Abstract
A new RNA virus has been identified from a sweet orange tree in southern Italy. This virus, tentatively named citrus virus A (CiVA), has a bipartite genome composed of (i) a negative-stranded (ns) RNA1, encoding the viral RNA-dependent RNA polymerase (RdRp), and (ii) an ambisense RNA2, coding for the putative movement protein (MP) and nucleocapsid protein (NP), with the two open reading frames separated by a long AU-rich intergenic region (IR) adopting a hairpin conformation. CiVA genomic RNAs and the encoded proteins resemble those of the recently discovered citrus concave gum-associated virus (CCGaV). This CCGaV, a nsRNA virus associated with the ancient citrus concave gum disease, has been proposed as the representative member of a new genus tentatively named Coguvirus. Molecular and phylogenetic analyses presented here support the classification of CiVA, and likely of other two recently described nsRNA viruses infecting plants, in this new genus. By showing that the evolutionary origin of the MP of all the putative coguviruses likely differs from that of their respective RdRp and NP, this study also provides evidence of a likely modular genome evolution for these viruses. Moreover, phylogenetic data support the proposal that, during the evolutionary history of nsRNA viruses, the plant-infecting viruses most likely emerged from an invertebrate-infecting ancestor several times as independent events. CiVA was identified in a field sweet orange tree not showing any obvious symptom and was graft-transmitted to sweet orange, grapefruit, rough lemon and Dweet tangor indicator plants that did not developed symptoms. The capacity of infecting citrus hosts of several species was also confirmed by a preliminary survey that identified orange, mandarin, clementine and lemon trees as natural hosts of CiVA in several fields of southern Italy, again without any obvious association with specific symptoms.
Highlights
Based on high-throughput sequencing (HTS) many new negative-stranded RNA viruses, most of which infecting invertebrates (Li et al, 2015; Shi et al, 2016; Tokarz et al, 2018), have been recently reported
A novel nsRNA virus, named citrus virus A, has been identified by HTS and its full-length genome completely sequenced by a classical molecular biology approach based on Sanger sequencing
citrus virus A (CiVA) is closely related to concave gumassociated virus (CCGaV), another nsRNA virus recently reported from citrus (Navarro et al, 2018)
Summary
Based on high-throughput sequencing (HTS) many new negative-stranded (ns) RNA viruses, most of which infecting invertebrates (Li et al, 2015; Shi et al, 2016; Tokarz et al, 2018), have been recently reported. A Novel Bunyavirus Infecting Citrus new order Bunyavirales to contain nine families (Maes et al, 2018). Citrus concave gum-associated virus (CCGaV), a novel bunyavirus infecting citrus trees, was identified by HTS and shown to be associated with a severe and ancient citrus disease called concave gum (CG) (Navarro et al, 2018). CCGaV is phylogenetically related to species in the family Phenuiviridae and to several yet not-classified viruses identified mainly in arthropodes (Navarro et al, 2018). We report a new nsRNA virus infecting citrus with molecular features and phylogenetic relationships with CCGaV, which strongly suggest that it is a prototype of a second species in the proposed genus Coguvirus. The results of preliminary field surveys in southern Italy documented the presence of this new virus, tentatively named citrus virus A (CiVA), in citrus trees of several species and in several citrus-growing areas
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