Stochastic processes constrain the within and between host evolution of influenza virus
- University of Michigan, United States
- Cited 29
- Views 2,867
- Annotations
Abstract
The evolutionary dynamics of influenza virus ultimately derive from processes that take place within and between infected individuals. Here we define influenza virus dynamics in human hosts through sequencing of 249 specimens from 200 individuals collected over 6290 person-seasons of observation. Because these viruses were collected from individuals in a prospective community-based cohort, they are broadly representative of natural infections with seasonal viruses. Consistent with a neutral model of evolution, sequence data from 49 serially sampled individuals illustrated the dynamic turnover of synonymous and nonsynonymous single nucleotide variants and provided little evidence for positive selection of antigenic variants. We also identified 43 genetically-validated transmission pairs in this cohort. Maximum likelihood optimization of multiple transmission models estimated an effective transmission bottleneck of 1-2 genomes. Our data suggest that positive selection is inefficient at the level of the individual host and that stochastic processes dominate the host-level evolution of influenza viruses.
Article and author information
Author details
Funding
Doris Duke Charitable Foundation (CSDA 2013105)
- Adam S Lauring
National Institute of Allergy and Infectious Diseases (R01 AI118886)
- Adam S Lauring
National Institute of General Medical Sciences (T32 GM007544)
- John T McCrone
Centers for Disease Control and Prevention (U01 IP00474)
- Arnold S Monto
National Institute of Allergy and Infectious Diseases (K08 AI119182)
- Robert J Woods
National Institute of Allergy and Infectious Diseases (R01 AI097150)
- Arnold S Monto
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Human subjects: This study was approved by the Institutional Review Board of the University of Michigan Medical School. Adults provided written informed consent for participation for themselves and their children; children 7-17 years provided oral assent.
Reviewing Editor
- Richard A Neher, University of Basel, Switzerland
Publication history
- Received: February 15, 2018
- Accepted: April 18, 2018
- Accepted Manuscript published: April 23, 2018 (version 1)
- Version of Record published: May 3, 2018 (version 2)
- Version of Record updated: June 29, 2018 (version 3)
Copyright
© 2018, McCrone 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.
Metrics
-
- 2,867
- Page views
-
- 418
- Downloads
-
- 29
- Citations
Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.
Download links
Downloads (link to download the article as PDF)
Download citations (links to download the citations from this article in formats compatible with various reference manager tools)
Open citations (links to open the citations from this article in various online reference manager services)
Further reading
-
- Evolutionary Biology
- Genetics and Genomics
-
- Computational and Systems Biology
- Evolutionary Biology
