FL.2 sublineage with Orf1b:K1383R circulating in China and other countries (350 seq) and then S:Q146K (71 seq)

[Walde1nsamkeit]

FL.2 + Orf1b:K1383R
GISAID Query: C11956T, T4579A, A17615G
Earliest Sequence: 02-23 Singapore (imported from Saudi) EPI_ISL_17146466
Latest Sequence: 05-16 Hubei, China EPI_ISL_17684404

Regions Detected:
China 331+2: Guangdong 223(2 detected at Zhuhai Custom, probably imported from Macao), Hubei 66, Shanghai 19 (including 1 from HK or Macao, 1 from Macao, 1 from Singapore, 1 from UAE, 1 from Russia, 1 from Thailand), Fujian 8 (including 1 from Thailand), Sichuan 7, Yunnan 4, Anhui 2, Heilongjiang 1, Shanxi 1; Hong Kong 2;
Japan 3 (2 from China), Malaysia 1, Singapore 4 (1 from Saudi, 1 from China, 1 from HK);
Austria 1, France 1, Netherlands 1, Russia 2, UK 2;
Canada 1, US 1.

Maybe circulate in low-sequencing regions e. g. Macao, UAE, Saudi etc.

Sequences:

EPI_ISL_17146466, EPI_ISL_17298736, EPI_ISL_17333208, EPI_ISL_17545640, EPI_ISL_17547923, EPI_ISL_17584630, EPI_ISL_17584634, EPI_ISL_17584636, EPI_ISL_17584640-17584642, EPI_ISL_17584645, EPI_ISL_17584649, EPI_ISL_17584653, EPI_ISL_17584655, EPI_ISL_17584676, EPI_ISL_17584688, EPI_ISL_17615002, EPI_ISL_17620290, EPI_ISL_17625276, EPI_ISL_17625279, EPI_ISL_17625305, EPI_ISL_17625310, EPI_ISL_17625315, EPI_ISL_17625324, EPI_ISL_17625329, EPI_ISL_17625339, EPI_ISL_17625341, EPI_ISL_17625344, EPI_ISL_17625353, EPI_ISL_17625360, EPI_ISL_17625383-17625384, EPI_ISL_17625386, EPI_ISL_17625389-17625390, EPI_ISL_17625413, EPI_ISL_17625431, EPI_ISL_17625462, EPI_ISL_17625484, EPI_ISL_17625499, EPI_ISL_17625517, EPI_ISL_17625561, EPI_ISL_17625567, EPI_ISL_17625585, EPI_ISL_17632975-17632976, EPI_ISL_17633004, EPI_ISL_17637623, EPI_ISL_17637640, EPI_ISL_17645421, EPI_ISL_17645435, EPI_ISL_17645472, EPI_ISL_17645476, EPI_ISL_17645482, EPI_ISL_17645485-17645486, EPI_ISL_17645513, EPI_ISL_17645516, EPI_ISL_17645689, EPI_ISL_17645761, EPI_ISL_17645781, EPI_ISL_17645945, EPI_ISL_17652315, EPI_ISL_17652358, EPI_ISL_17654834, EPI_ISL_17664527, EPI_ISL_17664543, EPI_ISL_17664763, EPI_ISL_17664766, EPI_ISL_17669410, EPI_ISL_17671914, EPI_ISL_17671919, EPI_ISL_17671928, EPI_ISL_17671938, EPI_ISL_17671944-17671945, EPI_ISL_17671949, EPI_ISL_17671951, EPI_ISL_17671956-17671957, EPI_ISL_17671976, EPI_ISL_17671985, EPI_ISL_17671997-17671998, EPI_ISL_17672004-17672005, EPI_ISL_17672017, EPI_ISL_17672024, EPI_ISL_17672062, EPI_ISL_17673622, EPI_ISL_17678284, EPI_ISL_17678311, EPI_ISL_17678338, EPI_ISL_17678369, EPI_ISL_17678372, EPI_ISL_17678427, EPI_ISL_17678450, EPI_ISL_17680003, EPI_ISL_17684000, EPI_ISL_17684028, EPI_ISL_17684038, EPI_ISL_17684126, EPI_ISL_17684191, EPI_ISL_17684328-17684329, EPI_ISL_17684360, EPI_ISL_17684398, EPI_ISL_17684401, EPI_ISL_17684403-17684404, EPI_ISL_17684406, EPI_ISL_17684412, EPI_ISL_17684426, EPI_ISL_17684430, EPI_ISL_17688136, EPI_ISL_17689324, EPI_ISL_17689340, EPI_ISL_17689358, EPI_ISL_17689360, EPI_ISL_17689391, EPI_ISL_17689401, EPI_ISL_17689404-17689405, EPI_ISL_17689777, EPI_ISL_17689831, EPI_ISL_17694789, EPI_ISL_17694888, EPI_ISL_17695035, EPI_ISL_17696747, EPI_ISL_17696835, EPI_ISL_17696885, EPI_ISL_17696896, EPI_ISL_17696903-17696904, EPI_ISL_17696909-17696911, EPI_ISL_17696