Codon Usage for Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Parvoviruses 2 through 7 (PPV2-PPV7).

Changzhan Xie,He Zhang,Ping Zhang,Ying Zhang,Zhuo Ha,Yubiao Xie,Ningyi Jin,Huijun Lu,Xianzhu Xia,Yimo Tao,Xiangyu Zhu

doi:10.3390/v14020170

Abstract

Porcine parvovirus (PPV) is the main pathogen of reproductive disorders. In recent years, a new type of porcine parvovirus has been discovered and named porcine parvovirus 2 to 7 (PPV2–PPV7), and it is associated with porcine circovirus type 2 in pigs. Codon usage patterns and their effects on the evolution and host adaptation of different PPV sub-types are still largely unknown. Here, we define six main sub-types based on the Bayesian method of structural proteins of each sub-type of PPV, including PPV2, PPV3, PPV4, PPV5, PPV6, and PPV7, which show different degrees of codon usage preferences. The effective number of codons (ENC) indicates that all PPV sub-types have low codon bias. According to the codon adaptation index (CAI), PPV3 and PPV7 have the highest similarity with the host, which is related to the main popular tendency of the host in the field; according to the frequency of optimal codons (FOP), PPV7 has the highest frequency of optimal codons, indicating the most frequently used codons in its genes; and according to the relative codon deoptimization index (RCDI), PPV3 has a higher degree. Therefore, it is determined that mutational stress has a certain impact on the codon usage preference of PPV genes, and natural selection plays a very decisive and dominant role in the codon usage pattern. Our research provides a new perspective on the evolution of porcine parvovirus (PPV) and may help provide a new method for future research on the origin, evolutionary model, and host adaptation of PPV.

Highlights

Introduction published maps and institutional affilThe family Parvoviridae encompasses small non-enveloped and negative single-strandedDNA viruses, including many human and animal pathogens, that infect a wide variety of species [1]
The results showed that the mutation rates of the amino acid codons encoded by the Porcine parvovirus (PPV)
Because the third codon has the highest mutation rate and the coby A3s (0.329 ± 0.129 in all), C3s (0.299 ± 0.123 in all), and G3s (0.284 ± 0.078 in all), the don has degeneracy, some mutations will not change the amino acid encoding the protein, third position of synonymous codons shows dissimilar composition patterns among these which makes the homology between PPV virus strains very high

Summary

Introduction

Introduction published maps and institutional affilThe family Parvoviridae encompasses small non-enveloped and negative single-strandedDNA viruses, including many human and animal pathogens, that infect a wide variety of species [1]. The family Parvoviridae encompasses small non-enveloped and negative single-stranded. DNA viruses, including many human and animal pathogens, that infect a wide variety of species [1]. Porcine parvoviruses (PPV) are important pathogens that cause reproductive failure in swine, resulting in enormous losses in the pig industry worldwide [2]. The. Parvoviridae family consists of three subfamilies: Parvovirinae, Hamaparvovirinae, and Densovirinae. Viruses infecting vertebrates and vertebrate cell cultures are assigned to the subfamily Parvovirinae, and Bocaparvovirus, Copiparvovirus, and Tetraparvovirus contain viruses that infect pigs. Eight species in four genera of parvovirus have been described to infect swine. Over the past few years, several new parvoviruses have been discovered in pigs

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Results

Conclusion