S RNA Intergenic Deletions Drive Viral Interference during Arenavirus Infections

Arenaviruses, a family of negative-sense RNA viruses spread by rodents, are a leading cause of severe hemorrhagic fever in humans. Due to a paucity of antivirals and vaccines for arenaviruses, there is a need to identify new mechanisms for interfering with arenavirus replication. In several negative-sense RNA viruses, natural viral interference results from the production of non-standard viral genomes (nsVGs) that activate the innate immune system and/or compete for essential viral products. Although it is well established that arenaviruses produce strong interfering activities, it is unknown if they produce interfering nsVGs. Here we show that arenaviruses produce deletions within the intergenic region of their Small (S) RNA genome, which prevents the production of viral mRNA and protein. These deletions are more abundant when arenaviruses are grown in high-interfering conditions and are associated with inhibited viral replication. Overall, we found that arenaviruses produce internal deletions within the S RNA intergenic region that are produced by arenaviruses and can block viral replication. These natural arenavirus interfering molecules provide a new target for the generation of antivirals as well as an alternative strategy for producing attenuated arenaviruses for vaccines. AUTHOR SUMMARYArenaviruses are hemorrhagic fever-causing pathogens that infect millions of people a year. There are currently no approved antivirals that target arenaviruses and understanding natural mechanisms that inhibit arenavirus replication is crucial for the development of effective therapeutics. Here, we identify multiple deletions within arenavirus genomes that are associated with the inhibition of viral replication. We show that these deletions prevent viral protein production through the removal of the intergenic region of the viral genome. These deletions were found in all arenaviruses tested in this study representing a novel mechanism for development of new antivirals and vaccines that broadly target the arenavirus family.