Australian terrestrial environments harbour extensive RNA virus diversity

Abstract

Australia is home to a diverse range of unique native fauna and flora. To address whether Australian ecosystems also harbour unique viruses, we performed meta-transcriptomic sequencing of 16 farmland and sediment samples taken from the east and west coasts of Australia. We identified 2,562 putatively novel viruses across 15 orders, the vast majority of which belonged to the microbe-associated phylum Lenarviricota. In many orders, the novel viruses identified here comprised entirely new clades, such as the Nodamuvirales and Ghabrivirales. Novel viruses also fell between established genera or families, such as in the Cystoviridae and Picornavirales, while highly divergent lineages were identified in the Martellivirales and Ghabrivirales. Viral abundance and alpha diversity were influenced by sampling site, soil type and land use, but not by depth from the surface. In sum, Australian soils and sediments are home to remarkable viral diversity, reflecting the biodiversity of local fauna and flora.

Genetic mechanisms underlying the structural elaboration and dissemination of viral internal ribosomal entry sites

“…Recombination has also been implicated in the transfer of IRESs between genomes of viruses belonging to different genera of Caliciviridae, Flaviviridae and Picornaviridae [11,13,14,16,17]. Here, we identified type 6 IRESs not only in Dicistroviridae, but also in Tombusviridae, Marnaviridae and the proposed Ripiresk picorna-like group of positive-sense RNA viruses [69], and in other instances, relocated to the 5'-terminal regions of dicistrovirus genomes. Recombination therefore serves to diversify the structure of type 6 IRESs by shuffling domains from different subsets of these IRESs, to move them to different locations in dicistrovirus genomes, and to transfer them horizontally between unrelated genomes.…”

“…Analysis of viral sequences and metagenomic datasets derived from arthropods, environmental samples and plant-associated material revealed 41 members of a structurally distinct group of type 6 IRES in picornavirus-like genomes or genome fragments (Table S11), including those of Hubei Picorna-like virus 51 [46], Robinvale bee virus 6 [47], Cherry virus Trakiya [66], Aphis glycines virus 1 [67] and rice curl dwarf-associated virus [68]. These viruses have recently been identified as members of a novel clade (Ripiresk picorna-like group) that falls between established Secoviridae and Iflaviridae families of the order Picornavirales [69]. These genomes are dicistronic, and the order of open reading frames that encode capsid proteins (ORF1) and non-structural proteins (ORF2) is reversed relative to the order in dicistroviruses.…”