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 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.

中文翻译：

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澳大利亚本土野生动物和非人类灵长类动物中的新型肝炎病毒和 pegi 病毒

摘要 黄病毒科是正义RNA病毒家族，包含寨卡病毒、登革热病毒和丙型肝炎病毒等人类和其他动物的重要病原体。黄病毒科目前分为四个属——肝炎病毒属、佩吉病毒属、瘟病毒属和黄病毒属——每个属都有不同的宿主范围。肝炎病毒属的成员与一系列动物物种有关，包括人类、非人类灵长类动物、其他哺乳动物物种以及鸟类和鱼类，而密切相关的 pegiviruses 已在各种哺乳动物类群中被发现，还包括人类。使用总 RNA 和全基因组测序的组合，我们在五种澳大利亚野生动物中鉴定了四种新型肝炎样病毒和一种已知肝炎病毒的新变体。受感染的宿主包括澳大利亚本土的有袋动物和鸟类，以及本土壁虎（Gehyra lauta）。从这些数据中，我们确定了一种独特的有袋类肝炎病毒进化枝，其中还包括在以澳大利亚长鼻袋狸 (Perameles nasuta) 为食时收集的一种充血的全息硬蜱蜱。还确定了与壁虎和鸟类相关的肝炎样病毒的不同谱系。通过挖掘 SRA 数据库，我们类似地从禽类和灵长类动物宿主中识别出三种新的肝炎样病毒，以及与灵长类动物相关的两种新型 pegi 样病毒。肝炎和pegi 样病毒作为一个整体的系统发育史，结合共同系统发育分析，为脊椎动物进化过程中病毒-宿主的共同分化提供了支持，尽管病毒之间存在频繁的跨物种传播。