Small RNA genomics of Aedes aegypti mosquitoes discovers infectious viruses that trigger an RNA interference response

We report a global survey of viral small RNAs (vsmRNAs) from >200 Aedes aegypti samples to identify many mosquito viruses that actively infect this prominent arboviral vector. Ae. aegypti viruses in the Americas are abundant, with some displaying geographical boundaries. Viruses infecting Asian Ae. aegypti are similar to those in the Americas and reveal the first wild example of dengue vsmRNAs. African Ae. aegypti display vsmRNAs from viruses unique to these African strains. Academic lab colonies generally lack viruses, yet two commercial strains are deeply infected by a tombus-like virus that is related to plant viruses. Comparing matched viral long RNAs to vsmRNAs reveal viral transcripts evading the mosquito RNA interference (RNAi) pathway. By infecting mosquito cells with Ae. aegypti homogenates, we generate stably infected cell lines which produce vsmRNAs that were comparable to native mosquito vsmRNA patterns. Lastly, we demonstrate that these stably infected mosquito cells producing vsmRNAs can exert gene silencing of reporters bearing viral sequence segments, providing a potential explanation for how Ae. aegypti can resist viral infections. This vsmRNA genomics approach in Ae. aegypti can add to existing vector surveillance approaches by discovering new viruses that persist in mosquito populations.