key: cord-0002184-snq9nij4 authors: Toplak, Ivan; Ipavec, Manica; Kuhar, Urška; Kušar, Darja; Papić, Bojan; Koren, Simon; Toplak, Nataša title: Complete Genome Sequence of the Porcine Epidemic Diarrhea Virus Strain SLO/JH-11/2015 date: 2016-04-07 journal: Genome Announc DOI: 10.1128/genomea.01725-15 sha: 105268027d44ab275991e358674462f77223e882 doc_id: 2184 cord_uid: snq9nij4 Porcine epidemic diarrhea virus (PEDV) was detected for the first time in Slovenia in January 2015. The complete genome sequence of PEDV strain SLO/JH-11/2015, obtained from a fecal sample of a fattening pig with diarrhea in September 2015, is closely related to recently detected European strains. England in 1971 and, until the end of the 1990s, sporadic cases have been reported throughout Europe (1, 2) . Since 2010, severe outbreaks with high mortality have also been reported from Asia (3) . In the United States, the virus was first detected in spring 2013 and emerged through swine herds (4) (5) (6) (7) . In January 2014, a novel PEDV variant named S INDEL strain OH851 was identified in the United States (7) . Between 2014 and 2015, the S INDEL strain was also identified in Germany, France, Belgium, and Japan (8) (9) (10) (11) . In December 2014, a clinical outbreak of diarrhea was observed at a pig-fattening farm, and PEDV was confirmed for the first time in Slovenia in January 2015 by real-time PCR (12) . At the same farm, PEDV was detected again in September 2015, in three fecal samples collected from fattening pigs with acute diarrhea. Direct total RNA extraction was performed using the QIAamp viral RNA kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions and subsequently using the standard TRIzol protocol. For sequencing the complete PEDV genome, an RNA library was prepared using the Ion total RNA sequencing kit version 2 (Thermo, Fisher Scientific-Ion Torrent, Carlsbad, CA, USA) according to the manufacturer's protocol. Emulsion PCR and enrichment were carried out using the Ion PGM template OT2 200 kit (Thermo, Fisher Scientific-Ion Torrent). The amplified library was sequenced on the Ion PGM platform using the Ion PGM HiQ sequencing kit and the Ion 314 Chip version 2 (Thermo, Fisher Scientific-Ion Torrent). Reads were mapped against the reference German PEDV strain L00721 (LM645057) genome and analyzed using the DNAStar Lasergene version 10.1.1 (DNAStar, Inc., Madison, WI, USA). The size of the PEDV strain SLO/JH-11/2015 genome was 28,028 nucleotides (nt), excluding the poly-A tail. The genomic organization was found to be the same as previously described for the isolate 15V010 from Belgium (9) To our knowledge, this is the first published complete PEDV sequence from Slovenia. The data confirm that the whole-PEDVgenome sequencing is possible from complex samples without the use of virus-specific primer sets. The obtained SLO/JH-11/2015 sequence will further our understanding of the genetic diversity of PEDV strains in Slovenia and facilitate future research on the epidemiology of PEDV circulating in Europe. Nucleotide sequence accession number. The complete genome sequence of PEDV SLO/JH-11/2015 has been deposited to GenBank under accession number KU297956. A new coronavirus-like particle associated with diarrhea in swine Completion of the porcine epidemic diarrhoea coronavirus (PEDV) genome sequence Complete genome sequence of a highly prevalent isolate of porcine epidemic diarrhea virus in South China Distinct characteristics and complex evolution of PEDV strains Complete genome sequence of porcine epidemic diarrhea virus strain USA/Colorado/2013 from the United States Isolation and characterization of porcine epidemic diarrhea viruses associated with the 2013 disease outbreak among swine in the United States New variant of porcine epidemic diarrhea virus Comparison of porcine epidemic diarrhea viruses from Germany and the United States Complete genome sequence of a porcine epidemic diarrhea virus from a novel outbreak in Belgium Complete genome sequence of a porcine epidemic diarrhea S gene indel strain isolated in France in December Isolation and experimental inoculation of an S indel strain of porcine epidemic diarrhea virus in Japan First detection of porcine epidemic diarrhoea virus in Slovenia This work was supported by the Slovenian Research Agency, Program Group Animal Health, Environment and Food Safety (P4-0092).