Hepatitis C virus evolutionary patterns studied through analysis of full-genome sequences.
The evolutionary patterns of hepatitis C virus (HCV), including the best-fitting nucleotide substitution model and the molecular clock hypothesis, were investigated by analyzing full-genome sequences available in the HCV database. The likelihood ratio test allowed us to discriminate among different evolutionary hypotheses. The phylogeny of the six major HCV types was accurately inferred, and the final tree was rooted by reconstructing the hypothetical HCV common ancestor with the maximum likelihood method. The presence of phylogenetic noise and the relative nucleotide substitution rates in the different HCV genes were also examined. These results offer a general guideline for the future of HCV phylogenetic analysis and also provide important insights on HCV origin and evolution.
Salemi
Marco
M
Rega Institute for Medical Research, KULeuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium. marco.salemi@uz.kuleuven.ac.be
Vandamme
Anne-Mieke
AM
D005075:Biological Evolution; D019143:Evolution, Molecular; D016679:Genome, Viral; D006526:Hepatitis C / Q000145:classification / Q000235:genetics*; D016013:Likelihood Functions; D010802:Phylogeny; D017423:Sequence Analysis, RNA