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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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New KP.3.3 branch with S:I844V emerged in Australia (148, 12 countries), two with S:ins643PAGV +S:Q644E from France #1674

Closed FedeGueli closed 4 days ago

FedeGueli commented 1 month ago

I have noticed a lineage circulating in Australia that has been sampled in 4 continents. For sure it won't be fast but interesting to track S:I844V mutation that should be close the fusion peptide. Defining : KP.3.3 > S:I844V (A24092G ) Query: A24092G,C25006T,T3565C Samples: 34 Countries: Australia (4 States), Canada (3 states) US (2 States), Japan, UK Tree:

Screenshot 2024-07-03 alle 00 29 21

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4ce95_45a280.json?f_userOrOld=uploaded%20sample&label=id:node_7004194

Note that a couple of samples from Canada have S:A344V (query: A24092G,C22593T)

IDs: EPI_ISL_19069391, EPI_ISL_19122434, EPI_ISL_19122480, EPI_ISL_19122548-19122549, EPI_ISL_19145755, EPI_ISL_19150394, EPI_ISL_19183843, EPI_ISL_19188044, EPI_ISL_19189289, EPI_ISL_19192870, EPI_ISL_19199086, EPI_ISL_19203036, EPI_ISL_19203071, EPI_ISL_19203093, EPI_ISL_19203130, EPI_ISL_19208145, EPI_ISL_19208244, EPI_ISL_19213524, EPI_ISL_19213780, EPI_ISL_19214041, EPI_ISL_19223298, EPI_ISL_19223643, EPI_ISL_19226556, EPI_ISL_19226562, EPI_ISL_19226784-19226785, EPI_ISL_19226791, EPI_ISL_19226800, EPI_ISL_19226804, EPI_ISL_19226825, EPI_ISL_19228576, EPI_ISL_19228989, EPI_ISL_19230952

Update July 26: One sequence of this sublineage popped up in France with an unusual insertion in S1 but toward the FCS S:ins643PAGV +S:Q644E, Spike_ins643PAGV + Spike_Q644E, ins23491CCAGCTGGGGTC

Screenshot 2024-07-26 alle 12 11 32
FedeGueli commented 1 month ago

37 new country Israel

FedeGueli commented 1 month ago

43

FedeGueli commented 1 month ago

This grew to 55 with two new countries likely worth getting designating @corneliusroemer

FedeGueli commented 1 month ago

75 from 10 countries new batch from NZL where it represents 2% of samples collected after June 15

FedeGueli commented 1 month ago

Edited the proposal to add the French singlet with S:ins643PAGV +S:Q644E cc @ryhisner

FedeGueli commented 4 weeks ago

84

FedeGueli commented 3 weeks ago

103

FedeGueli commented 2 weeks ago

109 now Singapore new country, as @ryhisner pointed out, there is one more sample with the insertion from France, it has also S:V642F not present in the other sample.

FedeGueli commented 1 week ago

131

FedeGueli commented 4 days ago

Proposed in https://github.com/cov-lineages/pango-designation/issues/2744