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

BACKGROUND: Porcine 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. METHODS: In 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. RESULTS: The 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)P > L(766) in the epitope SS6; two in the S(0)subdomain ((135)DN(136) > (135)SI(136) and N(144)> D(144)); two in subdomain S(HR1) at aa (1009)L > M(1009) and (1089)S > L(1089); one at aa (1279)P > S(1279) in subdomain S(HR2) of the S protein; two at aa (364)N > I(364) and (378)N > S(378) in the N protein; four at aa (25)L > S(25), (70)I > V(70), (107)C > F(107), and (168)D > N(168) in the ORF3 protein. We identified two insertions (at aa (59)NQGV(62) and aa (145)N) and one deletion (at aa (168)DI(169)) in S protein. Remarkable, eight amino acid substitutions ((294)I > M(294), (318)A > S(318), (335)V > I(335), (361)A > T(361), (497)R > T(497), (501)SH(502) > (501)IY(502), (506)I > T(506), (682)V > I(682), and (777)P > L(777)) were found in S(A) subdomain. Besides, N- and O-glycosylation analysis of S, N, and ORF3 protein reveals three known sites (25(G+), 123(N+), and 62(V+)) and three novel sites (144(D+), 1009(M+), and 1279(L+)) 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.