Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus

Abstract

Porcine epidemic diarrhea virus (PEDV) has caused severe economic losses both recently in the United States (US) and historically throughout Europe and Asia. Traditionally, analysis of the spike gene has been used to determine phylogenetic relationships between PEDV strains. We determined the complete genomes of 93 PEDV field samples from US swine and analyzed the data in conjunction with complete genome sequences available from GenBank (n=126) to determine the most variable genomic areas. Our results indicate high levels of variation within the ORF1 and spike regions while the C-terminal domains of structural genes were highly conserved. Analysis of the Receptor Binding Domains in the spike gene revealed a limited number of amino acid substitutions in US strains compared to Asian strains. Phylogenetic analysis of the complete genome sequence data revealed high rates of recombination, resulting in differing evolutionary patterns in phylogenies inferred for the spike region versus whole genomes. These finding suggest that significant genetic events outside of the spike region have contributed to the evolution of PEDV.

Keywords: Bayesian analysis; Complete genome; Molecular analysis; Porcine epidemic diarrhea virus.

Fig. 1

Nucleotide and amino acid entropy analysis. The x-axis represents position while the y-axis represents entropy level. The PEDV non-structural and structural proteins are annotated below each plot. (A) Entropy levels for nucleotide sequences. Black line represents the variance threshold of 0.8. (B) Entropy levels for amino acid sequences. Black line represents the variance threshold of 0.6. Arrows indicate general areas expressing high levels of variance.

Fig. 2

Areas of recombination in the PEDV genome. Recombinant regions within the PEDV genome. (A) The PEDV genome with excised recombinant areas highlighted in red. The red arrows designate excision of the recombinant sequence. (B) Recombination in strain Minnesota211, with major and minor parent sequences provided. The blue bars represent sequence originating from the major parent while red bars represent sequence originating from the minor (donor) parent.(For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 3

Concatenated genome bayesian phylogenetic tree. A time-scaled MCC phylogenetic tree of the full PEDV genome, excluding recombinant regions and sequences. The posterior probabilities are labeled at the major nodes. Branches are colored by country of origin. The red arrow denotes a clade of non-INDEL strains that group with US and European S-INDELs. Note the classical CV777 strain is not included in the figure. The historical strains are represented in clade A. The minor US clade includes the US and European S-INDELs (clade b) and the non-US INDEL (represented by the red arrow). The Major US clade includes a smaller subclade (clade C) separate out from the rest of the US major clade (clade D).(For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 4

S1 domain bayesian phylogenetic tree. A time-scaled MCC phylogenetic tree of the PEDV S1 domain. Branches are shaded by country of origin. Clade A consists of S-INDELs and classical strains, including sequences from America, Europe, and China. Clade B includes global non S-INDEL pathogenic sequences.

Fig. 5

S1 domain pAPN RBD alignment and protein models. Amino acid alignment and protein model visualizations of the pAPN RBD. (A) An alignment of the putative C-terminal receptor-binding domain (RBD) representing diverse residues within the American strains. Identical residues are represented as dots while residues that differ from the consensus are colored. Red boxes outline the four specific porcine aminopeptidase-N (pAPN) receptor binding regions. The attenuated vaccine strain is marked by a red dot while a S-INDEL strain is marked by a blue dot. (B) A tertiary model view of the C-terminal RBD, with the four regions of the pAPN RBD (labeled 1 through 4) are highlighted in orange, cyan, blue and magenta, respectively. (C) The pAPN RBD with the residue changes in North American strains compared to the vaccine strain DR13 highlighted in red. (D) The pAPN RBD with the residue changes in Asian strains compared to the vaccine strain DR13 highlighted in red. (E) A monomer model of the PEDV spike protein, with the C-terminal RBD represented in green, dark blue represents the S2 region, light blue represents the S1 region, and yellow represents the N-terminal RBD. (F) A theoretical tertiary structure model of the PEDV spike protein. Blue represents the S1 region, with the specific N- and C-terminal RBDs highlighted in yellow and green, respectively. The pAPN-RBD is shown in violet.(For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)