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bioRxiv · 10.1101/2020.04.17.046250

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

Lumby, C. K.·Zhao, L.·Breuer, J.·Illingworth, C. J. R.
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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 the importance of genetic drift to be minimal. Our result, supported by the analysis of 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.

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Lumby, C. K., Zhao, L., Breuer, J., Illingworth, C. J. R.. 2020-04-18. A large effective population size for within-host influenza virus infection. https://doi.org/10.1101/2020.04.17.046250

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