1. Evolutionary Biology
  2. Microbiology and Infectious Disease

A large effective population size for established within-host influenza virus infection

  1. Casper K Lumby
  2. Lei Zhao
  3. Judith Breuer
  4. Christopher J R Illingworth  Is a corresponding author
  1. University of Cambridge, United Kingdom
  2. University College London, United Kingdom
https://doi.org/10.7554/eLife.56915
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  1. Casper K Lumby
  2. Lei Zhao
  3. Judith Breuer
  4. Christopher J R Illingworth
(2020)
A large effective population size for established within-host influenza virus infection
eLife 9:e56915.
https://doi.org/10.7554/eLife.56915
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Abstract

Strains of the influenza virus form coherent global populations, yet exist at the level of single infections in individual hosts. The relationship between these scales is a critical topic for understanding viral evolution. Here we investigate the within-host relationship between selection and the stochastic effects of genetic drift, estimating an effective population size of infection Ne for influenza infection. Examining whole-genome sequence data describing a chronic case of influenza B in a severely immunocompromised child we infer an Ne of 2.5 x 107 (95% confidence range 1.0 x 107 to 9.0 x 107) suggesting that genetic drift is of minimal importance during an established influenza infection. Our result, supported by data from influenza A infection, suggests that positive selection during within-host infection is primarily limited by the typically short period of infection. Atypically long infections may have a disproportionate influence upon global patterns of viral evolution.

Data availability

All sequence data is taken from previous publications, and is available from the Sequence Read Archive. Where this is sensible, raw data underlying figures has been made available in files which accompany this document.

The following previously published data sets were used

Article and author information

Author details

  1. Casper K Lumby

    Department of Genetics, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8329-9228

  2. Lei Zhao

    Department of Genetics, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  3. Judith Breuer

    Division of Infection and Immunity, University College London, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  4. Christopher J R Illingworth

    Department of Genetics, University of Cambridge, Cambridge, United Kingdom
    For correspondence
    cjri2@cam.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0030-2784

Funding

Wellcome (101239/Z/13/Z)

  • Christopher J R Illingworth

Wellcome (101239/Z/13/A)

  • Christopher J R Illingworth

Wellcome (105365/Z/14/Z)

  • Casper K Lumby

Isaac Newton Trust

  • Christopher J R Illingworth

Helsingin Yliopisto

  • Christopher J R Illingworth

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

Reviewing Editor

  1. Armita Nourmohammad, University of Washington, United States

Version history

  1. Received: March 13, 2020
  2. Accepted: July 30, 2020
  3. Accepted Manuscript published: August 10, 2020 (version 1)
  4. Version of Record published: August 17, 2020 (version 2)

Copyright

© 2020, Lumby 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. Casper K Lumby
  2. Lei Zhao
  3. Judith Breuer
  4. Christopher J R Illingworth
(2020)
A large effective population size for established within-host influenza virus infection
eLife 9:e56915.
https://doi.org/10.7554/eLife.56915

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