BACKGROUND AND AIMS Runting-stunting syndrome (RSS) in chickens, also known as malabsorption syndrome, which is characterized by mild to severe enteritis and diagnosed through typical histopathologic examination as well as clinical signs, results in considerable economic losses. Despite the many studies carried out over decades to determine the etiologic agents of RSS involved in the disease, several outbreaks remained without the elucidation of, potentially multiple, etiologies involved. METHODS We performed comparative analysis of viral metagenomes from four chicken flocks affected with RSS using next-generation sequencing. Primers for the detection of chicken enteric viruses were designed from the sequencing data obtained with metagenomics. Multiplex reverse transcription-polymerase chain reaction (PCR) and PCR were performed to detect a variety of etiological agents previously described in natural cases of RSS. RESULTS The most abundant viral families identified in this study were Astroviridae, Picornaviridae, Parvoviridae, Caliciviridae, Reoviridae and Picobirnaviridae. Chicken astrovirus sequences were present in all four samples, suggesting an association between chicken astrovirus and RSS and chicken astrovirus as a candidate pathogen responsible for RSS. Picobirnavirus and the newly identified chapparvovirus were found in chickens in the Republic of Korea for the first time, and the genetic diversity of enteric viruses and viral communities was showed. CONCLUSIONS Chicken astrovirus was consistently detected in broilers affected with RSS and the result of this study may contribute to knowledge of enteric diseases and viruses in chickens.

中文翻译：

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对韩国患有矮小发育迟缓综合征的鸡进行病毒宏基因组分析。


背景与目的鸡矮小发育迟缓综合征(RSS)，也称为吸收不良综合征，其特征是轻度至重度肠炎，通过典型的组织病理学检查和临床体征进行诊断，导致相当大的经济损失。尽管数十年来进行了许多研究来确定与该疾病有关的 RSS 病因，但仍有几起疫情未阐明可能涉及的多种病因。方法 我们使用新一代测序技术对四个受 RSS 影响的鸡群的病毒宏基因组进行了比较分析。根据宏基因组学获得的测序数据设计了用于检测鸡肠道病毒的引物。进行多重逆转录聚合酶链反应 (PCR) 和 PCR 来检测先前在 RSS 自然病例中描述的多种病因。结果 本研究中确定的最丰富的病毒家族是星状病毒科、小核糖核酸病毒科、细小病毒科、杯状病毒科、呼肠孤病毒科和小核糖核酸病毒科。所有四个样本中均存在鸡星状病毒序列，表明鸡星状病毒和 RSS 之间存在关联，并且鸡星状病毒是导致 RSS 的候选病原体。首次在韩国的鸡中发现Picobirnavirus和新发现的chapparvovirus，显示了肠道病毒和病毒群落的遗传多样性。结论 在感染 RSS 的肉鸡中始终检测到鸡星状病毒，这项研究的结果可能有助于了解鸡的肠道疾病和病毒。