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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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EG.5.1 got S:F157L and growing rapidly (26 seqs - 8 countries) #394

Closed FedeGueli closed 1 year ago

FedeGueli commented 1 year ago

I want to thank @krosa1910 who turned the spotlight on S:F157 again L in #274 . I independently found a very recent EG.5.1 sublineage with S:F157L looking at GBW sequences on Gisaid ( US airport surveillance sequences)

Tree: Schermata 2023-07-12 alle 01 26 48 Schermata 2023-07-12 alle 01 27 12 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_283eb_de3bd0.json?label=id:node_6677659

Defining mutations: EG.5.1 >> > Orf1a:S1857L (C5835T), S:F157L (C22033A)

Gisaid query: C22033A,C5835T,G21718T,A18492G

Samples: 18 First: hCoV-19/England/PHEC-YYE4TUM/2023 | Original | EPI_ISL_17803964 | 2023-05-27 Last: hCoV-19/USA/FL-CDC-LC1045195/2023 | Original | EPI_ISL_17979092 | 2023-06-21

IDs: EPI_ISL_17803964, EPI_ISL_17818492, EPI_ISL_17838394, EPI_ISL_17885526, EPI_ISL_17885589, EPI_ISL_17926207, EPI_ISL_17949508, EPI_ISL_17951685, EPI_ISL_17952407, EPI_ISL_17952448, EPI_ISL_17956602, EPI_ISL_17960141, EPI_ISL_17971804, EPI_ISL_17971842, EPI_ISL_17972327, EPI_ISL_17974744, EPI_ISL_17975303, EPI_ISL_17979092,

Countries: 6 Schermata 2023-07-12 alle 01 32 02

FedeGueli commented 1 year ago

Ping @corneliusroemer i suggest direct designation of this one.

krosa1910 commented 1 year ago

Would make a lot of sense for this to be fast. It is EG.5.1, and S:157L is the only BA.2.75 early mutation (that XBB did not got due to it recom nature) that both showed up multiple times and seemed to show significant growth among XBB*.

Screenshot 2023-07-12 at 1 01 08 AM
FedeGueli commented 1 year ago

One of the three new sequences came from a traveller from Italy

FedeGueli commented 1 year ago

ping @corneliusroemer

FedeGueli commented 1 year ago

Designated EG.5.1.6 from https://github.com/cov-lineages/pango-designation/commit/a65b3221da89eca922fc3ea3e1941c2b7d01f83b

AngieHinrichs commented 1 year ago

Thanks @FedeGueli! Next time perhaps you can just add the milestone, and then let @aviczhl2 run the automated milestone update, and then you won't need to do the manual edit & pull request?

FedeGueli commented 1 year ago

Thanks @FedeGueli! Next time perhaps you can just add the milestone, and then let @aviczhl2 run the automated milestone update, and then you won't need to do the manual edit & pull request?

Ok thanks i ve not understand that it was no more needed manual update! thank you better this way!