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KP.2.3(with S:S31del)+C21816G(S:P85R)
GISAID query: C22000A,C21816G,G25593T
No. of seqs: 17(Denmark 1 UK 1 France 1 India 2 Japan 1(from Poland/Germany) Luxembourg 3 Portugal 2 Spain 2 USA 4(2 fro…
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KP.2.3+S:S31del+A22080G(S:Q173R)
GISAID query: C22000A, A22080G,G25593T
No. of seqs: 20(Canada 2 UK 2 Germany 1 Iceland 1 Ireland 1 Netherlands 3 Singapore 1 Switzerland 1 USA 8(2 from Greece))
…
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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…
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In the newest usher tree the placement is altered and JN.1.39.1 now starts from a weird A16011G node.
[usher](https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice10_genome_t…
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**KP.3.3>ORF1a:E1801K>S:Q52R**
- KP.3.3>ORF1a:E1801K GISAID Query:`G5666A,A19515G`
- KP.3.3>ORF1a:E1801K GISAID Query:`C14931T, A21717G,A7842`
EPI_ISL ID:
EPI_ISL_19169494, EPI_ISL_19175063, E…
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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…
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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1806
KS.1.1--JN.1
Breakpoint between 22929 and 24820
Additional mutations: C6701T, C19716T, T25510C, C29311T
Orf1a:L214…
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Besides KP.2.11, there seems to be a direct KP.2+S:L56V branch
KP.2+T21728G(S:L56V)
GISAID query: G17334T, T21728G, G22599C, -6543,-24819
No. of seqs: 25(Australia 1 Canada 2 France 1 India 1 I…
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It seems that there is a new convergent mutation of S:R190S. It usually couples with S:S31del.
Cov-spectrum shows its growth is negative with S:S31S, but large growth advantage with S:S31-. It see…
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From branch 36 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
JN.1+Orf10:P10S+S:F456L
Query: T22928C,C26753T,C18894T,-G24872T,-A532G
No. of seqs: 50 (Australia 1 Brazil 34 …