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EG.5.1.4+Orf3a:P240L+S:L455F,Orf3a:I47V (18 seqs, 2 countries) #644

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xz-keg opened this issue Aug 19, 2023 · 3 comments
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EG.5.1.4+Orf3a:P240L+S:L455F,Orf3a:I47V (18 seqs, 2 countries) #644

xz-keg opened this issue Aug 19, 2023 · 3 comments
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@xz-keg
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xz-keg commented Aug 19, 2023

EG.5.1.4+C26111T(Orf3a:P240L)+G22927T,A25531G(S:L455F,Orf3a:I47V)

GISAID query:G22927T,A25531G,C26111T
No. of seqs: 14(Japan 12 Hong Kong 1 Yunnan 1)

First: EPI_ISL_17997269, Hong Kong, 2023-6-29
Latest: EPI_ISL_18111828, Japan, 2023-8-4

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@FedeGueli FedeGueli added FLip = S:L455F / S:F456L S:456 S:455 labels Aug 19, 2023
@xz-keg xz-keg changed the title EG.5.1.4+Orf3a:P240L+S:L455F,Orf3a:I47V (14 seqs, 2 countries) EG.5.1.4+Orf3a:P240L+S:L455F,Orf3a:I47V (15 seqs, 2 countries) Aug 21, 2023
@xz-keg xz-keg changed the title EG.5.1.4+Orf3a:P240L+S:L455F,Orf3a:I47V (15 seqs, 2 countries) EG.5.1.4+Orf3a:P240L+S:L455F,Orf3a:I47V (17 seqs, 2 countries) Aug 22, 2023
@xz-keg xz-keg changed the title EG.5.1.4+Orf3a:P240L+S:L455F,Orf3a:I47V (17 seqs, 2 countries) EG.5.1.4+Orf3a:P240L+S:L455F,Orf3a:I47V (18 seqs, 2 countries) Aug 23, 2023
@alurqu
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alurqu commented Aug 23, 2023

Analyzing the Bloom and Neher estimates (from https://github.com/jbloomlab/SARS2-mut-fitness/blob/main/results/aa_fitness/aamut_fitness_by_clade.csv) of the fitness effects of the ORF3a non-synonymous mutations:

For ORF3a:P240L,

clade,gene,aa_mutation,delta_fitness
20A,ORF3a,P240L,1.0763
20B,ORF3a,P240L,0.76963
20C,ORF3a,P240L,0.91163
20E,ORF3a,P240L,0.82331
20G,ORF3a,P240L,0.78406
20I,ORF3a,P240L,1.0449
21C,ORF3a,P240L,1.0064
21I,ORF3a,P240L,1.1203
21J,ORF3a,P240L,1.0285
21K,ORF3a,P240L,0.62104
21L,ORF3a,P240L,0.8466
22A,ORF3a,P240L,0.68238
22B,ORF3a,P240L,0.83414
22C,ORF3a,P240L,0.81373
22D,ORF3a,P240L,0.8641
22E,ORF3a,P240L,0.85017
22F,ORF3a,P240L,0.9002
23A,ORF3a,P240L,0.83717

For ORF3a:I47V,

clade,gene,aa_mutation,delta_fitness
20A,ORF3a,I47V,1.0941
20B,ORF3a,I47V,1.402
20C,ORF3a,I47V,1.7551
20E,ORF3a,I47V,1.1609
20G,ORF3a,I47V,1.2443
20I,ORF3a,I47V,1.8361
21C,ORF3a,I47V,1.2892
21I,ORF3a,I47V,1.9313
21J,ORF3a,I47V,1.7654
21K,ORF3a,I47V,1.6804
21L,ORF3a,I47V,1.6262
22A,ORF3a,I47V,1.4997
22B,ORF3a,I47V,1.578
22C,ORF3a,I47V,1.0469
22D,ORF3a,I47V,1.2673
22E,ORF3a,I47V,1.2043
22F,ORF3a,I47V,1.0659
23A,ORF3a,I47V,1.2954

And of course, S:L455F along with EG.5's S:F456L likely improves fitness.

Unless there is some unexpected negative epistatic interaction, based on the new mutations this lineage may plausibly show an increase in viral fitness on top of an already fit lineage.

@FedeGueli
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Please propose it

@FedeGueli
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Designated JJ.1 via cov-lineages/pango-designation@36e3fb0

@FedeGueli FedeGueli removed this from the JJ.1 milestone Sep 2, 2023
@xz-keg xz-keg added this to the JJ.1 milestone Dec 17, 2023
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