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Porcine epidemic diarrhea virus (PEDV) is newly emerging in the United States. PEDV strain USA/Colorado/2013 (CO/13) was obtained from a 7-day-old piglet with severe diarrhea, and the complete genome was sequenced to further study the PEDV outbreak in the United States.
Porcine epidemic diarrhea virus (PEDV), a member of the Coronaviridae family, is an enveloped, positive-sense, single-strand RNA virus that causes severe diarrhea and dehydration in pigs. First identified in Europe in 1971, PEDV was characterized in feeder and fattening pigs and subsequently has been identified in Belgium, Hungary, Korea, Italy, Thailand, Japan, and China (1–10). More recently, PEDV outbreaks in China have been described as more clinically severe than historic strains (1, 11, 12). In the United States, PEDV was identified on 29 April 2013 by the Iowa State University Veterinary Diagnostic Laboratory and was corroborated by the National Veterinary Services Laboratories (NVSL) on 16 May 2013 (http://www.aasv.org/news/story.php?id=6444). To determine the phylogenetic relationship of the new U.S. strain and global PEDV strains, the complete genome of PEDV CO/13 was sequenced and analyzed.
At the University of Minnesota Veterinary Diagnostic Laboratory, a fecal sample from a 7-day-old pig was processed, RNA was extracted, and the sample was found to be positive for PEDV by reverse transcription-PCR (RT-PCR) using previously published methods (2, 13, 14). The RNA was submitted to the University of Minnesota Genomics Center for Illumina TruSeq (Illumina, San Diego, CA) library preparation and next-generation sequencing (NGS) on Illumina MiSeq (Illumina, San Diego, CA). Using a template assembly (SeqMan NGen, DNAStar version 11; Madison, WI), the CO/13 NGS reads were assembled using complete PEDV reference genomes from GenBank (9, 11, 12, 15–23). The GenBank reference strains were removed to create a single sequence of CO/13. Finally, the CO/13 NGS reads were remapped to the initial sequence of CO/13 to verify the accuracy of the initial assembly. The single genomic gap of CO/13 was closed using standard Sanger sequencing technology. The complete genomic sequence of CO/13 is 28,038 nucleotides (nt), excluding the 3′ poly(A) tail. The genome arrangement and corresponding nucleotide positions are as follows: 5′ untranslated region (UTR), nt 1 to 292; replicase, nt 293 to 12646 for 1a, and nt 12601 to 20637 for 1b; spike (S), nt 20634 to 24794; open reading frame 3 (ORF3), nt 24794 to 25468; envelope (E), nt 25449 to 25679; membrane (M), nt 25687 to 26367; nucleocapsid (N), nt 26379 to 27704; and 3′ untranslated region, nt 27706 to 28038.
The complete PEDV genome of CO/13 has a nucleotide identity of 96.5 to 99.5% with other complete PEDV genomes available in GenBank, with the highest nucleotide identity (99.5%) with Chinese strain AH2012 (GenBank accession no. KC210145) (9, 11, 12, 15–23). Comparing the complete genome of CO/13 to that of PEDV reference strain CV777, CO/13 contains a 1-nt insertion (at position 48) and deletions of 5 nt in the 5′ UTR (at positions 73 and 83 to 86), while the spike gene contains insertions of 16 nt (positions 20804, 20810 to 20820, 20843, and 21053 to 21055) and deletions of 7 nt (positions 20853 and 21118 to 21124) (18).
To our knowledge, this is the first complete U.S. PEDV sequence to be released. The PEDV USA/Colorado/2013 sequence data will further our understanding of the genetic diversity of PEDVs and facilitate future research on the epidemiology and evolution of PEDVs in the United States.
The USA/Colorado/2013 PEDV sequence data have been deposited in GenBank under the accession no. KF272920.
We thank Lotus Solmonson, Mark Diehl, Amanda Foss, and Lindsey Raymond for their technical assistance and Marie Culhane for her editing.
Funding for this project was provided by the Rapid Agricultural Response Fund, established by the Minnesota legislature and administered by the University of Minnesota Agricultural Experiment Station and the University of Minnesota Veterinary Diagnostic Laboratory.
Citation Marthaler D, Jiang Y, Otterson T, Goyal S, Rossow K, Collins J. 2013. Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States. Genome Announc. 1(4):e00555-13. doi:10.1128/genomeA.00555-13.