JD.1.1 (XBB.1.5.102 + FLip, S:A475V) Sublineage with S:T470N (10 sequences, 2 countries) #896
Comments
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If there's something with S:470 and S:475 we will see that in GK.3.1/GK.4/GW.5.1.1/FL.15.1.1 in a few weeks. Really suggest to use another AA-query. |
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S.T470N was in Sars1 |
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ping @corneliusroemer i suggest rapid designation here. |
FedeGueli
changed the title
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@ryhisner i think there are 8 not nine. |
Which one of the EPI_ISL's do you think doesn't belong? There appear to be nine on the Usher tree. One of them doesn't have ORF6:N26D or ORF1a:V1584M. Maybe we shouldn't count the coinfection/contamination one? EPI_ISL_18147899, EPI_ISL_18220202, EPI_ISL_18244938, EPI_ISL_18280964, EPI_ISL_18295837, EPI_ISL_18295898, EPI_ISL_18313958, EPI_ISL_18327415, EPI_ISL_18329981 |
FedeGueli
changed the title
the query gave 8 and miscounted on usher the french seqs sorry. so the query loses one. |
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I think C22971A, T28282C works just as well and also catches the French sequence, so I've changed the query. |
Thank you! |
FedeGueli
changed the title
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+1 Italy |
There seems to be homoplasy at 470N: currently, the Usher tree suggests one single event of 470N, but there are two branches with 2 private muts each and the smaller one has T16593C for which there are 2 basal French sequences, suggesting that 470N arose independently
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Designated JD.1.1.3 via cov-lineages/pango-designation@ec1bf5f |
Description
Sub-lineage of: JD.1.1
Earliest sequence: 2023-8-14, France — EPI_ISL_18220202
Most recent sequence: 2023-9-18, France — EPI_ISL_18327415
Countries circulating: France (8), Denmark (1)
Number of Sequences: 9
GISAID Nucleotide Query: C22971A, T28282C
CovSpectrum Query: Nextcladepangolineage:XBB.1.5* & C22986T & C22971A & [2-of: C14189T, C19158T, T28282C, C28087T]
Substitutions on top of JD.1.1:
Spike: T470N
Nucleotide: C19158T, C22971A ( C22971A, T28282C,C14189T to exclude old indian sequence but loses one of this)
Phylogenetic Order of Mutations: C19158T → C22971A (S:T470N)
USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/JD.1.1_T470N_France_9_seq.json?c=gt-S_470&gmax=25384&gmin=21563&label=id:node_3886280
Evidence
Despite there being only nine sequences, this has been detected in six different regions of France and Denmark. One of the most recent sequences appears to be a recombinant with EG.5.1. However, the presence of ORF1a:V1584M (in 8/9 sequences in this lineage) and the lack of ORF1a:T4175I (in EG.5.1) means this would need to have at least five breakpoints, two on either side of both ORF1a:V1584M and ORF1a:T4175I and one between S:52 and S:470. So it seems likely this is either coinfection or contamination.
Genomes
Genomes
EPI_ISL_18147899, EPI_ISL_18220202, EPI_ISL_18244938, EPI_ISL_18280964, EPI_ISL_18295837, EPI_ISL_18295898, EPI_ISL_18313958, EPI_ISL_18327415, EPI_ISL_18329981The text was updated successfully, but these errors were encountered: