Clinical signs of a European highly-pathogenic strain of China/US porcine epidemic diarrhoea 2a

Porcine Epidemic Diarrhoea (PEDv) was first recognised in the United Kingdom in 1970 (Wood 1977). In 2010 a variant of PEDv was recognised in China that resulted in severe mortality in piglets less than 10 days of age (Sun et al. 2012). In May 2013 this strain was subsequently isolated in the USA and resulted in a major outbreak from 2013 to 2015 in the Americas (Stevenson et al. 2013). It was suspected that this virus was present in Europe in 2014. To confirm this suspicion a specific property in the Ukraine was the focus of this study. It was expected that epidemiology methods would confirm that PEDv was present on this property in 2014.

The selected farm practiced weekly batches of 240 farrowing places weaning 3000 piglets per batch. The farm was specific pathogen free to Porcine Reproductive and Respiratory Syndrome virus, Mycoplasma hyopneumoniae, Aujeszky’s Disease, Brachyspira hyodysenteriae, Sarcoptes scabiei var suis, Toxigenic Pasteurella multocida, Transmissible Gastroenteritis Virus (TGE), and OIE pathogens. There were no clinical signs of Swine Influenza. The farm was conscious of biosecurity. The following infectious routes were ruled out: people; transport (feed wagons or slaughterhouse trucking) and feed. The infection was suspected to have been introduced, via the air, from a farm 1.5 km away and under different ownership. Examination of wind data demonstrated this explanation was feasible given the change in the wind direction directly between the two farms for two days prior to the first clinical signs appearing on the property under consideration.

Within hours of the believed introduction, the clinical signs of vomiting and profuse watery yellow diarrhoea spread around the farm in all age groups. The morbidity and mortality of pigs less than 10 days of age was 100%. An abortion outbreak in 36% of sows, 20 to 30 days of pregnancy occurred. A clinical diagnosis of PEDv was made following clinical and postmortem examination of the piglets. On-site testing using a lateral flow device (Antigen Rapid PED/TGE Ag Test Kit; Bionote, Korea) indicated the presence of PEDv antigen in the faeces. These findings were confirmed at the Animal and Plant Health Agency (UK), using an in-house PEDv polymerase chain reaction (PCR) and a commercially available PEDv/TGEv qRT-PCR kit (Qiagen, Hilden, Germany). The BLAST search of the 160 nucleotides RT-PCR amplicon revealed the highest similarity (99%) to several PED viruses from USA and China. The PEDv RNA was then subjected to DNase digest and converted to cDNA for preparation of sequencing libraries using a Nextera XT kit (Illumina; Illumina, San Diego, USA). Paired end sequencing was performed on an Illumina MiSeq. The consensus sequence was obtained by de novo assembly using Velvet 1.2.10 of the sequence reads that mapped to the NC003426 reference.

The discovery of this isolated PEDv virus was the first time that the China/US PED 2a strain had been isolated in Europe. The virus was catalogued as Ukraine/Poltava01/2014 strain genome (GenBank accession no. KP403954) and is 27,823 nucleotides in length (excluding the 3’ poly A tail). Nucleotide analyses of the full genome of the virus showed the highest similarity to PEDv strains reported recently from the USA, specifically strains USA/Kansas29/2013 (GenBank accession no. KJ645637.1) and USA/Colorado30/2013 (GenBank accession no. KJ645638.1) with 99.8% nucleotide identity.