Figure legends:
Figure 1 Geographical distribution and phylogenetic analysis of PEDV positive samples in China (A) Map of PEDV distribution in 17 provinces in China from March 2020 to March 2021. The blue solid triangle indicates the S-INDEL like strains detected in different provinces. Positive and negative departments are labelled with orange and grey. (B) Number of PEDV positive samples collected from China in each month from March 2020 to March 2021. The x-axis represents the month of the year during the study period and the y-axis represents the number of positive samples. S-INDEL like strains are highlighted with solid blue triangle in the x-axis. (C) Phylogenetic analysis of PEDV strains based on 91 S gene sequences identified in this study and 24 reference S gene sequences in Genbank. Multiple nucleotide sequence alignments are performed with ClustalW algorithm using MEGA 6.0 software. A neighbor-joining method based phylogenetic tree is automatically constructed with 1,000 bootstrap replicates using MEGA 6.0 software. The iTOL software is used for the display and annotation of the phylogenetic tree. Labels at branch tips refer to the strain name and GenBank accession number. Red taxa highlight the 91 PEDV S sequences detected in this study. Sequences from different genotypes are marked with different color. GI-a, GI-b, S-INDEL like strain, GII-a, and GII-b are labelled with yellow, blue, green, orange, and grey, respectively.
Figure 2 Molecular characterization of the emergent PEDV strains. (A) Alignment of partial S protein sequences of 7 S-INDEL like strains in this study and the prototype S-INDEL strains in the United States (OH851 and Minnesota58), South Korea (KNU-1406-1), and China (ZL29). (B) Locations of unique amino acid (aa) insertions identified in the 91 detected sequences. The symbol“-”indicates an aa deletion. Unique variations of aa are labelled with yellow.
Figure 3 Recombination analysis of six S-INDEL like strains.The recombinant events are identified by using a Simplot analysis. The query sequences from CH/HNBR/01/2021 (A), CH/JSXZ/12/2020 (B), CH/SCYB/12/2020 (C), CH/SCGA/03/2021(D), CH/SCST/04/2020 (E), and CH/HNSQ/02/2021(F) were used to compare with the parental sequences FR/001/2014 and AJ1102. The x-axis indicates the S gene sequences, and the y-axis represents the similarity value. The regions of recombinant breakpoint are shown within two red lines.
Figure 4 Comparison of the antigen epitopes of S proteins of field strains and the vaccine strains . Dots indicate the amino acids which are identical to those of reference strains. The colored amino acids indicate the mutations in the neutralizing epitopes S1A, COE, SS2, SS6, and 2C10.
Figure 5 Phylogenetic analysis based on the S genes of S-INDEL like strains and the reference S-INDEL strains around the world. The evolutionary tree was constructed by the neighbor-joining method using MEGA6 software. Bootstrap values are indicated for each node, based on 1,000 replicates. The positions of seven S-INDEL like strain are annotated by solid black circles.