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JN.1 +Orf3a:L85F + ORF1a:T2152I +S:T572I (650 ). With a S:F456L sub-branch (384) with Multiple branches of interest: 1) R346T Branch (62) 2) S:S60P,S:W64L branch (23) 3) Orf9b:E7V branch (44) #2461

Closed FedeGueli closed 2 months ago

FedeGueli commented 8 months ago

transferred from Branch 14 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1097 EDITED on June 19 Now JN.1.65: JN.1 >> Orf3a:L85F (G25647T) > T23629C > A5053G, ORF1a:T2152I (C6720T)> S:T572I (C23277T) Query: C23277T, A5053G ,C6720T Country: Uk Samples:469

IDs EPI_ISL_18684531, EPI_ISL_18684647-18684648, EPI_ISL_18684650-18684651, EPI_ISL_18684765, EPI_ISL_18688351, EPI_ISL_18688369, EPI_ISL_18688406, EPI_ISL_18688468, EPI_ISL_18688472, EPI_ISL_18688476, EPI_ISL_18694531, EPI_ISL_18707741, EPI_ISL_18707846, EPI_ISL_18712894, EPI_ISL_18712900, EPI_ISL_18727128, EPI_ISL_18735596, EPI_ISL_18735610, EPI_ISL_18735617, EPI_ISL_18735633, EPI_ISL_18735638, EPI_ISL_18763566, EPI_ISL_18763706, EPI_ISL_18763739, EPI_ISL_18763916, EPI_ISL_18763918, EPI_ISL_18764279, EPI_ISL_18764324, EPI_ISL_18764350, EPI_ISL_18764375, EPI_ISL_18771812, EPI_ISL_18782642, EPI_ISL_18782650, EPI_ISL_18782762, EPI_ISL_18793755, EPI_ISL_18800507, EPI_ISL_18800687, EPI_ISL_18800702, EPI_ISL_18800768, EPI_ISL_18809664, EPI_ISL_18809674, EPI_ISL_18809680, EPI_ISL_18809768, EPI_ISL_18809806, EPI_ISL_18821717, EPI_ISL_18825003, EPI_ISL_18825046, EPI_ISL_18830621, EPI_ISL_18831842, EPI_ISL_18842841, EPI_ISL_18854606-18854607, EPI_ISL_18854664, EPI_ISL_18854695, EPI_ISL_18854732, EPI_ISL_18860690, EPI_ISL_18860838, EPI_ISL_18867115, EPI_ISL_18867150, EPI_ISL_18867170-18867171, EPI_ISL_18867186, EPI_ISL_18867235, EPI_ISL_18867237, EPI_ISL_18867246, EPI_ISL_18877469, EPI_ISL_18877522, EPI_ISL_18877532-18877533, EPI_ISL_18881026, EPI_ISL_18881411, EPI_ISL_18881565, EPI_ISL_18881572, EPI_ISL_18881639, EPI_ISL_18881676, EPI_ISL_18881716, EPI_ISL_18881782, EPI_ISL_18881786, EPI_ISL_18885365, EPI_ISL_18890651, EPI_ISL_18890658, EPI_ISL_18901473, EPI_ISL_18901481, EPI_ISL_18910236, EPI_ISL_18910243, EPI_ISL_18910294, EPI_ISL_18910384, EPI_ISL_18910388, EPI_ISL_18910392, EPI_ISL_18913399, EPI_ISL_18913484, EPI_ISL_18926656, EPI_ISL_18926683, EPI_ISL_18932469, EPI_ISL_18932491, EPI_ISL_18932493, EPI_ISL_18932509, EPI_ISL_18932526, EPI_ISL_18932544, EPI_ISL_18932595, EPI_ISL_18932611, EPI_ISL_18932622, EPI_ISL_18932626, EPI_ISL_18932741, EPI_ISL_18932748, EPI_ISL_18932802, EPI_ISL_18932806, EPI_ISL_18936357, EPI_ISL_18936381, EPI_ISL_18936388, EPI_ISL_18936392, EPI_ISL_18944071, EPI_ISL_18944089, EPI_ISL_18944123, EPI_ISL_18944138, EPI_ISL_18951109, EPI_ISL_18951113, EPI_ISL_18951119, EPI_ISL_18969285, EPI_ISL_18969296, EPI_ISL_18969472, EPI_ISL_18969480, EPI_ISL_18969510, EPI_ISL_18969512, EPI_ISL_18976298, EPI_ISL_18983519, EPI_ISL_18987628, EPI_ISL_18987660, EPI_ISL_18987672, EPI_ISL_18987677, EPI_ISL_18987734, EPI_ISL_18993577, EPI_ISL_18993581, EPI_ISL_18993592, EPI_ISL_19002144, EPI_ISL_19002157, EPI_ISL_19002162, EPI_ISL_19006607, EPI_ISL_19006626, EPI_ISL_19006700, EPI_ISL_19006723, EPI_ISL_19010296, EPI_ISL_19010329, EPI_ISL_19010335-19010337, EPI_ISL_19010426, EPI_ISL_19022882, EPI_ISL_19022931, EPI_ISL_19022989, EPI_ISL_19023011, EPI_ISL_19023038, EPI_ISL_19023071, EPI_ISL_19023110, EPI_ISL_19025890, EPI_ISL_19025916, EPI_ISL_19025919, EPI_ISL_19033350, EPI_ISL_19033911, EPI_ISL_19033942, EPI_ISL_19036248, EPI_ISL_19044471, EPI_ISL_19044593, EPI_ISL_19044598, EPI_ISL_19050414, EPI_ISL_19050557, EPI_ISL_19053436, EPI_ISL_19053555, EPI_ISL_19055598, EPI_ISL_19055604-19055606, EPI_ISL_19055608, EPI_ISL_19055611, EPI_ISL_19055691, EPI_ISL_19062578, EPI_ISL_19062829, EPI_ISL_19069644, EPI_ISL_19069674, EPI_ISL_19072210-19072211, EPI_ISL_19086847, EPI_ISL_19088201, EPI_ISL_19094350, EPI_ISL_19095494, EPI_ISL_19108595, EPI_ISL_19108707, EPI_ISL_19109642, EPI_ISL_19131015, EPI_ISL_19131019, EPI_ISL_19132948, EPI_ISL_19132956, EPI_ISL_19139041, EPI_ISL_19139118, EPI_ISL_19139281, EPI_ISL_19140784, EPI_ISL_19140805, EPI_ISL_19140993, EPI_ISL_19141024, EPI_ISL_19141029, EPI_ISL_19141034, EPI_ISL_19141036-19141037, EPI_ISL_19141043, EPI_ISL_19143904-19143909, EPI_ISL_19143911, EPI_ISL_19143917, EPI_ISL_19143923, EPI_ISL_19144180, EPI_ISL_19144197, EPI_ISL_19144618, EPI_ISL_19145550, EPI_ISL_19146225, EPI_ISL_19146330, EPI_ISL_19146333, EPI_ISL_19146351, EPI_ISL_19146361, EPI_ISL_19146364, EPI_ISL_19147157, EPI_ISL_19151164, EPI_ISL_19151440, EPI_ISL_19157480-19157481, EPI_ISL_19157651, EPI_ISL_19157653, EPI_ISL_19159971-19159972, EPI_ISL_19161853, EPI_ISL_19162085, EPI_ISL_19163971-19163972, EPI_ISL_19164413, EPI_ISL_19164656, EPI_ISL_19164707, EPI_ISL_19164727, EPI_ISL_19164729-19164730, EPI_ISL_19165288, EPI_ISL_19165386, EPI_ISL_19165403, EPI_ISL_19165812, EPI_ISL_19165857, EPI_ISL_19165867, EPI_ISL_19165872, EPI_ISL_19165876-19165877, EPI_ISL_19165885, EPI_ISL_19166083, EPI_ISL_19166137, EPI_ISL_19166140, EPI_ISL_19166226, EPI_ISL_19167758, EPI_ISL_19167873, EPI_ISL_19167887, EPI_ISL_19175150, EPI_ISL_19175162-19175164, EPI_ISL_19175167, EPI_ISL_19175194-19175195, EPI_ISL_19175297-19175298, EPI_ISL_19175440, EPI_ISL_19175446, EPI_ISL_19175450, EPI_ISL_19175481, EPI_ISL_19175503, EPI_ISL_19175518-19175519, EPI_ISL_19175522, EPI_ISL_19176303-19176304, EPI_ISL_19176346, EPI_ISL_19176364, EPI_ISL_19176382, EPI_ISL_19176639, EPI_ISL_19176641, EPI_ISL_19176643, EPI_ISL_19176646, EPI_ISL_19176652, EPI_ISL_19176658, EPI_ISL_19176909, EPI_ISL_19177779, EPI_ISL_19178510-19178511, EPI_ISL_19178516-19178517, EPI_ISL_19178521, EPI_ISL