Phylogenetic and codon usage analysis for replicase and capsid genes of porcine circovirus 3

Abstract

Porcine circovirus type 3 (PCV3) is a highly contagious virus belonging to the family Circoviridae that causes the severe dermatitis and nephropathy syndrome. To date, PCV3 has a worldwide distribution and bring huge economic loss in swine industry. Replicase protein (Rep) and capsid protein (Cap) are two major proteins of PCV3. Considering that the large number of new PCV3 isolates were reported in the past few years and the research for the codon usage pattern of Rep and Cap genes was still a gap, phylogenetic and codon usage analysis of these two genes was performed. Phylogenetic analysis with all strains showed no clear clusters were displayed, but almost all strains of one genotype were separated into same clade. Relative synonymous codon usage (RSCU) analysis revealed that the codon usage bias existed and effective number of codon (ENC) analysis showed that the bias was slight low. ENC-GC3s plot indicated that mutational pressure and other factors both play a role in PCV3 codon usage and neutrality plot analysis showed that natural selection was the main force in uencing the codon usage pattern. In summary, the results provided the important basic data on codon usage pattern of Rep and Cap genes, and a better understanding of the evolution and potential origin of PCV3.

Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences

“…Such a finding would imply that composition constraints played an important role in PCV codon usage bias. The results were consistent with the previous studies on PCV-2 [32] and PCV-3 [33], respectively. Furthermore, the frequencies of A3, U3, G3, C3 were very different from the overall frequencies of A, U, G, C regardless of the PCV species studied, which indicated that selection pressure may play a role during the formation of PCV codon usage pattern.…”

“…The ENC values for all PCV species fluctuated around 54.7 ± 0.871, indicating a low bias in these viruses, which may improve the replication of PCVs in their host by reducing the competition during translation. Additionally, the ENC-plot suggested that besides mutation pressure, other factors also affected the codon usage pattern of PCVs, which was consistent with previous reports [31][32][33]. The imbalanced frequency of A3, U3 and G3, C3 in PCVs indicated by PR plot suggested a relevant role of natural selection in shaping the codon usage pattern of the viruses.…”

“…Additionally, the data from the neutrality plot indicated the natural selection pressure was set as the main force for PCVs codon usage patterns, which was consistent with the conclusion from a previous study on PCV-3 [33]. Furthermore, the expanding swine breeding herds also set a strong selection pressure on the codon usage pattern of these viruses.…”

“…This latter point is especially important for PCV-2 since vaccination may exert additional pressure on PCV-2 evolution [30], although it would be mainly related to particular epitope modifications. Therefore, although there are several previous studies focused on the codon usage bias of PCV-1, PCV-2 [31,32] and PCV-3 [33,34], with the emergence of PCV-4, a comprehensive analysis on the overall codon usage patterns of all PCV species allows a comparative evaluation of molecular evolution and host adaption of these viruses to their host, the pig.…”

Epidemiology and Evolution of Emerging Porcine Circovirus-like Viruses in Pigs with Hemorrhagic Dysentery and Diarrhea Symptoms in Central China from 2018 to 2021

“…In addition, the codon bias is always influenced by external factors to varying degrees. Natural selection has been shown to play a major role in PCV-2 and canine circovirus [50,51], but mutation is more important in duck circovirus codon bias [52]. Although these viruses are closely related, different factors have influenced their evolution.…”