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.
Article and author information
Author details
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
- Armita Nourmohammad, University of Washington, United States
Publication history
- Received: March 13, 2020
- Accepted: July 30, 2020
- Accepted Manuscript published: August 10, 2020 (version 1)
- 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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