Genomic Surveillance Elucidates HCV 1a Phylodynamics and Molecular Evolution

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• 作者：Kaifa Wei ; Yang Li ; Huiqin Chen ; Qiankun Zhang
• 刊名：Evolutionary Biology
• 出版年：2016
• 出版时间：September 2016
• 年：2016
• 卷：43
• 期：3
• 页码：380-391
• 全文大小：1,814 KB
• 刊物主题：Evolutionary Biology; Ecology; Developmental Biology; Human Genetics; Animal Genetics and Genomics;
• 出版者：Springer US
• ISSN：1934-2845
• 卷排序：43

文摘

The hepatitis C virus (HCV) infects at least 3 % of people worldwide, and continues to cause substantial morbidity and mortality. To better understand the phylodynamics and molecular evolution of the HCV 1a, a phylogenetic analysis of 186 full-length genomic sequences isolated from five countries between 1977 and 2009 was conducted in this study. Nucleotide substitution rates and molecular epidemiology were assessed by Bayesian coalescent analysis using time-stamped entire coding sequences. We showed that the substitution rates of ten genomic regions are diverse and higher than those of previously estimated. The coalescent analysis indicated that the transmission of subtype 1a probably started in the second half of the twentieth century and an explosion of epidemics occurred between 1960s and 1980s. Selection analysis suggested that the HCV 1a evolves under purifying selection. However, a total of 58 positively selected sites were detected and further analysis suggested that these sites may play an important role in adaptive evolution of HCV 1a strains. In addition, the codon usage and the factors accounting for shaping the codon usage pattern of HCV 1a were investigated to evaluate the dynamics of the virus evolution. Surveys of codon usage variation showed that mutational pressure and selection pressure account for HCV 1a codon usage pattern.KeywordsHCV 1aMolecular evolutionary rateEpidemicsNegative selectionCodon usage bias