Changes in the spike and nucleocapsid protein of porcine epidemic diarrhea virus strain in Vietnam—a molecular potential for the vaccine development?

PeerJ

article

Thach Xuan Tran¹  Nguyen T.K. Lien²  Ha T. Thu¹  Nguyen Dinh Duy¹  Bui T.T. Duong¹  Dong Van Quyen¹ 

[1] Dept of Molecular Microbiology, Institute of Biotechnology;Functional of Genomics Lab, Institute of Genome Research, Vietnam Academy of Science and Technology;University of Science and Technology of Ha Noi, Vietnam Academy of Science and Technology

关键词: Porcine epidemic diarrhea virus;    Spike protein;    Neutralizing antibodies;    Phylogenetic analysis;    Pigs;   

DOI  :  10.7717/peerj.12329

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

BackgroundPorcine epidemic diarrhea virus (PEDV) is a dangerous virus causing large piglet losses. PEDV spread rapidly between pig farms and caused the death of up to 90% of infected piglets. Current vaccines are only partially effective in providing immunity to suckling due to the rapid dissemination and ongoing evolution of PEDV.MethodsIn this study, the complete genome of a PEDV strain in Vietnam 2018 (IBT/VN/2018 strain) has been sequenced. The nucleotide sequence of each fragment was assembled to build a continuous complete sequence using the DNASTAR program. The complete nucleotide sequences and amino acid sequences of S, N, and ORF3 genes were aligned and analyzed to detect the mutations.ResultsThe full-length genome was determined with 28,031 nucleotides in length which consisted of the 5′UTR, ORF1ab, S protein, ORF3, E protein, M protein, N protein, and 3′UTR region. The phylogenetic analysis showed that the IBT/VN/2018 strain was highly virulent belonged to the G2b subgroup along with the Northern American and Asian S-INDEL strains. Multiple sequence alignment of deduced amino acids revealed numerous mutations in the S, N, and ORF3 regions including one substitution 766 L766 in the epitope SS6; two in the S0subdomain (135DN136 135SI136 and N144 D144); two in subdomain SHR1 at aa 1009 M1009 and 1089 L1089; one at aa 1279 S1279 in subdomain SHR2 of the S protein; two at aa 364 I364 and 378 S378 in the N protein; four at aa 25 S25, 70 V70, 107 F107, and 168 N168 in the ORF3 protein. We identified two insertions (at aa 59NQGV62 and aa 145N) and one deletion (at aa 168DI169) in S protein. Remarkable, eight amino acid substitutions (294 M294, 318 S318, 335 I335, 361 T361, 497 T497, 501SH502 501IY502, 506 T506, 682 I682, and 777 L777) were found in SA subdomain. Besides, N- and O-glycosylation analysis of S, N, and ORF3 protein reveals three known sites (25G+, 123N+, and 62V+) and three novel sites (144D+, 1009M+, and 1279L+) in the IBT/VN/2018 strain compared with the vaccine strains. Taken together, 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 an effective vaccine to control PEDV infections in Vietnam.

【 授权许可】

CC BY