Author response: A large effective population size for established within-host influenza virus infection [peer_review]

Casper K Lumby, Lei Zhao, Judith Breuer, Christopher JR Illingworth
2020 unpublished
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
more » ... of influenza B in a severely immunocompromised child we infer an N e of 2.5 Â 10 7 (95% confidence range 1.0 Â 10 7 to 9.0 Â 10 7 ) 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. Lumby et al. eLife 2020;9:e56915. DOI: https://doi.org/10.7554/eLife.56915 1 of 17 SHORT REPORT Lumby et al. eLife 2020;9:e56915.
doi:10.7554/elife.56915.sa2 fatcat:d6rawmfx7vcf7a4cthdyavhhzq