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Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses.
- Source :
-
Scientific reports [Sci Rep] 2018 Jan 10; Vol. 8 (1), pp. 373. Date of Electronic Publication: 2018 Jan 10. - Publication Year :
- 2018
-
Abstract
- Monitoring changes in influenza A virus genomes is crucial to understand its rapid evolution and adaptation to changing conditions e.g. establishment within novel host species. Selective sweeps represent a rapid mode of adaptation and are typically observed in human influenza A viruses. We describe Sweep Dynamics (SD) plots, a computational method combining phylogenetic algorithms with statistical techniques to characterize the molecular adaptation of rapidly evolving viruses from longitudinal sequence data. SD plots facilitate the identification of selective sweeps, the time periods in which these occurred and associated changes providing a selective advantage to the virus. We studied the past genome-wide adaptation of the 2009 pandemic H1N1 influenza A (pH1N1) and seasonal H3N2 influenza A (sH3N2) viruses. The pH1N1 influenza virus showed simultaneous amino acid changes in various proteins, particularly in seasons of high pH1N1 activity. Partially, these changes resulted in functional alterations facilitating sustained human-to-human transmission. In the evolution of sH3N2 influenza viruses, we detected changes characterizing vaccine strains, which were occasionally revealed in selective sweeps one season prior to the WHO recommendation. Taken together, SD plots allow monitoring and characterizing the adaptive evolution of influenza A viruses by identifying selective sweeps and their associated signatures.
- Subjects :
- Algorithms
Evolution, Molecular
Hemagglutinins, Viral chemistry
Hemagglutinins, Viral immunology
Humans
Influenza A Virus, H1N1 Subtype immunology
Influenza A Virus, H3N2 Subtype immunology
Influenza Vaccines genetics
Influenza Vaccines immunology
Influenza, Human immunology
Influenza, Human virology
Models, Molecular
Phylogeny
Protein Conformation
Sequence Analysis, RNA methods
Computational Biology methods
Hemagglutinins, Viral genetics
Influenza A Virus, H1N1 Subtype genetics
Influenza A Virus, H3N2 Subtype genetics
Subjects
Details
- Language :
- English
- ISSN :
- 2045-2322
- Volume :
- 8
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Scientific reports
- Publication Type :
- Academic Journal
- Accession number :
- 29321538
- Full Text :
- https://doi.org/10.1038/s41598-017-18791-z