Proposal for Australian AY.39.1 sub-lineage with S:12F that grew rapidly until Omicron arrived (3.5k seq, peak 30%)

[corneliusroemer]

Investigating potential donors for the putative Delta-Omicron recombinantin #437 I noticed that S:12F grew rapidly in Australia until Omicron arrived.

First sequence: around 2021-09-15
Growth to 500 sequences per week by early December
In total ~3.5k sequences

It's a mutation that's appeared a number of times over the last 2 years. It's predicted to confer a ~1.5% daily growth advantage by @fritzo's Pyro cov model https://github.com/broadinstitute/pyro-cov/blob/a0efed3f8eb7c67f169c5d8c831af76a6f1fc7df/paper/mutations.tsv#L391

It's a well separated, fairly long branch with 4-6 mutations:

T26187C, T28921C (optional)
C8964T,C21597T, C23029T, C25521T

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_6dd5_a8ec10.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:G27604A

Rather fast growth:
https://cov-spectrum.org/explore/Australia/AllSamples/Past6M/variants?aaMutations=S%3A12F&pangoLineage=AY.39.1*

[FedeGueli]

22% relative growth advantage vs delta baseline (World last 6m):

[FedeGueli]

S:12F has been described by Veesler et al
here: https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC7962585/

Luckily it doesnt seem to have the same immune escape effect as S:12P.

[InfrPopGen]

Thanks for submitting. We've added lineage AY.39.1.4 with 2945 newly designated sequences, and 1 updated designations. Defining mutation(s) C21597T (S:S12F), C23029T (synonymous).