A novel ISG15 transcript restricts influenza A virus infection

SUMMARY The interferon response orchestrates antiviral defense through the induction of interferon-stimulated genes (ISGs). Although nearly all human genes undergo alternative splicing, the identity and function of many ISG transcript isoforms remains poorly understood. Using long-read RNA sequencing of human cells that were undergoing an interferon response, we identified a previously unrecognized interferon-inducible ISG15 transcript. This non-canonical ISG15 (ncISG15) transcript contains a unique 5′ untranslated region and encodes an N-terminally truncated protein in frame with ISG15. During interferon stimulation, ncISG15 produces an ISGylation pattern distinct from canonical ISG15 and potently inhibits influenza A virus polymerase activity. The influenza A viral interferon antagonist protein NS1 counteracts ncISG15-mediated restriction; however, endogenous ncISG15 executes modest antiviral activity against NS1-encoding viruses. Antiviral activity of ncISG15 is largely independent of its function as a cytokine, through ISG augmentation, or by ISGylation. This novel transcript adds a new layer of regulatory complexity to the ISG15-driven antiviral network.