Geoghegan Jemma L, Di Giallonardo Francesca, Wille Michelle, Ortiz-Baez Ayda Susana, Costa Vincenzo A, Ghaly Timothy, Mifsud Jonathon C O, Turnbull Olivia M H, Bellwood David R, Williamson Jane E, Holmes Edward C
Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand.
Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
Virus Evol. 2021 Feb 4;7(1):veab005. doi: 10.1093/ve/veab005. eCollection 2021 Jan.
Revealing the determinants of virome composition is central to placing disease emergence in a broader evolutionary context. Fish are the most species-rich group of vertebrates and so provide an ideal model system to study the factors that shape virome compositions and their evolution. We characterized the viromes of nineteen wild-caught species of marine fish using total RNA sequencing (meta-transcriptomics) combined with analyses of sequence and protein structural homology to identify divergent viruses that often evade characterization. From this, we identified twenty-five new vertebrate-associated viruses and a further twenty-two viruses likely associated with fish diet or their microbiomes. The vertebrate-associated viruses identified here included the first fish virus in the (single-strand, negative-sense RNA virus) Other viruses fell within the , , , , , , , , , and , and were sometimes phylogenetically distinct from known fish viruses. We also show how key metrics of virome composition-viral richness, abundance, and diversity-can be analysed along with host ecological and biological factors as a means to understand virus ecology. Accordingly, these data suggest that that the vertebrate-associated viromes of the fish sampled here are predominantly shaped by the phylogenetic history (i.e. taxonomic order) of their hosts, along with several biological factors including water temperature, habitat depth, community diversity and swimming behaviour. No such correlations were found for viruses associated with porifera, molluscs, arthropods, fungi, and algae, that are unlikely to replicate in fish hosts. Overall, these data indicate that fish harbour particularly large and complex viromes and the vast majority of fish viromes are undescribed.
揭示病毒组组成的决定因素对于将疾病出现置于更广泛的进化背景中至关重要。鱼类是脊椎动物中物种最丰富的群体，因此提供了一个理想的模型系统来研究塑造病毒组组成及其进化的因素。我们使用总RNA测序（元转录组学）结合序列和蛋白质结构同源性分析，对19种野生捕获的海洋鱼类的病毒组进行了表征，以识别通常难以表征的 divergent 病毒。由此，我们鉴定出25种新的脊椎动物相关病毒以及另外22种可能与鱼类饮食或其微生物群相关的病毒。这里鉴定出的脊椎动物相关病毒包括 （单链、负义RNA病毒）中的第一种鱼类病毒。其他病毒属于 、 、 、 、 、 、 、 、 和 ，并且在系统发育上有时与已知的鱼类病毒不同。我们还展示了如何将病毒组组成的关键指标——病毒丰富度、丰度和多样性——与宿主生态和生物学因素一起进行分析，作为理解病毒生态学的一种手段。因此，这些数据表明，这里采样的鱼类的脊椎动物相关病毒组主要由其宿主的系统发育历史（即分类顺序）以及包括水温、栖息地深度、群落多样性和游泳行为在内的几个生物学因素塑造。对于与海绵动物、软体动物、节肢动物、真菌和藻类相关的病毒，未发现此类相关性，这些病毒不太可能在鱼类宿主中复制。总体而言，这些数据表明鱼类拥有特别庞大和复杂的病毒组，并且绝大多数鱼类病毒组尚未被描述。
