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Comparison of third-generation sequencing approaches to identify viral pathogens under public health emergency conditions

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Abstract

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.

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Data availability

The consensus sequences of Norovirus GII recovered by sequencing platforms are publicly available through the Supplementary material.

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Acknowledgements

We acknowledge Hebei General Hospital, Shijiazhuang, Hebei, China for providing fecal clinical samples.

Funding

This work was supported by grants from the China Mega-Projects for Infectious Disease (2018ZX10711001, 2017ZX10104001 and 2018ZX10713-002). The funder had no role in the design, execution, or analysis of the study, nor in the preparation or approval of manuscripts related to the study.

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Author notes

  1. Yang Li, Xiao-zhou He, and Ming-hui Li have contributed equally to the article.

Authors and Affiliations

  1. NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China

    Yang Li, Xiao-zhou He, Meng-jie Yang, Yi Zhang & Xue-jun Ma

  2. Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, 100011, China

    Ming-hui Li & Yao Xie

  3. State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100093, China

    Bo Li

  4. Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China

    Xue-jun Ma

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  1. Yang Li
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Contributions

Conceived or designed study: YL, XY, YZ, and XM. Performed research: YL, XH, ML, and YZ. Analyzed data: YL, XH, BL, and MY. Contributed new methods or models: YL, YZ, and XM. Wrote the paper: YL.

Corresponding authors

Correspondence to Yao Xie, Yi Zhang or Xue-jun Ma.

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All aspects of the study were performed in accordance with national ethics regulations and approved by the Institutional Review Boards of National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention.

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Edited by Detlev H. Kruger.

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Li, Y., He, Xz., Li, Mh. et al. Comparison of third-generation sequencing approaches to identify viral pathogens under public health emergency conditions. Virus Genes 56, 288–297 (2020). https://doi.org/10.1007/s11262-020-01746-4

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