The fishing and aquaculture industry is vital for global food security, yet viral diseases can result in mass fish die-off events. Determining the viromes of traditionally understudied species, such as fish, enhances our understanding of the global virosphere and the factors that influence virome composition and disease emergence. Very little is known about the viruses present in New Zealand’s native fish species, including the shortfin eel (Anguilla australis) and the longfin eel (Anguilla dieffenbachii), both of which are fished culturally by Māori (the indigenous population of New Zealand) and commercially. Through a total RNA metatranscriptomic analysis of longfin and shortfin eels across three different geographic locations in the South Island of New Zealand, we aimed to determine whether viruses had jumped between the two eel species and whether eel virome composition was impacted by life stage, species, and geographic location. We identified nine viral species spanning eight different families, thereby enhancing our understanding of eel virus diversity in New Zealand and the host range of these viral families. Viruses of the family Flaviviridae (genus Hepacivirus) were widespread and found in both longfin and shortfin eels, indicative of cross-species transmission or virus-host co-divergence. Notably, both host specificity and geographic location appeared to influence eel virome composition, highlighting the complex interaction between viruses, hosts, and their ecosystems. This study broadens our understanding of viromes in aquatic hosts and highlights the importance of gaining baseline knowledge of fish viral abundance and diversity, particularly in aquatic species that are facing population declines.

渔业和水产养殖业对全球粮食安全至关重要，但病毒性疾病可能导致大规模鱼类死亡事件。确定传统上研究不足的物种（例如鱼类）的病毒组可以增强我们对全球病毒圈以及影响病毒组组成和疾病出现的因素的了解。人们对新西兰本土鱼类中存在的病毒知之甚少，包括短鳍鳗鱼（Anguilla australis）和长鳍鳗鱼（Anguilla dieffenbachii），这两种鱼类均由毛利人（新西兰土著居民）进行文化捕捞和商业捕捞。通过对新西兰南岛三个不同地理位置的长鳍和短鳍鳗鱼进行总 RNA 宏转录组分析，我们的目的是确定病毒是否在这两个鳗鱼物种之间跳跃，以及鳗鱼病毒组的组成是否受到生命阶段、物种、和地理位置。我们鉴定了跨越八个不同科的九种病毒，从而增强了我们对新西兰鳗鱼病毒多样性以及这些病毒科的宿主范围的了解。黄病毒科（肝炎病毒属）的病毒广泛存在于长鳍鳗和短鳍鳗中，表明存在跨物种传播或病毒-宿主共分化。值得注意的是，宿主特异性和地理位置似乎都会影响鳗鱼病毒组的组成，凸显了病毒、宿主及其生态系统之间复杂的相互作用。这项研究拓宽了我们对水生宿主病毒组的理解，并强调了获得鱼类病毒丰度和多样性基线知识的重要性，特别是在面临种群数量下降的水生物种中。