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KP.2 with ORF1a:P1803L (nsp3_P985L = PLPro_P240L) and S:P793S (55 seqs, 14~18 countries) #1649

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NkRMnZr opened this issue Jun 25, 2024 · 6 comments
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KP.2 with ORF1a:P1803L (nsp3_P985L = PLPro_P240L) and S:P793S (55 seqs, 14~18 countries) #1649

NkRMnZr opened this issue Jun 25, 2024 · 6 comments
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest KP.2 PLPro s:793
Milestone
KP.2.25.3

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@NkRMnZr
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NkRMnZr commented Jun 25, 2024

Defining Mutations: KP.2 > C5673T(ORF1a:P1803L) > C14220T > C23939T(S:P793S)
Query: C7113T, C14220T, C23939T
Earliest seq: 2024-04-02 (EPI_ISL_19145665, Oman)
Latest seq: 2024-06-06 (EPI_ISL_19206138, GBW sample with travel history to: Qatar)
Sampled Countries: UK (10: EN); Kuwait (8); USA (6: OH/2; GBW samples with travel history to: Germany, Mexico, Qatar); Canada (3: AB; ON; QC); Japan (2); Oman (1); Portugal (1); Spain (1)

Genomes:

for lineages.csv commit:

Canada/AB-ABPHL-118607/2024
Canada/ON-PHL-202408700/2024
Canada/QC-L00744354001/2024
England/CLIMB-CM7Y8MIH/2024
England/CLIMB-CM7Y8WOT/2024
England/CLIMB-CM7YE9CW/2024
England/CLIMB-CM7YEIDW/2024
England/CLIMB-CM7YGEIZ/2024
England/CLIMB-CM7YGOFJ/2024
England/CLIMB-CM7YMKZF/2024
England/CLIMB-CM7YR7HX/2024
England/CLIMB-CM7YRPDN/2024
England/CLIMB-CM7YRXJX/2024
Japan/FR012-0177/2024
Japan/TKYnat17035/2024
Kuwait/Jaber20235200/2024
Kuwait/Jaber20269368/2024
Kuwait/Jaber20284395/2024
Kuwait/Jaber20295783/2024
Kuwait/Jaber20302365/2024
Kuwait/Jaber20317337/2024
Kuwait/Jaber20321317/2024
Kuwait/Jaber20324817/2024
Oman/CPHL_7242103/2024
Portugal/PT50983/2024
Spain/MC-HCUVA-20026263/2024
USA/CA-GBW-GKISBBBB38669/2024
USA/CA-GBW-GKISBBBC20350/2024
USA/CA-GBW-GKPLAAAA20616/2024
USA/NJ-GBW-GKISBBBC53819/2024
USA/OH-ODH-SC4031767/2024
USA/OH-ODH-SC4031778/2024

epi_isl accessions:
EPI_ISL_19211035, EPI_ISL_19188332, EPI_ISL_19202270, EPI_ISL_19213726, EPI_ISL_19190138, EPI_ISL_19213695, EPI_ISL_19108369, EPI_ISL_19108432, EPI_ISL_19108364, EPI_ISL_19108357, EPI_ISL_19108346, EPI_ISL_19108425, EPI_ISL_19108601, EPI_ISL_19197859, EPI_ISL_19178800, EPI_ISL_19213984, EPI_ISL_19213990, EPI_ISL_19213996, EPI_ISL_19213967, EPI_ISL_19213969, EPI_ISL_19213970, EPI_ISL_19213972, EPI_ISL_19213973, EPI_ISL_19145665, EPI_ISL_19190764, EPI_ISL_19178539, EPI_ISL_19206138, EPI_ISL_19205982, EPI_ISL_19191318, EPI_ISL_19162497, EPI_ISL_19134377, EPI_ISL_19183092

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_13feb_a66010.json?label=id:node_7006748
image

Trivia:

