key: cord-0001222-9zk7t1un authors: Marthaler, Douglas; Jiang, Yin; Otterson, Tracy; Goyal, Sagar; Rossow, Kurt; Collins, James title: Complete Genome Sequence of Porcine Epidemic Diarrhea Virus Strain USA/Colorado/2013 from the United States date: 2013-08-08 journal: Genome Announc DOI: 10.1128/genomea.00555-13 sha: 7763fdd2366c612dc01aaf0173ea6bb8f1ed0bf9 doc_id: 1222 cord_uid: 9zk7t1un 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. 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 ϭ6444). 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) (16) (17) (18) (19) (20) (21) (22) (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 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) (16) (17) (18) (19) (20) (21) (22) (23) . Comparing the complete genome of CO/13 to that of PEDV reference strain CV777, CO/13 contains a 1-nt insertion 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. Nucleotide sequence accession number. The USA/Colorado/ 2013 PEDV sequence data have been deposited in GenBank under the accession no. KF272920. 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