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

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.

Systematic analysis of the codon usage patterns of African swine fever virus genome coding sequences reveals its host adaptation phenotype

“…An ENC value >35 indicates a low CUB in the ASFV complete genome [ 25 ]. This finding aligns with previous studies on other porcine viruses, such as porcine circoviruses (54.71±0.87) [ 43 ], porcine parvoviruses (57.433±0.192) [ 44 ] and classical swine fever virus (52.69±0.47) [ 45 ]. The limited codon preference observed in these viruses may promote effective replication in diverse host cells [ 46 ].…”

A Subunit Vaccine Based on the VP2 Protein of Porcine Parvovirus 1 Induces a Strong Protective Effect in Pregnant Gilts

“…commercial inactivated vaccine, which includes nine strains of PPV1 belonging to the same branch of the NADL-2 strain, is widely used in China and plays a critical role in controlling the PPV1 epidemic [26]. The incidence of this disease has dropped considerably in the past ten years, with an incidence of 1-2.6% in parts of China.…”

“…However, immunization failure in large-scale pig farms can still occur owing to the presence of the basic variant of PPV1. Previous studies have shown that PPV1 isolates in China are located in different evolutionary lines [26,27].…”

Analysis of codon usage bias in Ziziphi Spinosae Semen based on transcriptome data

“…A species or a gene tends to use one or more speci c synonymous codons as the codon usage bias (CUB), and organisms have a certain preference for different codons, which is widespread in the biological community (Wang et al 2022b). Codon bias is in uenced by various factors, such as natural selection, mutational pressure, genetic drift, protein structure, and features, tRNA abundance, and GC content (Xie et al 2022). The chloroplast codon usage bias in Ginkgo biloba L. (Somaratne et al 2019a), Papilionoideae (Somaratne et al 2019b), and Helianthus annuus L. (Gao et al 2022) have been reported.…”