Distinct characteristics and complex evolution of PEDV strains, North America, May 2013-February 2014

Abstract

Porcine epidemic diarrhea virus (PEDV), which emerged in the United States in 2013, has spread throughout North America. Limited availability of PEDV complete genomes worldwide has impeded our understanding of PEDV introduction into the United States. To determine the relationship between the North American strains and global emerging and historic PEDV strains, we sequenced and analyzed complete genomes of 74 strains from North America; the strains clustered into 2 distinct clades. Compared with the initially reported virulent US PEDV strains, 7 (9.7%) strains from 4 states contained insertions and deletions in the spike gene (S INDELs). These S INDEL strains share 99.8%-100% nt identity with each other and 96.2%-96.7% nt identity with the initial US strains. Furthermore, the S INDEL strains form a distinct cluster within North American clade II, sharing 98.6%-100% nt identity overall. In the United States, the S INDEL and original PEDV strains are co-circulating and could have been introduced simultaneously.

Figure 1

Phylogenetic tree based on complete genome sequences of 112 North American porcine epidemic diarrhea virus strains. Blue represents US non–S INDEL strains; red represents US S INDEL strains; brown represents Mexican strains; purple represents worldwide non–S INDEL strains; and pink represents global S INDEL strains. Bootstrap values are represented at key nodes. Scale bar indicates nucleotide substitutions per site. CH, China; IA, Iowa; S INDEL, insertions and deletions in the spike gene; IN, Indiana; ISU, Iowa State University; MEX, Mexico; MN, Minnesota; USA, United States of America.

Figure 2

Phylogenetic tree based on the spike gene (S) sequence of 112 North American porcine epidemic diarrhea virus strains. Blue represents US non–S INDEL strains; red represents US S INDEL strains; brown represents Mexican strains; purple represents worldwide non–S INDEL strains; and pink represents global S INDEL strains. Bootstrap values are represented at key nodes. Scale bar indicates nucleotide substitutions per site. CH, China; IA, Iowa; S INDEL, insertions and deletions in the spike gene; IN, Indiana; ISU, Iowa State University; MEX, Mexico; MN, Minnesota; USA, United States of America.

Figure 3

Identification of US porcine epidemic diarrhea virus (PEDV) strains with insertions and deletions in the spike gene as potential recombinant strains. At each position of the window, the query sequence USA/Iowa107/2013 (A) or USA/Minnesota42/2013 (B) was compared with background sequences for 3 strains from China (CH/ZMZDY/11, CH/s, and AH2012). The x-axis represents the length of the PEDV genome, and the y-axis represents the similarity value. The red line represents PEDV strain CH/ZMDZY/11, the green line represents CH/S, and the blue line represents AH2012. When the query sequence is similar to the background sequence(s), the homologous regions are indicated as thick dashed lines (of the corresponding color) on the top of the plot. Arrows represent potential recombination breakpoints.