_19178524, EPI_ISL_19178534, EPI_ISL_19178536, EPI_ISL_19178540, EPI_ISL_19178548, EPI_ISL_19178550, EPI_ISL_19178558, EPI_ISL_19178561, EPI_ISL_19178568, EPI_ISL_19178573, EPI_ISL_19178576-19178577, EPI_ISL_19178588, EPI_ISL_19178596, EPI_ISL_19178602, EPI_ISL_19178605, EPI_ISL_19178870, EPI_ISL_19178877, EPI_ISL_19178881, EPI_ISL_19178963, EPI_ISL_19178968, EPI_ISL_19179031, EPI_ISL_19181403, EPI_ISL_19181412, EPI_ISL_19183236, EPI_ISL_19183639, EPI_ISL_19185413, EPI_ISL_19185416, EPI_ISL_19185472, EPI_ISL_19185639, EPI_ISL_19186480, EPI_ISL_19186482, EPI_ISL_19186670, EPI_ISL_19187535, EPI_ISL_19187545, EPI_ISL_19187554, EPI_ISL_19187605, EPI_ISL_19187716, EPI_ISL_19187917-19187918, EPI_ISL_19187921-19187922, EPI_ISL_19187935, EPI_ISL_19187953, EPI_ISL_19187955, EPI_ISL_19187959, EPI_ISL_19187967, EPI_ISL_19187974, EPI_ISL_19187981, EPI_ISL_19188092, EPI_ISL_19188097, EPI_ISL_19188099, EPI_ISL_19188410, EPI_ISL_19188424, EPI_ISL_19188428, EPI_ISL_19189750, EPI_ISL_19189775-19189776, EPI_ISL_19189812-19189816, EPI_ISL_19190049, EPI_ISL_19190058-19190060, EPI_ISL_19190062, EPI_ISL_19190077, EPI_ISL_19190366-19190367, EPI_ISL_19190380-19190381, EPI_ISL_19190384-19190385, EPI_ISL_19190387, EPI_ISL_19190904, EPI_ISL_19191191, EPI_ISL_19191280, EPI_ISL_19191290, EPI_ISL_19191312, EPI_ISL_19191398, EPI_ISL_19191417, EPI_ISL_19191426, EPI_ISL_19191556, EPI_ISL_19191784, EPI_ISL_19192197, EPI_ISL_19192205, EPI_ISL_19192207, EPI_ISL_19193420, EPI_ISL_19193860, EPI_ISL_19193876, EPI_ISL_19193916, EPI_ISL_19193921, EPI_ISL_19193928-19193929, EPI_ISL_19193932, EPI_ISL_19193942, EPI_ISL_19193945, EPI_ISL_19193995, EPI_ISL_19193997-19193999, EPI_ISL_19194005, EPI_ISL_19194009, EPI_ISL_19194013, EPI_ISL_19194462, EPI_ISL_19194764, EPI_ISL_19194771, EPI_ISL_19194784, EPI_ISL_19194786, EPI_ISL_19194791, EPI_ISL_19194804, EPI_ISL_19194813, EPI_ISL_19194817, EPI_ISL_19194828, EPI_ISL_19194843, EPI_ISL_19194845, EPI_ISL_19194855, EPI_ISL_19194893, EPI_ISL_19194905, EPI_ISL_19194914-19194915, EPI_ISL_19194953, EPI_ISL_19194961-19194962, EPI_ISL_19194983, EPI_ISL_19195000, EPI_ISL_19195009, EPI_ISL_19195035, EPI_ISL_19195044, EPI_ISL_19195060, EPI_ISL_19195063, EPI_ISL_19195095-19195096, EPI_ISL_19195104, EPI_ISL_19195119, EPI_ISL_19195781, EPI_ISL_19197010, EPI_ISL_19197150, EPI_ISL_19197181, EPI_ISL_19197900, EPI_ISL_19197910, EPI_ISL_19198462, EPI_ISL_19198471, EPI_ISL_19198523, EPI_ISL_19199255, EPI_ISL_19201275, EPI_ISL_19201303, EPI_ISL_19201314, EPI_ISL_19201371, EPI_ISL_19201427, EPI_ISL_19201513, EPI_ISL_19201521, EPI_ISL_19201526, EPI_ISL_19201589, EPI_ISL_19201592, EPI_ISL_19201634, EPI_ISL_19201646, EPI_ISL_19201652, EPI_ISL_19201696, EPI_ISL_19201699, EPI_ISL_19201704, EPI_ISL_19201716, EPI_ISL_19201728, EPI_ISL_19201730, EPI_ISL_19203586, EPI_ISL_19203623

