Closed Fearuncle closed 1 year ago
Can you estimate local prevalence in Shanghai after 1st of April or provide a gisaid query please?
11.9%
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
there is a growing mutation
ORF1ab:M1588V(A5027G) 19 seq.
I found 214 with A460G,T12730A, T3802C where do you find the other ones?
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
@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)
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)
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*.
43 seq
43? are u sure? or you mean new ones @Fearuncle
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.
how do i navigate gisaid to get accurate numbers
big upload
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)
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.
how do i navigate gisaid to get accurate numbers
Paste A460G,T12730A, T3802C
in GISAID's "Nucl Mutations" textbox.
NZ 2, China 4(Heilongjiang 3, Yunnan 1), S. Korea 1(from China), Australia 2 and Canada 1. 526 now.
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.
EDITED by mod.: Gisaid query A460G,T12730A, T3802C.