EG.5.1.4+Orf3a:P240L+S:L455F,Orf3a:I47V Exploding in Japan(27 seqs, 2 countries)

[xz-keg]

From sars-cov-2-variants/lineage-proposals#644

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

GISAID query:G22927T,A25531G,C26111T
No. of seqs: 18(Japan 16(Chiba, Tokyo, Kagawa, Hyogo,Tochigi) Hong Kong 1 Yunnan 1)

First: EPI_ISL_17997269, Hong Kong, 2023-6-29
Latest: EPI_ISL_18123086, Chiba, 2023-8-7

EG.5.1 is the current best backbone, S:L455F+S:F456L is the fittest Spike combo, Orf1b:2557 in EG.5.1.4 is also a fitness mutation, and Orf3a:P240L/I47V both have good fit advantage on Bloom and Neher estimates.

usher

[alurqu]

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]

Designated JJ.1 via 36e3fb0 milestone added to original issue

[FedeGueli]

milestone removed from the original issue.