Evolutionary and genotypic analyses of global porcine epidemic diarrhea virus strains

Abstract

Porcine epidemic diarrhea virus (PEDV), which re-emerged in China in October 2010, has spread rapidly worldwide. Detailed analyses of the complete genomes of different PEDV strains are essential to understand the relationships among re-emerging and historic strains worldwide. Here, we analysed the complete genomes of 409 strains from different countries, which were classified into five subgroup strains (i.e., GI-a, GI-b, GII-a, GII-b, and GII-c). Phylogenetic study of different genes in the PEDV strains revealed that the newly discovered subgroup GII-c exhibited inconsistent topologies between the spike gene and other genes. Furthermore, recombination analysis indicated that GII-c viruses evolved from a recombinant virus that acquired the 5' part of the spike gene from the GI-a subgroup and the remaining genomic regions from the GII-a subgroup. Molecular clock analysis showed that divergence of the GII-c subgroup spike gene occurred in April 2010, suggesting that the subgroup originated from recombination events before the PEDV re-emergence outbreaks. Interestingly, Ascaris suum, a large roundworm occurring in pigs, was found to be an unusual PEDV host, providing potential support for cross-host transmission. This study has significant implications for understanding ongoing global PEDV outbreaks and will guide future efforts to develop effective preventative measures against PEDV.

Isolation and characterization of a variant subgroup GII-a porcine epidemic diarrhea virus strain in China

“…The PEDV strains in the variant GII group appear to be genetically diverse with a gradual increase in number reported globally. reported that group GII PEDV strains can be classified into subgroups GII-a, GII-b, and GII-c, according to phylogenetic analysis of 409 complete genomes of global strains, of which the GII-c is a newly discovered subgroup [14]. In fact, the GII-c subgroup was genetically separated from the GII-a subgroup due to the inconsistent topologies between the S gene and other genes.…”

“…. Recently, analyzed the complete genomes of 409 PEDV strains form different countries, which were classified into five subgroups strains (GI-a, GI-b, GII-a, GII-b, and GII-c) [14]. Recombination analysis indicated that the GII-c subgroup strains evolved from a recombination event between subgroups GI-a and GII-a.…”

Current status of porcine epidemic diarrhoea (PED) in European pigs

“…Outbreaks of PED were observed in the Netherlands in 1989-1991, in Hungary in 1995, and in the UK in 1998. Typical epidemic outbreaks of PED with high mortality in neonatal piglets were also identified in Italy in [2005][2006] and China in 2010-2012 (8,32).…”

“…Besides porcine epidemic diarrhoea virus (PEDV), the porcine coronaviruses comprise transmissible gastroenteritis virus (TGEV), porcine respiratory coronavirus (PRCV), porcine haemagglutinating encephalomyelitis virus (PHEV), and porcine deltacoronavirus (PDCoV) (26). The clinical symptoms of PED are diarrhoea, vomiting, and dehydration which result in very high mortality among suckling piglets and large economic losses (5,8,21). Various factors influence the clinical signs of PED, mainly the age of the animals, the herd's immune status, and the virulence of the strain (18).…”

Significant inhibition of re-emerged and emerging swine enteric coronavirus in vitro using the multiple shRNA expression vector

“…Currently, vaccination is the primary measure for prevention of PEDV. However, genetic variants of PEDV have been identified in Asia, Europe, and North America since 2010 (Bevins et al, 2018;Guo et al, 2018;Su et al, 2018;Yu et al, 2018). Traditional inactivated and attenuated PEDV vaccines failed to provide robust protection against PEDV variants infection Li et al, , 2018bPark and Shin, 2018).…”