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01.12.2017 | Short Report | Ausgabe 1/2017 Open Access

Virology Journal 1/2017

Detection and phylogenetic analyses of spike genes in porcine epidemic diarrhea virus strains circulating in China in 2016–2017

Zeitschrift:
Virology Journal > Ausgabe 1/2017
Autoren:
Qiaoling Zhang, Xinsheng Liu, Yuzhen Fang, Peng Zhou, Yonglu Wang, Yongguang Zhang

Background

Porcine epidemic diarrhea (PED), which is caused by PED virus (PEDV), is an acute and highly contagious enteric disease in swine characterized by watery diarrhea and vomiting. From 1984 to early 2010, PEDV infections occurred in the pig population in China, but there were no large-scale outbreaks [1, 2]. However, a large-scale outbreak of PED occurred at the end of 2010 and led to the most severe PED epidemic in history [3].
PEDV is an enveloped, single-stranded, positive-sense RNA virus that belongs to the order Nidovirales, the family Coronaviridae and the genus Alphacoronavirus [4]. This virus’s spike (S) protein, which is a glycosylated protein located on the envelope of the virus, consists of S1, a receptor-binding subunit, and S2, a membrane fusion subunit. The S1 domain is important for recognizing and binding to cell receptors [5, 6]. In addition, the S1 domain contains several neutralizing epitopes that stimulate the induction of neutralizing antibodies in the natural host [7, 8]; therefore, the S protein has been the primary target for the development of vaccines against PEDV and for determining genetic relatedness among PEDV isolates.
In this study, a total of 110 diarrheal fecal samples and 6 intestinal contents samples were collected from swine farms in six Chinese provinces in 2016–2017. Samples were evaluated using RT-PCR and TaqMan real-time RT-qPCR (set up in our laboratory). To determine the frequency of co-infection, we also assessed samples for other enteric pathogens, such as PDCoV, TGEV and PKV, that are closely linked to porcine diarrhea. The complete S genes from 11 representative PEDV strains were amplified and sequenced, and the GenBank accession numbers for CH/HNXJ/2017, CH/HN7/2016, CH/GSTS/2016, CH/HNXY/2017, CH/HNCD/2017, CH/HNHB/2017, CH/XJKT/2016, CH/HNLB/2017, CH/HNPJ/2017, and CH/SXXY/2017 are MF152596, MF152597, MF152598, MF152599, MF152600, MF152601, MF152602, MF152603, MF152604, and MF152605, respectively. Seventy-four reference strains were obtained from GenBank for phylogenetic analysis. A phylogenetic tree was constructed using the neighbor-joining method and MEGA version 6 [9], with bootstrap values calculated for each node from 1000 replicates. Analysis of amino acid sequences was conducted using DNAStar software (Version 3.1; DNASTAR, Madison, WI, USA).

Results and discussion

Detection results showed that 52.6% (61/116) of the samples were positive for PEDV. The positive rate for porcine kobuvirus (PKV) in the samples was 19.8% (23/116), and the rate of co-infection with PEDV and PKV was 11.2% (13/116). However, porcine delta coronavirus (PDCoV) and porcine transmissible gastroenteritis virus (TGEV) were not detected in the samples. Rates of positivity for PEDV in Gansu, Xinjiang, Henan, Hainan, Hunan and Shanxi provinces were 16.7% (1/6), 75.0% (3/4), 37.5% (12/32), 59.5% (25/42), 59.2% (16/27), and 80.0% (4/5), respectively. PEDV-positive samples were detected for the first time in Hainan Province in China.
Sequence analysis results showed that all field strains shared 97–100% nucleotide and amino acid identity with each other as well as 93–94% nucleotide identity and 92–93% amino acid identity with the CV777 strain. Compared with the CV777 vaccine strain, the strains in this study had an insertion (A133) and a deletion (G155); in addition, all of the isolated strains except CH/HNZZ47/2016 had a continuous 4-amino-acid insertion (56NNTN59), whereas the CH/HNZZ47/2016 strain had a continuous 2-amino-acid insertion (58TN59). Mutant sites in these strains were primarily located in the S1 domain of the S protein. Moreover, the three epitope regions in CV777 (aa 498–637, aa 747–754 and aa 763–770) were examined to assess mutations in the field strains. We found that the amino acid sequence at aa 747–754 was conserved between the latest field strains and CV777; however, certain mutated regions were observed in the sequences at positions 498–637 and 747–754 (Table 1).
Table 1
Analysis of amino acid mutations in epitopes domains of field strains and the CV777 vaccine strain (aa 498–637, aa 747–754, aa 763–770)
Strains
499
520
523
524
545
565
566
569
597
604
611
629
637
766
767
769
CV777
I
A
G
H
D
S
K
D
G
F
S
T
Q
P
L
D
CH/HN7/2016
 
