Related Experiment Video
Updated: Jan 17, 2026
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Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
Published on: June 16, 2011
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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
1Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America.
Plos Computational Biology
|September 18, 2025
Summary
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.
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.
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