CP.5 alias BA.5.2.6., jolla on myös spike-mutaatio C1247F. Tälle on ilmentynyt alalinjaehdokas, jolla on kaksi spikemutaatiota lisäksi: T250I, N417T, nukleokapsidimutaatio G200S sekä ORF7a mutaatio Q90R.
ryhisner commented Nov 12, 2022
Description
Sub-lineage of: BA.5.2.6
Earliest sequence: 2022-10-4, Sweden, Orebro — EPI_ISL_15288391
Most recent sequence: 2022-10-26, Sweden, Orebro — EPI_ISL_15725064
Countries circulating: Sweden (All)
Number of Sequences: 11
GISAID Query: Spike_T250I, Spike_K417T, Spike_C1247F, Spike_R346T
CovSpectrum Query: Nextcladepangolineage:BA.5.2.6* & S:T250I & S:K417T
Substitutions on top of BA.5.2.6:
Spike: T250I, K417T, C1247F
N: G200S
ORF7a: Q90R
Nucleotide: C22311T, A22812C, A27662G, T28022C, G28871A
Evidence
S:K417T has never gone well together with S:L452R or S:R346T. The number
of sequences with K417T and L452R—just 111 sequences in 2022—is far
lower than you’d expect from their overall frequency. The same goes for
K417T and R346T, for which there have only ever been 208 sequences. Up
until now, it had seemed like K417T was straight-up incompatible with
R346T + L452R; there had only ever been one sequence with all three
mutations through October 3—and even that one sequence was very suspect
and may have resulted from contamination. But since October 4, 11
sequences with all three mutations have showed up in Sweden. I have no
idea why K417T has been so incompatible with R346T and L452R up to this
point. I assume there is some interaction between these residues. I’d be
curious to know if anyone with some knowledge of the RBD structure has
any ideas.
I also have no idea why, in this lineage, R346T, L452R, and K417T have, for apparently the first time, coexisted and transmitted, though S:T250I seems to be the only new mutation that could possibly ameliorate whatever detrimental interaction existed between those three mutations previously.
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