Closed NkRMnZr closed 1 year ago
Interesting thx Orf7a:39 is quite a hotspot of mutations . N:A398V seems the main branch circualting in China. Likely this is circulating in taiwan too.
Just noticed that a little sublineage of the N:A398V has one sample from Okinawa uploaded today (that is experimenting a bad covid wave right now) and two caught by american airport surveillance and one of these two was from Japan:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_267c7_dae1d0.json?c=userOrOld&label=id:node_10455558 . Not sure if the S:261V mutation is real. Japan had an issue in the past with that residue but the two american sequences have it too so maybe is it real this time?
Designated XBB.1.16.18 via https://github.com/cov-lineages/pango-designation/commit/489cbbcfd080c7dac4b97261cbde11c18bd65c58
Defining Mutations: XBB.1.16 > C27509T(ORF7a:T39I) Query: C29386T, A28447G, C27509T, -G284A, -T29410C, -A4681T, -C24382T, -G420T, -T3802C Earliest seq: 2023-03-08 (EPI_ISL_17270013, Gujarat, India) Latest seq: 2023-06-13 (EPI_ISL_17814779, Ontario, Canada) Sampled Countries: China (84, Shanghai/12, Sichuan/12, Guangdong/11, Liaoning/8, Hongkong/7, Fujian/6, Heilongjiang/5, Taiwan/5, Hubei/4, Yunnan/4, Henan/3, Jiangxi/2, Qinghai/2, Beijing/1, Gansu/1, Jiangsu/1), USA (43, California/15, Michigan/4, Virginia/4, Washington/4, Illinois/2, New Jersey/2, New York/2, Vermont/2, Arizona/1, Florida/1, Georgia/1, Hawaii/1, Kentucky/1, Missouri/1, Ohio/1, Tennessee/1), India (31, Gujarat/7, Maharashtra/7, Karnataka/5, Tamil Nadu/5, Rajasthan/2, Chhattisgarh/1, Madhya/1, Odisha/1, Puducherry/1, Telangana/1), South Korea (23), Australia (19, Victoria/10, NSW/8, ACT/1), UK (17, England/16, Scotland/1), Thailand (15), Japan (14), Israel (8), Singapore (7), Canada (6, Ontario/4, Alberta/1, New Brunswick/1), France (3), Germany (3), Indonesia (3), Sweden (2), Austria (1), Brunei (1), Finland (1), Mauritius(1), Norway (1), Russia (1),
Genomes:
EPI_ISL_17244711, EPI_ISL_17262440, EPI_ISL_17270013, EPI_ISL_17280612, EPI_ISL_17326775, EPI_ISL_17349567, EPI_ISL_17412158, EPI_ISL_17427663, EPI_ISL_17428150, EPI_ISL_17428388, EPI_ISL_17428399, EPI_ISL_17433585, EPI_ISL_17445754, EPI_ISL_17464002, EPI_ISL_17473050, EPI_ISL_17478181, EPI_ISL_17483727, EPI_ISL_17483810, EPI_ISL_17486535, EPI_ISL_17496228, EPI_ISL_17497497, EPI_ISL_17499634, EPI_ISL_17500475, EPI_ISL_17500630, EPI_ISL_17510925, EPI_ISL_17511452, EPI_ISL_17516232, EPI_ISL_17516413, EPI_ISL_17519019, EPI_ISL_17526968, EPI_ISL_17535358, EPI_ISL_17537793-17537794, EPI_ISL_17537805, EPI_ISL_17537888, EPI_ISL_17538761, EPI_ISL_17539405, EPI_ISL_17539422, EPI_ISL_17548048, EPI_ISL_17550869, EPI_ISL_17553754, EPI_ISL_17558112, EPI_ISL_17558193, EPI_ISL_17558205, EPI_ISL_17558242, EPI_ISL_17558261, EPI_ISL_17582142, EPI_ISL_17584665, EPI_ISL_17586056, EPI_ISL_17586421, EPI_ISL_17587053, EPI_ISL_17596142, EPI_ISL_17601910, EPI_ISL_17602000, EPI_ISL_17608686, EPI_ISL_17608878, EPI_ISL_17613527, EPI_ISL_17614352, EPI_ISL_17615846, EPI_ISL_17618288, EPI_ISL_17618342, EPI_ISL_17618350, EPI_ISL_17622208, EPI_ISL_17623946, EPI_ISL_17626983, EPI_ISL_17627112, EPI_ISL_17629763, EPI_ISL_17629966, EPI_ISL_17629977, EPI_ISL_17630458, EPI_ISL_17633743, EPI_ISL_17637617, EPI_ISL_17640505, EPI_ISL_17645661, EPI_ISL_17646192, EPI_ISL_17646979, EPI_ISL_17648909, EPI_ISL_17651424, EPI_ISL_17652383-17652384, EPI_ISL_17653070, EPI_ISL_17656890, EPI_ISL_17656904, EPI_ISL_17657004, EPI_ISL_17657018, EPI_ISL_17661343, EPI_ISL_17661767, EPI_ISL_17663275, EPI_ISL_17663286, EPI_ISL_17664557, EPI_ISL_17665938, EPI_ISL_17667465, EPI_ISL_17672435, EPI_ISL_17672467, EPI_ISL_17677425, EPI_ISL_17677520, EPI_ISL_17677527, EPI_ISL_17677650, EPI_ISL_17