Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak
Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak
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DOI：
10.1126/science.aau9343
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发表时间：
2019-01-04
期刊：
影响因子：
56.9
通讯作者：
Duraffour, S.
中科院分区：
文献类型：
--
作者：
Kafetzopoulou, L. E.;Pullan, S. T.;Duraffour, S.
2018年尼日利亚拉沙热季节出现了有史以来最大的病例激增，引发了人们对出现传播率上升的菌株的担忧。为了了解这一高峰的分子流行病学，我们首次在正在展开的疫情中心直接从患者样本中进行宏基因组纳米孔测序，这是一种由目标病原体高度可变的基因组决定的方法。基因组数据和系统发育重建已立即通报尼日利亚当局和世界卫生组织，以便为公共卫生应对提供信息。对36个基因组的实时分析以及随后对原产国全部120个测序样本的确认显示，与前几年的菌株存在广泛的多样性和系统发育混杂，表明存在独立的人畜共患传播事件，从而减轻了对突发菌株或广泛人际传播的担忧。
The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.