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

[tetano]

Elife


. 2020 Aug 10;9:e56915.
doi: 10.7554/eLife.56915. Online ahead of print.
A large effective population size for established within-host influenza virus infection


Casper K Lumby ¹ , Lei Zhao ¹ , Judith Breuer ² , Christopher J R Illingworth ¹



Affiliations

• PMID: 32773034
• DOI: 10.7554/eLife.56915

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 N_e for influenza infection. Examining whole-genome sequence data describing a chronic case of influenza B in a severely immunocompromised child we infer an N_e 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.

Keywords: evolutionary biology; infectious disease; microbiology; viruses.