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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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New JN.1 + S:T572I sublineage in Australia, Canada and New Zealand (213seqs - Australia and New Zealand) with a sublineage with S:G482S (5 ,Aus NZL) #2564

Closed FedeGueli closed 2 months ago

FedeGueli commented 5 months ago

JN.1 > C6896T > A19578G > S:T572I (C23277T) Query: C6896T , A19578G , C23277T, T3565C Samples: 77 Australia, New Zealand Canada Growth advantage: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=JN.1*&nucMutations1=C6896T%2CA19578G%2CC23277T%2CT3565C&analysisMode=CompareToBaseline&

Screenshot 2024-04-21 alle 11 26 17

Sublineage with S:G482S : Query: G23006A ,C28419T,T3565C Defining : #2564 >> Orf1a:L864F (C2855T), Orf1a:K1791R (A5637G), G21423A > Orf1a:E2268K (G7067A), C29708T > S:G482S (G23006A), N:t49I (C28419T)

Tree: (Upodated on June 10)

Screenshot 2024-06-11 alle 02 46 19

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice3_genome_test_5f1f3_798b10.json?label=id:node_7068308

IDs: EPI_ISL_18850360, EPI_ISL_18850499, EPI_ISL_18850678, EPI_ISL_18880336, EPI_ISL_18915695, EPI_ISL_18915705, EPI_ISL_18923412, EPI_ISL_18923442, EPI_ISL_18923448, EPI_ISL_18923472-18923473, EPI_ISL_18923481, EPI_ISL_18923497, EPI_ISL_18923501, EPI_ISL_18923528, EPI_ISL_18923563, EPI_ISL_18923576, EPI_ISL_18923706, EPI_ISL_18923813, EPI_ISL_18923821, EPI_ISL_18923870, EPI_ISL_18940335, EPI_ISL_18967378, EPI_ISL_18967404, EPI_ISL_18972780, EPI_ISL_18972786, EPI_ISL_18972790, EPI_ISL_18986980, EPI_ISL_18987147, EPI_ISL_18990521, EPI_ISL_19002719, EPI_ISL_19008079, EPI_ISL_19012041, EPI_ISL_19026559, EPI_ISL_19026584, EPI_ISL_19026586, EPI_ISL_19026596, EPI_ISL_19026637, EPI_ISL_19026677, EPI_ISL_19026741, EPI_ISL_19026760-19026762, EPI_ISL_19027028, EPI_ISL_19027059, EPI_ISL_19027090, EPI_ISL_19028239, EPI_ISL_19036966, EPI_ISL_19037092-19037093, EPI_ISL_19038703, EPI_ISL_19038725, EPI_ISL_19040631, EPI_ISL_19043117, EPI_ISL_19046865, EPI_ISL_19051326-19051327, EPI_ISL_19051413, EPI_ISL_19051423, EPI_ISL_19054812, EPI_ISL_19055775, EPI_ISL_19055793, EPI_ISL_19055814, EPI_ISL_19055816, EPI_ISL_19058900, EPI_ISL_19058907-19058908, EPI_ISL_19058966, EPI_ISL_19058971, EPI_ISL_19058976, EPI_ISL_19058979, EPI_ISL_19058981, EPI_ISL_19058990, EPI_ISL_19059011, EPI_ISL_19059049, EPI_ISL_19059051, EPI_ISL_19059057

IDs for 482S branch: EPI_ISL_19186723, EPI_ISL_19186777, EPI_ISL_19187076, EPI_ISL_19187091

FedeGueli commented 5 months ago

94 now big upload from NZL (17) , 3% of samples collected there after March 1

FedeGueli commented 5 months ago

109 with a batch from NSW it reaches 10% in April there. @corneliusroemer i suggest to designate it

FedeGueli commented 4 months ago

134 and 7% in SA in April

FedeGueli commented 4 months ago

Sorry i have mistakenly closed this one in the past weeks. @corneliusroemer one of the best 572I going around.

FedeGueli commented 3 months ago

185 still around but its share going down quickly closing it

FedeGueli commented 3 months ago

big upload from NZl of this with a new sublinegae with S:G482S predicted by Nextclade to be slighty beneficial for binding

FedeGueli commented 3 months ago

new sample with 482S from Australia

FedeGueli commented 2 months ago

213 but only two in June, hence closing this.