Multiple XBB.1.16 and EG.2 Lineages with S:K304X

[NkRMnZr]

Multiple XBB.1.16 and EG.2 Lineages with S:K304X

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1. Branch 1: Designated as XBB.1.16.23 , Transferred to XBB.1.16 with S:K304Q (100 seqs, 9 countries) cov-lineages/pango-designation#2187 XBB.1.16 > A22472C(S:K304Q)
2. Branch 2: Transferred to XBB.1.16 with ORF1b:Q1546H, ORF3a:L41F, ORF1a:Q2660H, ORF1b:A1620V, ORF1b:T284I and S:K304Q (31 seqs, 8 countries) cov-lineages/pango-designation#2244 XBB.1.16 > G18105T(ORF1b:Q1546H) > T16209C, C25513T(ORF3a:L41F) > A8245C(ORF1a:Q2660H), C16608T > C18326T(ORF1b:A1620V) > C14318T(ORF1b:T284I) > A22472C(S:K304Q) [Query: C14318T, C18326T, A22472C, 19 seqs, 08/30]
3. Branch 3: Designated as EG.2.2 , Transferred to EG.2 with S:K304N (45 seqs, mainly in Japan, 3 countries) cov-lineages/pango-designation#2188 EG.2 (XBB.1.9.2.2) > A6355T > C9430T, T18471C > A22474T(S:K304N) spotted by @FedeGueli

Branch 1

Transferred to Main Repo, Designated as XBB.1.16.23

Designated as XBB.1.16.23 via cov-lineages/pango-designation@9f68787

Transferred to cov-lineages/pango-designation#2187

Defining Mutations: XBB.1.16 > A22472C(S:K304Q)
Query: A22101T, A22472C, C29386T, -T16209C
Earliest seq: 2023-04-06 (EPI_ISL_17496355, Singapore)
Latest seq: 2023-07-15 (EPI_ISL_18050922, Fukushima, Japan)
Sampled Countries: Japan (7), Singapore (6), South Korea (6), USA (5, California/2, Indiana, North Carolina, Virginia), Canada (2, BC), India (2, Karnataka)

Genomes:

EPI_ISL_17496355, EPI_ISL_17539792, EPI_ISL_17596417, EPI_ISL_17631385, EPI_ISL_17695054, EPI_ISL_17777161, EPI_ISL_17807332, EPI_ISL_17837583, EPI_ISL_17856816, EPI_ISL_17884028, EPI_ISL_17927867, EPI_ISL_17927876, EPI_ISL_17930453, EPI_ISL_17949711, EPI_ISL_17956589, EPI_ISL_17984091, EPI_ISL_17996307, EPI_ISL_18006528, EPI_ISL_18006550, EPI_ISL_18008936, EPI_ISL_18009151, EPI_ISL_18038978, EPI_ISL_18044135, EPI_ISL_18045251, EPI_ISL_18045294, EPI_ISL_18050922, EPI_ISL_18050961, EPI_ISL_18051952

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_7587_7bc620.json?f_userOrOld=uploaded%20sample

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Branch 2

Transferred to Main Repo

Transferred to cov-lineages/pango-designation#2244

Defining Mutations: XBB.1.16 > G18105T(ORF1b:Q1546H/nsp14_Q22H) > T16209C, C25513T(ORF3a:L41F) > A8245C(ORF1a:Q2660H/nsp3_Q1842H), C16608T > C18326T(ORF1b:A1620V/nsp14_A96V) > C14318T(ORF1b:T284I/nsp12_T293I) > A22472C(S:K304Q)
Query: C14318T, C18326T, A22472C
Earliest seq: 2023-04-28 (EPI_ISL_17625420, Shanghai, China, travel history to: Singapore)
Latest seq: 2023-07-13 (EPI_ISL_18038504, Vientiane, Laos)
Sampled Countries: China (5, Heilongjiang/2, Hubei, Shanghai, Sichuan), Laos (1), South Korea (1), Switzerland (1), USA (1, New York)

Genomes:

EPI_ISL_17625420, EPI_ISL_17850378, EPI_ISL_17850453, EPI_ISL_17951213, EPI_ISL_17989079, EPI_ISL_18022610, EPI_ISL_18034134, EPI_ISL_18038504, EPI_ISL_18047554

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3f82_7bad10.json?f_userOrOld=uploaded%20sample

view from ORF1b:Q1546H branch

details

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Branch 3

Transferred to Main Repo, Designated as EG.2.2

Designated as EG.2.2 via cov-lineages/pango-designation@94fbed4

Transferred to cov-lineages/pango-designation#2188

Defining Mutations: EG.2 > A6355T > C9430T, T18471C > A22474T(S:K304N)
Query: A6355T, T18471C, A22474T
Earliest seq: 2023-03-31 (EPI_ISL_17546450, Jakarta, Indonesia)
Latest seq: 2023-07-24 (EPI_ISL_18051721, Yamaguchi, Japan)
Sampled Countries: Japan (18), Indonesia (2), USA (1, Arizona)

