The Complex World of Emaraviruses—Challenges, Insights, and Prospects

Abstract

Emaravirus (Order Bunyavirales; Family Fimoviridae) is a genus comprising over 20 emerging plant viruses with a worldwide distribution and economic impact. Emaraviruses infect a variety of host plants and have especially become prevalent in important long-living woody plants. These viruses are enveloped, with a segmented, single-stranded, negative-sense RNA genome and are transmitted by eriophyid mites or mechanical transmission. Emaraviruses have four core genome segments encoding an RNA-dependent RNA polymerase, a glycoprotein precursor, a nucleocapsid protein, and a movement protein. They also have additional genome segments, whose number varies widely. We report here that the proteins encoded by these segments form three main homology groups: a homolog of the sadwavirus Glu2 Pro glutamic protease; a protein involved in pathogenicity, which we named “ABC”; and a protein of unknown function, which we named “P55”. The distribution of these proteins parallels the emaravirus phylogeny and suggests, with other analyses, that emaraviruses should be split into at least two genera. Reliable diagnosis systems are urgently needed to detect emaraviruses, assess their economic and ecological importance, and take appropriate measures to prevent their spread (such as routine testing, hygiene measures, and control of mite vectors). Additional research needs include understanding the function of emaravirus proteins, breeding resistant plants, and clarifying transmission modes.

WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection

“…We had used it on earlier occasions (e.g. [5, 14, 15]), but not presented it in detail. The procedure can be decomposed into three principles…”

“…We had used it on earlier occasions (e.g. [5,14,15]), but not presented it in detail. The procedure can be decomposed into three principles Proteins detected by homology search programs such as PSI-blast are considered to be homologous to the query if the statistical significance of their sequence similarity with the query (called 'E-value') is below a certain cutoff (typically E≤10 −3 ) [22].…”

“…This procedure enabled us to identify a previously overlooked domain, WIV, present in nearly 100 arthropod viruses (the full list is in File S1). The procedure had already been used on several occasions to detect distant homologues [5,14,15] but not been presented in detail.…”

“…Contextual information has been used since the beginning of bioinformatics to detect distant homologues manually (e.g. [11][12][13]), but our previous experience suggested that it is particularly powerful in viruses [5,14,15].…”

Novel tri-segmented rhabdoviruses: A data mining expedition unveils the cryptic diversity of cytorhabdoviruses

“…On the other hand, no hits were found for P2, P3, P4, P6, P7, P8, P9, P10 or P11. Strikingly, P5 showed hits against the putative RNA silencing suppressor protein encoded by emaraviruses (family Fimoviridae ), plant viruses with segmented, linear, single-stranded, negative-sense genomes (Elbeaino et al, 2018) in the order Bunyavirales (Rehanek et al, 2022), while rhabdoviruses are classified in the order Mononegavirales (Walker et al, 2022). Viral RNA silencing suppressors are required for systemic infection of the plant host and the presence of these proteins suggests that the tri-segmented viruses detected here are plant-associated (Dolja et al, 2020).…”