The evolutionary rate dynamically tracks changes in HIV-1 epidemics

Maljkovic-berry, Irina; Athreya, Gayathri; Daniels, Marcus; Bruno, William; Korber, Bette; Kuiken, Carla; Ribeiro, Ruy M

doi:10.1016/j.epidem.2009.10.003

Title: The evolutionary rate dynamically tracks changes in HIV-1 epidemics

Journal Article · Thu Jan 01 00:00:00 EST 2009 · Epidemics

DOI:https://doi.org/10.1016/j.epidem.2009.10.003· OSTI ID:970967

Maljkovic-berry, Irina ^[1]; Athreya, Gayathri ^[1]; Daniels, Marcus ^[1]; Bruno, William ^[1]; Korber, Bette ^[1]; Kuiken, Carla ^[1]; Ribeiro, Ruy M ^[1]

Los Alamos National Laboratory

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.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC52-06NA25396

OSTI ID:: 970967

Report Number(s):: LA-UR-09-06062; LA-UR-09-6062; TRN: US201003%%311

Journal Information:: Epidemics, Journal Name: Epidemics

Country of Publication:: United States

Language:: English

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