title: The evolutionary rate dynamically tracks changes in HIV-1 epidemics: application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data.
abstract: Large-sequence datasets provide an opportunity to investigate the dynamics of pathogen epidemics. Thus, a fast method to estimate the evolutionary rate from large and numerous phylogenetic trees becomes necessary. Based on minimizing tip height variances, we optimize the root in a given phylogenetic tree to estimate the most homogenous evolutionary rate between samples from at least two different time points. Simulations showed that the method had no bias in the estimation of evolutionary rates and that it was robust to tree rooting and topological errors. We show that the evolutionary rates of HIV-1 subtype B and C epidemics have changed over time, with the rate of evolution inversely correlated to the rate of virus spread. For subtype B, the evolutionary rate slowed down and tracked the start of the HAART era in 1996. Subtype C in Ethiopia showed an increase in the evolutionary rate when the prevalence increase markedly slowed down in 1995. Thus, we show that the evolutionary rate of HIV-1 on the population level dynamically tracks epidemic events.
authors.affiliation: Theoretical Biology & Biophysics, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors.forename: Irina
authors.initials: I
authors.lastname: Maljkovic Berry
authors.forename: Gayathri
authors.initials: G
authors.lastname: Athreya
authors.forename: Moulik
authors.initials: M
authors.lastname: Kothari
authors.forename: Marcus
authors.initials: M
authors.lastname: Daniels
authors.forename: William J
authors.initials: WJ
authors.lastname: Bruno
authors.forename: Bette
authors.initials: B
authors.lastname: Korber
authors.forename: Carla
authors.initials: C
authors.lastname: Kuiken
authors.forename: Ruy M
authors.initials: RM
authors.lastname: Ribeiro
authors.forename: Thomas
authors.initials: T
authors.lastname: Leitner
mesh_terms: D023241:Antiretroviral Therapy, Highly Active; D003198:Computer Simulation; D005002:Ethiopia / Q000453:epidemiology; D005060:Europe / Q000453:epidemiology; D019143:Evolution, Molecular; D015658:HIV Infections / Q000188:drug therapy / Q000453:epidemiology* / Q000235:genetics*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D008137:Longitudinal Studies; D009010:Monte Carlo Method; D010802:Phylogeny; D014481:United States / Q000453:epidemiology