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...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-12-01
|
| Series: | Animals |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2615/12/23/3388 |
| _version_ | 1827643522209021952 |
|---|---|
| author | Baicheng Huang Guoqian Gu Yunjing Zhang Zhenzhen Chen Kegong Tian |
| author_facet | Baicheng Huang Guoqian Gu Yunjing Zhang Zhenzhen Chen Kegong Tian |
| author_sort | Baicheng Huang |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T17:55:29Z |
| format | Article |
| id | doaj.art-a68e1a0cc9784768a22b3db2e6b7069c |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-09T17:55:29Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-a68e1a0cc9784768a22b3db2e6b7069c2023-11-24T10:26:18ZengMDPI AGAnimals2076-26152022-12-011223338810.3390/ani12233388Molecular and Structural Evolution of Porcine Epidemic Diarrhea VirusBaicheng Huang0Guoqian Gu1Yunjing Zhang2Zhenzhen Chen3Kegong Tian4National Research Center for Veterinary Medicine, Luoyang 471000, ChinaDepartment of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Hong Kong SAR 999077, ChinaNational Research Center for Veterinary Medicine, Luoyang 471000, ChinaNational Research Center for Veterinary Medicine, Luoyang 471000, ChinaNational Research Center for Veterinary Medicine, Luoyang 471000, ChinaTo 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.https://www.mdpi.com/2076-2615/12/23/3388porcine epidemic diarrhea virusmolecular evolutionpositive selectionstructural assayhaplotypes |
| spellingShingle | Baicheng Huang Guoqian Gu Yunjing Zhang Zhenzhen Chen Kegong Tian Molecular and Structural Evolution of Porcine Epidemic Diarrhea Virus Animals porcine epidemic diarrhea virus molecular evolution positive selection structural assay haplotypes |
| title | Molecular and Structural Evolution of Porcine Epidemic Diarrhea Virus |
| title_full | Molecular and Structural Evolution of Porcine Epidemic Diarrhea Virus |
| title_fullStr | Molecular and Structural Evolution of Porcine Epidemic Diarrhea Virus |
| title_full_unstemmed | Molecular and Structural Evolution of Porcine Epidemic Diarrhea Virus |
| title_short | Molecular and Structural Evolution of Porcine Epidemic Diarrhea Virus |
| title_sort | molecular and structural evolution of porcine epidemic diarrhea virus |
| topic | porcine epidemic diarrhea virus molecular evolution positive selection structural assay haplotypes |
| url | https://www.mdpi.com/2076-2615/12/23/3388 |
| work_keys_str_mv | AT baichenghuang molecularandstructuralevolutionofporcineepidemicdiarrheavirus AT guoqiangu molecularandstructuralevolutionofporcineepidemicdiarrheavirus AT yunjingzhang molecularandstructuralevolutionofporcineepidemicdiarrheavirus AT zhenzhenchen molecularandstructuralevolutionofporcineepidemicdiarrheavirus AT kegongtian molecularandstructuralevolutionofporcineepidemicdiarrheavirus |