Abstract
Outbreaks of porcine epidemic diarrhoea virus (PEDV) have caused great economic losses to the global pig industry. PEDV strains with variants in the spike (S) gene have been reported in several countries. To better understand the molecular epidemiology and genetic diversity of PEDV field isolates, in this study, we characterised the complete genome sequence of a novel PEDV variant JSCZ1601 from a outbreak in China in 2016. The PEDV isolate was 28,033 nucleotides (nt) in length without the polyadenylated sequences. Phylogenetic analysis based on the full-length genome sequence of JSCZ1601 grouped it with the pandemic variants determined post-2010 into group 2 (G2). However, the S gene of JSCZ1601 formed a new subgroup separated from the subgroups containing the other G2 strains. Comparative analysis of the amino acids encoded by the S genes revealed the N-terminal of the deduced JSCZ1601 S protein had a novel two-amino-acid deletion (N58 and S59) compared with all identified genogroups. Further, compared with the reference strains, a ‘G’ insertion was detected in the 5′ terminal of the 5′UTR of the JSCZ1601. The animal experiment revealed that this strain was high pathogenic to neonatal pigs. Taken together, a PEDV strain with the new molecular characterizations and phylogenies was found in mainland China. It is necessary to strengthen the monitoring of PEDV variations.
Highlights
Porcine epidemic diarrhoea (PED) is characterised by severe watery diarrhoea, leading to dehydration and high mortality among piglets
This study showed that a porcine epidemic diarrhoea virus (PEDV) strain with the new molecular characterizations and phylogenies was found in mainland China
The comparative analyses showed that the nucleotide identities between JSCZ1601 and the strains identified post-2010 (e.g., Chinese strains JS-HZ2012, GD-A, and AH2012, and American strains PC21A, USA/Minnesota61/2013, and USA/Michigan252/2014) ranged from 98.0–99.0%, while the nucleotide identities with genomes determined ante-2010 (CV777, JS2008, DR13, and attenuated DR13) ranged from 96.6–97.4%
Summary
Porcine epidemic diarrhoea (PED) is characterised by severe watery diarrhoea, leading to dehydration and high mortality among piglets. Thereby, a comprehensive study is necessary to better understand the genetic variations and relationships between different strains, and would be helpful to find out the reason of the continuously outbreak of PEDV and develop new strategy to control and prevent PEDV infection. We found a novel PEDV field strain JSCZ1601 with amino acid deletions in the protein encoded by the S gene, and a ‘G’ insertion in the 5′terminal of the 5′UTR. This study showed that a PEDV strain with the new molecular characterizations and phylogenies was found in mainland China. This will be useful to take into consideration in the control and prevention of this disease
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