913, EPI_ISL_17697568, EPI_ISL_17697577, EPI_ISL_17697580, EPI_ISL_17697585-17697586, EPI_ISL_17697589, EPI_ISL_17697595, EPI_ISL_17697606, EPI_ISL_17697623-17697624, EPI_ISL_17697627, EPI_ISL_17697630, EPI_ISL_17697635-17697636, EPI_ISL_17697644, EPI_ISL_17697646, EPI_ISL_17697652, EPI_ISL_17697660, EPI_ISL_17697671-17697672, EPI_ISL_17697683, EPI_ISL_17697688, EPI_ISL_17697691, EPI_ISL_17697695, EPI_ISL_17697697-17697698, EPI_ISL_17697700, EPI_ISL_17697702, EPI_ISL_17697709, EPI_ISL_17697711, EPI_ISL_17697713, EPI_ISL_17697715, EPI_ISL_17697719, EPI_ISL_17697721, EPI_ISL_17697723, EPI_ISL_17697728, EPI_ISL_17697732, EPI_ISL_17697735, EPI_ISL_17697739-17697741, EPI_ISL_17697755, EPI_ISL_17697759-17697760, EPI_ISL_17697763-17697765, EPI_ISL_17697767, EPI_ISL_17697769, EPI_ISL_17697777-17697778, EPI_ISL_17697782, EPI_ISL_17697785-17697786, EPI_ISL_17697793-17697794, EPI_ISL_17697803, EPI_ISL_17697810-17697812, EPI_ISL_17697814, EPI_ISL_17697818-17697819, EPI_ISL_17697822, EPI_ISL_17697834, EPI_ISL_17697836-17697838, EPI_ISL_17697844, EPI_ISL_17697846-17697853, EPI_ISL_17697857, EPI_ISL_17697860-17697863, EPI_ISL_17697866-17697868, EPI_ISL_17697880, EPI_ISL_17697883-17697884, EPI_ISL_17697887, EPI_ISL_17697891, EPI_ISL_17697900, EPI_ISL_17697902, EPI_ISL_17697906-17697907, EPI_ISL_17697911, EPI_ISL_17697914, EPI_ISL_17697936, EPI_ISL_17697939, EPI_ISL_17697942, EPI_ISL_17697949, EPI_ISL_17697956, EPI_ISL_17697958-17697960, EPI_ISL_17697966, EPI_ISL_17697970, EPI_ISL_17697972-17697973, EPI_ISL_17697976-17697977, EPI_ISL_17697980, EPI_ISL_17697987, EPI_ISL_17697997, EPI_ISL_17698002, EPI_ISL_17698007, EPI_ISL_17698011-17698015, EPI_ISL_17698020, EPI_ISL_17698022, EPI_ISL_17698024, EPI_ISL_17698026, EPI_ISL_17698028-17698029, EPI_ISL_17698032-17698034, EPI_ISL_17698036, EPI_ISL_17698038, EPI_ISL_17698045-17698046, EPI_ISL_17698049, EPI_ISL_17698060, EPI_ISL_17698063, EPI_ISL_17698067, EPI_ISL_17698069-17698070, EPI_ISL_17698073, EPI_ISL_17698077-17698080, EPI_ISL_17698084, EPI_ISL_17698087, EPI_ISL_17698090, EPI_ISL_17698092, EPI_ISL_17698094, EPI_ISL_17698104-17698105, EPI_ISL_17698112, EPI_ISL_17698116-17698117, EPI_ISL_17698119, EPI_ISL_17698123, EPI_ISL_17698134, EPI_ISL_17698137, EPI_ISL_17698140, EPI_ISL_17698144-17698145, EPI_ISL_17698152, EPI_ISL_17698155, EPI_ISL_17698158, EPI_ISL_17698164, EPI_ISL_17698172, EPI_ISL_17698175-17698177, EPI_ISL_17698179, EPI_ISL_17698189, EPI_ISL_17698191-17698193, EPI_ISL_17698199, EPI_ISL_17698203, EPI_ISL_17698205, EPI_ISL_17698207, EPI_ISL_17698221, EPI_ISL_17698226, EPI_ISL_17698233-17698234, EPI_ISL_17698236, EPI_ISL_17698240-17698241, EPI_ISL_17698243, EPI_ISL_17698248, EPI_ISL_17698250, EPI_ISL_17698253, EPI_ISL_17698259-17698260, EPI_ISL_17698263-17698264, EPI_ISL_17698267, EPI_ISL_17698270, EPI_ISL_17698275, EPI_ISL_17698277, EPI_ISL_17698284, EPI_ISL_17698288, EPI_ISL_17698290, EPI_ISL_17698292, EPI_ISL_17698298, EPI_ISL_17698300, EPI_ISL_17698304-17698306, EPI_ISL_17698319, EPI_ISL_17698323-17698324, EPI_ISL_17698326, EPI_ISL_17698328

Shanghai/SCDC-3299/2023|EPI_ISL_17625484|2023-04-24 seems to be a recombinant.
Hubei/HCDC-1001/2023|EPI_ISL_17625388|2023-04-27(17615A) seems to be a recombinant between FL.2* and BA.5.2.48*.

