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wavess: An R package for simulation of adaptive within-host virus sequence evolution.

Narmada Sambaturu1,2, Zena Lapp1, Fernando D K Tria1

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Summary
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This study introduces wavess, a new R package for simulating virus evolution within hosts. It models recombination and selection, validating against HIV-1 data and showing realistic immune response heterogeneity.

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Area of Science:

  • Virology
  • Computational Biology
  • Evolutionary Biology

Background:

  • Understanding within-host virus evolution is crucial for studying viral diversification and adaptation.
  • Factors like recombination and host immune responses significantly shape virus evolution.

Purpose of the Study:

  • To introduce wavess, a novel software and R package for simulating within-host virus evolution.
  • To provide a user-friendly tool for modeling recombination, immune responses, and selection pressures.
  • To validate the model's performance against empirical viral sequence data.

Main Methods:

  • Developed wavess as a discrete-time, individual-based model.
  • Implemented simulation of recombination, latent infected cells, and multiple selection types (conserved sites, replicative, immune).
  • Created an R package with functions for input generation and output analysis.

Main Results:

  • Applied wavess to simulate HIV-1 env sequence evolution in 11 individuals.
  • Demonstrated that immune cost varied across individuals, reflecting heterogeneous immune responses.
  • Showed that phylogenies from simulated sequences closely matched those from real sequences.

Conclusions:

  • wavess is a rigorously validated tool for simulating within-host virus evolution.
  • The R package offers a comprehensive solution for modeling complex evolutionary dynamics.
  • The model accurately captures key evolutionary processes, including immune-driven adaptation.