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. 2021 May 11;12:2642. doi: 10.1038/s41467-021-22905-7

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 7 — a Synonymous constraint elements (blue) match nearly perfectly 41-codon ORFc dual-coding region boundaries (black), and PhyloCSF protein-coding evolutionary signatures (green) switch between frame 1 and 2 (rows) in the dual-coding region, with frame-2 signal (negative flanking ORF3c) increasing to near-zero, and frame-1 signal (high flanking ORF3c) dropping to near-zero. b, c Codon-resolution evolutionary signatures (colors, CodAlignView³³) annotating genomic alignment (letters) spanning ORF3a start and dual-coding region, in frame-1 (top) and frame-2 (bottom), highlighting (yellow boxes): (b, frame-2, ORF3c) radical codon substitutions (red) and stop codons (yellow, magenta, cyan) prior to ORF3c start; synonymous (light green) and conservative (dark green) substitutions in ORF3c; ORF3c’s start codon is conserved, except in one strain (row 4) with near-cognate GUG; ORF3c’s stop codon is conserved except for one-codon extension in two strains (rows 2–3); no intermediate stop codons in ORF3c; (c, frame-1, ORF3a) abundant synonymous and conservative substitutions in ORF3a prior to dual-coding region; increase in fully conserved codons (white) over dual-coding region indicating synonymous constraint. Short 61-nucleotide (nt) interval with only one weak-Kozak-context intervening start codon indicates ORF3c may be translated from ORF3a’s subgenomic RNA via leaky scanning.