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Elife. 2017 Jun 27;6. pii: e26875. doi: 10.7554/eLife.26875.

Parallel evolution of influenza across multiple spatiotemporal scales.

Author information

1
Department of Genome Sciences, University of Washington, Seattle, United States.
2
Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, United States.
3
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States.
4
Seattle Children's Research Institute, Seattle, United States.
5
Department of Pediatrics, University of Washington, Seattle, United States.
6
Department of Medicine, University of Washington, Seattle, United States.
7
Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States.

Abstract

Viral variants that arise in the global influenza population begin as de novo mutations in single infected hosts, but the evolutionary dynamics that transform within-host variation to global genetic diversity are poorly understood. Here, we demonstrate that influenza evolution within infected humans recapitulates many evolutionary dynamics observed at the global scale. We deep-sequence longitudinal samples from four immunocompromised patients with long-term H3N2 influenza infections. We find parallel evolution across three scales: within individual patients, in different patients in our study, and in the global influenza population. In hemagglutinin, a small set of mutations arises independently in multiple patients. These same mutations emerge repeatedly within single patients and compete with one another, providing a vivid clinical example of clonal interference. Many of these recurrent within-host mutations also reach a high global frequency in the decade following the patient infections. Our results demonstrate surprising concordance in evolutionary dynamics across multiple spatiotemporal scales.

KEYWORDS:

antigenic evolution; clonal interference; deep sequencing; epidemiology; evolutionary biology; genomics; hemagglutinin; human; infectious disease; influenza; microbiology; virus

PMID:
28653624
PMCID:
PMC5487208
DOI:
10.7554/eLife.26875
[Indexed for MEDLINE]
Free PMC Article

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