Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses.

2.50
Hdl Handle:
http://hdl.handle.net/10033/621312
Title:
Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses.
Authors:
Klingen, Thorsten R; Reimering, Susanne; Loers, Jens; Mooren, Kyra; Klawonn, Frank; Krey, Thomas; Gabriel, Gülsah; McHardy, Alice Carolyn
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.
Affiliation:
BRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56, 38106 Braunschweig, Germany.
Citation:
Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses. 2018, 8 (1):373 Sci Rep
Journal:
Scientific reports
Issue Date:
10-Jan-2018
URI:
http://hdl.handle.net/10033/621312
DOI:
10.1038/s41598-017-18791-z
PubMed ID:
29321538
Type:
Article
Language:
en
ISSN:
2045-2322
Appears in Collections:
publications of the research group cellular proteom research (CPRO); publications of the research group bioinformatics in infection research ([BRICS] BIFO)

Full metadata record

DC FieldValue Language
dc.contributor.authorKlingen, Thorsten Ren
dc.contributor.authorReimering, Susanneen
dc.contributor.authorLoers, Jensen
dc.contributor.authorMooren, Kyraen
dc.contributor.authorKlawonn, Franken
dc.contributor.authorKrey, Thomasen
dc.contributor.authorGabriel, Gülsahen
dc.contributor.authorMcHardy, Alice Carolynen
dc.date.accessioned2018-03-07T15:17:04Z-
dc.date.available2018-03-07T15:17:04Z-
dc.date.issued2018-01-10-
dc.identifier.citationSweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses. 2018, 8 (1):373 Sci Repen
dc.identifier.issn2045-2322-
dc.identifier.pmid29321538-
dc.identifier.doi10.1038/s41598-017-18791-z-
dc.identifier.urihttp://hdl.handle.net/10033/621312-
dc.description.abstractMonitoring 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.en
dc.language.isoenen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.titleSweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses.en
dc.typeArticleen
dc.contributor.departmentBRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56, 38106 Braunschweig, Germany.en
dc.identifier.journalScientific reportsen

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