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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1662
S:T22N seems currently as fast as S:S31del globally. This derives by many different combinations so i think it is prudent …
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From branch 33 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1502
KP.2.5+C592T+C2377T, del21653_21655(Orf1a:N704K,S:S31del)
GISAID query: T592C,T2377G,A22115G
No. of seqs: …
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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1738
A new Orf9b mutation occurs under KP.3.3. Note that Orf9b mutations are not shown on usher so hard to notice.
KP.3.3+A97…
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From branch 9 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1502
JN.1.4+T18453C+del21653_21655,G22599C,A27675C(S:S31del, S:R346T, Orf7a:Q94H)
I cannot decide the order.
…
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I've noticed that the attachments field remains empty without linking the PDF file associated with the Zotero entry. I have verified that the PDF is properly attached in Zotero, and the citation key …
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After finishing the SARS-CoV-2 support in #549, do more extensive testing with published sample data. List of samples to [download] and the [toolkit] to download with.
Find more samples from [SRA] …
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I suggest using the poreCov pipeline as the backend for SARS-CoV-2 wastewater lineage deconvolution from nanopore long reads. You already added `freyja` ( #274 #270), which is great as the current com…
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From branch 4 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1768
KP.2+C5673T(Orf1a:P1803L)+C14220T+C3619T, C18657T,G23236T, C26936T, del21656_21658(S:K558N, F32del)
GISAID q…
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KR.1 got its DeFLiRT sublineage likely in Philippines
Defining mutations: KR.1 >> C6568T > C6388T, S:S31del (del21653-55)
(New) Query: C6568T,C6388T,T3565C,C897A (by @aviczhl2 )
Samples: 3
Countr…
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Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/1643
KP.2.2+C23277T(S:T572I)
GISAID query: C23277T, A25359G, T21737C, -A2745G, -24364,-28468,-25455,-29410
No. of …