NOW JN.1.65.1: BRANCH with S:F456L There is a further COMBO branch with S:F456L spotted and tracked by @aviczhl2 JN.1 >> Orf3a:L85F (G25647T) > T23629C > A5053G, ORF1a:T2152I (C6720T)> S:T572I (C23277T)>C5884T, Orf1b:S2339F (C20483T), C29149T > S:F456L (T22928C) A5053G ,C6720T,T22928C, 229 seqs, Spain, Italy, Netherlands, France, US, Portugal, Canada, Canary Isl.,Israel, England

IDs EPI_ISL_19033350, EPI_ISL_19036248, EPI_ISL_19050414, EPI_ISL_19072210-19072211, EPI_ISL_19094350, EPI_ISL_19095494, EPI_ISL_19108707, EPI_ISL_19109642, EPI_ISL_19131015, EPI_ISL_19131019, EPI_ISL_19132948, EPI_ISL_19132956, EPI_ISL_19139281, EPI_ISL_19140784, EPI_ISL_19140805, EPI_ISL_19140993, EPI_ISL_19141024, EPI_ISL_19141034, EPI_ISL_19141036-19141037, EPI_ISL_19141043, EPI_ISL_19144180, EPI_ISL_19144197, EPI_ISL_19144618, EPI_ISL_19145550, EPI_ISL_19146330, EPI_ISL_19146333, EPI_ISL_19146351, EPI_ISL_19146361, EPI_ISL_19146364, EPI_ISL_19151440, EPI_ISL_19157480-19157481, EPI_ISL_19157651, EPI_ISL_19157653, EPI_ISL_19162085, EPI_ISL_19163971-19163972, EPI_ISL_19164413, EPI_ISL_19164656, EPI_ISL_19164707, EPI_ISL_19164727, EPI_ISL_19164729-19164730, EPI_ISL_19165386, EPI_ISL_19165403, EPI_ISL_19165812, EPI_ISL_19165857, EPI_ISL_19165867, EPI_ISL_19165872, EPI_ISL_19165876-19165877, EPI_ISL_19165885, EPI_ISL_19166083, EPI_ISL_19166137, EPI_ISL_19166140, EPI_ISL_19166226, EPI_ISL_19167758, EPI_ISL_19167873, EPI_ISL_19167887, EPI_ISL_19175150, EPI_ISL_19175162-19175164, EPI_ISL_19175167, EPI_ISL_19175194-19175195, EPI_ISL_19175297-19175298, EPI_ISL_19175440, EPI_ISL_19175446, EPI_ISL_19175481, EPI_ISL_19175503, EPI_ISL_19175518-19175519, EPI_ISL_19175522, EPI_ISL_19176303-19176304, EPI_ISL_19176346, EPI_ISL_19176364, EPI_ISL_19176382, EPI_ISL_19177779, EPI_ISL_19178548, EPI_ISL_19178550, EPI_ISL_19178558, EPI_ISL_19178561, EPI_ISL_19178568, EPI_ISL_19178573, EPI_ISL_19178576-19178577, EPI_ISL_19178588, EPI_ISL_19178596, EPI_ISL_19178602, EPI_ISL_19178605, EPI_ISL_19178870, EPI_ISL_19178877, EPI_ISL_19178881, EPI_ISL_19178963, EPI_ISL_19178968, EPI_ISL_19179031, EPI_ISL_19181403, EPI_ISL_19181412, EPI_ISL_19183639, EPI_ISL_19185413, EPI_ISL_19185416, EPI_ISL_19185472, EPI_ISL_19185639, EPI_ISL_19186480, EPI_ISL_19186482, EPI_ISL_19186670, EPI_ISL_19187535, EPI_ISL_19187545, EPI_ISL_19187554, EPI_ISL_19187605, EPI_ISL_19187917-19187918, EPI_ISL_19187921-19187922, EPI_ISL_19187935, EPI_ISL_19187953, EPI_ISL_19187955, EPI_ISL_19188092, EPI_ISL_19188097, EPI_ISL_19188099, EPI_ISL_19189750, EPI_ISL_19189775-19189776, EPI_ISL_19189812-19189816, EPI_ISL_19190049, EPI_ISL_19190058-19190060, EPI_ISL_19190062, EPI_ISL_19190077, EPI_ISL_19190366-19190367, EPI_ISL_19190904, EPI_ISL_19191191, EPI_ISL_19191280, EPI_ISL_19191290, EPI_ISL_19191312, EPI_ISL_19191398, EPI_ISL_19191417, EPI_ISL_19191426, EPI_ISL_19191556, EPI_ISL_19191784, EPI_ISL_19192197, EPI_ISL_19192205, EPI_ISL_19192207, EPI_ISL_19193420, EPI_ISL_19193860, EPI_ISL_19193876, EPI_ISL_19193916, EPI_ISL_19193921, EPI_ISL_19193928-19193929, EPI_ISL_19193932, EPI_ISL_19193942, EPI_ISL_19193945, EPI_ISL_19193995, EPI_ISL_19193997-19193999, EPI_ISL_19194005, EPI_ISL_19194009, EPI_ISL_19194013, EPI_ISL_19194462, EPI_ISL_19194764, EPI_ISL_19194771, EPI_ISL_19194784, EPI_ISL_19194786, EPI_ISL_19194791, EPI_ISL_19194804, EPI_ISL_19194813, EPI_ISL_19194817, EPI_ISL_19194843, EPI_ISL_19194845, EPI_ISL_19194855, EPI_ISL_19194893, EPI_ISL_19194905, EPI_ISL_19194914-19194915, EPI_ISL_19194924, EPI_ISL_19194953, EPI_ISL_19194961-19194962, EPI_ISL_19194983, EPI_ISL_19195009, EPI_ISL_19195035, EPI_ISL_19195044, EPI_ISL_19195060, EPI_ISL_19195063, EPI_ISL_19195095-19195096, EPI_ISL_19195104, EPI_ISL_19195781, EPI_ISL_19197010, EPI_ISL_19197900, EPI_ISL_19197910, EPI_ISL_19198462, EPI_ISL_19198471, EPI_ISL_19198523, EPI_ISL_19199255, EPI_ISL_19201275, EPI_ISL_19201303, EPI_ISL_19201314, EPI_ISL_19201371, EPI_ISL_19201418, EPI_ISL_19201427, EPI_ISL_19201513, EPI_ISL_19201521, EPI_ISL_19201526, EPI_ISL_19201589, EPI_ISL_19201592, EPI_ISL_19201634, EPI_ISL_19201646, EPI_ISL_19201652, EPI_ISL_19201696, EPI_ISL_19201699, EPI_ISL_19201704, EPI_ISL_19201716, EPI_ISL_19201728, EPI_ISL_19201730, EPI_ISL_19203623

