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

Autor:	Tran TX; Dept of Molecular Microbiology, Institute of Biotechnology, Hanoi, Vietnam., Lien NTK; Functional of Genomics Lab, Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam., Thu HT; Dept of Molecular Microbiology, Institute of Biotechnology, Hanoi, Vietnam., Duy ND; Dept of Molecular Microbiology, Institute of Biotechnology, Hanoi, Vietnam., Duong BTT; Dept of Molecular Microbiology, Institute of Biotechnology, Hanoi, Vietnam., Quyen DV; Dept of Molecular Microbiology, Institute of Biotechnology, Hanoi, Vietnam.; University of Science and Technology of Ha Noi, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
Jazyk:	angličtina
Zdroj:	PeerJ [PeerJ] 2021 Oct 18; Vol. 9, pp. e12329. Date of Electronic Publication: 2021 Oct 18 (Print Publication: 2021).
DOI:	10.7717/peerj.12329
Abstrakt:	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. Competing Interests: The authors declare there are no competing interests. (©2021 Tran et al.)
Databáze:	MEDLINE
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