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

Philippe Lemey, Sergei L. Kosakovsky Pond, Alexei J. Drummond, Oliver G. Pybus, Beth Shapiro, Helena Barroso, Nuno Taveira, Andrew Rambaut

Research output: Contribution to journalArticlepeer-review

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 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 languageEnglish
Article numbere29
Pages (from-to)282-292
Number of pages11
JournalPLoS Computational Biology
Volume3
Issue number2
DOIs
Publication statusPublished - Feb 2007

Keywords

  • HUMAN-IMMUNODEFICIENCY-VIRUS
  • AMINO-ACID SITES
  • DETECTING POSITIVE SELECTION
  • TYPE-1 INFECTION
  • NEUTRALIZING ANTIBODIES
  • MOLECULAR EVOLUTION
  • IMMUNE ACTIVATION
  • LIKELIHOOD METHOD
  • CORECEPTOR USAGE
  • C2V3 SEQUENCES

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