Discovery of a Novel Jingmenvirus in Australian Sugarcane Soldier Fly (Inopus flavus) Larvae

Abstract

In Australia, soldier flies are major pests of sugarcane, and they can cause significant yield losses in some areas, possibly due to the 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 the 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 the larvae matched the IFJV1 sequences. Moreover, they were found to be 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 the possible pathogenicity to its host or the sugarcane it parasitizes requires the development of a stable replication model.

Keywords: soldier fly; sugarcane pest; virome.

Figure 1

Genome organization of IFJV1. Segments are represented as black boxes with open reading frames highlighted in colors. The signal peptide of VP2 in segment 4 is represented in red. SP: signal peptide; aa: amino acid. Genbank accession numbers: OM869459-OM869462.

Figure 2

Phylogenetic analysis of the amino acid sequence of NSP1 (a) and NSP2 (b) of Inopus flavus jingmenvirus 1, aligned with reference jingmenviruses. These maximum-likelihood phylogenies were inferred using a JTT substitution matrix and assumed a discretized gamma rate distribution with four rate categories and with 100 bootstraps. Bar: branch length. The identified virus in this study is shown with an arrow.

Figure 3

Length profile and distribution of IFJV1−derived sRNAs. The virus−derived sRNA length profiles are on the left: (a) segment 1; (b) segment 2; (c) segment 3; (d) segment 4, and the distribution of 21 nt-long IFJV1-derived sRNA mapped back to the virus in positive (black) and negative (grey) sense nucleotide sequences are on the right.