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Research Article

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics

  • Philippe Lemey mail,

    To whom correspondence should be addressed. E-mail: philippe.lemey@zoo.ox.ac.uk

    Affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom

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  • Sergei L Kosakovsky Pond,

    Affiliation: Department of Pathology, University of California San Diego, La Jolla, United States of America

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  • Alexei J Drummond,

    Affiliation: Department of Computer Science, University of Auckland, Auckland, New Zealand

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  • Oliver G Pybus,

    Affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom

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  • Beth Shapiro,

    Affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom

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  • Helena Barroso,

    Affiliations: Centro de Patogénese Molecular, Faculdade de Farmácia de Lisboa, Lisbon, Portugal, Instituto Superior de Ciências da Saúde Egas Moniz, Lisbon, Portugal

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  • Nuno Taveira,

    Affiliations: Centro de Patogénese Molecular, Faculdade de Farmácia de Lisboa, Lisbon, Portugal, Instituto Superior de Ciências da Saúde Egas Moniz, Lisbon, Portugal

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  • Andrew Rambaut

    Affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom

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  • Published: February 16, 2007
  • DOI: 10.1371/journal.pcbi.0030029

About the Authors

Philippe Lemey, Oliver G Pybus, Beth Shapiro
Department of Zoology, University of Oxford, Oxford, United Kingdom
Sergei L Kosakovsky Pond
Department of Pathology, University of California San Diego, La Jolla, United States of America
Alexei J Drummond
Department of Computer Science, University of Auckland, Auckland, New Zealand
Helena Barroso, Nuno Taveira
Centro de Patogénese Molecular, Faculdade de Farmácia de Lisboa, Lisbon, Portugal
Helena Barroso, Nuno Taveira
Instituto Superior de Ciências da Saúde Egas Moniz, Lisbon, Portugal
Andrew Rambaut
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom

Corresponding Author

Email: philippe.lemey@zoo.ox.ac.uk

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

PL, OGP, and AR designed the analysis strategy. PL analysed the data and wrote the paper. SLKP assisted in HYPHY analyses. AJD and AR provided programming assistance. BS, AJD, and AR assisted in BEAST analyses. NT and HB contributed unpublished HIV-2 transmission chain data.