DataSheet_1_Metatranscriptomic assessment of diarrhoeic faeces reveals diverse RNA viruses in rotavirus group A infected piglets and calves from India.pdf

RNA viruses are a major group contributing to emerging infectious diseases and neonatal diarrhoea, causing morbidity and mortality in humans and animals. Hence, the present study investigated the metatranscriptomic-derived faecal RNA virome in rotavirus group A (RVA)-infected diarrheic piglets and calves from India. The viral genomes retrieved belonged to Astroviridae in both species, while Reoviridae and Picornaviridae were found only in piglets. The nearly complete genomes of porcine RVA (2), astrovirus (AstV) (6), enterovirus G (EVG) (2), porcine sapelovirus (PSV) (2), Aichivirus C (1), and porcine teschovirus (PTV) (1) were identified and characterised. In the piglet, AstVs of PAstV2 (MAstV-26) and PAstV4 (MAstV-31) lineages were predominant, followed by porcine RVA, EVG, PSV, Aichivirus C, teschovirus (PTV-17) in decreasing order of sequence reads. In contrast, AstV accounted for the majority of reads in bovines and belonged to MAstV-28 and a proposed MAstV-35. Both RVA G4P[6] strains exhibited prototype Gottfried strains like a genotypic constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. Ten out of eleven genes were of porcine origin, while the VP7 gene clustered with G4-lineage-1, consisting of human strains, suggesting a natural porcine-human reassortant. In the recombination analysis, multiple recombination events were detected in the PAstV4 and PAstV2 genomes, pointing out that these viruses were potential recombinants. Finally, the study finds diverse RNA virome in Indian piglets and calves for the first time, which may have contributed to diarrhoea. In the future, the investigation of RNA virome in animals will help in revealing pathogen diversity in multifactorial diseases, disease outbreaks, monitoring circulating viruses, viral discovery, and evaluation of their zoonotic potential.

RNA病毒是一群重要的病原体，其导致的新兴传染病和新生儿腹泻在人类和动物中引起了发病率和死亡率。因此，本研究对来自印度的A组轮状病毒（RVA）感染腹泻猪崽和小牛的元转录组来源粪便RNA病毒群进行了研究。从两种物种中检索到的病毒基因组属于星状病毒科，而在猪崽中仅发现呼肠孤病毒科和微小病毒科。鉴定并特征化了猪源RVA（2）、星状病毒（AstV）（6）、肠道病毒G（EVG）（2）、猪圆环病毒（PSV）（2）、Aichivirus C（1）和猪肠病毒（PTV）（1）的几乎完整的基因组。在猪崽中，PAstV2（MAstV-26）和PAstV4（MAstV-31）谱系的AstV占主导地位，其次是猪源RVA、EVG、PSV、Aichivirus C、肠病毒（PTV-17），其序列读取量依次递减。相比之下，AstV在牛中占多数读取量，属于MAstV-28和提议的MAstV-35。G4P[6]的RVA菌株表现出原型Gottfried菌株的基因型星座，即G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1。11个基因中有10个来自猪源，而VP7基因与G4-lineage-1聚类，包括人类菌株，表明这是一种天然的猪-人重组体。在重组分析中，检测到PAstV4和PAstV2基因组中的多次重组事件，指出这些病毒是潜在的重组体。最后，该研究首次发现印度猪崽和小牛中存在多样的RNA病毒群，这可能导致腹泻。在未来，对动物中RNA病毒群的研究将有助于揭示多因素疾病的病原体多样性、疾病爆发、流行病毒监测、病毒发现及其动物源性潜力的评估。