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Porcine epidemic diarrhea (PEDV) virus is a member of the Coronaviridae family, causing serious diarrhea in pigs. This epidemic has a high mortality rate in piglets under two weeks of age. PEDV was thought to be a concern of the pig industry worldwide. Unfortunately, there are currently no effective vaccines available to prevent PEDV disease. Recently, a novel strain of PED virus (HUA-PED45) belongs to the G2b group was found in Vietnam, causing severe economic losses to domestic pig farming. Frequent mutation in the coding sequence of antigenic spike (S) protein of PEDV strain HUA-PED45 may result in the deterioration of the protective potential of vaccines against to the local strains and may reduce the detection by the existing diagnostic kits. In this study, the codon-optimized PED45S1C epitope alone (residue 502-641 aa) and 2C10 epitope fusion genes (PED45S1C-CT24) were over-expressed by using pQE30 expression vector (Qiagen, Germany). To find out the optimal time of expression after IPTG induction, IPTG concentration was optimized as well. The highly pure and homogeneous S1C and S1C-CT24 fusion protein were obtained by using Ni-NTA affinity chromatography. The purified antigens have the potential to be utilized to develop as subunit vaccine candidates, as well as provide the material for related studies of this dangerous virus strain.