Significance: Influenza A viruses cause annual influenza epidemics and occasional severe pandemics. Their genome is segmented into eight RNA fragments, which offers evolutionary advantages but complicates genomic packaging. The existence of a selective mechanism ensuring specific packaging of one copy of each RNA into each virion is suspected, but its molecular details remain unknown. We identified a direct interaction between two viral genomic RNA segments of an influenza A virus and demonstrated that this interaction takes place in infected cells, is required for optimal viral replication, and favors copackaging of the interacting RNA segments. Collectively, our experiments indicate that viral RNA segments can promote selective packaging of the influenza A virus genome by forming a sequence-dependent supramolecular network of interactions.

Human immunodeficiency virus type 1 (HIV-1) replication is a highly regulated process requiring the recruitment of viral and cellular components to the plasma membrane for assembly into infectious particles. This review highlights the recent process of understanding the selection of the genomic RNA (gRNA) by the viral Pr55^Gag precursor polyprotein, and the processes leading to its incorporation into viral particles.

Programmed ribosomal frameshifting (PRF) is a fundamental gene expression event in many viruses, including SARS-CoV-2. It allows production of essential viral, structural and replicative enzymes that are encoded in an alternative reading frame. Despite the importance of PRF for the viral life cycle, it is still largely unknown how and to what extent cellular factors alter mechanical properties of frameshift elements and thereby impact virulence. This prompted us to comprehensively dissect the interplay between the SARS-CoV-2 frameshift element and the host proteome. We reveal that the short isoform of the zinc-finger antiviral protein (ZAP-S) is a direct regulator of PRF in SARS-CoV-2 infected cells. ZAP-S overexpression strongly impairs frameshifting and inhibits viral replication. Using in vitro ensemble and single-molecule techniques, we further demonstrate that ZAP-S directly interacts with the SARS-CoV-2 RNA and interferes with the folding of the frameshift RNA element. Together, these data identify ZAP-S as a host-encoded inhibitor of SARS-CoV-2 frameshifting and expand our understanding of RNA-based gene regulation.