Bayesian Coalescent Analysis Reveals a High Rate of Molecular Evolution in GB Virus C

• Published in: Journal of molecular evolution Vol. 66; no. 3; pp. 292 - 297
• Main Authors: Romano, Camila M, Zanotto, Paolo M. de A, Holmes, Edward C
• Format: Journal Article
• Language: English
• Published: New York New York : Springer-Verlag 01.03.2008; Springer-Verlag; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Bayes Theorem; Bayesian analysis; Biomedical and Life Sciences; Cell Biology; Evolution, Molecular; Evolutionary Biology; Flaviviridae; GB virus; GB virus C - genetics; Hepatitis; Life Sciences; Microbiology; Molecular biology; Mutation; Plant Genetics and Genomics; Plant Sciences; Primates; Viruses; GB virus C; Substitution rate; Phylogeny; Coalescent theory; Codivergence; Molecular clock
• ISSN: 0022-2844; 1432-1432
• DOI: 10.1007/s00239-008-9087-3

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.