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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 may apply more generally to HIV evolution, since we also observed an overall low synonymous substitution rate for HIV-2, which is known to be less pathogenic than HIV-1 and capable of tempering the detrimental effects of immune activation. Humoral immune responses, on the other hand, are the major determinant of nonsynonymous rate changes through time in the envelope gene, and our relaxed-clock estimates support a decrease in selective pressure as a consequence of immune system collapse.

Original publication

DOI

10.1371/journal.pcbi.0030029

Type

Journal article

Journal

PLoS computational biology

Publication Date

02/2007

Volume

3

Addresses

Department of Zoology, University of Oxford, Oxford, United Kingdom. philippe.lemey@zoo.ox.ac.uk

Keywords

Humans, HIV Infections, Disease Progression, Genetic Predisposition to Disease, Viral Envelope Proteins, Codon, Amino Acid Substitution, DNA Mutational Analysis, Evolution, Molecular, Virus Replication, Virus Activation, Amino Acid Sequence, Models, Genetic, Computer Simulation, Molecular Sequence Data, Genetic Variation