Updated Phylogenetic Analysis of the Spike Gene and Identification of a Novel Recombinant Porcine Epidemic Diarrhoea Virus Strain in Taiwan.

New variants of porcine epidemic diarrhoea virus (PEDV) causing a highly contagious intestinal disease, porcine epidemic diarrhoea virus (PED), have resulted in high mortality in suckling pigs across several countries since 2013. After 2015, the prevalence of the genogroup 2b (G2b) PEDVs decreased in a cyclical pattern with endemic seasonal outbreaks occasionally seen. To better understand the genetic diversity of PEDVs recently circulating in Taiwan, full-length spike (S) genes of 31 PEDV strains from 28 pig farms collected during 2016-2018 were sequenced. While the majority of S gene sequences (from 27/28 farms) were closely related to the previous G2b PEDV strains, increased genetic diversities leading to several nonsynonymous mutations scattering in the neutralizing epitopes of the S gene were detected in PEDVs recently circulating in Taiwan. Furthermore, novel recombinant variants, the PEDV TW/Yunlin550/2018 strains exhibiting recombinant events between a previously isolated Taiwan PEDV G2b strain and a wild-type PEDV G1a strain, were identified and further classified into a new genogroup, G1c. These results provide updated information about the genetic diversity of currently circulating PEDVs in the field and could help to develop more suitable strategies for controlling this disease.

[1]  I. Cheng,et al.  Identification of Neutralizing Monoclonal Antibodies Targeting Novel Conformational Epitopes of the Porcine Epidemic Diarrhoea Virus Spike Protein , 2019, Scientific Reports.

[2]  S. Xiao,et al.  Evolutionary and genotypic analyses of global porcine epidemic diarrhea virus strains , 2018, Transboundary and emerging diseases.

[3]  Changhee Lee,et al.  Genomic and antigenic characterization of porcine epidemic diarrhoea virus strains isolated from South Korea, 2017 , 2018, Transboundary and emerging diseases.

[4]  Z. Poljak,et al.  Herd‐level prevalence and incidence of porcine epidemic diarrhoea virus (PEDV) and porcine deltacoronavirus (PDCoV) in swine herds in Ontario, Canada , 2018, Transboundary and emerging diseases.

[5]  T. Hirai,et al.  Molecular characterization of US-like and Asian non-S INDEL strains of porcine epidemic diarrhea virus (PEDV) that circulated in Japan during 2013–2016 and PEDVs collected from recurrent outbreaks , 2018, BMC Veterinary Research.

[6]  P. Gauger,et al.  Identification of porcine epidemic diarrhea virus variant with a large spike gene deletion from a clinical swine sample in the United States , 2018, Virus Genes.

[7]  T. Opriessnig,et al.  Evaluation of the efficacy of a commercial inactivated genogroup 2b-based porcine epidemic diarrhea virus (PEDV) vaccine and experimental live genogroup 1b exposure against 2b challenge , 2017, Veterinary Research.

[8]  Xinsheng Liu,et al.  Detection and phylogenetic analyses of spike genes in porcine epidemic diarrhea virus strains circulating in China in 2016–2017 , 2017, Virology Journal.

[9]  J. Christopher-Hennings,et al.  The S2 glycoprotein subunit of porcine epidemic diarrhea virus contains immunodominant neutralizing epitopes , 2017, Virology.

[10]  Xiaoya Zhao,et al.  Sequence analysis of the spike gene of Porcine epidemic diarrhea virus isolated from South China during 2011–2015 , 2017, Journal of veterinary science.

[11]  I. Cheng,et al.  Evaluation and Comparison of the Pathogenicity and Host Immune Responses Induced by a G2b Taiwan Porcine Epidemic Diarrhea Virus (Strain Pintung 52) and Its Highly Cell-Culture Passaged Strain in Conventional 5-Week-Old Pigs , 2017, Viruses.

[12]  B. Bosch,et al.  Cell Attachment Domains of the Porcine Epidemic Diarrhea Virus Spike Protein Are Key Targets of Neutralizing Antibodies , 2017, Journal of Virology.

