Identification and RNAi profile of a novel iflavirus infecting Senegalese Aedes vexans arabiensis mosquitoes

The inland floodwater mosquito Aedes vexans (Meigen, 1830) has widespread Afrotropical distribution and is the most common cosmopolitan mosquito in Europe. Ae. vexans is a competent vector of numerous arthropod-borne viruses such as Rift Valley fever virus (Bunyavirales), Zika virus and West Nile virus (Flaviviridae). Small RNA sequences of female Ae. vexans arabiensis samples originating from Barkédji village, Senegal were de novo assembled and bioinformatically screened for virus infection. This resulted in the complete assembly of a novel 9,494nt iflavivirus designated as Aedes vexans iflavirus (AvIFV). AvIFV is most closely related to Venturia canescens picorna-like virus with 56.77% amino acid identity. Annotation of the AvIFV genome reveals typical iflavirus genome features such as a large 2783 amino acid polyprotein, but additionally two small ~130 aa transmembrane proteins. Analysis of virus-derived small RNAs indicated that AvIFV is exclusively targeted by the RNA interference response in whole mosquitoes with a majority ~60% of AvIFV reads corresponding to 21nt virus-derived short interfering RNAs. Additional small RNA sequencing data and RT-PCR screens were undertaken from colony samples originating from France, Germany and the United Kingdom suggesting that AvIFV is absent in these samples. This is the second report of an iflavirus infecting mosquitoes and provides insight into genome evolution and host response towards iflaviruses.