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Here i want to propose a CM.8.1 sublineage that appeared first in phillipines and has been exported fastly in several countries.
I was digging a bit samples from Philippines or travel realted with Ph…
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Hi there,
I just ran an analysis and came across a case of BQ.1.13.1. This lineage is not to find in the annotation-json file.
--> looks like this is solved.
I am still missing XBB.1.9 (?)
G…
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When using ```Aliasor()``` to uncompress/compress aliased/unaliased lineages, there are instances when an unexpected lineage is returned. When running the following:
```
from pango_aliasor.aliasor…
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Hello!
I'm trying to use pyseer's elastic net feature to assess the effects of different variant groups on the phenotype, i.e. to find biologically plausible combinations of variants that predict t…
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I noticed a potential BJ.1/BA.2.75 recombinant in today's upload from Singapore.
A more extensive search using the simple GISAID query: `E_T11A,Spike_V83A` (ORF1ab/NTD BJ.1, S2 to 3' BA.2.75) revea…
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Came across a BA.2.75 that had S:346T, S:486S and S:444T which looks like a combination that could be quite fit.
GISAID query: `Spike_R346T, Spike_F486S,Spike_K444T`
Found 3 sequences that clust…
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Defining mutations (used in GISAID query): XBB.1>T28297C>T23018C(S:F486P)>A22161G(S:Y200C)
GISAID query: T28297C, T23018C, T23019C, A22161G
Earliest seq: 2023-01-12 (USA, EPI_ISL_16729101)
Most …
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Looking at BA.5.1.16 I investigated the two defining mutations: A2969G, G27470A
G27470A is very close to the BA.5.1 defining mutation T27438C (32 bases away), it has almost never been seen in Japan…
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After analysing the Whole Genome Sequence of a positive SARS-CoV-2 sample collected on 31/01/2023,
I determined the lineage of the strain using both Nexclade and Pangolin
**The Output of Nexclade wa…
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Description
Sub-lineage of:CH.1.1(BA.2.75.3.4.1.1.1.1)
Earliest sequence:2022-12-30(New Zealand)
Countries circulating:New Zealand10, United Kingdom6, Austria4, Germany4, Australia3, Netherlands2, …