Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates

Abstract

The Flaviviridae family of positive-sense RNA viruses contains important pathogens of humans and other animals, including Zika virus, dengue virus and hepatitis C virus. The Flaviviridae are currently divided into four genera - Hepacivirus, Pegivirus, Pestivirus and Flavivirus – each with a diverse host range. Members of the genus Hepacivirus are associated with an array of animal species, including humans, non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa, also including humans. Using a combination of total RNA and whole genome sequencing we identified four novel hepaci-like viruses and one novel variant of a known hepacivirus in five species of Australian wildlife. The hosts infected comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). From these data we identified a distinct marsupial clade of hepaci-like viruses that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Distinct lineages of hepaci-like viruses associated with geckos and birds were also identified. By mining the short-read archive (SRA) database we similarly identified three new hepaci-like viruses from avian and primate hosts, as well as two novel pegi-like viruses associated with primates. The phylogenetic history of the hepaci- and pegi-like viruses as a whole, combined with co-phylogenetic analysis, provided support for virus-host co-divergence over the course of vertebrate evolution, although with frequent cross-species virus transmission. Overall, our work highlights the diversity of the Hepacivirus and Pegivirus genera as well as the uncertain phylogenetic distinction between.

Molecular detection and genomic characterization of diverse hepaciviruses in African rodents

“…To date, those include mammalian hosts such as bats ( Quan et al 2013 ), cows ( Baechlein et al 2015 ; Corman et al 2015 ), dogs ( Kapoor et al 2011 ; El-Attar et al 2015 ), horses ( Burbelo et al 2012 ; Lyons et al 2012 ), non-human primates ( Lauck et al 2013 ; Canuti et al 2019 ; Porter et al 2020 ), possums ( Chang et al 2019 ), shrews ( Guo et al 2019 ), sloths ( Moreira-Soto et al 2020 ) and rodents ( Drexler et al 2013 ; Kapoor et al 2013 ; Firth et al 2014 ; Van Nguyen et al 2018 ). Non-mammalian hosts harbouring hepaciviruses have also been identified in birds ( Chu et al 2019 ; Goldberg et al 2019 ; Porter et al 2020 ), fish and reptiles ( Shi et al 2018 ). Finally, divergent hepaciviruses were very recently detected in the first non-vertebrate hosts, specifically in a Culex annulirostris mosquito ( Williams et al 2020 ) and an Ixodes holocyclus tick species ( Harvey et al 2018 ).…”

“…The most closely related viruses to HCV have been identified in horses ( Burbelo et al 2012 ; Lyons et al 2012 ) and this lineage has also been introduced in dogs ( Pybus and Thézé 2016 ) and donkeys ( Walter et al 2017 ). Very recently, a hepaci-like virus sampled from a Senegal bushbaby was shown to group with the equine lineage ( Porter et al 2020 ). Rodent hepaciviruses (RHVs) show the greatest genetic heterogeneity among mammalian host clades and were hypothesized to constitute the primary zoonotic source of mammalian hepaciviruses ( Pybus and Gray 2013 ; Hartlage et al 2016 ; Pybus and Thézé 2016 ).…”

Metagenomic identification of viral sequences in laboratory reagents

“…These viruses occupied diverse locations across the phylogeny, although they were closely related to some previously identified reagent-associated viruses: Avon-Heathcote estuary associated circular viruses, Circoviridae sp. subtypes, Dromedary stool-associated circular virus subtypes, and Sandworm circovirus [5, 9] ( Figure 2 ). It is notable that the CRESS viruses analysed derive from a variety of environments, and there is no clear pattern according to the host species of sample origin, which is anticipated in the case of contaminant sequences.…”

“…Specifically, we used a combination of e-value, hit length, and percentage similarity to determine the potential of a contig to be a viral sequence. The abundance of reagent-associated reads was calculated by comparing the number of contig reads to the total number of library reads (via mapping trimmed reads back to the contigs) as performed in previous studies [5, 8].…”

Retrospective meta-transcriptomic identification of severe dengue in a traveller returning from Africa to Sweden, 1990

“…In five of the sequencing libraries (Table 1), partly confirmed with PCR, we noted the presence of HPgV, phylogenetically indicated to be of non-African origin (Figure 1). HPgV is a common virus, present in up to 5% of healthy blood-donors [6], and is most closely related to simian pegiviruses [11]. HPgV is currently not definitively associated with any disease [12], and the majority of individuals clear the infection within two years [6].…”