- Ho, Jessica Sook Yuin;
- Angel, Matthew;
- Ma, Yixuan;
- Sloan, Elizabeth;
- Wang, Guojun;
- Martinez-Romero, Carles;
- Alenquer, Marta;
- Roudko, Vladimir;
- Chung, Liliane;
- Zheng, Simin;
- Chang, Max;
- Fstkchyan, Yesai;
- Clohisey, Sara;
- Dinan, Adam M;
- Gibbs, James;
- Gifford, Robert;
- Shen, Rong;
- Gu, Quan;
- Irigoyen, Nerea;
- Campisi, Laura;
- Huang, Cheng;
- Zhao, Nan;
- Jones, Joshua D;
- van Knippenberg, Ingeborg;
- Zhu, Zeyu;
- Moshkina, Natasha;
- Meyer, Léa;
- Noel, Justine;
- Peralta, Zuleyma;
- Rezelj, Veronica;
- Kaake, Robyn;
- Rosenberg, Brad;
- Wang, Bo;
- Wei, Jiajie;
- Paessler, Slobodan;
- Wise, Helen M;
- Johnson, Jeffrey;
- Vannini, Alessandro;
- Amorim, Maria João;
- Baillie, J Kenneth;
- Miraldi, Emily R;
- Benner, Christopher;
- Brierley, Ian;
- Digard, Paul;
- Łuksza, Marta;
- Firth, Andrew E;
- Krogan, Nevan;
- Greenbaum, Benjamin D;
- MacLeod, Megan K;
- van Bakel, Harm;
- Garcìa-Sastre, Adolfo;
- Yewdell, Jonathan W;
- Hutchinson, Edward;
- Marazzi, Ivan
RNA viruses are a major human health threat. The life cycles of many highly pathogenic RNA viruses like influenza A virus (IAV) and Lassa virus depends on host mRNA, because viral polymerases cleave 5'-m7G-capped host transcripts to prime viral mRNA synthesis ("cap-snatching"). We hypothesized that start codons within cap-snatched host transcripts could generate chimeric human-viral mRNAs with coding potential. We report the existence of this mechanism of gene origination, which we named "start-snatching." Depending on the reading frame, start-snatching allows the translation of host and viral "untranslated regions" (UTRs) to create N-terminally extended viral proteins or entirely novel polypeptides by genetic overprinting. We show that both types of chimeric proteins are made in IAV-infected cells, generate T cell responses, and contribute to virulence. Our results indicate that during infection with IAV, and likely a multitude of other human, animal and plant viruses, a host-dependent mechanism allows the genesis of hybrid genes.