KP.3.3 plus S:A27P, 92 samples 7 countries

[JosetteSchoenma]

KP.3.3 plus S:A27P, 5 samples Japan 3 from Saitama and 2 from Tokyo Query: Spike_A27P, Spike_Q493E NEW Nuc Query: C7299T, C28291A, -A4364C, -C6543T (by @Over-There-Is ) (Old Nuc Query: T21610C,C7299T,C28291A )

[FedeGueli]

i ve added a nuc query T21610C,C7299T,C28291A

[JosetteSchoenma]

i ve added a nuc query T21610C,C7299T,C28291A

Thanks, @FedeGueli !

[FedeGueli]

+1 Jap

[FedeGueli]

10 all from Japan likely slow.

[xz-keg]

19 and in USA, Germany and France

[FedeGueli]

Please propose it a quite big batch from South Korea with it, 2/13 samples from there in August.

[FedeGueli]

52 now, @JosetteSchoenma would you propose it please?

[xz-keg]

I only find 46 using the nuc query.

[DailyCovidCases]

I think this is nearly dead, so please close this issue

[FedeGueli]

I think this is nearly dead, so please close this issue

15/51 in august, it is not dead @JosetteSchoenma please ignore .

[FedeGueli]

Instead propose it please @JosetteSchoenma

[Over-There-Is]

S:A27P is T21632C in GISAID. T21610C, T21632C, C7299T,C28291A=48 -T21610C, T21632C, C7299T,C28291A=33 T21610C, -T21632C, C7299T,C28291A=5

[Over-There-Is]

S:A27P is T21632C in GISAID. T21610C, T21632C, C7299T,C28291A=48 -T21610C, T21632C, C7299T,C28291A=33 T21610C, -T21632C, C7299T,C28291A=5 -T21610C, -T21632C, C7299T,C28291A=1

T21610C is a well-known misinterpretation of ins21608, it's unrelated to S:27.

sequences without T21632C: hCoV-19/Germany/SH-RKI-I-1143903/2024|EPI_ISL_19283857|2024-07-04 KP.3.3.4 hCoV-19/South_Korea/KDCA293904/2024|EPI_ISL_19340653|2024-07-22 21610-21641N shares A20013G and C2470T with other sequences, it should belong to this lineage.(-T21610C) hCoV-19/Canada/BC-BCCDC-726017/2024|EPI_ISL_19345984|2024-07-26 KP.3.3.4 hCoV-19/USA/NV-SNPHL-817177/2024|EPI_ISL_19350782|2024-08-13 21611-21641N KP.3.3.4 hCoV-19/South_Korea/KDCA294215/2024|EPI_ISL_19352431|2024-07-27 on a C6543T branch. hCoV-19/USA/CO-CDPHE-42195353/2024|EPI_ISL_19406336|2024-07-29 KP.3.3.4

A better query would be: C7299T, C28291A, -A4364C, -C6543T Totally 82 now: KR41 JP21 US17 CA1 CN-HK1 FR1

[Over-There-Is]

And it would be 84 if adding non-GISAID sequences like USA/NJ-CDC-QDX21693001/2024|PQ212164.1|2024-07-31 and USA/NC-CDC-LC1115476/2024|PQ237566.1|2024-08-16.

[Over-There-Is]

In usher's database it's T21632C, but in uploaded sequences, it will be interpreted as G21641C and unable to be combined with existing tree. https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_39026_bc9640.json?c=country&label=id:node_11656771

[FedeGueli]

Added the new query: C7299T, C28291A, -A4364C, -C6543T

[FedeGueli]

S:A27P is T21632C in GISAID. T21610C, T21632C, C7299T,C28291A=48 -T21610C, T21632C, C7299T,C28291A=33 T21610C, -T21632C, C7299T,C28291A=5 -T21610C, -T21632C, C7299T,C28291A=1

T21610C is a well-known misinterpretation of ins21608, it's unrelated to S:27.

sequences without T21632C: hCoV-19/Germany/SH-RKI-I-1143903/2024|EPI_ISL_19283857|2024-07-04 KP.3.3.4 hCoV-19/South_Korea/KDCA293904/2024|EPI_ISL_19340653|2024-07-22 21610-21641N shares A20013G and C2470T with other sequences, it should belong to this lineage.(-T21610C) hCoV-19/Canada/BC-BCCDC-726017/2024|EPI_ISL_19345984|2024-07-26 KP.3.3.4 hCoV-19/USA/NV-SNPHL-817177/2024|EPI_ISL_19350782|2024-08-13 21611-21641N KP.3.3.4 hCoV-19/South_Korea/KDCA294215/2024|EPI_ISL_19352431|2024-07-27 on a C6543T branch. hCoV-19/USA/CO-CDPHE-42195353/2024|EPI_ISL_19406336|2024-07-29 KP.3.3.4

A better query would be: C7299T, C28291A, -A4364C, -C6543T Totally 82 now: KR41 JP21 US17 CA1 CN-HK1 FR1

Thx

[Over-There-Is]

Japan +3, 85(or including non-GISAID sequences 87)

[Over-There-Is]

Korea+5, 90

[xz-keg]

92, Netherlands

[FedeGueli]

only 4 in September, weird lineage still going but slowly

[Over-There-Is]

95

[FedeGueli]

7/95 after September 1 . likely dying off