The value of next-generation sequencing (NGS)-based applications for testing purposes in human medicine is widely recognized. Although NGS-based metagenomic screening may be of interest in veterinary medicine, in particular for intensively farmed livestock species such as pigs, there is a lack of protocols tailored to veterinary requirements, likely because of the high diversity of species and samples. Therefore, we developed an NGS-based protocol for use in veterinary virology and present here different applications in porcine medicine. To develop the protocol, each step of sample preparation was optimized using porcine samples spiked with various RNA and DNA viruses. The resulting protocol was tested with clinical samples previously confirmed to be positive for specific viruses by a diagnostic laboratory. Additionally, we validated the protocol in an NGS viral metagenomics ring trial and tested the protocol on viral multiplex reference material (NIBSC, U.K.). We applied our ViroScreen protocol successfully for 1) virus identification, 2) virus characterization, and 3) herd screening. We identified torque teno sus virus and atypical porcine pestivirus in a neurologic case, determined the full-length genome sequence of swine influenza A virus in field samples, and screened pigs using pen floor fecal samples and chewing rope liquid.

基于下一代测序 (NGS) 的应用在人类医学测试方面的价值得到了广泛认可。尽管基于 NGS 的宏基因组筛查可能对兽医学感兴趣，特别是对于集约化养殖的牲畜物种，如猪，但缺乏针对兽医要求的协议，这可能是因为物种和样本的高度多样性。因此，我们开发了一种基于 NGS 的协议，用于兽医病毒学，并在此展示了在猪医学中的不同应用。为了制定该协议，我们使用掺有各种 RNA 和 DNA 病毒的猪样品对样品制备的每个步骤进行了优化。由此产生的协议用之前被诊断实验室确认对特定病毒呈阳性的临床样本进行了测试。此外，我们在 NGS 病毒宏基因组学环形试验中验证了该方案，并在病毒多重参考材料（NIBSC，英国）上测试了该方案。我们成功地将 ViroScreen 协议应用于 1) 病毒识别、2) 病毒表征和 3) 群体筛选。我们在一个神经系统病例中鉴定了扭力腱索病毒和非典型猪瘟病毒，确定了田间样本中猪甲型流感病毒的全长基因组序列，并使用围栏地板粪便样本和咀嚼绳液对猪进行了筛查。