Abstract
The discovery of hepaciviruses in non-human hosts has accelerated following the advancement of high-throughput sequencing technology. Hepaciviruses have now been described in reptiles, fish, birds, and an extensive array of mammals. Using metagenomic sequencing on pooled samples of field-collected Culex annulirostris mosquitoes, we discovered a divergent hepacivirus-like sequence, named Jogalong virus, from the Kimberley region in northern Western Australia. Using PCR, we screened the same 300 individual mosquitoes and found just a single positive sample (1/300, 0.33%). Phylogenetic analysis of the hepacivirus NS5B protein places Jogalong virus within the genus Hepacivirus but on a distinct and deeply rooted monophyletic branch shared with duck hepacivirus, suggesting a notably different evolutionary history. Vertebrate barcoding PCR targeting two mitochondrial genes, cytochrome c oxidase subunit I and cytochrome b, indicated that the Jogalong virus-positive mosquito had recently fed on the tawny frogmouth (Podargus strigoides), although it is currently unknown whether this bird species contributes to the natural ecology of this virus.
Highlights
Hepaciviruses are positive-sense RNA viruses in the family Flaviviridae
A total of 20,556 Cx. annulirostris was collected from the six traps located in three sites from across the Kimberley region in the north west of Australia (Table 1, Fig 1); 50 female mosquitoes were randomly selected from each trap for virome analyses
We identified nucleic acid sequences of a virus tentatively named Jogalong virus that is related to members of the genus Hepacivirus
Summary
Hepaciviruses are positive-sense RNA viruses in the family Flaviviridae. Hepaciviruses are difficult to culture; their diversity was underappreciated until the advent of high throughput sequencing (HTS). The genus Hepacivirus comprises at least fourteen species that infect humans [1], and other mammals including rodents [2,3,4,5,6], cows [7, 8], horses [9], primates [10, 11], and bats [12]. A survey of Australian ticks identified a hepacivirus from an Ixodes holocyclus tick that fed on a long-nosed bandicoot [13].
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