Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic.

Focusing instead on the shorter ORF3d-2 isoform, this protein contains zero predicted epitopes, which is a highly significant depletion given its own amino acid content (p=0.001) and compared to short unannotated ORFs (p=0.001).

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Between-host diversity was sufficient to detect marginally significant purifying selection across all genes ( π N / π S = 0.50, p=0.0613, Z -test; Figure 5—figure supplement 1 ) but not most individual genes ( Figure 5 ).

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