Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids)

Abstract

Although Australian marsupials are characterised by unique biology and geographic isolation, little is known about the viruses present in these iconic wildlife species. The Dasyuromorphia are an order of marsupial carnivores found only in Australia that include both the extinct Tasmanian tiger (thylacine) and the highly threatened Tasmanian devil. Several other members of the order are similarly under threat of extinction due to habitat loss, hunting, disease, and competition and predation by introduced species such as feral cats. We utilised publicly available RNA-seq data from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database to document the viral diversity within four Dasyuromorph species. Accordingly, we identified fifteen novel virus sequences from five DNA virus families (Adenoviridae, Anelloviridae, Gammaherpesvirinae, Papillomaviridae, and Polyomaviridae) and three RNA virus taxa: the order Jingchuvirales, the genus Hepacivirus, and the delta-like virus group. Of particular note was the identification of a marsupial-specific clade of delta-like viruses that may indicate an association of deltaviruses with marsupial species. In addition, we identified a highly divergent hepacivirus in a numbat liver transcriptome that falls outside of the larger mammalian clade. We also detect what may be the first Jingchuvirales virus in a mammalian host—a chu-like virus in Tasmanian devils—thereby expanding the host range beyond invertebrates and ectothermic vertebrates. As many of these Dasyuromorphia species are currently being used in translocation efforts to reseed populations across Australia, understanding their virome is of key importance to prevent the spread of viruses to naive populations.

A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record

“…In addition, these phylogenies revealed a robustly supported relationship between chuvirus EVEs in the Tibetan frog ( Nanorana parkeri ) and zebrafish ( Danio rerio ) genomes. Taken together, these results provide evidence for the existence of numerous diverse lineages of chuviruses in vertebrates, adding to recent evidence for the presence of exogenous chuviruses in marsupials [ 64 ].…”

“…4 Exogenous versus endogenous distribution of virus families that have been incorporated into the vertebrate germline. Circles indicate the known presence of exogenous viruses in vertebrate groups, determined through reference to the NCBI virus genomes resource [ 56 ], supplemented with information obtained from recently published papers [ 64 – 70 ]. Shaded boxes indicate the presence of endogenous viral elements, as determined in the present study.…”

“…These issues, combined with rapid data accumulation, coverage limitations, and assembly errors—make generation of complete and accurate annotations difficult [ 83 , 85 ]. Consequently, labor-intensive manual genome annotation remains important [ 64 , 78 ], and most published whole genome sequences are comprised of genomic “dark matter”.…”

Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities

“…With an expanded diversity of environments sampled as well as a growing re-assessment of publicly available sequencing data and the continuous development of tools and resources, this field has experienced massive growth in recent years, with no signs of deceleration in sight (Figure 1) (8,(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29).…”

Emerging viral threats in Australia

“…To date, metagenomic virus discovery studies have been conducted for several native and invasive species in Australia including rabbits, 36 foxes, 37 bats, 38 dasyurids (marsupial carnivores), 39 koalas 40 and shorebirds, 41 but expanding the number of species studied and the geographical range of these studies is needed to understand the dynamics of the Australian 'virome'. It is particularly important to conduct unbiased metagenomic screening of domestic species in frequent contact with humans, wildlife at the human-animal interface, and common invertebrate vectors of disease (e.g.…”