TY - JOUR T1 - Estimating the heritability of viral traits using phylogenetic trees JF - bioRxiv DO - 10.1101/046797 SP - 046797 AU - Gabriel E. Leventhal AU - Sebastian Bonhoeffer Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/04/03/046797.abstract N2 - In HIV patients, the set-point viral load (SPVL) is the most widely used predictor of disease severity. Yet SPVL varies over several orders of magnitude between patients. The heritability of SPVL quantifies how much of the variation in SPVL is due to transmissible viral genetics. There is currently no clear consensus on the value of SPVL heritability, as multiple studies have reported apparently discrepant estimates. Here we illustrate that the discrepancies in estimates are most likely due to differences in the estimation methods, rather than the study populations. Importantly, phylogenetic estimates run the risk of being strongly confounded by unrealistic model assumptions. Care must be taken when interpreting and comparing the different estimates to each other.Asymptomatic phaseHIV infections are generally split into three characteristic stages: (I) Primary infection; (II) Asymptomatic phase; (III) AIDS phase.Viral loadThe density of virus in the blood of a patient. It is a proxy for the amount of virus in the rest of the body.Set-point viral loadThe viral load during phase II fluctuates around a remarkably stable level, the set-point viral load.Genetic varianceAmount of variance in the trait (e.g. SPVL) that is due to differences in transmissible viral genetics.Environmental varianceAmount of variance in the trait (e.g. SPVL) that is due to anything other then viral genetics.Viral heritabilityThe fraction of phenotypic variance that is explained by transmissible genetic factors.Donor-recipient regressionMethod to estimate heritability by regressing the trait values in the recipients on the traits values of the donors.SeronegativeNegative for HIV infection.Serodiscordant couplesSexual partnerships where only a single individual is infected.PedigreeAncestral tree linking parents to their offspring.Genetic bottlneckSudden decrease in population size where only a few genetic variants are selected. This leads to a drastic decrease in genetic variation in the population.Genetic driftChange in the genotype distribution over time due to the finite size of a population. ER -