Based on the Results of PEDV Phylogenetic Analysis of the Most Recent Isolates in China, the Occurrence of Further Mutations in the Antigenic Site S1° and COE of the S Protein Which Is the Target Protein of the Vaccine

Abstract

The continuous challenge of existing vaccine systems by porcine epidemic diarrhea virus (PEDV) variant strains in recent years, it caused significant economic losses in the global swine industry. A PEDV virulent strain CH/HLJBQL/2022 was successfully isolated in China in this study. A genome-wide based phylogenetic analysis suggests that CH/HLJBQL/2022 belongs to the GII subtype, and 96.3%–99.6% homology existed in the whole genomes of other strains. For the first time, simultaneous mutations of four amino acids were found in the highly conserved membrane (M) and nucleocapsid (N) proteins, as well as five amino acid mutations that differed from the vast majority of strains in the spike (S) protein. Mutations in the M and S proteins were found to produce coils with different angles by building 2D and 3D structural models. Epitope analysis indicated that the isolates produced specific changes and that the transmembrane function of the M protein had not been affected. In addition, typing markers exist during strain evolution, but isolates are using the fusion of specific amino acids from multiple variant strains to add additional features, as also demonstrated by protein alignments and 3D models of numerous subtype strains. These results suggest that aa mutations in the M and S proteins may have changed the structure and antigenic epitope of the isolates and PEDV is evolving again on the basis of variants that have been found to counteract the immune network of the new vaccine.

Immunoinformatics approach for designing a multi-epitope subunit vaccine against porcine epidemic diarrhea virus genotype IIA spike protein

“…One-hundred-eight (108) spike (S) proteins were extracted from the proteomes of PEDV GIIa strains retrieved from Yao, Qiao, et al . (2023) , Yao, Zhu, et al . (2023) , and Liu et al .…”

“…One hundred eight PEDV GIIa strains used in the study were referenced from the phylogenetic trees constructed by Yao, Qiao, et al . (2023) , Yao, Zhu, et al . (2023) , and Liu et al .…”

“…Specifically, highly virulent strains, such as PEDV strain CH/HLJJS/2022 from China, belong to the GIIa subtype ( Yao et al . 2023a ; Yao et al ., 2023b ). Sequence analysis of PEDV isolates in the Philippines revealed that both GI and GII strains are present in the country ( Salamat et al ., 2021 ).…”

Towards a Safer Future: Enhancing Vaccine Development to Combat Animal Coronaviruses

“…Notably, a majority of coronavirus subunit vaccines in development target the RBD. Moreover, the NTD of S proteins from diverse animal coronaviruses have demonstrated carbohydrate receptor-binding activity, as observed in TGEV and IBV [ 208 , 209 ]. Recent studies have also indicated further mutations in the antigenic site S1° and COE of the PEDV S protein, making it a main candidate target for animal vaccine development [ 209 ].…”