Porcine Epidemic Diarrhea Virus and Discovery of a Recombinant Swine Enteric Coronavirus, Italy.

M Beatrice Boniotti,Douglas Marthaler,Enrica Sozzi,Antonio Lavazza,Alice Papetti,Chiara Chiapponi,Paolo Bonilauri,Silvia Faccini,Giovanni Alborali,Paolo Cordioli

doi:10.3201/eid2201.150544

Abstract

Porcine epidemic diarrhea virus (PEDV) has been detected sporadically in Italy since the 1990s. We report the phylogenetic relationship of swine enteric coronaviruses collected in Italy during 2007–2014 and identify a drastic shift in PEDV strain variability and a new swine enteric coronavirus generated by recombination of transmissible gastroenteritis virus and PEDV.

Highlights

Porcine epidemic diarrhea virus (PEDV) has been detected sporadically in Italy since the 1990s
During 2007–2014, most (92%) samples collected from the Po Valley in Italy were positive for PEDV by ELISA; only 72% were positive by pan-CoV PCR
Because we were investigating the presence of PEDV or Transmissible gastroenteritis virus (TGEV) in samples with clinical signs of diarrhea, the high occurrence of PEDV may not reflect the actual prevalence of PEDV in Italy

Summary

Cluster III Cluster III Cluster III

On the basis of the partial sequences from RdRp and the S1 and M genes, the strains from Italy clustered into 3 temporally divided groups, suggesting 3 independent virus entries. Cluster II was identified in Emilia Romagna (n = 1) and Lombardia (n = 8). Cluster III was identified in Emilia Romagna at 2 swine farms. Swine Enteric Coronaviruses, Italy single S1 gene segment was sequenced from clusters I and II (PEDV/Italy/7239/2009 and SeCoV/Italy/213306/2009, respectively). Because of the recent outbreak of PEDV in Europe, the 2 positive samples from cluster III (PEDV/ Italy/178509/2014 and PEDV/Italy/200885/2014) were sequenced (Figure 1, panel A). The whole genome was obtained from only clusters I and II (PEDV/Italy/7239/2009 and SeCoV/Italy/213306/2009, respectively; Figure 1, panel B). The complete S gene of SeCoV/Italy/213306/2009 shared 92% and 90% nt identity with the prototype European strain PEDV CV777 and the original highly virulent North American strain Colorado 2013, respectively, and the remaining genome shared a 97% nt identity with the virulent strains TGEV H16 and TGEV Miller M6. Wholegenome analysis of PEDV/Italy/7239/2009 showed that it grouped with the global PEDV strains [6] and shared ≈97% nt identity with PEDV strains CV777, DR13 virulent, and North American S-INDEL strain OH851 (Table 2)

Conclusions

Findings

Strain identification