Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution. Methods in Ecology and Evolution
Vrancken et al. developed a novel Bayesian inference method to estimate the evolutionary history and phylogenetic signal for setpoint viral load (spVL) and declining slope of CD4+ T-cell (dsCD4) from molecular sequence data from the SHCS to study virulence heritability in HIV. As a control trait they included the estimated probability that a treatment-naïve virus is resistant to zidovudine (prAZT) from the pol sequence. They found a relatively high phylogenetic signal for spVL in the men who have sex with men subset and a low phylogenetic signal for prAZT. For dsCD4 the phylogenetic signals were generally lower.
In conclusion, comparative phylogenetic approaches can be used for understanding HIV dynamics.