Fifty patients with unexplained fever and poor outcomes presented at Irrua Specialist Teaching Hospital (ISTH) in Edo State, Nigeria, an area endemic for Lassa fever, between September 2018 - January 2019. After ruling out Lassa fever, plasma samples from these epidemiologically-linked cases were sent to the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria, where we carried out metagenomic sequencing which implicated yellow fever virus (YFV) as the etiology of this outbreak. Twenty-nine of the 50 samples were confirmed positive for YFV by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), 14 of which resulted in genome assembly. Maximum likelihood phylogenetic analysis revealed that these YFV sequences formed a tightly clustered clade more closely related to sequences from Senegal than sequences from earlier Nigerian isolates, suggesting that the YFV clade responsible for this outbreak in Edo State does not descend directly from the Nigerian YFV outbreaks of the last century, but instead reflects a broader diversity and dynamics of YFV in West Africa. Here we demonstrate the power of metagenomic sequencing for identifying ongoing outbreaks and their etiologies and informing real-time public health responses, resulting in accurate and prompt disease management and control.

译文

:2018年9月至2019年1月,在拉萨热的地方病地区尼日利亚伊多州伊鲁亚专科教学医院(ISTH)呈现了50例原因不明的发烧和转归不良的患者。关联的病例被发送到尼日利亚奥德州埃德的救世主大学非洲传染病基因组学卓越中心(ACEGID),我们在其中进行了宏基因组测序,其中涉及黄热病病毒(YFV)作为此次暴发的病因。通过逆转录酶定量聚合酶链反应(RT-qPCR),确认了50份样品中有29份YFV阳性,其中14份导致基因组装配。最大似然系统发育分析表明,这些YFV序列形成了紧密塞密的进化枝,与来自塞内加尔的序列比来自早期尼日利亚分离株的序列更紧密相关,这表明造成此疫情的YFV进化枝并非直接源自尼日利亚YFV爆发。上个世纪,但反而反映了西非YFV的更广泛的多样性和动态。在这里,我们展示了宏基因组测序的功能,可用于识别持续不断的暴发及其病因,并告知实时的公共卫生应对措施,从而实现准确,及时的疾病管理和控制。

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