Integrated Transcriptomic and Translatomic Profiling Reveals Noncanonical RNA Junctions and Hidden Coding Potential in Porcine Epidemic Diarrhea Virus

In Porcine epidemic diarrhea virus at 3–5 hpi, noncanonical RNA junctions are widespread (43,635 distinct), yet canonical sgRNA junctions still account for 95.5% of junction-supporting reads.

• Why it matters: The classical coronavirus discontinuous transcription model and standard genome annotations do not fully capture junction diversity or potentially undercount viral protein-coding capacity.
• What they did: They integrated time-resolved RNA-seq, CHX- and HAR-treated Ribo-seq, comparative genomics, and peptide mass spectrometry to map junctions, hidden ORFs, translation signals, and confirm peptides.
• The result: They found 68 hidden ORFs longer than 40 amino acids in the +1 frame versus three in the +2 frame, and mass spectrometry detected a characteristic peptide for N-x1 in infected samples.

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