Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

ABSTRACT: Upon HIV transmission, some patients develop AIDS in only a few months, while others remain disease free for 20 or more years. This variation in the rate of disease progression is poorly understood and has been attributed to host genetics, host immune responses, co-infection, viral genetics, and adaptation. Here, we develop a new "relaxed-clock" phylogenetic method to estimate absolute rates of synonymous and nonsynonymous substitution through time. We identify an unexpected association between the synonymous substitution rate of HIV and disease progression parameters. Since immune activation is the major determinant of HIV disease progression, we propose that this process can also determine viral generation times, by creating favourable conditions for HIV replication. These conclusions ma

SUBMITTER: Lemey P 

PROVIDER: S-EPMC1797821 | biostudies-literature | 2007 Feb

REPOSITORIES: biostudies-literature