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

Abstract

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 766P > L766 in the epitope SS6; two in the S0subdomain (135DN136 > 135SI136 and N144> D144); two in subdomain SHR1 at aa 1009L > M1009 and 1089S > L1089; one at aa 1279P > S1279 in subdomain SHR2 of the S protein; two at aa 364N > I364 and 378N > S378 in the N protein; four at aa 25L > S25, 70I > V70, 107C > F107, and 168D > 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 (294I > M294, 318A > S318, 335V > I335, 361A > T361, 497R > T497, 501SH502 > 501IY502, 506I > T506, 682V > I682, and 777P > 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.

Development of an Indirect Enzyme-Linked Immunosorbent Assay Based on the Yeast-Expressed CO-26K-Equivalent Epitope-Containing Antigen for Detection of Serum Antibodies against Porcine Epidemic Diarrhea Virus

“…Studies have reported that the amino acid variations of the PEDV S protein might result in antigenicity differences [15,33]. As a consequence, the selection of conserved antigen regions is very important for total antibody level and neutralizing antibody detection.…”

“…These structural proteins have already been used as target coating proteins to establish iELISAs for detecting anti-PEDV antibodies [11]; however, researchers found that N protein or M protein-based iELISAs exhibit high cross-reactivity for other swine coronaviruses [12,13] while S proteinbased iELISA is more sensitive than N protein one [11]. Meanwhile, it has been proven that the S protein has higher antigenicity than other ones, and anti-S antibodies produced in PEDV-infected pigs could persist longer than anti-N antibodies [14,15]. Moreover, because the S protein harbors more virus-neutralizing epitopes, it is also recognized as the target for neutralizing antibody induction [16,17].…”

Porcine Epidemic Diarrhea: Insights and Progress on Vaccines

“…The evolution of PEDV has been complex and rapid, with potential recombination events occurring between the G1a and G2 lineages and leading to new lineages such as S-INDEL (G1b) and the newly identified G2c [ 10 , 27 , 28 , 29 ]. Changes in the S gene through mutation and recombination can alter the pathogenicity of the virus and its ability to infect different tissues or species [ 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 ]. The S protein is also vital for infection, as it induces the production of neutralizing antibodies and is a key target for vaccine development, both for live attenuated and subunit vaccines [ 22 ].…”

Molecular analysis reveals a distinct subgenogroup of porcine epidemic diarrhea virus in northern Vietnam in 2018–2019

“…Despite vaccination, severe outbreaks of PED have been occurring continually in pig herds throughout the whole country. The reasons for vaccine failure might be found by examining genetic variations within the genomes of the currently circulating PEDV strains [ 28 , 29 , 31 , 32 ]. There remains a need for molecular analysis of the S1 protein sequences of the clinical strains recently or currently circulating in Vietnam.…”

“…The complete S1 spike sequence phylogeny will give higher resolution, and the complete genomic sequence analysis will better resolve the taxonomic status of these isolates. Further detailed genome characterization and protein structure prediction, as well as testing their antigenicity/immunogenicity will be useful for developing a strategy for making alternative vaccines in the near future [ 32 ]. This research highlights the need for frequent vaccine updates to ensure protection efficacy despite the continuous evolution of PEDV [ 37 , 41 , 42 ].…”