Two novel flavi-like viruses shed light on the plant infecting koshoviruses

The family Flaviviridae is composed of viruses with a positive sense single-stranded RNA genome and includes viruses that are important veterinary and human pathogens. Most members of the family are arthropod and vertebrate-infecting viruses but more recently flavi-like divergent viruses have been identified in marine invertebrate and vertebrate hosts. The striking discovery of gentian Kobu-sho-associated virus (GKaV) expanded the host range of flaviviruses to plants, which was complemented by a recently reported flavi-like virus in carrot, suggesting they could be grouped in a proposed Koshovirus genus. Here, we report the identification in transcriptomic datasets and characterization of two novel RNA viruses from the flowering plants Coptis teeta and Sonchus asper , which have genetic and evolutionary affinity to koshoviruses. These two new viruses are members of novel species which were dubbed Coptis flavi-like virus 1 (CopV1) and Sonchus flavi-like virus 1 (SonV1) and with a viral monopartite RNA of ca. 24 kb, likely have the longest genomes among plant-associated RNA viruses yet. Structural and functional annotations of the polyproteins of all koshoviruses resulted in the detection not only of the expected helicase and RNA-dependent RNA polymerase, but also several additional divergent domains such as AlkB oxigenase, Trypsin-like serine protease, methyltransferase, and envelope E1 flavi-like domains. Phylogenetic analysis groups in a monophyletic clade CopV1, SonV1, GKaV and the carrot flavi-like virus robustly supporting the recently proposed genus Koshovirus of plant infecting flavi-like viruses.