期刊
INFECTION GENETICS AND EVOLUTION
卷 35, 期 -, 页码 27-33出版社
ELSEVIER
DOI: 10.1016/j.meegid.2015.07.024
关键词
Tembusu virus; Codon usage pattern; Mutation pressure; Cross-species transmission
资金
- National Natural Science Foundation of China [31201891]
- Sichuan Provincial Cultivation Program for Leaders of Disciplines in Science [2012JQ0040]
- Major Project of Education Department in Sichuan Province [12ZA107]
- Specialized Research Fund for the Doctoral Program of Higher Education [20125103120012]
- Innovative Research Team Program in Education Department of Sichuan Province [12TD005, 2013TD0015]
- National Science and Technology Support Program [2015BAD12B05]
- National Special Fund for Agro-scientific Research in the Public Interest [201003012]
- China Agricultural Research System [CARS-43-8]
Tembusu virus (TMUV) is a single-stranded, positive-sense RNA virus. As reported, TMUV infection has resulted in significant poultry losses, and the virus may also pose a threat to public health. To characterize TMUV evolutionarily and to understand the factors accounting for codon usage properties, we performed, for the first time, a comprehensive analysis of codon usage bias for the genomes of 60 TMUV strains. The most recently published TMUV strains were found to be widely distributed in coastal cities of southeastern China. Codon preference among TMUV genomes exhibits a low bias (effective number of codons (ENC) = 53.287) and is maintained at a stable level. ENC-GC3 plots and the high correlation between composition constraints and principal component factor analysis of codon usage demonstrated that mutation pressure dominates over natural selection pressure in shaping the TMUV coding sequence composition. The high correlation between the major components of the codon usage pattern and hydrophobicity (Gravy) or aromaticity (Aromo) was obvious, indicating that properties of viral proteins also account for the observed variation in TMUV codon usage. Principal component analysis (PCA) showed that CQW1 isolated from Chongqing may have evolved from GX2013H or GX2013G isolated from Guangxi, thus indicating that TMUV likely disseminated from southeastern China to the mainland. Moreover, the preferred codons encoding eight amino acids were consistent with the optimal codons for human cells, indicating that TMUV may pose a threat to public health due to possible cross-species transmission (birds to birds or birds to humans). The results of this study not only have theoretical value for uncovering the characteristics of synonymous codon usage patterns in TMUV genomes but also have significant meaning with regard to the molecular evolutionary tendencies of TMUV. (C) 2015 Elsevier B.V. All rights reserved.
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