Potential BA.2.3.17/BA.2.75.2 recombinant (66 seqs as of 2022-11-12)

[c19850727]

I am proposing this potential recombinant with only 18 sequences based on its geographical distribution and potential growth advantage during recent few days.

Description

Recombinant between: BA.2.3.17 and BA.2.75.2
Earliest sequence: 2022/07/27 (Nepal)
Most recent sequence: 2022/10/10 (Singapore ex-Nepal)
Countries circulating: Nepal (2/17), Brunei (3/17), UK-England (1/17), France (5/17), Germany (1/17), Israel (2/17), Malaysia (1/17), Singapore ex-Nepal (1/17), Singapore local (1/17)

Potential breakpoint: somewhere between NSP12 and Spike NTD (15451-22000)
Potential BA.2.3.17 donor: EPI_ISL_12874157 or EPI_ISL_12788684 or EPI_ISL_12788514 from US-CA or US-HI.

Mutation profile:

Private mutations: none
GISAID query: Spike_D1199N, NSP12_A97V, -NSP8_N118S, -NSP3_P822S, -NSP16_G671S (there are 2 unrelated random sequences picked up by this query, both from early 2021, so it's easily identifiable by dates of collection)
Cov-spectrum query: T3796C, T3927C, T4586C, T5183C, G12444A, A15451G, C13730T, C7528T, G25157A

Evidence

Usher tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_db2c_dffb30.json?branchLabel=aa%20mutations&c=gt-nuc_3796&label=nuc%20mutations:T3796C,T3927C,T4586C,T5183C,G12444A,A15451G

Genomes:

EPI_ISL_14807682, EPI_ISL_14959369, EPI_ISL_14960037, EPI_ISL_15031974, EPI_ISL_15136400, EPI_ISL_15140939, EPI_ISL_15244536-15244537, EPI_ISL_15244551, EPI_ISL_15296261, EPI_ISL_15313055, EPI_ISL_15325673, EPI_ISL_15330221, EPI_ISL_15335186, EPI_ISL_15384119, EPI_ISL_15385024, EPI_ISL_15385056-15385057

[c19850727]

19 sequences as of 2022-10-19. Newly found in Malaysia.

[c19850727]

20 sequences as of 2022-10-20.

[c19850727]

29 sequences as of 2022-10-22. 10 from Brunei and 1 from Nepal.

[FedeGueli]

E_T11A,Spike_D1199N, NSP12_A97V, -NSP8_N118S, -NSP3_P822S, -NSP16_G671S finds 28 all belonging this lineage.

[c19850727]

31 sequences as of 2022-10-24. Newly found in Australia.

BTW @FedeGueli some of these genomes have dropouts in E protein so I didn't use E_T11A in my query.

[corneliusroemer]

Thanks @c19850727, I agree this one looks interesting due to geographic spread and growth

[c19850727]

34 genomes. 3 more from Brunei.

[FedeGueli]

2 new sequences from Germany it should be 36 (even if my query finds 35 in Gisaid)

[c19850727]

yeah Fede 2 more from Germany emerged after my daily coffee-time GISAID screening -o-

[c19850727]

41 sequences as of 2022-10-30. Newly found in France, and 3 more from Brunei.

[FedeGueli]

i see one more from Malaysia and one more from Japan

[Sam8138]

The entry of BE.1.4.4 incorrectly lists the alias as: B.1.1.529.5.3.1.1.4.3 It should be: B.1.1.529.5.3.1.1.4.4

[AngieHinrichs]

Thanks for reporting the typo @Sam8138, fixed now.

[Sam8138]

In the entry for BA.2.23.1: Alias of Alias of B.1.1.529.2.23.1, mainly found in England, USA and Denmark, from pango-designation issue #532 Should read: ("Alias of " is duplicated) Alias of B.1.1.529.2.23.1, mainly found in England, USA and Denmark, from pango-designation issue #532

[FedeGueli]

In the entry for BA.2.23.1: Alias of Alias of B.1.1.529.2.23.1, mainly found in England, USA and Denmark, from pango-designation issue #532 Should read: ("Alias of " is duplicated) Alias of B.1.1.529.2.23.1, mainly found in England, USA and Denmark, from pango-designation issue #532

is this related to this issue?

[FedeGueli]

i found 45 sequences as today with Spike_T478K,Spike_D1199N, NSP12_A97V, -NSP8_N118S, -NSP3_P822S, -NSP16_G671S

[Sam8138]

In the entry for BA.2.23.1: Alias of Alias of B.1.1.529.2.23.1, mainly found in England, USA and Denmark, from pango-designation issue #532 Should read: ("Alias of " is duplicated) Alias of B.1.1.529.2.23.1, mainly found in England, USA and Denmark, from pango-designation issue #532 In entry for CU.1: Alias of BA.5.1.529.5.1.26.1, Central/Eastern Europe, S:T95I, S:T547K Should read: Alias of B.1.1.529.5.1.26.1, Central/Eastern Europe, S:T95I, S:T547K

[AngieHinrichs]

@Sam8138 thanks for reporting the typos. If you find any more, please open a new issue:

https://github.com/cov-lineages/pango-designation/issues/new

That will help to keep the discussion in this issue focused on the potential recombinant lineage.

[c19850727]

46 sequences as of 2022-11-03. Newly found in Japan (local case).

[FedeGueli]

47seqs as today

[FedeGueli]

51 as today

[c19850727]

53 as of 2022-11-07. Newly found in Turkey.

[c19850727]

63 as of 2022-11-08. Another big upload from Brunei (10/75).

[c19850727]

64 sequences as of 2022-11-10.

[InfrPopGen]

Thanks for submitting. We've added recombinant lineage XBH with 36 newly designated sequences, and 0 updated designations. Defining mutations C7528T (ORF1b:A88V), nt:C13730T (following BA.2.75.2 G25157A (S:D1199N) on current tree).