Abstract
BACKGROUND: The Jerusalem sage (Phlomis fruticosa) is a popular ornamental in Europe. In 2022, typical virus-like symptoms consisting of chlorotic rings and irregular patches were identified on leaves of this plant species in Lausanne, Switzerland. METHODS: High-throughput sequencing was used on symptomatic samples, which was followed by transmission electron microscopy, sap inoculations of indicator species, and RT-PCR analyses. RESULTS: Two RNA viruses were identified. The first one represents a novel isolate of tobacco rattle virus (TRV) named “Phlo”. Its presence was confirmed in symptomatic plants but not in asymptomatic ones. Phlo is distinguished by its exceptionally long RNA2 that harbours a peculiar genetic make-up, which 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 bi-segmented, ambisense RNA genome encoding a replicase, nucleocapsid, and putative movement protein. PPV1 is related to muscari virus A, and together they likely constitute a new genus for which the name “Maladivirus” is proposed. CONCLUSIONS: TRV Phlo is most likely responsible for the symptoms observed on the Jerusalem sages. PPV1 may be latent on this species, although there are still uncertainties regarding its host. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12985-025-02896-3.