通过实时纳米孔测序分析对临床样本中的病毒病原体进行快速宏基因组鉴定。

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis.

作者信息

Greninger Alexander L, Naccache Samia N, Federman Scot, Yu Guixia, Mbala Placide, Bres Vanessa, Stryke Doug, Bouquet Jerome, Somasekar Sneha, Linnen Jeffrey M, Dodd Roger, Mulembakani Prime, Schneider Bradley S, Muyembe-Tamfum Jean-Jacques, Stramer Susan L, Chiu Charles Y

机构信息

Department of Laboratory Medicine, University of California, San Francisco, CA, 94107, USA.

UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, 91407, USA.

出版信息

Genome Med. 2015 Sep 29;7:99. doi: 10.1186/s13073-015-0220-9.

We report unbiased metagenomic detection of chikungunya virus (CHIKV), Ebola virus (EBOV), and hepatitis C virus (HCV) from four human blood samples by MinION nanopore sequencing coupled to a newly developed, web-based pipeline for real-time bioinformatics analysis on a computational server or laptop (MetaPORE). At titers ranging from 10(7)-10(8) copies per milliliter, reads to EBOV from two patients with acute hemorrhagic fever and CHIKV from an asymptomatic blood donor were detected within 4 to 10 min of data acquisition, while lower titer HCV virus (1 × 10(5) copies per milliliter) was detected within 40 min. Analysis of mapped nanopore reads alone, despite an average individual error rate of 24 % (range 8-49 %), permitted identification of the correct viral strain in all four isolates, and 90 % of the genome of CHIKV was recovered with 97-99 % accuracy. Using nanopore sequencing, metagenomic detection of viral pathogens directly from clinical samples was performed within an unprecedented <6 hr sample-to-answer turnaround time, and in a timeframe amenable to actionable clinical and public health diagnostics.

我们报告了通过MinION纳米孔测序与新开发的基于网络的管道相结合，在计算服务器或笔记本电脑上进行实时生物信息学分析（MetaPORE），从四个人类血液样本中对基孔肯雅病毒（CHIKV）、埃博拉病毒（EBOV）和丙型肝炎病毒（HCV）进行无偏宏基因组检测。在每毫升10⁷ - 10⁸拷贝的滴度范围内，在数据采集的4至10分钟内检测到来自两名急性出血热患者的EBOV读数以及来自一名无症状献血者的CHIKV读数，而较低滴度的HCV病毒（每毫升1×10⁵拷贝）在40分钟内被检测到。仅对映射的纳米孔读数进行分析，尽管平均个体错误率为24%（范围为8 - 49%），但仍能在所有四个分离株中鉴定出正确的病毒株，并且以97 - 99%的准确率 recovered了CHIKV基因组的90%。使用纳米孔测序，直接从临床样本中对病毒病原体进行宏基因组检测，在前所未有的<6小时样本到答案周转时间内完成，且在适合进行可操作的临床和公共卫生诊断的时间范围内。（注：“recovered”这里可能是“获得”“重建”等意思，结合语境较难准确翻译，暂保留英文）