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Monitoring Influenza Virus Survival Outside the Host Using Real-Time Cell Analysis
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Evolutionary Rate Variation at Predicted PTM Sites Reveals Localized Host-Associated Patterns in Influenza A Virus.

Ashley I Teufel1, Md Imran Hasan2, Davida S Smyth1

  • 1Department of Natural Sciences, Texas A&M University-San Antonio, Texas, One University Way, San Antonio, Texas 78224, USA.

Genome Biology and Evolution
|June 4, 2026
PubMed
Summary

This study reveals how post-translational modification sites on influenza A virus (IAV) proteins evolve. It identifies specific sites with altered evolutionary rates, offering insights into viral adaptation and host interactions.

Keywords:
PTM site predictionevolutionary rate analysishost adaptationinfluenza A virusposttranslational modificationsviral evolution

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Area of Science:

  • Virology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Influenza A viruses (IAVs) pose a significant global health risk due to their adaptability.
  • Post-translational modifications (PTMs) regulate viral protein function, but their evolutionary dynamics in IAVs are poorly understood.

Purpose of the Study:

  • To computationally predict potential PTM sites across IAV proteins.
  • To analyze the evolutionary dynamics and rate variation at these predicted PTM sites across different IAV strains (H1N1, H5N1, H7N9).

Main Methods:

  • Utilized MusiteDeep for computational prediction of PTM sites in IAV proteins.
  • Modeled PTM states as discrete evolutionary traits.
  • Applied Bayesian phylogenetic methods to examine evolutionary rate variation at PTM sites.

Main Results:

  • Identified 34 positions at predicted PTM sites with significantly altered evolutionary rates (11 elevated, 23 reduced).
  • Fast-evolving sites were concentrated in polymerase proteins and surface glycoproteins.
  • Slowly evolving sites were prevalent in PB1 polymerase and NS1 proteins, with some showing host-associated rate differences.

Conclusions:

  • Evolutionary pressures on IAV PTM sites vary, impacting viral adaptation.
  • Specific PTM sites exhibit distinct evolutionary patterns, potentially influencing host specificity and viral fitness.
  • Findings suggest host-specific selective pressures on PTM sites across different IAV lineages.