Two Distinct Genotypes of Porcine Epidemic Diarrhoea Virus in Vaccinated Pig Flocks in Shandong Province of China, 2012-2015

Abstract

As one of the top pork producers in China, Shandong Province suffered frequent outbreaks of porcine epidemic diarrhoea virus (PEDV) on pig farms from January 2012 to July 2015, resulting in significant economic losses. To better understand the prevalence situation, we conducted molecular epidemiological analyses of 38 PEDV strains isolated from 13 cities in Shandong Province. The detection rate of PEDV was 71.2% (146/205) by reverse transcription polymerase chain reaction (RT-PCR). The S genes of the 38 isolated samples were 4146 to 4161 nt in length and shared high levels of sequence identity (93.3-99.6% nt, 92.1-99.4% aa) with those of the 41 reference strains. Among the 38 strains, 31 strains that occupied 12 cities were classed into G3 genotype, while the other seven that only existed in four cities were classed into G2 genotype. In addition, the strains CH-SDLY-2-2014 and CH-SDLY-3-2014 isolated from Linyi were classed into the Gd subgenotype. Notably, there were multiple insertions or deletions in the S genes and several mutations in the neutralizing epitopes of the PEDV S protein. Overall, the results revealed that G2 and G3 are the predominant PEDV genotypes circulating in Shandong Province during 2012-2015, and Gd subgenotype in G3 group had already spread towards northern China in 2014.

Keywords: Gd subgenotype; S gene; genotype; mutation; porcine epidemic diarrhoea virus.

Figure 1

The rooted phylogenetic tree of 38 field strains homolog and other representative S gene constructed by the neighbour‐joining method within the Mega 6.0 software. Bootstrap majority consensus values on 1000 replicates are indicated at each branch point in per cent. Black solid circles indicate the 38 porcine epidemic diarrhoea virus strains isolated in this study. Bootstrap values are represented at key nodes. Scale bar represents nucleotide substitutions per site.

Figure 2

Map representing the 17 cities of Shandong Province in China. The 38 porcine epidemic diarrhoea virus (PEDV) strains were collected from 13 cities in Shandong. Black dot represents the PEDV strains in G3 genotype; black triangled dot represents the PEDV strains in Gd subgenotype; star represents the PEDV strains in G2 genotype.

Figure 3

Comparison of the antigen epitopes of S proteins of strains and reference strains. Ellipses represent the consensus amino acids. COE, SS6, SS2 and 2C10 are in the box. Strains in this study are marked with asterisks (*).