Heterogeneity in spike protein genes of porcine epidemic diarrhea viruses isolated in Korea

Abstract

Porcine epidemic diarrhea virus (PEDV) has plagued the domestic swine industry in Korea causing significant economic impacts on pig production nationwide. In the present study, we determined the complete nucleotide sequences of the spike (S) glycoprotein genes of seven Korean PEDV isolates. The entire S genes of all isolates were found to be nine nucleotides longer in length than other PEDV reference strains. This size difference was due to the combined presence of notable 15 bp insertion and 6 bp deletion within the N-terminal region of the S1 domain of the Korean isolates. In addition, the largest number of amino acid variations was accumulated in the S1 N-terminal region, leading to the presence of hypervariability in the isolates. Sequence comparisons at the peptide level of the S proteins revealed that all seven Korean isolates shared diverse similarities ranging from a 93.6% to 99.6% identity with each other but exhibited a 92.2% to 93.7% identity with other reference strains. Collectively, the sequence analysis data indicate the diversity of the PEDV isolates currently prevalent in Korea that represents a heterogeneous group. Phylogenetic analyses showed two separate clusters, in which all Korean field isolates were grouped together in the second cluster (group 2). The results indicate that prevailing isolates in Korea are phylogenetically more closely related to each other rather than other reference strains. Interestingly, the tree topology based on the nucleotide sequences representing the S1 domain or the S1 N-terminal region most nearly resembled the full S gene-based phylogenetic tree. Therefore, our data implicates a potential usefulness of the partial S protein gene including the N-terminal region in unveiling genetic relatedness of PEDV isolates.

Complete Genome Sequence of a Porcine Epidemic Diarrhea Virus Variant

“…The second domain is located at positions 1428 to 1914. These regions are also found in the S genes of Korean PEDV isolates (3).…”

“…Among the six genes of CH/ FJND-3/2011, the S gene has the lowest sequence identity (93.75%) with that of CH/S and is 9 nt longer than those of CV777 and CH/S. The PEDV S gene plays an important role in the molecular epidemiology of PEDV in the field and in the genetic variation of PEDV field isolates (3,4,5). The alignment in the S1 region (nt 1 to 2217) of the S gene reveals two domains exhibiting increased divergence compared to the remaining part of the sequence.…”

Optimization of expression and purification of recombinant S1 domain of the porcine epidemic diarrhea virus spike (PEDV- S1) protein inEscherichia coli

“…As shown in Figure 8(b), lanes 8-10, PEDV-S1 was highly enriched. Therefore, eluted fractions (19)(20)(21)(22)(23)(24)(25)(26) containing relatively pure camel were pooled. After Ni-NTA chromatography, ̴ 17 mg highly enriched Ni-NTA chromatography system is a rapid and convenient purification technique.…”

“…It contains a putative signal peptide (aa , a large extracellular region, a single transmembrane domain (aa 1334-1356), and a short cytoplasmic tail. Although PEDV has an uncleaved S protein because it lacks a furin cleavage site, the S protein can be divided into S1 (aa 1-735) and S2 (736-the last aa) domains based on homology with S proteins of other coronaviruses [14][15][16][17]. Like other coronavirus S proteins, the PEDV S protein is known to play a pivotal role, interacting with the cellular receptor to mediate viral entry and inducing neutralizing antibodies in the natural host [18,19].…”

“…More precisely, previous studies have shown that the S1 domain includes the main neutralizing epitopes and the receptor-binding region [20,21]. Furthermore, along with the full-length S gene, the S1 portion is known to be a suitable region for determining genetic relatedness among the different PEDV isolates and for developing differential diagnostic assays [22,23]. Considering these molecular and biological features of the S1 domain, it would be an appropriate target for developing effective vaccines against PEDV.…”