Molecular and Structural Evolution of Porcine Epidemic Diarrhea Virus

Abstract

To analyze the evolutionary characteristics of the highly contagious porcine epidemic diarrhea virus (PEDV) at the molecular and structural levels, we analyzed the complete genomes of 647 strains retrieved from the GenBank database. The results showed that the spike (S) gene exhibited larger dS (synonymous substitutions per synonymous site) values than other PEDV genes. In the selective pressure analysis, eight amino acid (aa) sites of the S protein showed strong signals of positive selection, and seven of them were located on the surface of the S protein (S1 domain), suggesting a high selection pressure of S protein. Topologically, the S gene is more representative of the evolutionary relationship at the genome-wide level than are other genes. Structurally, the evolutionary pattern is highly S1 domain-related. The haplotype networks of the S gene showed that the strains are obviously clustered geographically in the lineages corresponding to genotypes GI and GII. The alignment analysis on representative strains of the main haplotypes revealed three distinguishable nucleic acid sites among those strains, suggesting a putative evolutionary mechanism in PEDV. These findings provide several new fundamental insights into the evolution of PEDV and guidance for developing effective prevention countermeasures against PEDV.

Research progress of porcine epidemic diarrhea virus S protein

“…Adaptive mutations at these three positively selected sites may enhance viral infectivity, help the virus evade host immunity, and enable continual environmental adaptation ( Ao, 2020 ). A study conducted in 2022 on the evolution of the molecular structure of PEDV confirmed the presence of these three positively selected nucleic acid sites and their impact on virus virulence ( Huang et al, 2022 ).…”

“…Adaptive mutations at these three positively selected sites may enhance viral infectivity, help the virus evade host immunity, and enable continual environmental adaptation (Ao, 2020). A study conducted in 2022 on the evolution of the molecular structure of PEDV confirmed the presence of these three positively selected nucleic acid sites and their impact on virus virulence (Huang et al, 2022). Cheng et al (2023) amplified the S1 gene sequence of 11 PEDV endemic strains isolated from Zhejiang from 2015 to 2017 by RT-PCR and compared the amino acid sequence variations of the S1 protein.…”

Epitope screening and vaccine molecule design of PRRSV GP3 and GP5 protein based on immunoinformatics

“…Predicting the interactions between TLR‐3 (PDB ID: 2A0Z) as a receptor and the candidate vaccine proteins as a ligand was made using the server pyDockWEB (https://life.bsc.es/pid/pydockweb; Access:2023.02). The computer software LigPLot+ was used to determine the interface between the vaccine ligand and TLR‐3 receptor and whether there are hydrogen bonds and hydrophobic interaction between amino acid residues 29,30 …”

“…The computer software LigPLot+ was used to determine the interface between the vaccine ligand and TLR‐3 receptor and whether there are hydrogen bonds and hydrophobic interaction between amino acid residues. 29 , 30 …”

Phylogenetic and Spatiotemporal Analyses of Porcine Epidemic Diarrhea Virus in Guangxi, China during 2017–2022

“…The first reported porcine epidemic diarrhea (PED) outbreak occurred in 1971 in UK pig herds [ 6 , 7 ]. Before 2010, PEDV was effectively controlled through the use of the CV777 vaccine [ 8 ].…”