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Identifying selection in the within-host evolution of influenza using viral sequence data.
Christopher J R Illingworth1, Andrej Fischer2, Ville Mustonen2
1Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
Plos Computational Biology
|August 1, 2014
Summary
Researchers developed a new method to study influenza virus evolution within a host. This analysis of pig infections revealed signatures of selection shaping the virus during infection.
Area of Science:
- Virology
- Evolutionary Biology
- Genomics
Background:
- Within-host evolution of influenza viruses is critical for epidemiology.
- Understanding the role of selection in viral population dynamics during infection is key.
Purpose of the Study:
- To develop and apply a method for measuring selection on influenza virus within a host using time-resolved genome sequence data.
- To investigate the evolutionary forces shaping the influenza virus during infection in pigs.
Main Methods:
- Developed a novel method to analyze time-resolved genome sequence data from influenza infections.
- Applied the method to sequence data from the HA1 gene of influenza virus in a pig transmission study.
- Accounted for linkage disequilibrium in the analysis, crucial for non-recombining viruses like influenza.
Main Results:
- Detected signatures of non-neutral evolution in 6 out of 16 pig infections.
- Observed both positive and negative selection acting on specific viral alleles.
- Identified time-dependent selection in three infections and a potential immune response driving selection in one case.
Conclusions:
- The developed method provides new insights into influenza virus population dynamics within a host.
- Selection plays a significant role in shaping influenza virus evolution during infection.
- The findings highlight the importance of considering evolutionary forces in understanding influenza epidemiology.
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