678543, EPI_ISL_17680399, EPI_ISL_17681290, EPI_ISL_17681565, EPI_ISL_17683537, EPI_ISL_17683553, EPI_ISL_17683653, EPI_ISL_17684097, EPI_ISL_17684102, EPI_ISL_17684323, EPI_ISL_17686328, EPI_ISL_17686446, EPI_ISL_17687869, EPI_ISL_17689361, EPI_ISL_17689771, EPI_ISL_17689817, EPI_ISL_17689927, EPI_ISL_17690966, EPI_ISL_17692067, EPI_ISL_17692121, EPI_ISL_17692243, EPI_ISL_17694956, EPI_ISL_17696973, EPI_ISL_17697656, EPI_ISL_17697680, EPI_ISL_17697749, EPI_ISL_17697921, EPI_ISL_17697971, EPI_ISL_17698006, EPI_ISL_17698051, EPI_ISL_17698096, EPI_ISL_17698242, EPI_ISL_17698291, EPI_ISL_17699415, EPI_ISL_17700670, EPI_ISL_17701808, EPI_ISL_17703937, EPI_ISL_17704274, EPI_ISL_17704816, EPI_ISL_17705155, EPI_ISL_17706045, EPI_ISL_17706088, EPI_ISL_17707087, EPI_ISL_17709517, EPI_ISL_17710126, EPI_ISL_17711148, EPI_ISL_17711237, EPI_ISL_17714338-17714339, EPI_ISL_17714349, EPI_ISL_17714850, EPI_ISL_17716152, EPI_ISL_17718766, EPI_ISL_17718845, EPI_ISL_17719669, EPI_ISL_17719936, EPI_ISL_17720422, EPI_ISL_17720457, EPI_ISL_17720567, EPI_ISL_17720641, EPI_ISL_17720790, EPI_ISL_17721632, EPI_ISL_17723274, EPI_ISL_17724053, EPI_ISL_17725420, EPI_ISL_17729601, EPI_ISL_17729872, EPI_ISL_17730007, EPI_ISL_17730156, EPI_ISL_17731819, EPI_ISL_17731855, EPI_ISL_17732753, EPI_ISL_17734635, EPI_ISL_17734708, EPI_ISL_17736030, EPI_ISL_17739679, EPI_ISL_17739835, EPI_ISL_17741544, EPI_ISL_17741763, EPI_ISL_17742209, EPI_ISL_17742212, EPI_ISL_17742230, EPI_ISL_17743936, EPI_ISL_17744360, EPI_ISL_17744692, EPI_ISL_17744731, EPI_ISL_17762917, EPI_ISL_17763272, EPI_ISL_17764843, EPI_ISL_17766577, EPI_ISL_17766663, EPI_ISL_17769930, EPI_ISL_17770243, EPI_ISL_17773392, EPI_ISL_17774373, EPI_ISL_17775074, EPI_ISL_17779142, EPI_ISL_17779384, EPI_ISL_17780695, EPI_ISL_17784190, EPI_ISL_17784231, EPI_ISL_17785016, EPI_ISL_17785906, EPI_ISL_17785915, EPI_ISL_17786917, EPI_ISL_17786927, EPI_ISL_17786992, EPI_ISL_17789897, EPI_ISL_17790228, EPI_ISL_17790657, EPI_ISL_17790703, EPI_ISL_17791900, EPI_ISL_17791914, EPI_ISL_17791937, EPI_ISL_17792389, EPI_ISL_17792551, EPI_ISL_17794030, EPI_ISL_17794818, EPI_ISL_17794879, EPI_ISL_17795227, EPI_ISL_17795531, EPI_ISL_17801918, EPI_ISL_17801987, EPI_ISL_17802056, EPI_ISL_17802701, EPI_ISL_17802714, EPI_ISL_17802848, EPI_ISL_17803241, EPI_ISL_17803764, EPI_ISL_17804063, EPI_ISL_17807341, EPI_ISL_17807568, EPI_ISL_17808006, EPI_ISL_17808110, EPI_ISL_17808123, EPI_ISL_17808435, EPI_ISL_17811334, EPI_ISL_17811342, EPI_ISL_17811344, EPI_ISL_17811408, EPI_ISL_17811686, EPI_ISL_17813244, EPI_ISL_17814779, EPI_ISL_17815036, EPI_ISL_17816278, EPI_ISL_17816297, EPI_ISL_17816349, EPI_ISL_17816625, EPI_ISL_17816985, EPI_ISL_17819801, EPI_ISL_17830369, EPI_ISL_17830690, EPI_ISL_17834778, EPI_ISL_17834899, EPI_ISL_17834931, EPI_ISL_17835095, EPI_ISL_17835154, EPI_ISL_17835711, EPI_ISL_17836108, EPI_ISL_17836639, EPI_ISL_17837055, EPI_ISL_17838108, EPI_ISL_17838232, EPI_ISL_17838386, EPI_ISL_17838407, EPI_ISL_17848414, EPI_ISL_17848446, EPI_ISL_17850196, EPI_ISL_17850300, EPI_ISL_17850409, EPI_ISL_17850593, EPI_ISL_17850624, EPI_ISL_17850628, EPI_ISL_17850702, EPI_ISL_17850729, EPI_ISL_17850732, EPI_ISL_17850773-17850774, EPI_ISL_17850778-17850779, EPI_ISL_17850782, EPI_ISL_17852289, EPI_ISL_17854578, EPI_ISL_17879336, EPI_ISL_17880193, EPI_ISL_17880230,UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1eab9_d3d9d0.json?c=country&label=id:node_6611214
view from XBB.1.16 polytomy![overview](https://github.com/sars-cov-2-variants/lineage-proposals/assets/125747944/c4a3ea58-13d3-4999-b2f3-fe413adb9cb6)
ORF7a:T39I branch diversity check:
notable mutations like N:A398V, S:Q675H and XBB's definition-changing N:P13F(from N:P13L) are on the rise.
Trivia: