XBB.1.16 with ORF7a:T39I (422 seqs, 22 countries), further gained N:P13F, S:D1153Y, and S:F456L (2 seqs, France)

[NkRMnZr]

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

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:

• One of the large, undesignated branches of XBB.1.16.
• Despite low seqs count, there seems to be a 8% prevalence rate in Thailand at some point, and many seqs from airport screening with metadata shows travel history to India or Thailand.
• Newly emerged N:P13F + S:D1153Y + S:F456L, query: T22928C, G25019T, C16134T, 2

[FedeGueli]

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.

[FedeGueli]

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?

[NkRMnZr]

Update 1: 23-06-29, 15 seqs from 3 countries

Diversity from this batch: 

12 seqs from Japan:

EPI_ISL_17880193, EPI_ISL_17880230, EPI_ISL_17881641, EPI_ISL_17881689, EPI_ISL_17882109, EPI_ISL_17882263, EPI_ISL_17882589, EPI_ISL_17883331, EPI_ISL_17883907, EPI_ISL_17883910, EPI_ISL_17883912, EPI_ISL_17883996

1 from England, UK: EPI_ISL_17884520 1 from Scotland, UK: EPI_ISL_17884587 new entry: 1 from Georgia

Update 2: 23-07-02, 18 seqs from 6 countries

Diversity from this batch: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_ed1a_27ca60.json?f_userOrOld=uploaded%20sample 

5 seqs from South Korea:

4 good seqs: EPI_ISL_17927764, EPI_ISL_17927814, EPI_ISL_17927821, EPI_ISL_17932550 1 with Ns: EPI_ISL_17932497

3 from China, follows:

2 from Shanxi: EPI_ISL_17951320, EPI_ISL_17951321 1 from Hong Kong: EPI_ISL_17952688

4 from USA, follows:

2 from California: EPI_ISL_17950720, EPI_ISL_17951095 1 from Hawaii: EPI_ISL_17951526 1 from Florida: EPI_ISL_17951688

3from UK, follows:

2 from England: EPI_ISL_17951961, EPI_ISL_17951966 1 from Scotland: EPI_ISL_17952145

2 from Japan EPI_ISL_17941082, EPI_ISL_17941093 New entry: 1 from Spain EPI_ISL_17949806

Update 3: 23-07-06, 22 seqs from 8 countries


5 from China, follows

1 from Henan: EPI_ISL_17956786 1 from Tianjin: EPI_ISL_17956735 1 from Hong Kong: EPI_ISL_17952688 2 from Fujian: EPI_ISL_17956769, EPI_ISL_17956749

1 from England, UK: EPI_ISL_17953411 5 from Japan: EPI_ISL_17958477, EPI_ISL_17958529, EPI_ISL_17958565, EPI_ISL_17958988, EPI_ISL_17960097 5 from India: EPI_ISL_17957825, EPI_ISL_17957849, EPI_ISL_17957854, EPI_ISL_17957795, EPI_ISL_17957841 1 from Thailand: EPI_ISL_17959848 1 from Hawaii, USA: EPI_ISL_17961063 1 from Alberta, Canada: EPI_ISL_17960919 New Entry: 3 from New Zealand: EPI_ISL_17961690, EPI_ISL_17962238, EPI_ISL_17962458

Update 4: 23-07-08, 20 seqs from 3 countries

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2a78_93bf70.json?f_userOrOld=uploaded%20sample  1 from Yunan, China: EPI_ISL_17966398 3 from Shanxi, China: EPI_ISL_17972980, EPI_ISL_17973017, EPI_ISL_17973022 4 from Liaoning, China: EPI_ISL_17972866, EPI_ISL_17972895, EPI_ISL_17972904, EPI_ISL_17972931 2 from California, US: EPI_ISL_17966038, EPI_ISL_17966068 1 from Hawaii, US: EPI_ISL_17970917 9 from South Korea: EPI_ISL_17966521, EPI_ISL_17969767, EPI_ISL_17970025, EPI_ISL_17970203, EPI_ISL_17970345, EPI_ISL_17970372, EPI_ISL_17970461, EPI_ISL_17970540

