ArticleVirus evolution2019
A non-parametric analytic framework for within-host viral phylogenies and a test for HIV-1 founder multiplicity.
Article in Virus evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Influence of the broadly neutralizing antibody VRC01 on HIV breakthrough virus populations in antibody-mediated prevention trials.Nature communications · 2026Trial
- Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand.PLoS pathogens · 2020Trial
- Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies.PLoS pathogens · 2023Article
- Article
- Optimal sequence-based design for multi-antigen HIV-1 vaccines using minimally distant antigens.PLoS computational biology · 2022Article
- Evolution during primary HIV infection does not require adaptive immune selection.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Factors influencing estimates of HIV-1 infection timing using BEAST.PLoS computational biology · 2021Article
- RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection.Virus evolution · 2021Article
- A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
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2 authors.
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Abstract
Phylogenetics is a powerful tool for understanding the diversification dynamics of viral pathogens. Here we present an extension of the spectral density profile of the modified graph Laplacian, which facilitates the characterization of within-host molecular evolution of viruses and the direct comparison of diversification dynamics between hosts. This approach is non-parametric and therefore fast and model-free. We used simulations of within-host evolutionary scenarios to evaluate the efficiency of our approach and to demonstrate the significance of interpreting a viral phylogeny by its spectral density profile in terms of diversification dynamics. The key features that are captured by the profile are positive selection on the viral gene (or genome), temporal changes in substitution rates, mutational fitness, and time between sampling. Using sequences from individuals infected with HIV-1, we showed the utility of this approach for characterizing within-host diversification dynamics, for comparing dynamics between hosts, and for charting disease progression in infected individuals sampled over multiple years. We furthermore propose a heuristic test for assessing founder heterogeneity, which allows us to classify infections with single and multiple HIV-1 founder viruses. This non-parametric approach can be a valuable complement to existing parametric approaches.
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