Public Health England, National Infection Service, Porton Down, UK.
National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.
Science. 2019 Jan 4;363(6422):74-77. doi: 10.1126/science.aau9343.
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.
2018 年尼日利亚拉沙热疫情爆发，为历史最大规模，这引起了人们对病毒传播率上升的担忧。为了了解此次疫情的分子流行病学特征，我们首次在疫情爆发的中心，直接对患者样本进行了宏基因组纳米孔测序，这种方法是由目标病原体高度多变的基因组决定的。基因组数据和系统发育重建结果被立即传达给尼日利亚当局和世界卫生组织，为公共卫生应对措施提供了信息。对 36 个基因组进行实时分析，并对该国测序的 120 个样本进行后续确认，结果显示存在广泛的多样性和与往年病毒株的系统发育混合，表明存在独立的人畜共患病传播事件，从而消除了新出现的病毒株或广泛的人际传播的担忧。
