FU.1 with A460G 516 seq. mostly China mostly Shanghai ( >18% prevalence in Shanghai)

[Fearuncle]

first sequenced: 3-30-23 Most recent Sequence: 4-26-23

EDITED by mod.: Gisaid query A460G,T12730A, T3802C.

[FedeGueli]

Can you estimate local prevalence in Shanghai after 1st of April or provide a gisaid query please?

[Fearuncle]

11.9%

[FedeGueli]

I think it could be more than 13% actually. It is already at 200 seqs found with the query A460G,T12730A, T3802C on Gisaid. It represents 177 out of 1294 samples collected in Shanghai after 1st of April.

@corneliusroemer i suggest to directly designate it in the next systemic tree review of XBB.1.16 ( due to the fact it is not permitted to propose lineages with just nucletotide mutations.

I ve edited headline and proposal to ease the Cornelius work

[Fearuncle]

there is a growing mutation ORF1ab:M1588V(A5027G) 19 seq.

[FedeGueli]

I found 214 with A460G,T12730A, T3802C where do you find the other ones?

[Fearuncle]

[FedeGueli]

Consider that some sequences could be duplicated cause Usher pulls seqs from the chinese gen bank too and there are seqs also uploaded in Gisaid. i will look at the tree later to see if this is the case

[Fearuncle]

[Fearuncle]

[FedeGueli]

@corneliusroemer i would consider a designation of this one in your next designathlon. (we cant propose in the pango page due the nuc only mut)

[FedeGueli]

321 samples on Gisaid with A460G,T12730A, T3802C . Found also in travellers from Taiwan.

@corneliusroemer i suggest a direct designation of this one (missing an AA defining mutation it could not be propose officially)

[Fearuncle]

[Over-There-Is]

Among 15 FU.1 sequences collected in Guangdong, 12 have A460G mutation. Additionally, Guangdong/GDCDC_JM_0092/2023|EPI_ISL_17698225|2023-05-10 (assigned by GISAID as XBB.1.9.1 and assigned by Nextclade as XBB.1.22) is probably a recombinant between FU.1+A460G and XBB.1.9.2*.

[Fearuncle]

43 seq

[FedeGueli]

43? are u sure? or you mean new ones @Fearuncle

[Over-There-Is]

Exactly there are only 25 seq with A460G and Orf1a:V3367I right now, most of these are uploaded to both GISAID and GenBase and duplicated.

[Fearuncle]

how do i navigate gisaid to get accurate numbers

[Fearuncle]

big upload

[Over-There-Is]

Totally 525 now, GISAID query: Spike_T547I, A460G Among 154 sequences uploaded by Shanghai at 05-29, at least 47 are imported (tagged as HG), 3 from Hong Kong SAR, 4 from Macao SAR, 1 from Taiwan Province; 14 from Thailand, 5 from South Korea, 3 from Singapore, 3 from UAE, 3 from Japan, 2 from US, 2 from Egypt, and Algeria, Sweden, UK, Switzerland, Vietnam each one, and 2 not tagged their travelling information.

And then, Yunnan 1, US 1(from S. Korea), Anhui 5(4 Bozhou and 1 Lu'an), Fujian 5(2 Amoy, 2 Sanming and 1 Nanping), 1 Hubei(Jingzhou), South Korea 3(2 from China and 1 from Turkey) and Sichuan 3(Guangyuan, Luzhou and Yibin each one).

Earliest Sequence: EPI_ISL_17232963 SFO Airport, California, US (from Deutschland) 03-06 Latest Sequence: EPI_ISL_17730875 South Korea (from China) 05-21

Accumulated: China 495+3: Shanghai 396, 56 imported: 3 HK, 4 Macao, 1 TW; 19 Thailand, 5 S. Korea, 4 UAE, 3 Singapore, 3 Japan, 2 US, 2 Egypt, 2 Vietnam, 1 Deutschland, 1 Malaysia, 1 Algeria, 1 Sweden, 1 UK, 1 Switzerland, 2 travelling info unavailable. Hubei 24: 5 Jingzhou, 4 Huanggang, 3 Huangshi, 3 Ezhou, 2 Jingzhou, 2 Xiangyang, 1 Wuhan, 1 Xiaogan, 1 Enshi, 1 Shiyan and 1 Xianning. Fujian 24: 12 Fuzhou, 3 Longyan, 3 Sanming, 2 Amoy, 2 Nanping, 1 Zhangzhou and 1 Quanzhou. Anhui 13: 6 Bozhou, 5 Lu'an and 2 Fuyang. Guangdong 12: 7 Shenzhen, 2 Guangzhou, 1 Meizhou, 1 Zhanjiang and 1 Dongguan. Sichuan 8: 2 Yibin, 2 Luzhou, 1 Neijiang, 1 Ya'an, 1 Guangyuan, 1 Liangshan. Yunnan 8, city not assigned. Jiangsu 4: 2 Zhenjiang, 1 Wuxi, 1 Changzhou. Henan 2: 1 Hebi and 1 Xinyang. Taiwan 3, all from Mainland. Beijing 1, Zhejiang 1(Hangzhou?), Heilongjiang 1, Shanxi 1(Jincheng).

US 9: 1 from Deutschland, 1 from China Mainland,1 from Taiwan, 1 from South Korea, 3 Airport Screening, 2 local cases in Washington State South Korea 8: 3 from China, 2 from Switzerland, 1 from Turkey. Japan 6, 5 Imported, at least 3 from China. Singapore 2, all Local. Austria 1(Vienna) Australia 1(SA)

[Over-There-Is]

With Fede's query, only 516 is found. 1 seq in Jingzhou dropped 12730 out, 4 seq in Shanghai (all local), 1 seq in Wuxi, 1 seq in Changzhou and 1 seq in Fuzhou dropped 3802 out, and 1 Shanghai local seq dropped out both.

[Over-There-Is]

how do i navigate gisaid to get accurate numbers

Paste A460G,T12730A, T3802C in GISAID's "Nucl Mutations" textbox.

[Over-There-Is]

NZ 2, China 4(Heilongjiang 3, Yunnan 1), S. Korea 1(from China), Australia 2 and Canada 1. 526 now.

[FedeGueli]

At this point please transfer this to the main page , it doesnt accomplish the pango criteria so maybe put it as possible systemic designation needed to describe the tree.