  • There are 3 seqs currently placed under a F456L-dropout subbranch, those are: EPI_ISL_19145665, EPI_ISL_19202270, EPI_ISL_19178539
@FedeGueli FedeGueli changed the title KP.2 with ORF1a:P1803L (nsp3_P985L) and S:P793S (29~32 seqs, 8~11 countries) KP.2 with ORF1a:P1803L (nsp3_P985L = PLPro_P240L) and S:P793S (29~32 seqs, 8~11 countries) Jun 25, 2024
@FedeGueli FedeGueli added PLPro Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest labels Jun 25, 2024
@NkRMnZr NkRMnZr changed the title KP.2 with ORF1a:P1803L (nsp3_P985L = PLPro_P240L) and S:P793S (29~32 seqs, 8~11 countries) KP.2 with ORF1a:P1803L (nsp3_P985L = PLPro_P240L) and S:P793S (36~39 seqs, 10~13 countries) Jul 3, 2024
@NkRMnZr NkRMnZr mentioned this issue Jul 6, 2024
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@NkRMnZr NkRMnZr changed the title KP.2 with ORF1a:P1803L (nsp3_P985L = PLPro_P240L) and S:P793S (36~39 seqs, 10~13 countries) KP.2 with ORF1a:P1803L (nsp3_P985L = PLPro_P240L) and S:P793S (38~41 seqs, 11~14 countries) Jul 6, 2024
@FedeGueli FedeGueli added s:793 and removed S:739 labels Jul 6, 2024
@NkRMnZr
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NkRMnZr commented Jul 12, 2024

New entry: Japan, Israel, Italy (thru GBW), Sweden, Netherlands

@NkRMnZr NkRMnZr changed the title KP.2 with ORF1a:P1803L (nsp3_P985L = PLPro_P240L) and S:P793S (38~41 seqs, 11~14 countries) KP.2 with ORF1a:P1803L (nsp3_P985L = PLPro_P240L) and S:P793S (43~46 seqs, 12~16 countries) Jul 12, 2024
@FedeGueli
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FedeGueli commented Jul 12, 2024 •
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PLPRO_P240L could be interesting it is placed at the itnerface between Palm and Fingers of Pocket 2 of SC2 PLpRO
I have no idea of what kind of impact it could have tough. Maybe @ryhisner studied that a bit ?
Screenshot 2024-07-12 alle 12 53 06
pic from https://www.biorxiv.org/content/10.1101/2023.05.16.540953v3.full

@NkRMnZr NkRMnZr changed the title KP.2 with ORF1a:P1803L (nsp3_P985L = PLPro_P240L) and S:P793S (43~46 seqs, 12~16 countries) KP.2 with ORF1a:P1803L (nsp3_P985L = PLPro_P240L) and S:P793S (46~49 seqs, 12~16 countries) Jul 25, 2024
@NkRMnZr NkRMnZr changed the title KP.2 with ORF1a:P1803L (nsp3_P985L = PLPro_P240L) and S:P793S (46~49 seqs, 12~16 countries) KP.2 with ORF1a:P1803L (nsp3_P985L = PLPro_P240L) and S:P793S (50~53 seqs, 14~18 countries) Aug 9, 2024
@NkRMnZr
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NkRMnZr commented Aug 9, 2024

New entry: France, Hungary

@FedeGueli FedeGueli changed the title KP.2 with ORF1a:P1803L (nsp3_P985L = PLPro_P240L) and S:P793S (50~53 seqs, 14~18 countries) KP.2 with ORF1a:P1803L (nsp3_P985L = PLPro_P240L) and S:P793S (55 seqs, 14~18 countries) Aug 19, 2024
@FedeGueli
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55 one recent sample from Scotland in August,but it is still fading away

@FedeGueli FedeGueli added the Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. label Aug 19, 2024
@NkRMnZr
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NkRMnZr commented Aug 26, 2024

slowed, closing for now

@NkRMnZr NkRMnZr closed this as not planned Won't fix, can't repro, duplicate, stale Aug 26, 2024
@FedeGueli FedeGueli added this to the KP.2.25.3 milestone Oct 20, 2024
@FedeGueli
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Designated KP.2.25.3 via cov-lineages/pango-designation@a3d38ca#diff-ead4244ff49c81bc758e9f068f5ef42156bd985b9c86de8fa4d6fcd7f2829090R1204

FedeGueli referenced this issue in cov-lineages/pango-designation Oct 20, 2024
@corneliusroemer
Designate KP.2.25 and sublineages
a3d38ca
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest KP.2 PLPro s:793
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@FedeGueli @NkRMnZr