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The porcine epidemic diarrhea virus (PEDV) has caused severe economic losses in the pig industry. Since its discovery, the virus has spread in pig herds for more than 50 years. Many new features have been found in the PEDV spike genes. In this study, 123 representative S genes were used to analyze their characteristics across strains. Phylogenetic analysis revealed that PEDV can be divided into nine groups: G1a, G1b, G1c, G1d, G2a, G2b, G2c, G2d, and G3. In addition, 21 different lengths of the S gene were found. Analysis of the amino acid insertion and deletion sites revealed that most deletions and insertions occurred in the loops of the spike quaternary structure, primarily in the D0 and N‐terminal domains (NTDs). According to the above results, PEDV has undergone considerable evolution, possibly under the immune pressure of vaccination. These results are highly important for understanding the current epidemic situation of PEDV. [ABSTRACT FROM AUTHOR]