Abstract In Australia, soldier flies are major pests of sugarcane, and they can cause significant yield losses in some areas, possibly due to virus transmission to the plants. We sequenced fly larvae salivary glands and identified a novel jingmenvirus, putatively named Inopus flavus jingmenvirus 1 (IFJV1). Phylogenetic trees confirmed that IFJV1 groups with insect-associated jingmenviruses, newly identified flavivirus-like viruses with a segmented genome. After the design and validation of molecular detection systems for IFJV1, larval homogenates were passaged on insect and vertebrate cells but IFJV1 could only be detected in the first two passages in insect cells and not at all in vertebrate cells. Despite this lack of consistent replication in laboratory models, this virus does replicate in its host Inopus flavus , as sequenced small RNA from larvae match the IFJV1 sequences, are predominantly 21 nucleotides-long and map to the whole sequences on both strands, which is typical of an actively replicating virus. This discovery confirms the worldwide presence of jingmenviruses, which until now had only been detected on four continents. However, the study of IFJV1 tropism and of the possible pathogenicity to its host or the sugarcane it parasitizes requires the development of a stable replication model.

Discovery of a novel jingmenvirus in Australian sugarcane Soldier fly (Inopus flavus) larvae