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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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KP.2 subbranch with S:del32 (95 sequences, 9 countries, most with Orf1a:P2079L, mainly in Ecuador) and further S:V1164I (11 sequences, 3 countries) on T22795G branch #1916

Closed Over-There-Is closed 1 month ago

Over-There-Is commented 1 month ago

KP.2> T22795G> C16887T, del21655-21657(S:del32), T24637G> C6501T(Orf1a:P2079L)> G25052A(S:V1164I)) Query: del21656_21658, T24637G, -G25593T Query for sequences without del21655-21657: T22795G, -del21656_21658, T24637G (in these sequences, deleted bases are replaced by N's.) Query for dropout sequence without T24637G: C16887T, G17334T, -T24637G, del21656_21658 Query for S:V1164I branch: C6501T, T22795G, G25052A

Earliest sequence: 05-02 England, United Kingdom EPI_ISL_19139240 Latest sequence: 08-26 New Jersey, USA EPI_ISL_19394749 Regions detected: Ecuador 56, US 29(3 not on GISAID, 4 from Ecuador, 2 from Colombia, 1 from Brazil, 2 airport pooled), UK 4, Spain 3, Canada 1, Czech Republic 1, Dominican Republic 1

Some British sequences have N's on 21655~21657. They have C16887T and T24637G too, which indicates these sequences belong to this branch. But some of them are misplaced. Some sequences have too much reversions and got misplaced on usher. https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_51b45_d0000.json?c=country&label=id:node_7070982 image

Sequences: EPI_ISL_19139240, EPI_ISL_19179140, EPI_ISL_19209073-19209074, EPI_ISL_19216243, EPI_ISL_19232443, EPI_ISL_19238242, EPI_ISL_19261814, EPI_ISL_19262887, EPI_ISL_19262891-19262893, EPI_ISL_19262899-19262900, EPI_ISL_19263257, EPI_ISL_19277841, EPI_ISL_19287274-19287276, EPI_ISL_19287278, EPI_ISL_19287286, EPI_ISL_19289273, EPI_ISL_19300528, EPI_ISL_19307626, EPI_ISL_19307809, EPI_ISL_19322192, EPI_ISL_19324558, EPI_ISL_19326010, EPI_ISL_19328830, EPI_ISL_19339216, EPI_ISL_19339232, EPI_ISL_19349639, EPI_ISL_19350907, EPI_ISL_19351885-19351886, EPI_ISL_19351897, EPI_ISL_19351905, EPI_ISL_19351916, EPI_ISL_19351918, EPI_ISL_19354916-19354918, EPI_ISL_19354920-19354921, EPI_ISL_19354929, EPI_ISL_19354931, EPI_ISL_19354935, EPI_ISL_19354940, EPI_ISL_19354943, EPI_ISL_19354948, EPI_ISL_19354950, EPI_ISL_19354953, EPI_ISL_19356550, EPI_ISL_19356557-19356558, EPI_ISL_19356562-19356563, EPI_ISL_19359974, EPI_ISL_19361340, EPI_ISL_19361414, EPI_ISL_19362281, EPI_ISL_19362674, EPI_ISL_19364760, EPI_ISL_19366076, EPI_ISL_19369496, EPI_ISL_19369896, EPI_ISL_19369910, EPI_ISL_19371830, EPI_ISL_19379468, EPI_ISL_19379580, EPI_ISL_19382704, EPI_ISL_19382709-19382713, EPI_ISL_19382715, EPI_ISL_19391057, EPI_ISL_19391064-19391065, EPI_ISL_19391071, EPI_ISL_19391075, EPI_ISL_19391085, EPI_ISL_19391089, EPI_ISL_19391091-19391092, EPI_ISL_19391094, EPI_ISL_19391097-19391098, EPI_ISL_19394496, EPI_ISL_19394545, EPI_ISL_19394749, PP994108.1, PQ206828.1, PQ212377.1

Over-There-Is commented 1 month ago

The original proposal is a subbranch of an S:F32- branch. @FedeGueli @aviczhl2

Over-There-Is commented 1 month ago

duplicated with https://github.com/cov-lineages/pango-designation/issues/2715