Single-cell transcriptional dynamics of flavivirus infection

  1. Fabio Zanini  Is a corresponding author
  2. Szu-Yuan Pu
  3. Elena Bekerman
  4. Shirit Einav
  5. Stephen R Quake  Is a corresponding author
  1. Stanford University, United States

Abstract

Dengue and Zika viral infections affect millions of people annually and can be complicated by hemorrhage or neurological manifestations, respectively. However, a thorough understanding of the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach to probe the host transcriptome together with intracellular viral RNA at the single cell level. We applied viscRNA-Seq to monitor dengue and Zika virus infection in cultured cells and discovered extreme heterogeneity in virus abundance. We exploited this variation to identify host factors that show complex dynamics and a high degree of specificity for either virus, including proteins involved in the endoplasmic reticulum translocon, signal peptide processing, and membrane trafficking. We validated the viscRNA-Seq hits and discovered novel proviral and antiviral factors. viscRNA-Seq is a powerful approach to assess the genome-wide virus-host dynamics at single cell level.

Article and author information

Author details

  1. Fabio Zanini

    Department of Bioengineering, Stanford University, Stanford, United States
    For correspondence
    fabio.zanini@stanford.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7097-8539
  2. Szu-Yuan Pu

    Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Elena Bekerman

    Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Shirit Einav

    Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Stephen R Quake

    Department of Bioengineering, Stanford University, Stanford, United States
    For correspondence
    quake@stanford.edu
    Competing interests
    The authors declare that no competing interests exist.

Funding

National Institute of Allergy and Infectious Diseases (1U19 AI10966201)

  • Shirit Einav

Stanford Bio-X

  • Shirit Einav

Stanford Institute for Immunity, Transplantation, and Infection

  • Shirit Einav

European Molecular Biology Organization (ALTF 269-2016)

  • Fabio Zanini

Child Health Research Institute

  • Szu-Yuan Pu

Lucile Packard Foundation for Children's Health

  • Szu-Yuan Pu

Stanford Clinical and Translational Science Award (UL1​ ​ TR000093)

  • Szu-Yuan Pu

National Institute of Allergy and Infectious Diseases (5T32AI007502)

  • Elena Bekerman

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Arup K Chakraborty, Massachusetts Institute of Technology, United States

Publication history

  1. Received: October 19, 2017
  2. Accepted: February 8, 2018
  3. Accepted Manuscript published: February 16, 2018 (version 1)
  4. Version of Record published: February 26, 2018 (version 2)

Copyright

© 2018, Zanini et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Fabio Zanini
  2. Szu-Yuan Pu
  3. Elena Bekerman
  4. Shirit Einav
  5. Stephen R Quake
(2018)
Single-cell transcriptional dynamics of flavivirus infection
eLife 7:e32942.
https://doi.org/10.7554/eLife.32942
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    Severe pneumonia is one of the common acute diseases caused by pathogenic bacteria infection, especially by pathogenic bacteria, leading to sepsis with a high morbidity and mortality rate. However, the existing bacteria cultivation method cannot satisfy current clinical needs requiring rapid identification of bacteria strain for antibiotic selection. Therefore, developing a sensitive liquid biopsy system demonstrates the enormous value of detecting pathogenic bacterium species in pneumonia patients.

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    In this study, we developed a tool named Species-Specific Bacterial Detector (SSBD, pronounce as "speed") for detecting selected bacterium. Newly designed diagnostic tools combining specific DNA-tag screened by our algorithm and CRISPR/Cas12a, which were first tested in the lab to confirm the accuracy, followed by validating its specificity and sensitivity via applying on bronchoalveolar lavage fluid (BALF) from pneumonia patients. In the validation I stage, we compared the SSBD results with traditional cultivation results. In the validation II stage, a randomized and controlled clinical trial was completed at the ICU of Nanjing Drum Tower Hospital to evaluate the benefit SSBD brought to the treatment.

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    Clinical trial:

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