Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada.
Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, Canada.
PLoS Pathog. 2023 Jun 22;19(6):e1011386. doi: 10.1371/journal.ppat.1011386. eCollection 2023 Jun.
Sea lice, the major ectoparasites of fish, have significant economic impacts on wild and farmed finfish, and have been implicated in the decline of wild salmon populations. As blood-feeding arthropods, sea lice may also be reservoirs for viruses infecting fish. However, except for two groups of negative-strand RNA viruses within the order Mononegavirales, nothing is known about viruses of sea lice. Here, we used transcriptomic data from three key species of sea lice (Lepeophtheirus salmonis, Caligus clemensi, and Caligus rogercresseyi) to identify 32 previously unknown RNA viruses. The viruses encompassed all the existing phyla of RNA viruses, with many placed in deeply branching lineages that likely represent new families and genera. Importantly, the presence of canonical virus-derived small interfering RNAs (viRNAs) indicates that most of these viruses infect sea lice, even though in some cases their closest classified relatives are only known to infect plants or fungi. We also identified both viRNAs and PIWI-interacting RNAs (piRNAs) from sequences of a bunya-like and two qin-like viruses in C. rogercresseyi. Our analyses showed that most of the viruses found in C. rogercresseyi occurred in multiple life stages, spanning from planktonic to parasitic stages. Phylogenetic analysis revealed that many of the viruses infecting sea lice were closely related to those that infect a wide array of eukaryotes with which arthropods associate, including fungi and parasitic tapeworms, implying that over evolutionary time there has been cross-phylum and cross-kingdom switching of viruses between arthropods and other eukaryotes. Overall, this study greatly expands our view of virus diversity in crustaceans, identifies viruses that infect and replicate in sea lice, and provides evidence that over evolutionary time, viruses have switched between arthropods and eukaryotic hosts in other phyla and kingdoms.
海虱是鱼类的主要外寄生虫，对野生和养殖鱼类有重大的经济影响，并被认为是野生三文鱼数量下降的原因之一。作为吸血节肢动物，海虱也可能是感染鱼类的病毒的宿主。然而，除了单链负股 RNA 病毒目中的两个病毒群之外，我们对海虱的病毒一无所知。在这里，我们使用了三种关键的海虱（鲑鱼虱、克莱门氏海虱和罗杰氏海虱）的转录组数据，鉴定出了 32 种以前未知的 RNA 病毒。这些病毒涵盖了所有现有的 RNA 病毒门，其中许多处于深分枝的进化分支，可能代表新的科和属。重要的是，存在典型的病毒衍生小干扰 RNA（viRNA）表明，这些病毒中的大多数都感染了海虱，尽管在某些情况下，它们最近被分类的近亲仅已知感染植物或真菌。我们还从 C. rogercresseyi 的 bunya 样病毒和两种 qin 样病毒的序列中鉴定出了 viRNA 和 PIWI 相互作用 RNA（piRNA）。我们的分析表明，在 C. rogercresseyi 中发现的大多数病毒存在于多个生命阶段，从浮游阶段到寄生阶段都有。系统发育分析显示，感染海虱的许多病毒与感染包括真菌和寄生绦虫在内的广泛真核生物的病毒密切相关，这表明在进化过程中，病毒在节肢动物和其他真核生物之间发生了跨门和跨界的切换。总的来说，这项研究极大地扩展了我们对甲壳类动物病毒多样性的认识，鉴定出了感染和在海虱中复制的病毒，并提供了证据表明，在进化过程中，病毒在节肢动物和其他门和界的真核宿主之间发生了切换。
