Potentially ancestral BA.4 sublineage without ORF7b:L11F (24 seq, mostly South Africa)

[silcn]

There is a genuine-looking sublineage of BA.4 in which the defining mutation ORF7b:L11F is reverted to WT. It does not carry any further defining mutations, and so could potentially be ancestral to the rest of BA.4, in a similar way to 9866C vs T in BA.2. The absence of ORF7b:L11F can cause classification issues, with Nextclade in particular often calling it as B.1.1.529.

24 sequences so far: 23 from South Africa and 1 from Singapore. Earliest is 2022-03-12.

I suppose it won't be possible to know for sure if this is really ancestral or the result of a reversion, but the oldest sequences are from Gauteng which is where we might expect to find a hypothetical ancestral branch. Maybe some kind of mutation-rate analysis could shed light on it? In any case it should probably be treated as a reversion from a designation point of view. Not saying this or any of its sublineages are worth designating at the moment - just pointing out that it exists so it can be monitored.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_24a7a_e8f300.json?branchLabel=Spike%20mutations&c=gt-ORF7b_11&label=nuc%20mutations:T27788G

Unfortunately this is hard to track with a cov-spectrum query without picking up dropouts and artefacts too.

EPI_ISLs

EPI_ISL_11674432
EPI_ISL_11999077
EPI_ISL_12097352
EPI_ISL_12097357
EPI_ISL_12212572
EPI_ISL_12267762
EPI_ISL_12307600
EPI_ISL_12307624
EPI_ISL_12401079
EPI_ISL_12401118
EPI_ISL_12401132
EPI_ISL_12401159
EPI_ISL_12474452
EPI_ISL_12477007
EPI_ISL_12520010
EPI_ISL_12520035
EPI_ISL_12520057
EPI_ISL_12587902
EPI_ISL_12765570
EPI_ISL_12765575
EPI_ISL_12769203
EPI_ISL_12903477
EPI_ISL_12903599
EPI_ISL_12903737