Bayesian Coalescent Analysis Reveals a High Rate of Molecular Evolution in GB Virus C |
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Authors: | Camila M Romano Paolo M de A Zanotto Edward C Holmes |
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Institution: | 1. Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute–ICBII, University of S?o Paulo, S?o Paulo, Brazil 2. Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA, 16802, USA 3. Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
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Abstract: | GB virus C/hepatitis G (GBV-C) is an RNA virus of the family Flaviviridae. Despite replicating with an RNA-dependent RNA polymerase, some previous estimates of rates of evolutionary change in GBV-C
suggest that it fixes mutations at the anomalously low rate of ∼10−7 nucleotide substitution per site, per year. However, these estimates were largely based on the assumption that GBV-C and
its close relative GBV-A (New World monkey GB viruses) codiverged with their primate hosts over millions of years. Herein,
we estimated the substitution rate of GBV-C using the largest set of dated GBV-C isolates compiled to date and a Bayesian
coalescent approach that utilizes the year of sampling and so is independent of the assumption of codivergence. This revealed
a rate of evolutionary change approximately four orders of magnitude higher than that estimated previously, in the range of
10−2 to 10−3 sub/site/year, and hence in line with those previously determined for RNA viruses in general and the Flaviviridae in particular. In addition, we tested the assumption of host-virus codivergence in GBV-A by performing a reconciliation analysis
of host and virus phylogenies. Strikingly, we found no statistical evidence for host-virus codivergence in GBV-A, indicating
that substitution rates in the GB viruses should not be estimated from host divergence times. |
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Keywords: | GB virus C Molecular clock Substitution rate Codivergence Phylogeny Coalescent theory |
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