Plant biosecurity threats detected using metatranscriptomic sequencing of animal gut contents

Ribgrass mosaic virus (RMV) and related viruses of the genus Tobamovirus (family Virgaviridae) are cruciferous plant pathogens that represent a threat to global horticultural systems. In Australia, they are considered exotic biosecurity threats, and an incursion of these viruses would require rapid and strict control efforts. However, current surveillance methods for these viruses are limited. We examined whether RMV and related tobamoviruses could be detected through the analysis of mammalian gut metatranscriptomes. Accordingly, we identified five different tobamoviruses in one or more gut metatranscriptomes of the Eastern grey kangaroo, fallow deer, domestic dog, spotted-tailed quoll, feral cat, and the Tasmanian devil. One of the tobamoviruses was also detected in a tick metatranscriptome. The five tobamoviruses detected were: (i) RMV, (ii) a novel relative of RMV, (iii and iv) two highly diverse novel tobamoviruses, and (v) the plant pathogen tobacco mild green mosaic virus (TMGMV) already known to be present in Australia. Subsequent phylogenetic analysis provided information on their origin and spread through Australia. RMV was detected at multiple sites in both the Australian Capital Territory (ACT) and Tasmania, two regions separated by ~700 km of land and 200 km of water. The novel relative of RMV was detected in the ACT and New South Wales (NSW), the highly divergent novel tobamoviruses were each detected in a single state (NSW and Queensland, QLD), while TMGMV was detected in QLD. This work highlights the potential utility of metatranscriptomic sequencing of wild animal gut samples for the surveillance of biosecurity threats to native and agricultural plant species and for studying their evolution in new environments.