Fig. 8. More variant alleles of clinical relevance arose de novo and persisted in spike for Delta lineage compared to Beta, with key variants being co-inherited.

Each line and sample number refers to a select viral sample being passaged. P0 and P10 are identical across samples, given that it was passaged in a single animal up to P10. VAF: variant allele frequency. P refers to passage. Variant allele incidence by sample in Delta lineage virus. Larger points represent variant alleles with a within-sample, Illumina-derived allele-frequency of 1.0, smaller ones 0.5. Stars in a given passage represent alleles that are likely co-inherited per Nanopore sequencing.