Molecular and Structural Evolution of Porcine Epidemic Diarrhea Virus

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 (syn...

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Bibliographic Details
Published in:Animals (Basel) 2022-12, Vol.12 (23), p.3388
Main Authors: Huang, Baicheng, Gu, Guoqian, Zhang, Yunjing, Chen, Zhenzhen, Tian, Kegong
Format: Article
Language:English
Subjects:
Amino acids
Coronaviruses
Diarrhea
Epidemics
Evolution
Genes
Genomes
Genotypes
Haplotypes
Hogs
molecular evolution
Mutation
Nucleic acids
Phylogenetics
porcine epidemic diarrhea virus
Positive selection
Prevention
Proteins
S gene
Strains (organisms)
structural assay
Transmissible gastroenteritis
Viruses
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Summary: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.
ISSN:2076-2615
2076-2615
DOI:10.3390/ani12233388