353, EPI_ISL_18564429, EPI_ISL_18564485, EPI_ISL_18564563, EPI_ISL_18564590, EPI_ISL_18564919, EPI_ISL_18564965, EPI_ISL_18565021, EPI_ISL_18565027, EPI_ISL_18565104, EPI_ISL_18565120, EPI_ISL_18565132, EPI_ISL_18565173, EPI_ISL_18570049`

12-14, 25 seqs from China, S. Korea, Luxembourg, Poland, Sweden, USA

`EPI_ISL_18580300, EPI_ISL_18580590, EPI_ISL_18580593, EPI_ISL_18580600, EPI_ISL_18580612, EPI_ISL_18597072, EPI_ISL_18597139, EPI_ISL_18597334, EPI_ISL_18597557, EPI_ISL_18597572, EPI_ISL_18597673, EPI_ISL_18597840, EPI_ISL_18597986, EPI_ISL_18598044, EPI_ISL_18601478, EPI_ISL_18607499, EPI_ISL_18611812, EPI_ISL_18614622, EPI_ISL_18614940, EPI_ISL_18625243, EPI_ISL_18631123, EPI_ISL_18631129, EPI_ISL_18631551, EPI_ISL_18633701, EPI_ISL_18633706`

24-01-13, 65 seqs from Canada, China, S. Korea, Luxembourg, Poland, Russia, Ukraine and USA

`EPI_ISL_18634061, EPI_ISL_18634088, EPI_ISL_18634094, EPI_ISL_18634101, EPI_ISL_18634157, EPI_ISL_18634160, EPI_ISL_18634163, EPI_ISL_18634173, EPI_ISL_18634176, EPI_ISL_18634279, EPI_ISL_18634294, EPI_ISL_18634304, EPI_ISL_18638484-18638485, EPI_ISL_18638501, EPI_ISL_18638547, EPI_ISL_18638567, EPI_ISL_18639441, EPI_ISL_18639888, EPI_ISL_18639957, EPI_ISL_18643272, EPI_ISL_18646376, EPI_ISL_18662730, EPI_ISL_18663501, EPI_ISL_18672047, EPI_ISL_18672049, EPI_ISL_18672078, EPI_ISL_18672091, EPI_ISL_18672095, EPI_ISL_18672107, EPI_ISL_18674345, EPI_ISL_18674429, EPI_ISL_18679859, EPI_ISL_18679879, EPI_ISL_18683297, EPI_ISL_18685300, EPI_ISL_18685781, EPI_ISL_18686111, EPI_ISL_18686725, EPI_ISL_18687063, EPI_ISL_18687636, EPI_ISL_18690523, EPI_ISL_18697514, EPI_ISL_18697851, EPI_ISL_18697871, EPI_ISL_18700290, EPI_ISL_18700329, EPI_ISL_18700333, EPI_ISL_18706542, EPI_ISL_18707155, EPI_ISL_18710528, EPI_ISL_18711495, EPI_ISL_18711917, EPI_ISL_18712023, EPI_ISL_18712205, EPI_ISL_18715061, EPI_ISL_18723486, EPI_ISL_18728043, EPI_ISL_18732939, EPI_ISL_18733402, EPI_ISL_18733506, EPI_ISL_18736258, EPI_ISL_18736623, EPI_ISL_18751720, EPI_ISL_18751820`

[FedeGueli]

77 as today

Ass the most of lineages little hopes vs HK.3 : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=C6541T%2CT23042C%2CG25855C&analysisMode=CompareToBaseline&

[DailyCovidCases]

Please close this issue