Identifying the genetic variation, evolutionary origin of acute diarrhea virus strains in pigs caused by Procine Epidemic Diarrhea virus (PEDV) in Northern Vietnam.

Theoretical results: The study has identified the evolutionary origin of PEDV strains causing acute diarrhea in pigs circulating in Vietnam. Identifying genetic variations of PEDV strains circulating in the country compared with virus strains in other countries around the world as well as compared with vaccine strains.
- Collected 52 samples including small intestine tissue and feces samples and idendified 28/52 samples are PEDV- positive from some provinces in the North of Vietnam including Hai Duong, Ha Noi, Hung Yen, Nam Dinh, Thanh Hoa, Tuyen Quang and Vinh Phuc.
- Sequenced 28 S1 gene of PEDV strains isolated in the North of Vietnam and registered on genbank with accession numbers OM681587, OM681588, OM681589, OM681590, OM681591, MZ787937, MT198679, OM681592, OM681593, OM681594, OM681595, OM681596, OM681597, OM681598, MW345262, OM681599, OM681600, MW345261, OM681601, OM681602, OM681603, MZ787936, MW345260, OM681604, OM681605, MW345259, OM681606, OM681607.
- Have sequenced 03 complete genomes of PEDV strains circulating in the country including IBT/VN/2018, TQ/VN/2018 and HN/VN/2018 and deposited on genbank with corresponding accession numbers MT198679, MZ787936 and MZ787937. The study has identified that Vietnamese PEDV strains belong to the G2b clade along with other S-INDEL mutant strains from North America and Asia. These are highly virulent strains.  
- Analyzed mutations in the S, N and ORF3 protein, in which the S gene have highly
variable with seven substitutions and two substitutions in the N gene. S protein 3D structure of the IBT/VN/2018 strain is the most similar to the AJ1102, DR13 strain, and slightly different with CV777, SM98 strains and 6U7K reference structure. The results of homologous modeling showed that the acquired mutations found in S protein of the IBT/VN/2018 strain including mutations in the S0 domain does not remarkably affect its overall 3D structure.
- Have identified 6 glycosylation sites (25G+, 123N+, 62V+, 144D+, 1009M+ and 1279L+) in ORF3, N and S when compared with vaccine strains. Among them, 3 new glycosylation sites are present in IBT/VN/2018 including 144D+, 1009M+ và 1279L+. The results showed that mutations in the S, N, and ORF3 genes can affect receptor specificity, viral pathogenicity, and the ability to evade the host immune system of the IBT/VN/2018 strain. Our results highlight the importance of molecular characterization of field strains of PEDV for the development of diagnostic kit and effective vaccine to control PEDV infections in Vietnam.
Applied results: Provided genetic materials for the development of effective vaccines to control PEDV infections in Vietnam.

The study has provided the scientific basis for selecting virus strains as vaccine strains, providing genetic materials for the production of new generation vaccines with high immunological similarity with the field pathogenic virus strains. in the country to improve the protective effectiveness of vaccines; In addition, the project also provides genetic materials and scientific basis for developing diagnostic kits for detection of PEDV causing disease in pigs in Vietnam.

- Scientific papers in referred journals (list): 01
Tran TX, Lien NTK, Thu HT, Duy ND, Duong BTT, Quyen DV. 2021. Changes in the spike and nucleocapsid protein of porcine epidemic diarrhea virus strain in Vietnam—a molecular potential for the vaccine development?. PeerJ 9:e12329
http://doi.org/10.7717/peerj.12329.
- Patents (list):
- Technological products (describe in details: technical characteristics, place):
+ Sequence of S1 of PEDV circulating in Vietnam: 28 S1 gene sequences of PEDV strains isolated in Hai Duong, Ha Noi, Hung Yen, Nam Dinh, Thanh Hoa, Tuyen Quang, Vinh Phuc. They have been registered on genbank with the accession numbers OM681587, OM681588, OM681589, OM681590, OM681591, MZ787937, MT198679, OM681592, OM681593, OM681594, OM681595, OM681596, OM681597, OM681598, MW345262, OM681599, OM681600, MW345261, OM681601, OM681602, OM681603, MZ787936, MW345260, OM681604, OM681605, MW345259, OM681606, OM681607.
+ Complete PEDV genome sequence: 03 complete genome sequences of PEDV circulating in Vietnam designated as IBT/VN/2018, TQ/VN/2018 and HN/VN/2018 have been sequenced and registered on the genbank with the accession numbers MT198679, MZ787936 and MZ787937, respectively.
+ A detailed report on genetic characteristics, evolutionary origin of the PEDV strain causing disease in pigs in the North of Vietnam.
- Other products (if applicable):
+ 01 manuscript submited to an ISI journal.

Our study emphasize that it is necessary to continuously evaluate the genetic variation and evolutionary origins of the PEDV strains circulating in Vietnam. Compare the immunological similarity between the field strains and the vaccine strains being used in the country for the selection and/or production of highly protective vaccines to control PEDV infection in Vietnam.