There are further branches of interest:

Now MF.1: Branch with TRIO (346T 456L 572I): thanks to @NkRMnZr for highlighting the previous query was not catching most of them JN.1 >> Orf3a:L85F (G25647T) > T23629C > A5053G, ORF1a:T2152I (C6720T)> S:T572I (C23277T)>C5884T, Orf1b:S2339F (C20483T), C29149T > S:F456L (T22928C)> Reversion Orf1b:F2339FS (T20483C)> SIlent S:Y473Y (T22981C) > Silent S:Y37Y (T21673C), S:R346T (G22599C)
Query: T22981C,T21673C ,G22599C Samples:30 (Spain , US, France, Israel, Italy)

IDs EPI_ISL_19094350, EPI_ISL_19141036, EPI_ISL_19175162, EPI_ISL_19176364, EPI_ISL_19177779, EPI_ISL_19179031, EPI_ISL_19183639, EPI_ISL_19187921, EPI_ISL_19188424, EPI_ISL_19189750, EPI_ISL_19189775-19189776, EPI_ISL_19191398, EPI_ISL_19191417, EPI_ISL_19191426, EPI_ISL_19191556, EPI_ISL_19193928, EPI_ISL_19194773, EPI_ISL_19194845, EPI_ISL_19194914-19194915, EPI_ISL_19195096, EPI_ISL_19195104, EPI_ISL_19197181, EPI_ISL_19198523, EPI_ISL_19201589, EPI_ISL_19201592, EPI_ISL_19201646, EPI_ISL_19201716, EPI_ISL_19203623

NOW MF.2: On the S:F456L Branch Sublineage with further S:S60P S:W64L spotted by @NkRMnZr (see comments) JN.1 >> Orf3a:L85F (G25647T) > T23629C > A5053G, ORF1a:T2152I (C6720T)> S:T572I (C23277T)>C5884T, Orf1b:S2339F (C20483T), C29149T > S:F456L (T22928C) > S:S60P (T21740C), S:W64L (G21753T) Query: T21740C,G21753T,T3565C [EDITED there was a typo between S:W64L (correct)and S:W64R(wrong)] Samples: 19 (Spain, England, Ireland, US)

IDs EPI_ISL_19164730, EPI_ISL_19176639, EPI_ISL_19178558, EPI_ISL_19178568, EPI_ISL_19178596, EPI_ISL_19178605, EPI_ISL_19187637, EPI_ISL_19187967, EPI_ISL_19193916, EPI_ISL_19193921, EPI_ISL_19194771, EPI_ISL_19194784, EPI_ISL_19194786, EPI_ISL_19201526, EPI_ISL_19201652, EPI_ISL_19201696, EPI_ISL_19201699, EPI_ISL_19201704, EPI_ISL_19201730

On the S:F456L Branch sublineage with further S:V503I JN.1 >> Orf3a:L85F (G25647T) > T23629C > A5053G, ORF1a:T2152I (C6720T)> S:T572I (C23277T)>C5884T, Orf1b:S2339F (C20483T), C29149T > S:F456L (T22928C)> Reversion Orf1b:F2339FS (T20483C) > T22981C> S:V503I (G23069A) Query: T22981C ,G23069A, A10420G Samples: 5 (Spain and France)

IDs EPI_ISL_19146333, EPI_ISL_19189812, EPI_ISL_19194804, EPI_ISL_19194905, EPI_ISL_19194983

New Update on June 21: It seems that this lineage has got a fast sublineage defined by Orf9:E7V too: JN.1 >> Orf3a:L85F (G25647T) > T23629C > A5053G, ORF1a:T2152I (C6720T)> S:T572I (C23277T)>C5884T, Orf1b:S2339F (C20483T), C29149T > S:F456L (T22928C)> **Reversion Orf1b:F2339FS (T20483C) > T22981C > G19800A, C21342T, Orf9b:E7V (A28303T) Query:G19800A, A28303T ,C21342T Samples: 35 (Spain, Netherlands, England Italy-GBW and France)

