Whole genome sequencing of the porcine epidemic diarrhea virus by Ion Torrent sequencing technology

In 2014, the first clinical case of porcine epidemic diarrhoea (PED) in Europe was described. In January 2015, the first PED virus-infected herd in Slovenia was confirmed by polymerase chain reaction. The determination of the whole viral genome has been conducted from stool samples, collected from infected herd in September 2015. Ion Torrent next-generation sequencing technology has been used for the first time. Whole genome analysis of PEDV strain SLO/JH-11/2015 and the phylogenetic comparison with the other PEDV strains have confirmed the emergence of previously confirmed SINDEL strain identified in Germany, France and Belgium. The PEDV genome obtained in this research is, according to our knowledge, the fourth published whole genome of PEDV in Europe and the first in Slovenia.