JN.1 + S:N185S(105 seq, 12 countries)

cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme

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JN.1 + S:N185S(105 seq, 12 countries) #2471

Closed DoropFan closed 3 months ago

DoropFan commented 6 months ago

Transferred from:https://github.com/sars-cov-2-variants/lineage-proposals/issues/1214

Sub-lineage of:JN.1(BA.2.86.1.1) Earliest sequence:2023-10-31(Spain)EPI_ISL_18724688

UShER Tree JN.1>C11833T, T27863C>C27434T(ORF7a:T14I)>T14100C, A22116G(S:N185S), C27810T(ORF7b:L19F(rev) https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1409e_f214d0.json?c=gt-nuc_22116&gmax=23116&gmin=21116&label=id:node_6846872 GISAID:T14100C, A22116G, C27434T JN1+185Sp2

CovSpectrum Genomes

corneliusroemer commented 5 months ago

The reversion is weird - it sort of points at recombination but there's not much other evidence for it.

FedeGueli commented 5 months ago

aviczhl2 commented 4 months ago

T27863C>C27434T

The prevalence of two nearby mutations lower the chance for recomb. If it is a recomb it has to be a sandwich recomb with BP 1 between 27435 and 27809 and BP 2 between 27811 and 27862.

FedeGueli commented 3 months ago

this slowed down a lot. 105 now.

DoropFan commented 3 months ago

There seems to be no new sequence, so I'll close it.

DoropFan commented 3 months ago

There seems to be no new sequence, so I'll close it.

FedeGueli commented 3 months ago

Thank you