A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the "FAIR" (Findable, Accessible, Interoperable, and Reusable) data principles.

中文翻译：

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农场动物中的病毒元基因组学：系统评价。

大多数新兴传染病是人畜共患病起源的。超基因组下一代测序（mNGS）已被用于识别罕见和新颖的传染病因，并表征人，动物和环境样品中的病毒多样性。在这里，我们系统地回顾了在普通牲畜（牛，小反刍动物，家禽和猪）中进行病毒mNGS的研究。在第一次和第二次筛选后，我们鉴定了2481条记录，最终包括120条记录。猪是研究最频繁的牲畜，在家禽样品中发现的病毒多样性最高。已知文献报道了已知的动物病毒，人畜共患病毒和新型病毒，这表明mNGS能够识别已知和新型病毒。但是，宏基因组学研究的覆盖面很小，有关小反刍动物的病毒和所研究牲畜的呼吸病毒的数据很少。现有文献很少提及诸如牲畜年龄和农场类型之类的基本元数据，并且只有10.8％的数据集可公开获得。对动物病毒的深入了解对于发现潜在的人畜共患病和动物病原体以及“一站式”卫生至关重要。元基因组学研究可以提供这种背景，但前提是与基本元数据结合并遵循“公平”（可查找，可访问，可互操作和可重用）数据原理。深入了解家畜病毒感染对于检测潜在的人畜共患病和动物病原体以及“一个健康”的准备至关重要。元基因组学研究可以提供这种背景，但前提是与基本元数据结合并遵循“公平”（可查找，可访问，可互操作和可重用）数据原理。对动物病毒的深入了解对于发现潜在的人畜共患病和动物病原体以及“一站式”卫生至关重要。元基因组学研究可以提供这种背景，但前提是与基本元数据结合并遵循“公平”（可查找，可访问，可互操作和可重用）数据原理。