Since the Shanghai sequences uploaded in 05-18 are not released on GenBase, it is yet not available to access the travelling information of the hosts.

Some sequences with S:F486P and Orf1b:K1383R have only one of 11956T or 4579A. These sequences are probably related to this sublineage.

And 71 of these sequences have C21998A (S:Q146K) mutation.

Earliest Sequence: 04-07 Guangdong, China EPI_ISL_17584630
Latest Sequence: 05-10 Hubei, China EPI_ISL_17671945

Almost all of these sequences are collected in China:
Hubei 20, Shanghai 9 (1 from UAE, 1 from HK or Macao, 1 from Macao), Sichuan 4, Guangdong 36, Yunnan 1; UK 1.

Sequences:

EPI_ISL_17545640, EPI_ISL_17584630, EPI_ISL_17615002, EPI_ISL_17625276, EPI_ISL_17625305, EPI_ISL_17625315, EPI_ISL_17625324, EPI_ISL_17625360, EPI_ISL_17625389, EPI_ISL_17625431, EPI_ISL_17625499, EPI_ISL_17625567, EPI_ISL_17625585, EPI_ISL_17632975-17632976, EPI_ISL_17645472, EPI_ISL_17645513, EPI_ISL_17664527, EPI_ISL_17671914, EPI_ISL_17671919, EPI_ISL_17671944-17671945, EPI_ISL_17671949, EPI_ISL_17671951, EPI_ISL_17671956-17671957, EPI_ISL_17672024, EPI_ISL_17678284, EPI_ISL_17678372, EPI_ISL_17678427, EPI_ISL_17678450, EPI_ISL_17680003, EPI_ISL_17684000, EPI_ISL_17684191, EPI_ISL_17684329, EPI_ISL_17696835, EPI_ISL_17697630, EPI_ISL_17697636, EPI_ISL_17697691, EPI_ISL_17697695, EPI_ISL_17697698, EPI_ISL_17697760, EPI_ISL_17697763, EPI_ISL_17697767, EPI_ISL_17697786, EPI_ISL_17697803, EPI_ISL_17697836, EPI_ISL_17697849-17697850, EPI_ISL_17697880, EPI_ISL_17697883, EPI_ISL_17697914, EPI_ISL_17698013, EPI_ISL_17698015, EPI_ISL_17698032, EPI_ISL_17698034, EPI_ISL_17698046, EPI_ISL_17698073, EPI_ISL_17698078, EPI_ISL_17698087, EPI_ISL_17698104, EPI_ISL_17698123, EPI_ISL_17698226, EPI_ISL_17698233-17698234, EPI_ISL_17698248, EPI_ISL_17698260, EPI_ISL_17698267, EPI_ISL_17698275, EPI_ISL_17698284, EPI_ISL_17698292

Hubei/HCDC-1003/2023|EPI_ISL_17625389|2023-04-27 seems to develop Q146K separately.

[Walde1nsamkeit]

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_3a56c_8f9160.json?c=gt-S_146&f_userOrOld=uploaded%20sample&label=id:node_8458197
Maybe containing artefact reversions.

[Walde1nsamkeit]

https://nextstrain.org/fetch/github.com/Over-There-Is/subtreeAuspice/raw/main/subtreeAuspice_genome_3a56c_8f9170.json

[oobb45729]

Orf1b:K1383R is in one of the main subbranches of Alpha, although Alpha+Orf1b:K1383R might have a disadvantage over other Alphas.

[Walde1nsamkeit]

3 more sequences in Singapore: 1 from China Mainland, 1 from HK and 1 local

[Walde1nsamkeit]

221 more sequences: Guangdong 211(2 detected at Zhuhai Custom, probably imported from Macao), Hubei 8, Shanghai 1 and Shanxi 1. 35 sequences in Guangdong and 1 in Shanghai have additional Q146K.

[Walde1nsamkeit]

7 more sequences: US 6(all imported, 1 from Germany, 1 from Taiwan, 1 from South Korea and 3 from Airport pool test), and 1 Ireland.

[FedeGueli]

cc @corneliusroemer this is a big branch maybe already under your radar

[Walde1nsamkeit]

Transfer to cov-lineages/pango-designation

[FedeGueli]

Hi @Over-There-Is i would like to suggest if you can update issues less frequently just to say once every 5 days or when there is a big upload (10-20 seqs in one shot) cause while it is very useful to me as moderator to be updated daily on things so i am not forced to check on my own con sider that this page and the official one are read and subscribed by a lot of people, readers or scientists and your daily update could sort the opposite effect on the lineage you proposed. What you can do as do @alurqu is to update the title/headline only with numbers of sequences and variation for example : XYZ.1 +S:1rev (10seqs Korea,China / +1 Korea). The title changes wont be notified to everyone but i can still get the message.

Thank you very much for your work!