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.