Genomic Motifs as a Novel Indicator of the Relationship between Strains Isolated from the Epidemic of Porcine Epidemic Diarrhea in 2013-2014

Abstract

Porcine epidemic diarrhea virus (PEDV) is a positive-sense RNA virus that causes infectious gastroenteritis in pigs. Following a PED outbreak that occurred in China in 2010, the disease was identified for the first time in the United States in April 2013, and was reported in many other countries worldwide from 2013 to 2014. As a novel approach to elucidate the epidemiological relationship between PEDV strains, we explored their genome sequences to identify the motifs that were shared within related strains. Of PED outbreaks reported in many countries during 2013-2014, 119 PEDV strains in Japan, USA, Canada, Mexico, Germany, and Korea were selected and used in this study. We developed a motif mining program, which aimed to identify a specific region of the genome that was exclusively shared by a group of PEDV strains. Eight motifs were identified (M1-M8) and they were observed in 41, 9, 18, 6, 10, 14, 2, and 2 strains, respectively. Motifs M1-M6 were shared by strains from more than two countries, and seemed to originate from one PEDV strain, Indiana12.83/USA/2013, among the 119 strains studied. BLAST search for motifs M1-M6 revealed that M3-M5 were almost identical to the strain ZMDZY identified in 2011 in China, while M1 and M2 were similar to other Chinese strains isolated in 2011-2012. Consequently, the PED outbreaks in these six countries may be closely related, and multiple transmissions of PEDV strains between these countries may have occurred during 2013-2014. Although tools such as phylogenetic tree analysis with whole genome sequences are increasingly applied to reveal the connection between isolates, its interpretation is sometimes inconclusive. Application of motifs as a tool to examine the whole genome sequences of causative agents will be more objective and will be an explicit indicator of their relationship.

Fig 1. Location of the sequence motifs in the genome of PEDV.

The numbers on the x-axis represent the position of the motifs in the PEDV genome as the number of nucleotides from the 5’UTR.

Fig 2. Phylogenic tree for 119 PEDV strains and identified motifs.

(A) Phylogenetic tree based on the genomes of 119 PEDV strains isolated in 2013–2014. Phylogenetic analysis was performed using a maximum-likelihood method with general time reversible nucleotide substitution model and with a bootstrap test using 1000 replicates in the MEGA6 program. Notations on the very left side represent the clades shown by Vlasova et al. (9). (B) The presence of sequence motifs in each strain. (C) Color chart of nucleotides in the sites having inconsistencies within the 119 PEDV strains. Nucleotides in agreement with the sequence of Indiana12.83/USA/2013 are colored with respect to the type of nucleotide (a: red, t: blue, c: green, and g: yellow). To increase the discriminability of motifs, nucleotides in sites with only one inconsistent strain were not colored.