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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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KP.3.1 subbranch with S:N>K679R(190 seqs, 20 regions, mainly in Spain) and further S:L176F(38, 8 regions) #2743

Open Over-There-Is opened 2 months ago

Over-There-Is commented 2 months ago

Transferred from sars-cov-2-variants/lineage-proposals#1802

Found with @aviczhl2 's phylogenic tree analysis tool. Spotted first by @aviczhl2 .

KP.3.1> A1620G(Orf1a:E452G), del29728-29776(#2646)> T2593C> C8616T(Orf1a:A2784V)> C14216T(Orf1b:T250I), A23598G(S:K679R)> C22088T(S:L176F) Query: C14216T, A23598G, -G932A Query for S:L176F branch: C14216T, C22088T, A23598G This branch is misplaced on a T29728G> C14216T, A23598G> G29728T flip-flop branch yet due to the deletion.

Earliest sequence: 04-21 Madrid, Spain EPI_ISL_19164708 Latest sequence: 08-12 Denmark EPI_ISL_19348042 Regions detected: Spain 54(including 1 from Canary Islands), UK 8, France 6, Sweden 6, Denmark 4, Ireland 4, Italy 2, Portugal 2, Finland 1, Greece 1, Netherlands 1, Luxembourg 1; US 8(1 from Greece, 1 from Spain), Canada 1; Israel 1.

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3044b_6cd8c0.json?c=country&label=id:node_7028471 image

Sequences: EPI_ISL_19164708, EPI_ISL_19164712, EPI_ISL_19176965, EPI_ISL_19178589, EPI_ISL_19179515, EPI_ISL_19185426, EPI_ISL_19186676, EPI_ISL_19189621, EPI_ISL_19194760, EPI_ISL_19194769, EPI_ISL_19195261, EPI_ISL_19197928, EPI_ISL_19201438, EPI_ISL_19201738, EPI_ISL_19214624, EPI_ISL_19215264, EPI_ISL_19215276, EPI_ISL_19216662, EPI_ISL_19218924, EPI_ISL_19219465, EPI_ISL_19220641, EPI_ISL_19221168, EPI_ISL_19221172, EPI_ISL_19221310, EPI_ISL_19221771, EPI_ISL_19222000, EPI_ISL_19225530, EPI_ISL_19225568, EPI_ISL_19225573, EPI_ISL_19229220, EPI_ISL_19229223, EPI_ISL_19231626, EPI_ISL_19232532-19232533, EPI_ISL_19232597, EPI_ISL_19235907, EPI_ISL_19252937, EPI_ISL_19258573, EPI_ISL_19261329, EPI_ISL_19261586, EPI_ISL_19263174, EPI_ISL_19263232, EPI_ISL_19263264, EPI_ISL_19263302, EPI_ISL_19263321, EPI_ISL_19264890, EPI_ISL_19265498, EPI_ISL_19265509, EPI_ISL_19266060, EPI_ISL_19267058, EPI_ISL_19267060, EPI_ISL_19270338, EPI_ISL_19271730, EPI_ISL_19273215, EPI_ISL_19276263, EPI_ISL_19276287, EPI_ISL_19277304, EPI_ISL_19280649, EPI_ISL_19280673, EPI_ISL_19280872, EPI_ISL_19281671, EPI_ISL_19287047, EPI_ISL_19289400, EPI_ISL_19290827, EPI_ISL_19291541, EPI_ISL_19292706, EPI_ISL_19293241, EPI_ISL_19296711, EPI_ISL_19296910, EPI_ISL_19300146, EPI_ISL_19305441, EPI_ISL_19305699, EPI_ISL_19307088, EPI_ISL_19309647, EPI_ISL_19310720, EPI_ISL_19311299, EPI_ISL_19312405, EPI_ISL_19312486, EPI_ISL_19312559, EPI_ISL_19313452, EPI_ISL_19319581, EPI_ISL_19322327, EPI_ISL_19322362, EPI_ISL_19322545, EPI_ISL_19323296, EPI_ISL_19323471, EPI_ISL_19326372, EPI_ISL_19327347, EPI_ISL_19331142, EPI_ISL_19331714, EPI_ISL_19332615, EPI_ISL_19332675, EPI_ISL_19332799, EPI_ISL_19333749, EPI_ISL_19333767, EPI_ISL_19335088, EPI_ISL_19338465, EPI_ISL_19338542, EPI_ISL_19341069, EPI_ISL_19348042
xz-keg commented 2 months ago

This branch is sub-branch of https://github.com/cov-lineages/pango-designation/issues/2646 so it has the del29728_29776 large deletion thing.

Over-There-Is commented 2 months ago

This branch is sub-branch of #2646 so it has the del29728_29776 large deletion thing.

so T29728G is an artefact.

Over-There-Is commented 1 month ago

Poland

Over-There-Is commented 1 month ago

US+20

Over-There-Is commented 1 month ago

Brazil

DailyCovidCases commented 3 weeks ago

Now 171/32 seqs: usher Screenshot (247) @corneliusroemer Is this branch worth a designation?

FedeGueli commented 3 weeks ago

8 in September from 5 different countries

Over-There-Is commented 2 weeks ago

Costa Rica, Slovenia