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XBB.1.42 (S:Q613H) + S:478R (29 Seqs as 14/07)circulating in Austria (around 2% in June) #198

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Fearuncle opened this issue Jun 15, 2023 · 5 comments
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XBB.1.42 (S:Q613H) + S:478R (29 Seqs as 14/07)circulating in Austria (around 2% in June) #198

Fearuncle opened this issue Jun 15, 2023 · 5 comments
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Convergent evolution Lineages with convergent mutations designated S:478
Milestone
XBB.1.42.1

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@Fearuncle
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Fearuncle commented Jun 15, 2023 •
edited by FedeGueli
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image
tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2974f_b6e660.json?c=gt-S_478&label=id:node_6627370
first seq: 2023-04-21
most recent: 2023-05-30
EPI_ISL_17743532 EPI_ISL_17619026 EPI_ISL_17669720 EPI_ISL_17782534 EPI_ISL_17782156 EPI_ISL_17782351 EPI_ISL_17782430

Gisaid query:
-G23345A,-A22101T,C22995G,T23018C,T28297C,C12789T,-G5720A,A16878T,-A27507C,-C11956T,-C26322T,-A2514G

Edited this query finds all the 7 sequences but be aware that could catch samples from unrelated lineages in the next weeks .
@FedeGueli FedeGueli added Convergent evolution Lineages with convergent mutations S:478 labels Jun 15, 2023
@FedeGueli
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Very good catch XBB.1.42 recombinant lineage is expanding m likely faster than we think.

@FedeGueli FedeGueli changed the title XBB.1.42 + S:478R 7 seq. XBB.1.42 + S:478R (10Seqs) Jun 19, 2023
@FedeGueli
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New tree shows ten sequences for this lineage: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_d936_c9120.json?c=userOrOld&label=id:node_6632239
Schermata 2023-06-19 alle 23 34 31

@FedeGueli FedeGueli changed the title XBB.1.42 + S:478R (10Seqs) XBB.1.42 (S:Q613H) + S:478R (10Seqs) Jun 19, 2023
@FedeGueli FedeGueli changed the title XBB.1.42 (S:Q613H) + S:478R (10Seqs) XBB.1.42 (S:Q613H) + S:478R (17Seqs as 23/06)circualting in Austria (around 2% in June) Jun 23, 2023
@FedeGueli FedeGueli changed the title XBB.1.42 (S:Q613H) + S:478R (17Seqs as 23/06)circualting in Austria (around 2% in June) XBB.1.42 (S:Q613H) + S:478R (17Seqs as 23/06)circulating in Austria (around 2% in June) Jun 23, 2023
@FedeGueli
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17 today a batch uploaded yesterday from Vienna all from June. This could be something.

@FedeGueli FedeGueli changed the title XBB.1.42 (S:Q613H) + S:478R (17Seqs as 23/06)circulating in Austria (around 2% in June) XBB.1.42 (S:Q613H) + S:478R (19 Seqs as 26/06)circulating in Austria (around 2% in June) Jun 26, 2023
@FedeGueli FedeGueli changed the title XBB.1.42 (S:Q613H) + S:478R (19 Seqs as 26/06)circulating in Austria (around 2% in June) XBB.1.42 (S:Q613H) + S:478R (24 Seqs as 30/06)circulating in Austria (around 2% in June) Jul 1, 2023
@FedeGueli FedeGueli changed the title XBB.1.42 (S:Q613H) + S:478R (24 Seqs as 30/06)circulating in Austria (around 2% in June) XBB.1.42 (S:Q613H) + S:478R (22 Seqs as 30/06)circulating in Austria (around 2% in June) Jul 1, 2023
@FedeGueli
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new query: -G23345A,-A22101T,C22995G,T23018C,T28297C,C12789T,-G5720A,A16878T,-A27507C,-C11956T,-C26322T,-A2514G finds 22

New tree:
Schermata 2023-07-01 alle 11 48 26
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_d02_ff4f30.json?c=userOrOld&label=id:node_6679449

please keep this updated. It is likely something to propose soon.

@Fearuncle Fearuncle changed the title XBB.1.42 (S:Q613H) + S:478R (22 Seqs as 30/06)circulating in Austria (around 2% in June) XBB.1.42 (S:Q613H) + S:478R (23 Seqs as 03/07)circulating in Austria (around 2% in June) Jul 3, 2023
@Fearuncle Fearuncle changed the title XBB.1.42 (S:Q613H) + S:478R (23 Seqs as 03/07)circulating in Austria (around 2% in June) XBB.1.42 (S:Q613H) + S:478R (25 Seqs as 03/07)circulating in Austria (around 2% in June) Jul 6, 2023
@Fearuncle Fearuncle changed the title XBB.1.42 (S:Q613H) + S:478R (25 Seqs as 03/07)circulating in Austria (around 2% in June) XBB.1.42 (S:Q613H) + S:478R (27 Seqs as 03/07)circulating in Austria (around 2% in June) Jul 10, 2023
@Fearuncle Fearuncle changed the title XBB.1.42 (S:Q613H) + S:478R (27 Seqs as 03/07)circulating in Austria (around 2% in June) XBB.1.42 (S:Q613H) + S:478R (29 Seqs as 14/07)circulating in Austria (around 2% in June) Jul 15, 2023
@Fearuncle
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Designated as XBB.1.42.1

Fearuncle referenced this issue in cov-lineages/pango-designation Jul 17, 2023
@corneliusroemer
Designate XBB.1.42.1 (S:478R) with 30 seqs
6031f74
FedeGueli added a commit to FedeGueli/pango-designation that referenced this issue Jul 17, 2023
@FedeGueli
Update lineage_notes.txt
47b2bc1 
Add issue sars-cov-2-variants/lineage-proposals#198 to XBB.1.42.1
Add issue sars-cov-2-variants/lineage-proposals#336 to XBB.1.12.1
@FedeGueli FedeGueli mentioned this issue Jul 17, 2023
Merged
corneliusroemer pushed a commit to cov-lineages/pango-designation that referenced this issue Jul 17, 2023
@FedeGueli
Update lineage_notes.txt (#2102)
568a2df 
Add issue sars-cov-2-variants/lineage-proposals#198 to XBB.1.42.1
Add issue sars-cov-2-variants/lineage-proposals#336 to XBB.1.12.1
@xz-keg xz-keg added this to the XBB.1.42.1 milestone Dec 17, 2023
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