Neonatal diarrhea in piglets may cause major losses in affected pig herds. The present study used random high-throughput RNA sequencing (metagenomic next generation sequencing, mNGS) to investigate the virome of sows from a farm with persistent neonatal piglet diarrhea in comparison to two control farms without diarrhea problems. A variety of known swine gastrointestinal viruses was detected in the control farms as well as in the problem farm (Mamastrovirus, Enterovirus, Picobirnavirus, Posavirus 1, Kobuvirus, Proprismacovirus). A substantial increase in normalized viral read counts was observed in the affected farm compared to the control farms. The increase was attributable to a single viral species in each of the sampled sows (porcine astrovirus 4 and Posavirus 1). The complete genomes of a porcine astrovirus 4 and two co-infecting Posavirus 1 were de novo assembled and characterized. The 6734 nt single-stranded RNA genome of porcine astrovirus 4 (PoAstV-4) strain Belgium/2019 contains three overlapping open reading frames (nonstructural protein 1ab, nonstructural protein 1a, capsid protein). Posavirus 1 strains Belgium/01/2019 and Belgium/02/2019 have a 9814 nt single-stranded positive-sense RNA genome encoding a single open reading frame (polyprotein precursor) containing the five expected Picornavirales-conserved protein domains. The study highlights the potential of mNGS workflows to study unexplained neonatal diarrhea in piglets and contributes to the scarce availability of both PoAstV-4 and Posavirus-1 whole genome sequences from Western Europe.

仔猪的新生儿腹泻可能会在受影响的猪群中造成重大损失。本研究使用随机高通量RNA测序（基因组下一代测序，mNGS）来调查与两个没有腹泻问题的对照猪场相比，有持续性新生仔猪腹泻的猪场的母猪病毒。在控制农场以及问题场中的（检测到各种已知猪胃肠病毒Mamastrovirus，肠道病毒，Picobirnavirus，Posavirus 1，Kobuvirus，Proprismacovirus）。与对照农场相比，在受影响的农场中观察到标准化病毒读取计数的大幅增加。该增加归因于每个采样母猪中的单一病毒种类（猪星状病毒4和马铃薯病毒1）。从头开始组装并鉴定猪星状病毒4和两个共同感染的Posavirus 1的完整基因组。比利时/ 2019年猪星状病毒4（PoAstV-4）菌株的6734 nt单链RNA基因组包含三个重叠的开放阅读框（非结构蛋白1ab，非结构蛋白1a，衣壳蛋白）。杆状病毒1株比利时01/2019和比利时02/2019拥有一个9814 nt单链正义RNA基因组，该基因组编码一个包含五个预期的Picornavirales保守蛋白结构域的开放阅读框（多蛋白前体）。这项研究强调了mNGS工作流程研究仔猪无法解释的新生儿腹泻的潜力，并有助于西欧PoAstV-4和Posavirus -1全基因组序列的稀缺性。