The characteristic of codon usage pattern and its evolution of hepatitis C virus

Evolutionary characterization of Tembusu virus infection through identification of codon usage patterns

“…The synonymous codon usage among TMUV CDSs was relatively low (ENC=53.287, S.D.=0.149), in agreement with previous results for RNA virus genomes, including West Nile virus (ENC=53.81)(Moratorio et al, 2013), Hepatitis C virus (ENC=52.62)(Hu et al, 2011), Newcastle disease virus(ENC= 56.15)…”

“…To date, analyses of Flavivirus codon usage are fragmentary, and such studies have primarily focused on particular virus species, as previously described (Hu et al, 2011;Moratorio et al, 2013;Zhou et al, 2013). Conversely, the evolutionary characteristics and genetic relationships of codon usage bias in the TMUV genome have not been systematically studied; indeed, only a few genomic sequences of TMUV have been sequenced to date, with many studies only recently performed.…”

“…For viruses, little information exists regarding the extent and origin of synonymous codon variation. Recent efforts to elucidate codon usage biases in Flaviviridae have concentrated mainly on Dengue virus (DGV) (Zhou et al, 2013), West Nile virus (WNV) (Moratorio et al, 2013), and Hepatitis C virus (HCV) (Hu et al, 2011). In contrast, investigations of TMUV have primarily focused on viral isolation and identification Tang et al, 2013a), the establishment and application of diagnostic methods (Li et al, 2012b;Yun et al, 2012), and genetic analyses of complete genome sequences Wan et al, 2012;Zhu et al, 2012), whereas information regarding codon usage patterns is not available.…”

Analysis of synonymous codon usage patterns in duck hepatitis A virus: a comparison on the roles of mutual pressure and natural selection

“…The genome size of hepatitis virus has around 7500 nucleotides. Synonymous codon usage bias patterns of hepatitis viruses have been extensively quantified in recent studies for all the five subtypes (A, B, C, D, and E) [1,3,7,10,23]. However, the analysis on HAV was incomplete [23], because in that previous study, only 21 genomes were analyzed.…”

Comprehensive Analysis of Codon Usage on Rabies Virus and Other Lyssaviruses

“…Previous studies have already reported low codon usage bias for RABV genes including, N [32] and G [33]. In addition, low codon usage bias has been identified in other RNA viruses, such as H5N1 influenza virus (50.91) [34], H3N8 Equine influenza virus (52.09) [35], Ebola virus (57.23) [36] and hepatitis C virus (HCV) (52.62) [37]. Low codon usage bias can help overcome host defense mechanisms and reduce the barriers for virus replication [38,39,40].…”