[13]  H. Chiou,et al.  Phylogenetic Analysis of the Spike (S) Gene of the New Variants of Porcine Epidemic Diarrhoea Virus in Taiwan , 2017, Transboundary and emerging diseases.

[14]  N. V. Diep,et al.  Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation , 2017, PloS one.

[15]  Gaiping Zhang,et al.  Genome sequencing and analysis of a novel recombinant porcine epidemic diarrhea virus strain from Henan, China , 2016, Virus Genes.

[16]  F. Schmoll,et al.  First detection, clinical presentation and phylogenetic characterization of Porcine epidemic diarrhea virus in Austria , 2015, BMC Veterinary Research.

[17]  Changhee Lee.  Porcine epidemic diarrhea virus: An emerging and re-emerging epizootic swine virus , 2015, Virology Journal.

[18]  A. Petrov,et al.  Comparison of Porcine Epidemic Diarrhea Viruses from Germany and the United States, 2014 , 2015, Emerging infectious diseases.

[19]  Bongkyun Park,et al.  Novel Porcine Epidemic Diarrhea Virus Variant with Large Genomic Deletion, South Korea , 2014, Emerging infectious diseases.

[20]  A. Vlasova,et al.  Distinct Characteristics and Complex Evolution of PEDV Strains, North America, May 2013–February 2014 , 2014, Emerging infectious diseases.

[21]  Jiyong Zhou,et al.  Evidence of Recombinant Strains of Porcine Epidemic Diarrhea Virus, United States, 2013 , 2014, Emerging infectious diseases.

[22]  Y. Berhane,et al.  Investigation into the Role of Potentially Contaminated Feed as a Source of the First‐Detected Outbreaks of Porcine Epidemic Diarrhea in Canada , 2014, Transboundary and emerging diseases.

[23]  R. Morrison,et al.  Evidence of infectivity of airborne porcine epidemic diarrhea virus and detection of airborne viral RNA at long distances from infected herds , 2014, Veterinary Research.

[24]  M. Chiou,et al.  US-Like Strain of Porcine Epidemic Diarrhea Virus Outbreaks in Taiwan, 2013–2014 , 2014, The Journal of veterinary medical science.

[25]  Leyi Wang,et al.  New Variant of Porcine Epidemic Diarrhea Virus, United States, 2014 , 2014, Emerging infectious diseases.

[26]  K. Schwartz,et al.  Emergence of Porcine epidemic diarrhea virus in the United States: clinical signs, lesions, and viral genomic sequences , 2013, Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc.

[27]  Vincent Moulton,et al.  RDP3: a flexible and fast computer program for analyzing recombination , 2010, Bioinform..

[28]  Changhee Lee,et al.  Contribution of the porcine aminopeptidase N (CD13) receptor density to porcine epidemic diarrhea virus infection , 2009, Veterinary Microbiology.

[29]  Jianfei Chen,et al.  Identification of two novel B cell epitopes on porcine epidemic diarrhea virus spike protein , 2008, Veterinary Microbiology.

[30]  B. X. Li,et al.  Porcine aminopeptidase N is a functional receptor for the PEDV coronavirus , 2007, Virology.

[31]  V. Shepherd,et al.  Virus glycosylation: role in virulence and immune interactions , 2007, Trends in Microbiology.

[32]  Chul-Joong Kim,et al.  Phage-displayed peptides having antigenic similarities with porcine epidemic diarrhea virus (PEDV) neutralizing epitopes , 2006, Virology.

[33]  R. Baric,et al.  Coronavirus Genome Structure and Replication , 2005, Current topics in microbiology and immunology.

[34]  M. Pensaert,et al.  A new coronavirus-like particle associated with diarrhea in swine , 2005, Archives of Virology.

[35]  A. Bridgen,et al.  Completion of the Porcine Epidemic Diarrhoea Coronavirus (PEDV) Genome Sequence , 2004, Virus Genes.

[36]  Y. Jang,et al.  Identification of the epitope region capable of inducing neutralizing antibodies against the porcine epidemic diarrhea virus. , 2002, Molecules and cells.

[37]  M. Pensaert,et al.  Prevalence of infections with enzootic respiratory and enteric viruses in feeder pigs entering fattening herds , 1994, Veterinary Record.