IDs EPI_ISL_19139281, EPI_ISL_19140784, EPI_ISL_19146330, EPI_ISL_19157480-19157481, EPI_ISL_19164413, EPI_ISL_19167887, EPI_ISL_19175163-19175164, EPI_ISL_19175167, EPI_ISL_19175519, EPI_ISL_19178588, EPI_ISL_19188097, EPI_ISL_19189814-19189816, EPI_ISL_19193876, EPI_ISL_19193929, EPI_ISL_19193945, EPI_ISL_19193995, EPI_ISL_19193997-19193999, EPI_ISL_19194009, EPI_ISL_19194013, EPI_ISL_19194764-19194765, EPI_ISL_19194961, EPI_ISL_19197900, EPI_ISL_19197910, EPI_ISL_19201275, EPI_ISL_19201314, EPI_ISL_19201521, EPI_ISL_19206061, EPI_ISL_19210123

Tree as of June 21:

Screenshot 2024-06-22 alle 02 38 01 Screenshot 2024-06-22 alle 02 39 41 Screenshot 2024-06-22 alle 02 40 21

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_26d0d_61a540.json?c=gt-nuc_28303&gmax=29303&gmin=27303&label=id:node_6941360

Many thanks to @aviczhl2 and @NkRMnZr for helping in tracking this lineage

FedeGueli commented 8 months ago

46 now but only England.

FedeGueli commented 8 months ago

51

FedeGueli commented 8 months ago

67

FedeGueli commented 7 months ago

93 still uk only

FedeGueli commented 7 months ago

109

xz-keg commented 5 months ago

There is an S:F456L branch under this now.

Query: C23277T, A5053G ,C6720T,T22928C, 2 seqs, Spain

FedeGueli commented 5 months ago

190 now with 9 carrying 456L

FedeGueli commented 4 months ago

194 and 13 with 456L

FedeGueli commented 4 months ago

Jump to 26 for the 572I+456L branch. Dunno why it seems going up very fastly

FedeGueli commented 4 months ago

@corneliusroemer i suggest to look at this.

FedeGueli commented 4 months ago

@corneliusroemer the 456L branch quite unexplicably has started to climb the charts, i suspect that the ongoing starting wave in Spain shortened very much time from collecting to uploading artificially booosting the growth of lineages based in Spain ( Spain represents around 5% of samples in May when it was around 2% in March)

FedeGueli commented 4 months ago

@corneliusroemer likely this one the only one quite fast ( togetrher with the 456L + M:L46F from China) that you missed in your superlative night effort in designations.

FedeGueli commented 4 months ago

77 for the 456L branch, @corneliusroemer i suggest to designate it because it is around 5% (23/435) in Spain after May 10, and Spain is experiencing a wave right now, with a prevalence of 10% in Galicia in May that is the worst hit region in Spain.

FedeGueli commented 4 months ago

One more Trio sequence added from Andalusia right now.

FedeGueli commented 3 months ago

333 - 115 - 3

FedeGueli commented 3 months ago

142 +17 today

NkRMnZr commented 3 months ago

There's further S:R346T after T572I then F456L, remarkable steps. image

FedeGueli commented 3 months ago

439 with 203 Flirt @corneliusroemer another designation needed here

Memorablea commented 3 months ago

@corneliusroemer

NkRMnZr commented 3 months ago

image

also there's an S:S60P, W64L branch emerged

FedeGueli commented 3 months ago

Thanks @NkRMnZr great catches i am updating the proposal right now

FedeGueli commented 3 months ago

@corneliusroemer please take a look at this collective work in tracking this lineage that is urgent to designate. All three and samples updated as of today.

xz-keg commented 3 months ago

Trio branch is 62 now. Query: T21673C,T22981C,G22599C

@corneliusroemer the whole thing of this needs designation

FedeGueli commented 3 months ago

thx @Aviczhl2 i have updated, this should be designate , it is quite a textbook example of stepwise evo.

DailyCovidCases commented 2 months ago

Designated JN.1.65, JN.1.65.1, MF.1 (JN.1.65.1.1), MF.2 (JN.1.65.1.2)

FedeGueli commented 2 months ago

all designated JN.1.65 (572I) , JN.1.65.1 (456L) MF.1 (Trio) MF.2 ( S:S60P,S:W64L) via https://github.com/cov-lineages/pango-designation/commit/0720b7772f5e12cd6e7b550f2acb215c462e32e1