The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses timely makes it a powerful tool for public health emergency response. Third-generation sequencing (TGS) offers advantages in speed and length of detection over second-generation sequencing (SGS). Here, we presented the end-to-end workflows for both Oxford Nanopore MinION and Pacbio Sequel on a viral disease emergency event, along with Ion Torrent PGM as a reference. A specific pipeline for comparative analysis on viral genomes recovered by each platform was assembled, given the high errors of base-calling for TGS platforms. All the three platforms successfully identified and recovered at least 85% Norovirus GII genomes. Oxford Nanopore MinION spent the least sample-to-answer turnaround time with relatively low but enough accuracy for taxonomy classification. Pacbio Sequel recovered the most accurate viral genome, while spending the longest time. Overall, Nanopore metagenomics can rapidly characterize viruses, and Pacbio Sequel can accurately recover viruses. This study provides a framework for designing the appropriate experiments that are likely to lead to accurate and rapid virus emergency response.

中文翻译：

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在公共卫生紧急情况下鉴定病毒病原体的第三代测序方法的比较。

高通量测序（HTS）能够及时检测已知和未知病毒，这使其成为公共卫生应急响应的强大工具。与第二代测序（SGS）相比，第三代测序（TGS）在检测速度和检测长度方面具有优势。在这里，我们介绍了牛津纳米孔MinION和Pacbio Sequel在病毒性疾病紧急事件上的端到端工作流程，并提供了Ion Torrent PGM作为参考。考虑到TGS平台碱基检出的错误率很高，因此组装了一个用于对每个平台回收的病毒基因组进行比较分析的特定管道。所有这三个平台均成功鉴定并回收了至少85％的诺如病毒GII基因组。Oxford Nanopore MinION花了最少的样本到答案的周转时间，相对较低，但足够用于分类法分类。Pacbio Sequel恢复了最准确的病毒基因组，同时花费了最长的时间。总体而言，纳米孔宏基因组学可以快速表征病毒，Pacbio Sequel可以准确地恢复病毒。这项研究为设计适当的实验提供了框架，这些实验可能导致准确而快速的病毒紧急响应。