ArticleMolecular biology and evolution2018
A Practical Guide to Estimating the Heritability of Pathogen Traits.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
- Attenuation of HIV severity by slightly deleterious mutations can explain the long-term trajectory of virulence evolution.PLoS computational biology · 2025Article
- Temperature and Pressure Shaped the Evolution of Antifreeze Proteins in Polar and Deep Sea Zoarcoid Fishes.Molecular biology and evolution · 2025Article
- High peak viraemia followed by spontaneous HIV-1 control in women living with HIV-1 subtype A1 in East Africa.Journal of the International AIDS Society · 2025Article
- The genetic architecture of HIV-1 virulence.Virus evolution · 2025Article
- Evidence for circulation of high-virulence HIV-1 subtype B variants in the United Kingdom.Virus evolution · 2025Article
- Reconciling founder variant multiplicity of HIV-1 infection with the rate of CD4Journal of the Royal Society, Interface · 2024Article
- Self-reported neurocognitive complaints in the Swiss HIV Cohort Study: a viral genome-wide association study.Brain communications · 2024Article
- A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits.Molecular biology and evolution · 2022Article
- HIV-1 infections with multiple founders associate with the development of neutralization breadth.PLoS pathogens · 2022Article
- Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements.Journal of the American Statistical Association · 2022Article
- Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load.Virus evolution · 2022Article
- Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART.Nature communications · 2020Article
- Few amino acid signatures distinguish HIV-1 subtype B pandemic and non-pandemic strains.PloS one · 2020Article
- Natural selection favoring more transmissible HIV detected in United States molecular transmission network.Nature communications · 2019Article
- Automatic generation of evolutionary hypotheses using mixed Gaussian phylogenetic models.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- A non-parametric analytic framework for within-host viral phylogenies and a test for HIV-1 founder multiplicity.Virus evolution · 2019Article
- Article
- A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda.eLife · 2016Article
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2 authors.
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Abstract
Pathogen traits, such as the virulence of an infection, can vary significantly between patients. A major challenge is to measure the extent to which genetic differences between infecting strains explain the observed variation of the trait. This is quantified by the trait's broad-sense heritability, H2. A recent discrepancy between estimates of the heritability of HIV-virulence has opened a debate on the estimators' accuracy. Here, we show that the discrepancy originates from model limitations and important lifecycle differences between sexually reproducing organisms and transmittable pathogens. In particular, current quantitative genetics methods, such as donor-recipient regression of surveyed serodiscordant couples and the phylogenetic mixed model (PMM), are prone to underestimate H2, because they neglect or do not fit to the loss of resemblance between transmission partners caused by within-host evolution. In a phylogenetic analysis of 8,483 HIV patients from the United Kingdom, we show that the phenotypic correlation between transmission partners decays with the amount of within-host evolution of the virus. We reproduce this pattern in toy-model simulations and show that a phylogenetic Ornstein-Uhlenbeck model (POUMM) outperforms the PMM in capturing this correlation pattern and in quantifying H2. In particular, we show that POUMM outperforms PMM even in simulations without selection-as it captures the mentioned correlation pattern-which has not been appreciated until now. By cross-validating the POUMM estimates with ANOVA on closest phylogenetic pairs, we obtain H2 ≈ 0.2, meaning ∼20% of the variation in HIV-virulence is explained by the virus genome both for European and African data.
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