XDV.1+Orf3a:G174C+S:K478I (25 seqs, 9 places mostly in rural Hubei, 4 with S:478T cycle reversion)

[xz-keg]

There seems to be a lot of S:478 mutation branches on XDV.1. This one is only in Hubei, but appears in 7 different regions, mostly of rural areas. Consider neighboring provinces aren't uploading any seqs this may be very widespread in rural areas of central China. And 1 seq also detected in Japan.

XDV.1+C8140T+G25912T,C29546T(Orf3a:G174C)+T19110C+A22995T(S:K478I) +C9803T+T22995C(S:I478T cycle reversion)

GISAID query: T19110C,C8140T, -22995A No. of seqs: 20(Hubei 19(Jingzhou, Shiyan, Huangshi, Wuhan, Xianning, Shennongjia, Jingmen), Japan 1)

First: EPI_ISL_19384776, 2024-7-17, Shennongjia Latest: EPI_ISL_19429270, 2024-9-9, Jingmen

GISAID query for S:I478T sub-branch: T19110C,C8140T,-22995 (3 seqs)

usher

Notes (edited): the 478T branch is a mini saltation with ORF1a:P3134S (C9665T), A13512G, ORF1b:S1159N (G16943A), A18036G, C25587T, ORF3a:A110T (G25720A), ORF7b:F16C (T27802G)

[FedeGueli]

Thx for spotting , it seems to seem that 478X could not work well with 493E and maybe also with 31del but i should look at it more closely

Yeah it seems confirmed, roughly, by data: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?%2FAllSamples%2FPast3M%2Fvariants%3FnextcladePangoLineage=JN.1*&variantQuery=S%3A478+%26+%21S%3A478K++&

[xz-keg]

Yeah it seems confirmed, roughly, by data: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?%2FAllSamples%2FPast3M%2Fvariants%3FnextcladePangoLineage=JN.1*&variantQuery=S%3A478+%26+%21S%3A478K++&

S:478X seems to be a new convergent spot for JN.1-Spike. 478R was mostly appeared in the XBB era while 478T rev appears most now.

[xz-keg]

Yeah it seems confirmed, roughly, by data: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?%2FAllSamples%2FPast3M%2Fvariants%3FnextcladePangoLineage=JN.1*&variantQuery=S%3A478+%26+%21S%3A478K++&

I just realize this branch actually has a cycle reversion branch exported to Japan. S:478T->K->I->T cycle mutation.

[xz-keg]

1 more seq from Hubei, a new city of Huanggang.

[FedeGueli]

22 for a very recent sample uploaded today with 478T from Hubei

[FedeGueli]

Added a note to keep track of the mini saltation where 478T appeared

[DailyCovidCases]

Likely dying off now

[FedeGueli]

+2 Heilongjiang