Sequence analysis of the partial spike glycoprotein gene of porcine epidemic diarrhea viruses isolated in Korea

Abstract

Porcine epidemic diarrhea virus (PEDV) causes a devastating enteric disease with acute diarrhea, dehydration and significant mortality in swine, thereby incurring heavy economic losses in Korea. Spike (S) glycoprotein has been suggested as an important determinant for PEDV biological properties. In this study, the nucleotide and deduced amino acid sequences of the partial S glycoprotein genes of Korean PEDV isolates, including epitope region that is capable of inducing PEDV-neutralizing antibodies, were determined. The partial S glycoprotein genes were amplified by RT-PCR, cloned, sequenced, and compared with each other as well as with reference PEDV strains. By phylogenetic analysis, the Korean PEDV isolates were divided into three groups (G1, G2, G3), which had three subgroups (G1-1, G1-2, G1-3). Group1 (G1) Korean PEDV isolates were highly homologous to CV777, Br1/87, JS-2004-2, KPED-9, P-5V, SM98-1, parent DR13, and attenuated DR13, group2 (G2) Korean PEDV isolates were highly homologous to Spk1, and group3 (G3) was Chinju99 at the nucleotide and deduced amino acid sequence levels. In addition, the G1 Korean PEDV isolates didn't had several specific nucleotides and amino acids which were found in the G2 and G3 Korean PEDV isolates, and especially the G1-1 Korean PEDV isolates had specific nucleotides and amino acids which were not found in the G1-2, G1-3, G2, and G3 Korean PEDV isolates. It was suggested that many Korean PEDV isolates are closely related to the G1 including CV777, Br1/87, JS-2004-2, KPED-9, P-5 V, SM98-1, parent DR13, and attenuated DR13 rather than to the G2 and G3 including Spk1 and Chinju99, and notably more prevalent PEDVs isolated in Korea are especially close to the Chinese PEDV strain JS-2004-2 rather than Korean PEDV strains Spk1, Chinju99, KPED-9, SM98-1, parent DR13, and attenuated DR13.

Evaluation of two real-time polymerase chain reaction assays for Porcine epidemic diarrhea virus (PEDV) to assess PEDV transmission in growing pigs

“…Primers and a probe, labeled at the 5'-end with the reporter dye 6-carboxyfluorescein (FAM) and at the 3′-end with the 3′-quencher BHQ1, were targeted to the partial gS gene 17,20,23 at nucleotides 1910-2021, which yielded a 111-bp DNA fragment. 2 Primers and a probe, labeled at the 5′-end with FAM and at the 3′-end with BHQ1, for gN real-time RT-PCR were targeted to the gN gene at nucleotides 941-1028, which yielded a 87-bp DNA fragment.…”

A novel strain of porcine epidemic diarrhea virus in Vietnamese pigs

“…It plays an important role in molecular epidemiology and in assessing the genetic variation of PEDV field strains [7,25]. The calculation method employing the neighborjoining (NJ) method of the MEGA 6.06 program [26] was used to further investigate genetic diversity of Vietnamese strains.…”

Complete Genome Sequence of a Porcine Epidemic Diarrhea Virus Variant

“…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.…”