search

cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
Other
1.03k stars 97 forks source link

JN.3+N:H300Y(57 seq, 12 countries) and further S:F456V(23 seq, 8 countries) #2445

Closed Over-There-Is closed 6 months ago

Over-There-Is commented 6 months ago

Transferred from sars-cov-2-variants/lineage-proposals#1160

JN.3> C2939T(Orf1a:P892S)> C29171T(N:H300Y)> A17637G, T22928G(S:F456V), C29095T, C29253T(N:S327L)

S:F456V branch is spotted by @Huachuan1120 on 12-04. A recombinant of S:F456V branch with EG.5.1.3 has been spotted and proposed by @aviczhl2 in sars-cov-2-variants/lineage-proposals#1267.

Query: C2939T, A6183, C29171(4 dropout, 7 not on GISAID) Query for S:F456V branch: A17637G, T22928G (including the recombinant, 2 dropout) Alternative query for S:F456V branch: C6525T, C29095T, C29253T (not including the recombinant)

Earliest Sequence: 09-18 Auvergne-Rhône-Alpes, France EPI_ISL_18327129 Latest Sequence: 12-30 England, UK EPI_ISL18764443 Regions Detected: France 3 +10_(ARA 6, HDF 3, Bretagne 1, IDF 1, Normandie 1, PDL 1), UK 2 +9(Scotland 9, England 2), Germany 10(Bayern 6, Berlin 3, BW 1), Switzerland 3(Berne 2, Zürich 1), Ireland 3(Dublin 2, Kildare 1), Denmark 2, Italy 1(Friuli-Venezia Giulia), Netherlands 1(Limburg); US 1 +7(Michigan 7, NJ 1), Canada 3(Ontario); China 1(HK), Singapore 1

https://nextstrain.org/fetch/github.com/Over-There-Is/subtreeAuspice/raw/main/subtreeAuspice_genome_6c9b_389ab0.json?c=country&label=id:node_4507656 2024-01-10 (1)

Sequences: EPI_ISL_18327129, EPI_ISL_18345205, EPI_ISL_18393016, EPI_ISL_18398880, EPI_ISL_18421665, EPI_ISL_18421669, EPI_ISL_18444789, EPI_ISL_18444795, EPI_ISL_18444860, EPI_ISL_18444880, EPI_ISL_18493326, EPI_ISL_18510026, EPI_ISL_18541096, EPI_ISL_18547047, EPI_ISL_18577281, EPI_ISL_18577373, EPI_ISL_18592282, EPI_ISL_18596299, EPI_ISL_18598210, EPI_ISL_18599846, EPI_ISL_18599863, EPI_ISL_18606074, EPI_ISL_18605945, EPI_ISL_18619751, EPI_ISL_18631463, EPI_ISL_18632934, EPI_ISL_18633152, EPI_ISL_18645464, EPI_ISL_18652958, EPI_ISL_18661656, EPI_ISL_18674685, EPI_ISL_18676345, EPI_ISL_18676927, EPI_ISL_18680575, EPI_ISL_18688159, EPI_ISL_18688784, EPI_ISL_18695237, EPI_ISL_18700645, EPI_ISL_18708522, EPI_ISL_18713427, EPI_ISL_18716994, EPI_ISL_18717245, EPI_ISL_18724621, EPI_ISL_18726821, EPI_ISL_18742238, EPI_ISL_18749823, EPI_ISL_18755890, EPI_ISL_18755899, EPI_ISL_18764443, EPI_ISL_18768801 American sequences not uploaded to GISAID: OR981977.1, PP002773.1, PP002783.1, PP002856.1, PP099237.1, PP099810.1, PP099826.1 Potential recombinant with EG.5.1.3: EPI_ISL_18705445, EPI_ISL_18724545, CLIMB-CM7YFQ6T
FedeGueli commented 6 months ago

ping @corneliusroemer

Over-There-Is commented 6 months ago

Italy