BACKGROUND Diarrhoea is a major cause of death in neonate pigs and most of the viruses that cause it are RNA viruses. Next Generation Sequencing (NGS) deeply characterize the genetic diversity among rapidly mutating virus populations at the interspecific as well as the intraspecific level. The diversity of RNA viruses present in faeces of neonatal piglets suffering from diarrhoea in 47 farms, plus 4 samples from non-diarrhoeic piglets has been evaluated by NGS. Samples were selected among the cases submitted to the Veterinary Diagnostic Laboratories of Infectious Diseases of the Universitat Autònoma de Barcelona (Barcelona, Spain) and Universidad de León (León, Spain). RESULTS The analyses identified the presence of 12 virus species corresponding to 8 genera of RNA viruses. Most samples were co-infected by several viruses. Kobuvirus and Rotavirus were more commonly reported, with Sapovirus, Astrovirus 3, 4 and 5, Enterovirus G, Porcine epidemic diarrhoea virus, Pasivirus and Posavirus being less frequently detected. Most sequences showed a low identity with the sequences deposited in GenBank, allowing us to propose several new VP4 and VP7 genotypes for Rotavirus B and Rotavirus C. CONCLUSIONS Among the cases analysed, Rotaviruses were the main aetiological agents of diarrhoea in neonate pigs. Besides, in a small number of cases Kobuvirus and Sapovirus may also have an aetiological role. Even most animals were co-infected in early life, the association with enteric disease among the other examined viruses was unclear. The NGS method applied successfully characterized the RNA virome present in faeces and detected a high level of unreported intraspecific diversity.

中文翻译：

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腹泻新生仔猪粪便中 RNA 病毒存在高水平的未报告的种内多样性。


背景技术腹泻是新生猪死亡的主要原因，并且大多数引起腹泻的病毒是RNA病毒。下一代测序（NGS）在种间和种内水平上深入表征快速突变病毒群体的遗传多样性。 NGS 评估了 47 个农场患有腹泻的新生仔猪粪便中存在的 RNA 病毒多样性，以及来自非腹泻仔猪的 4 个样本。样本是从提交给巴塞罗那自治大学（西班牙巴塞罗那）和莱昂大学（西班牙莱昂）传染病兽医诊断实验室的病例中选择的。结果 分析确定存在 12 种病毒，对应 8 个 RNA 病毒属。大多数样本同时受到多种病毒的感染。科布病毒和轮状病毒较为常见，沙波病毒、星状病毒3、4和5型、肠道病毒G、猪流行性腹泻病毒、马赛病毒和马沙病毒则较少被发现。大多数序列与 GenBank 中保藏的序列的同一性较低，这使我们能够为轮状病毒 B 和轮状病毒 C 提出几种新的 VP4 和 VP7 基因型。 结论 在分析的病例中，轮状病毒是新生猪腹泻的主要病原体。此外，在少数病例中，科布病毒和沙波病毒也可能具有病原学作用。即使大多数动物在生命早期都被共同感染，其他受检病毒与肠道疾病的关联尚不清楚。应用的 NGS 方法成功地表征了粪便中存在的 RNA 病毒组，并检测到了高水平的未报告的种内多样性。