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Mol Phylogenet Evol. 2019 Sep 16;141:106618. doi: 10.1016/j.ympev.2019.106618. [Epub ahead of print]

Comprehensive codon usage analysis of porcine deltacoronavirus.

Author information

1
MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
2
MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: shuosu@njau.edu.cn.
3
MOA Key Laboratory of Animal Virology, Department of Veterinary Medicine and Veterinary Medical Research Center, Zhejiang University, Hangzhou 310058, China; Institute of Preventive Veterinary Sciences, Zhejiang University, Hangzhou 310058, China; Collaborative Innovation Center and State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University, Hangzhou 310003, China. Electronic address: jyzhou@zju.edu.cn.

Abstract

Porcine deltacoronavirus (PDCoV) is a newly identified coronavirus of pigs that was first reported in Hong Kong in 2012. Since then, many PDCoV isolates have been identified worldwide. In this study, we analyzed the codon usage pattern of the S gene using complete coding sequences and complete PDCoV genomes to gain a deeper understanding of their genetic relationships and evolutionary history. We found that during evolution three groups evolved with a relatively low codon usage bias (effective number of codons (ENC) of 52). The factors driving bias were complex. However, the primary element influencing the codon bias of PDCoVs was natural selection. Our results revealed that different natural environments may have a significant impact on the genetic characteristics of the strains. In the future, more epidemiological surveys are required to examine the factors that resulted in the emergence and outbreak of this virus.

KEYWORDS:

Codon usage; Evolution; Mutation pressure; Nature selection; PDCoV

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