Codon volatility of hemagglutinin genes of H5N1 avian influenza viruses from different clades

Abstract

Codon volatility is a method recently developed to estimate selective pressures on proteins on the basis of their synonymous codon usage. Volatility of a codon was defined as the fraction of single nucleotide substitutions that would be nonsynonymous. Higher volatility may indicate that the gene has been under more positive selection in the recent past. We analyzed volatility of hemagglutinin genes of H5N1 viruses in the recent outbreaks and observed differences in the volatility among viruses of different clades. The codon volatility of subclade 2.1 viruses from Indonesia was the lowest among all H5N1 clades and subclades. Time series analyses since the beginning of the epidemic in 2004 showed that codon volatility of subclade 2.1 has gradually decreased, while those of other major clades have been increasing. This may reflect differences in the recent evolution of these viruses.

Analysis of the codon usage pattern in Middle East Respiratory Syndrome Coronavirus

“…The codon usage bias was further confirmed by the mean ENC value of 49.82. For comparison, the mean ENC value for other studied viruses were: Porcine epidemic diarrhea virus (mean ENC=47.91) [ 13 ], SARS (mean ENC = 48.99)[ 39 ], Foot and mouth disease virus (mean ENC = 51.42) [ 40 ], H5N1 influenza A virus (mean ENC = 50.91) [ 41 ], Duck enteritis virus (mean ENC = 52.17) [ 42 ], Classical swine fever virus (mean ENC = 51.7) [ 43 ] and Hepatitis A virus (mean ENC = 39.78)[ 44 ]. An ENC value greater than 45 is considered as a lower codon usage bias.…”

Characterization of the porcine epidemic diarrhea virus codon usage bias

“…The results indicate that codon usage bias exists and that the PEDV preferred codons ending in (U)T. The codon usage bias was further confirmed by the mean ENC value of 47.91. For comparison, the mean ENC value for the following other studied viruses is: (1) foot and mouth disease virus (mean ENC = 51.42) (Zhou et al, 2010), (2) H5N1 influenza A virus (mean ENC = 50.91) (Auewarakul et al, 2009), (3) duck enteritis virus (mean ENC = 52.17) (Jia et al, 2009), (4) SARS (mean ENC = 48.99) (Zhao et al, 2008), (5) classical swine fever virus (mean ENC = 51.7) (Tao et al, 2009), and (6) Hepatitis A virus (mean ENC = 39.78) (D'Andrea et al, 2011). An ENC value greater than 45 is considered to represent a low codon usage bias.…”

“…This phenomenon is called codon usage bias. Codon usage bias has been confirmed in many viruses (Auewarakul et al, 2009;Fu, 2010; D'Andrea et al, 2011;Li et al, 2012;Liu et al, 2010a;Shi et al, 2013;Wang et al, 2011;Wong et al, 2010;Zhou et al, 2010). Synonymous codon usage bias is strong in some viruses, such as the hepatitis A virus (D'Andrea et al, 2011).…”

A(H5N1) Virus Evolution in South East Asia

“…H5N1 HPAI viruses from clade 2.1 (found in Indonesia) may be under a lower positive selective pressure compared to the other clades [74]. Although such an observation is difficult to interpret, there may be a reduced necessity for the virus to evolve and adapt in Indonesia due to the high endemicity of the disease.…”

“…Although such an observation is difficult to interpret, there may be a reduced necessity for the virus to evolve and adapt in Indonesia due to the high endemicity of the disease. The persistence in poultry reduces the need for the virus to jump from one species to another, especially to mammalian species, in order to maintain the chain of transmission [74]. …”