1. Microbiology and Infectious Disease

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
https://doi.org/10.7554/eLife.32942
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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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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.

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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.

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

Share this article

https://doi.org/10.7554/eLife.32942

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Further reading

    1. Microbiology and Infectious Disease

    Extreme heterogeneity of influenza virus infection in single cells

    Alistair B Russell, Cole Trapnell, Jesse D Bloom
    Research Article Updated

    Viral infection can dramatically alter a cell’s transcriptome. However, these changes have mostly been studied by bulk measurements on many cells. Here we use single-cell mRNA sequencing to examine the transcriptional consequences of influenza virus infection. We find extremely wide cell-to-cell variation in the productivity of viral transcription – viral transcripts comprise less than a percent of total mRNA in many infected cells, but a few cells derive over half their mRNA from virus. Some infected cells fail to express at least one viral gene, but this gene absence only partially explains variation in viral transcriptional load. Despite variation in viral load, the relative abundances of viral mRNAs are fairly consistent across infected cells. Activation of innate immune pathways is rare, but some cellular genes co-vary in abundance with the amount of viral mRNA. Overall, our results highlight the complexity of viral infection at the level of single cells.