Characterization of an unusual tobacco rattle virus isolate and a novel phenuivirid in the Jerusalem sage

Two RNA viruses were identified by high-throughput sequencing analysis of leaf samples of Jerusalem sages ( Phlomis fruticosa ) in Switzerland. The first virus, representing a novel isolate of tobacco rattle virus (TRV) named "Phlo", was identified in symptomatic plants but not in healthy ones. Phlo is distinguished by its exceptionally long RNA2 that harbours two ORFs preceding the CP ORF. This peculiar genetic make-up is shared by a set of closely-related European TRV RNA2s, and it could be associated with host-specific systemic infection ability. The second virus, detected both in symptomatic and asymptomatic sages, is a novel member of the family Phenuiviridae named "Phlomis phenuivirus 1" (PPV1). PPV1 exhibits a “cogu-like” architecture with a probable bi-segmented, ambisense RNA genome encoding a replicase, nucleocapsid, and putative movement protein (MP). PPV1 is related to Muscari virus A, a virus identified in an ornamental in Australia, and together they likely constitute a new genus for which the name "Maladivirus" is proposed. This taxon represents a sister clade of the genus Entovirus , whose members have been identified in a fungus and diverse environmental samples. Intriguingly, the putative MPs of maladiviruses and entoviruses cluster with those of lentinuviruses (i.e. cogu-like mycoviruses) and with putative endogenous viral elements from a mycorrhizal fungus, suggesting a role in fungal hosts.