纳米孔测序技术在病原体现场快速确认中的应用与挑战

Application and challenge of nanopore sequencing technology in rapid identification of pathogens in the field

国外暴发的埃博拉出血热、寨卡病毒病和拉萨热疫情表明,我们亟需一种快速、有效的病原体现场检测技术来应对新发和烈性传染病。现有的二代测序平台能实现病原体快速鉴别,但对运行环境要求比较苛刻,样本制备过程相对复杂,测序运行时间较长,数据分析也依赖高性能计算设备,限制了其在非实验室环境下的现场检测应用。而作为三代测序技术代表之一的Oxford Nanopore Technologies(ONT)纳米孔测序平台具有实时、长读长、测序通量高、流转时间短、文库制备流程简易等优势,而ONT测序平台MinION更是以便携、低成本的特性而独具病原体现场快速确认的能力。本文主要对纳米孔测序技术在病原体现场快速确认中的应用与挑战进行综述。

The recent overseas outbreaks of Ebola haemorrhagic fever,Zika virus disease and Lassa fever called for a rapid and effective pathogen detection technology in the field to cope with the emerging and fulminant infectious diseases.Next-generation sequencing platforms provide the ability of rapid identification of pathogens without bias.However,current next-generation sequencing platforms demand favorable lab environments and are characterized by a relatively complex sample preparation procedure,a relatively long sequencing time,and high performance computing equipments for downstream analyses,which therefore limits the field application of these platforms under non-laboratory conditions.As a representative of the third-generation sequencing technology,nanopore sequencing released by Oxford Nanopore Technologies(ONT) has such advantages as real time,long read,high throughput,short turnaround time and simple sample preparation procedure.Particularly,the ONT platform MinION,also characterized by portability and low-cost in addition to above advantages,could well handle rapid pathogen detection in the field.This review mainly summarizes the applications and challenges of nanopore sequencing technology in rapid identification of pathogens in the field.