-
LB.1+G23593T(S:Q677H)
GISAID query: G23593T, del21653, G22111T,-18131,-4784,-3724,-19669,-4683,-15960,-19560
No. of seqs: 6(Spain 1 USA 1 UK 1 Canada 3)
First: EPI_ISL_19230847, Canada, 2024-6-…
-
This S98F seems to be a new convergent site.
KP.2.3(with 31del)+C28714T+C20233T(Orf1b:P2256S)+C11575T+T15207C,C21855T(S:S98F)
GISAID query: C21855T,C28714T, C20233T
No. of seqs: 16(USA 4 Canada 1…
-
From branch 6 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1771
LB.1.7+G22132T(S:R190S)
GISAID query: G22132T, G22111T, C4784T, -22096,-16376,-11109,-17439,-27292, G11727A
N…
-
KP.1.1.1+C12400T+G24757T+del21653_21655,G1655A, T6522A, T19389C, A22995C, C25989A, T27438C, C29296T,A22995C(rev)
(Orf1a:V464I,I2086N, S:S31del, S:K478T(rev), Orf3a:D199E)
GISAID query: C12400T,G24…
-
There seems another KP.2.3-445P branch now.
KP.2.3+S:S31del+C28714T+C7948T+A22896C(S:H445P)+C21816A(S:P85Q)
GISAID query: C21816A, T22896C,T22200G,C7948T
No. of seqs: 4( Japan 1(from India) USA …
-
From branch 31 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1771
This S:R190S becomes convergent in KP.3.1.1, too.
KP.3.1.1+G22132T(S:R190S)
GISAID query: C12616T,A13121T,…
-
MH.1+C10183T+C25413T+A178T+C5770T+C3587T(Orf1a:H1108Y)+C21815T(S:P85S)
GISAID query: C21815T, C3587T, C25413T
No. of seqs: 19(France 1 Israel 12 China 1 USA 5(2 from Netherlands))
First: EPI_IS…
-
We are using Usher to integrate new sequences into an existing tree. However, in some rare cases, the topology of the original input tree is _not_ preserved.
For example, if you have the tree: (((A…
-
Most Chinese sequences are now open, this should be a useful addition to open data
Usher now pulls these, it seems to work. We can probably copy the approach, see https://github.com/yatisht/usher/i…
-
From https://github.com/sars-cov-2-variants/lineage-proposals/issues/2084
Recently I train a GPT model on viral evolution for SARS-Cov-2 using data up to early-JN.1, and T22119C-S:F186S is its top …