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Repository for suggesting new lineages that should be added to the current scheme
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FY.3.1 sublineage with nucleotide deletion 22294-22296 (S:L244- and S:H245F) -78 seqs in 6 countries, mainly in China #2147

Open HynnSpylor opened 11 months ago

HynnSpylor commented 11 months ago

*Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/322

Defining mutations: FY.3.1>G4109T (ORF1a:D1282Y)>The possible branch (Usher could not show the deletion branch?) GISAID query: A22161G, G4109T, del22295 Earliest seq: 2023-05-09 (Anhui Province, China- EPI_ISL_17808319) Most recent seq: 2023-07-06 (Canada- EPI_ISL_18037090) Countries detected: Countries detected: China (43, mostly in Shanghai Municipality and Jiangsu Province), South Korea (2), US (2), Austria (1), Israel (1), Canada (1)

Usher Tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3ea13_25e350.json

屏幕截图 2023-07-27 201004

The actual deletion nucs are 22294-22296, and it seems that Usher could not show the deletion branch clearly. However, 49 of all the 50 samples get nuc mutation C245A, while all other FY.3.1 samples do not get the mutation, hence I think C245A is also associated with the branch.

image

屏幕截图 2023-07-27 201203

Besides, it contains a single seq with saltation (2 Spike mutation S:T286I, S:T883N and 6 non-Spike aa mutations)

Genomes: EPI_ISL_17725081, EPI_ISL_17725083, EPI_ISL_17770021, EPI_ISL_17770080, EPI_ISL_17775215, EPI_ISL_17794024, EPI_ISL_17794027, EPI_ISL_17795397, EPI_ISL_17808139, EPI_ISL_17808598, EPI_ISL_17818552, EPI_ISL_17835387, EPI_ISL_17835606, EPI_ISL_17836850, EPI_ISL_17836901, EPI_ISL_17953563, EPI_ISL_17956863, EPI_ISL_17956886, EPI_ISL_17957166, EPI_ISL_17971793, EPI_ISL_17978368-17978369, EPI_ISL_17978371, EPI_ISL_17978373, EPI_ISL_17978378-17978379, EPI_ISL_17978430, EPI_ISL_17978455, EPI_ISL_17978467, EPI_ISL_17978478, EPI_ISL_17978480, EPI_ISL_17978504, EPI_ISL_17987513, EPI_ISL_17988159-17988160, EPI_ISL_17988169-17988170, EPI_ISL_17988226, EPI_ISL_17988309, EPI_ISL_17994509, EPI_ISL_17999217, EPI_ISL_18033565, EPI_ISL_18033758, EPI_ISL_18036098, EPI_ISL_18036412, EPI_ISL_18036596, EPI_ISL_18037090, EPI_ISL_18037330, EPI_ISL_18037373, EPI_ISL_18037400

HynnSpylor commented 11 months ago

65 seqs now

FedeGueli commented 11 months ago

65 seqs now

you made me fainting on the other issue ;)

HynnSpylor commented 11 months ago

78 seqs now

DailyCovidCases commented 2 months ago

Please close this issue