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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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LB.1.3 + S:T>A376S circulating in South Africa (38, 4 places, 40% South Africa after OCT 1) with a sublineage with S:K147R #2825

Open FedeGueli opened 1 week ago

FedeGueli commented 1 week ago

LB.1.3>> Orf1a:G432S (G1559A) > S:A376S (G22688T) > S:k147R (A22002G) Query:22688T,G1559A Samples: 38 (South Africa 34, Denmark 2, Canada 1,Portugal 1) First sampled on 2024-08-06 in a traveler from SA

Query for S:K147R branch: A22002G,22688T Samples: 6

The tree is split in two with one branch belonging to a South African LB.1.3 branch with ORF1a:T1581M (C5007T). Both branches show interesting spike diversity with 445R or 147R and other mutations:

Screenshot 2024-11-16 alle 01 00 53

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_45f5b_7e1820.json?f_userOrOld=uploaded%20sample

IDs: EPI_ISL_19339131, EPI_ISL_19438359, EPI_ISL_19453873-19453874, EPI_ISL_19453879, EPI_ISL_19453891, EPI_ISL_19463191, EPI_ISL_19463196-19463197, EPI_ISL_19463199, EPI_ISL_19467580, EPI_ISL_19467656, EPI_ISL_19485379, EPI_ISL_19485390, EPI_ISL_19522660, EPI_ISL_19531084, EPI_ISL_19531086, EPI_ISL_19546684, EPI_ISL_19546686-19546687, EPI_ISL_19546690-19546691, EPI_ISL_19546694-19546699, EPI_ISL_19546701-19546704, EPI_ISL_19546706, EPI_ISL_19546708-19546710, EPI_ISL_19546714, EPI_ISL_19546718,

FedeGueli commented 1 day ago

38 now, 14/33 after OCT.1 in South Africa, @corneliusroemer this needs a rapid designation.

FedeGueli commented 1 day ago

Re updating the tree, there is also a K147R branch of it