How effectively can HIV phylogenies be used to measure heritability?
Shirreff G., Alizon S., Cori A., Günthard HF., Laeyendecker O., van Sighem A., Bezemer D., Fraser C.
BACKGROUND AND OBJECTIVES: The severity of HIV-1 infection, measured by set-point viral load (SPVL), is highly variable between individuals. Its heritability between infections quantifies the control the pathogen genotype has over disease severity. Heritability estimates vary widely between studies, but differences in methods make comparison difficult. Phylogenetic comparative analysis offers measures of phylogenetic signal, but it is unclear how to interpret them in terms of the fraction of variance in SPVL controlled by the virus genotype. METHODOLOGY: We present computational methods which link statistics summarizing phylogenetic signal to heritability, h(2) in order to test for and quantify it. We re-analyse data from Switzerland and Uganda, and apply it to new data from the Netherlands. We systematically compare established and new (e.g. phylogenetic pairs, PP) phylogenetic signal statistics. RESULTS: Heritability estimates varied by method and dataset. Several methods were consistently able to detect simulated heritability above , but none below. Pagel’s λ was the most robust and sensitive. The PP method found no heritability in the Netherlands data, whereas Pagel’s λ found significant heritability only in a narrow subdivision (P = 0.038). Heritability was estimated at h(2) = 0.52 (95% confidence interval 0.00-0.63). CONCLUSIONS AND IMPLICATIONS: This standardized measure, h(2), allows comparability of heritability between cohorts. We confirm high heritability in Swiss data, but neither in Ugandan data nor in the Netherlands, where it is barely significant or undetectable. Existing phylogenetic methods are ill-suited for detecting heritability below , which may nonetheless be biologically important.