Genomes:

EPI_ISL_17546450, EPI_ISL_17551534, EPI_ISL_17958643, EPI_ISL_18012733, EPI_ISL_18040498, EPI_ISL_18041432, EPI_ISL_18041478, EPI_ISL_18050913, EPI_ISL_18050968, EPI_ISL_18051721, EPI_ISL_18053832, EPI_ISL_18065217, EPI_ISL_18065997, EPI_ISL_18066036, EPI_ISL_18066169, EPI_ISL_18066186, EPI_ISL_18066189, EPI_ISL_18066243, EPI_ISL_18066260, EPI_ISL_18066370, EPI_ISL_18066401

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2724c_e55150.json?f_userOrOld=uploaded%20sample

note that most of this lineage has a B.1.1 defining mutation altered, N:G204R>P (G28884C over existing G28883C)

[FedeGueli]

I spotted a EG.2 + S:K304N today: A22474T,C9430T, T18471C,A6355T

[NkRMnZr]

Tracking updates:

08-05, Branch 1 +4 (Canada, Japan, South Korea; Branch 2 +3 (China, South Korea, USA)

4 seqs from Canada, Japan, and South Korea on Branch 1: EPI_ISL_18055280, EPI_ISL_18058363, EPI_ISL_18063130, EPI_ISL_18067271;
3 seqs from China, South Korea and USA on Branch 2: EPI_ISL_18055693, EPI_ISL_18057798, EPI_ISL_18067375

08-08: Branch 1, +3 (Japan and USA); Branch 3, +3 (Japan)

08-13: Branch 1, +4 (Japan, USA); Branch 2, +1 (USA); Branch 3, +7 (Japan)

08-18, Branch 2: +3 from China and USA

08-25, Branch 2: +2 from China and Singapore

[NkRMnZr]

I spotted a EG.2 + S:K304N today: A22474T,C9430T, T18471C,A6355T

I'm adding it to tasklist, it seems to be jumping fast this week

[FedeGueli]

Thanks @NkRMnZr for noticing and adding :it represents 7 out of 212 samples from okinawa Japan in July

[NkRMnZr]

Thanks @NkRMnZr for noticing and adding :it represents 7 out of 212 samples from okinawa Japan in July

And there's N:G204R>P mutation on many of the sequences

[NkRMnZr]

08-08: Branch 1, +3 (Japan and USA); Branch 3, +3 (Japan)
Branch 1, 3 seqs from Japan and USA: EPI_ISL_18071590, EPI_ISL_18073723, EPI_ISL_18073893
Branch 3, 3 seqs from Japan: EPI_ISL_18075785, EPI_ISL_18075812, EPI_ISL_18077847

[NkRMnZr]

08-13: Branch 1, +4 (Japan, USA); Branch 2, +1 (USA); Branch 3, +7 (Japan)
Branch 1, 4 seqs from Japan and USA: EPI_ISL_18081404, EPI_ISL_18081957, EPI_ISL_18082731, EPI_ISL_18095875
Branch 2, 1 more from USA: EPI_ISL_18080211
Branch 3, 7 seqs from Japan: EPI_ISL_18081861, EPI_ISL_18082809, EPI_ISL_18082915, EPI_ISL_18082917, EPI_ISL_18082927, EPI_ISL_18082929, EPI_ISL_18082982

Update of Branch 1 on UShER

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_237b3_8edee0.json?f_userOrOld=uploaded%20sample

Update of Branch 3 on UShER

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_23c06_8ee3a0.json?f_userOrOld=uploaded%20sample

[FedeGueli]

Please propose Branch 1 (see - uncertain)
and
Branch 3 : see, a bit clearer

[NkRMnZr]

08-18, Branch 2: +3 from China and USA
1 from New York: EPI_ISL_18104523
1 from Shanghai: EPI_ISL_18105848
1 from Jiangsu: EPI_ISL_18105951

[NkRMnZr]

08-25, Branch 2: +2 from China and Singapore EPI_ISL_18127506, EPI_ISL_18138323

[FedeGueli]

Brnch 3 designated EG.2.2 from cov-lineages/pango-designation@94fbed4

[FedeGueli]

Branch 1 designated XBB.1.16.23 via cov-lineages/pango-designation@9f68787

[FedeGueli]

I think @NkRMnZr you should propose the last branch in the other repo so maybe Cornelius goes to designate it too.

[NkRMnZr]

Branch 2 transferred to cov-lineages/pango-designation#2244

[FedeGueli]

Branch 2 transferred to cov-lineages/pango-designation#2244

Thank you