Update 5: 23-07-11, 17 seqs from 5 countries, S:F456L Emerged

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_26a95_d79cb0.json?f_userOrOld=uploaded%20sample  3 from France: EPI_ISL_17974702, EPI_ISL_17974742, EPI_ISL_17974743 3 from Japan: EPI_ISL_17973212, EPI_ISL_17973213, EPI_ISL_17978803 1 from Sichuan, China: EPI_ISL_17978561 1 from Xinjiang, China: EPI_ISL_17978632 1 from California, USA: EPI_ISL_17977789 1 from Maryland, USA: EPI_ISL_17976808 1 from New Jersey, USA: EPI_ISL_17976535 5 from Georgia, USA: EPI_ISL_17976674, EPI_ISL_17976676, EPI_ISL_17976680, EPI_ISL_17976731, EPI_ISL_17976734 new entry: 1 from Italy: EPI_ISL_17975705 newly emerged N:P13F + S:D1153Y (G25019T) + S:F456L (T22928C), follows: Main proposal > C28310T(N:P13F over existing N:P13L/C28311T > G25019T(S:D1153Y) > C16134T > T22928C(S:F456L) query: T22928C, G25019T, C16134T, 2

Update 6: 23-07-15, 11 seqs from 4 countries

 2 from Japan: EPI_ISL_17980753, EPI_ISL_17980765 1 from BC, Canada: EPI_ISL_17986849 7 from South Korea: EPI_ISL_17983676, EPI_ISL_17983999-17984001, EPI_ISL_17984352, EPI_ISL_17984508, EPI_ISL_17984537 new entry: 1 from Ireland: EPI_ISL_17980444

Update 7: 23-07-18, 11 seqs from 4 countries

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1f158_670380.json?f_userOrOld=uploaded%20sample  1 from Thailand: EPI_ISL_17994655 1 from Japan: EPI_ISL_17994314 1 from Washington, USA: EPI_ISL_17994126

8 from China:

2 from Gansu: EPI_ISL_17987976, EPI_ISL_17987979 1 from Jiangsu: EPI_ISL_17988208 2 from Shanghai: EPI_ISL_17987667, EPI_ISL_17994603 2 from Sichuan: EPI_ISL_17988986, EPI_ISL_17988997 1 from Yunnan: EPI_ISL_17987867

Update 8: 23-07-20, 16 seqs from 5 countries

 1 from Australia: EPI_ISL_17999585 2 from Fujian: EPI_ISL_17999088, EPI_ISL_17999114 1 from Henan: EPI_ISL_18006130 4 from Japan: EPI_ISL_17996491, EPI_ISL_18000601, EPI_ISL_18000639, EPI_ISL_18006984 3 from Singapore: EPI_ISL_17996592, EPI_ISL_17996595, EPI_ISL_17996601 1 from Arizona: EPI_ISL_18005310 1 from California: EPI_ISL_17997414 1 from Massachusetts: EPI_ISL_17998428 2 from Washington with travel history to Japan: EPI_ISL_17996082, EPI_ISL_17996128

Update 9: 23-07-23, 10 seqs from 6 countries

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3b23_d54f10.json?f_userOrOld=uploaded%20sample  1 from Henan, China: EPI_ISL_18012357 3 from Sichuan, China: EPI_ISL_18012386, EPI_ISL_18012387, EPI_ISL_18012389 1 from Japan: EPI_ISL_18008228 1 from Scotland, UK: EPI_ISL_18010698 1 from Thailand: EPI_ISL_18007808 1 from California, USA: EPI_ISL_18008810 1 from Massachusetts, USA: EPI_ISL_18011197 New Entry: 1 from Mexico: EPI_ISL_18011932

[FedeGueli]

Designated XBB.1.16.18 via https://github.com/cov-lineages/pango-designation/commit/489cbbcfd080c7dac4b97261cbde11c18bd65c58