A Negative-Stranded RNA Virus Infecting Citrus Trees: The Second Member of a New Genus Within the Order Bunyavirales

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 gumassociated
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 invertebrateinfecting
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.