S
      
S
   
E
 
S
S
CH/HNXJ/2017
T
V
D
     
S
   
E
L
S
S
CH/HNCD/2017
T
S
      
S
   
E
 
P
S
CH/HNHB/2017
 
S
    
N
 
S
L
  
E
 
S
S
CH/XJKT/2016
T
V
      
S
   
E
L
S
S
CH/HNLB/2017
T
 
D
R
  
V
V
S
   
E
 
S
S
CH/HNPJ/2017
T
  
L
    
S
   
E
 
S
S
CH/GSTS/2016
 
S
  
S
   
S
 
G
I
E
 
S
S
CH/SXXY/2017
 
S
      
S
   
E
 
S
S
CH/HNXY/2017
T
S
 
R
  
N
 
S
   
E
 
S
S
CH/HNZZ47/2016
 
S
   
F
  
S
   
V
 
S
S
In the phylogenetic tree based on the S gene, the S protein-encoding genes indicated that all 11 PEDV epidemic strains were of subtype G2 (Fig. 1). More specifically, CH/HNXY/2017, CH/HNCD/2017, CH/HNHB/2017, CH/SXXY/2017, CH/HN7/2016, CH/GSTS/2016 and CH/HNZZ47/2016 were categorized as subtype G2a, whereas CH/HNLB/2017, CH/HNXJ/2017, CH/HNPJ/2017, and CH/XJKT/2016 were categorized as subtype G2b (Fig. 1). In contrast, early PEDV isolates in China, such as CH/S, LZC, and the CV777 vaccine strain, are classical G1 strains.
In this study, the rate of positivity for PEDV in China in 2016–2017 exceeded 50%, indicating that PEDV has remained prevalent in China; this rate was significantly higher than those determined for earlier PEDV outbreaks in China. Although no previous reports indicated that PEDV existed in Hainan Province, in this study, PEDV was detected in samples collected from that location (with a positive rate of 59.2% (25/42)). This result indicates that PEDV has spread to Hainan Province, with positivity for PEDV detected in a high proportion of clinical samples from that province. Therefore, PEDV infection is trending toward becoming a national epidemic in China. PEDV positive provinces of China was shown in Fig. 2.
Currently, many enteric viruses are known to induce porcine diarrhea, including PEDV, TGEV, PKV, PDCoV, and porcine rotavirus (PRoV), which are closely linked to porcine diarrheal disease. An epidemiological study conducted in 2012–2014 showed that co-infection with PKV and PEDV was detected in 15.0% (47/314) of samples and that co-infection with PKV and one or more of TGEV, PDCoV, and PRoV was common [10]. In this study, the rate of co-infection with PEDV and PKV was 11.2% (13/116) in diarrhea samples. However, co-infection with PEDV and TGEV or PDCoV was not detected. Additionally, the rate of PEDV positivity was 52.6% (61/116) for samples from 2016 to 2017. The infection rate in the assessed samples was higher for PEDV than for other diarrhea viruses; this result was consistent with the findings of certain prior epidemiological surveys conducted in China [1012]. Thus, the aforementioned results indicate that PEDV remained the main pathogen causing swine diarrhea in China.
The S gene is a significant structural gene of PEDV and is thought to encode the most antigenic protein for inducing neutralizing antibodies against PEDV [13, 14]. Therefore, the S gene is used to analyze the molecular epidemiology and genetic relatedness of PEDV. In this study, the 11 field strains were classified into the G2 group according to a phylogenetic tree. This result indicated that virulent strains were prevalent in China and were responsible for PEDV outbreaks in 2016–2017. In addition, to an extent, the examined strains differed from early PEDV isolates (LZC, CH/S and CV777). This difference explains why PED outbreaks continued to occur in cases involving the use of CV777-based vaccines. Based on the amino acid sequence of the S gene, the mutant sites in these strains were primarily located in the S1 domain of the S protein. The CV777 vaccine strain has three major neutralizing epitopes: aa 498–637 (the COE gene), aa 747–754 (YSNIGVCK) and aa 763–770 (LQDGQVKI) [2, 14]. We found that strains in this study had sequence mutations at positions 498–637 and 747–754; however, the amino acid sequence at aa 747–754 was conserved between the field strain most recently isolated in our study and CV777. This result is consistent with the observation that CV777-based vaccines provided partial cross-protection against PEDV epidemic strains in China. In summary, current field strains of PEDV found in China in 2016–2017 are primarily virulent strains, and genetic variations in these strains may have led to antigenic changes and the failure of immunization.

Acknowledgments

This study was supported by the National Natural Science Foundation of China (Grant No. 31602095), the National Key Research and Development Program (2016YFD0501505) and the National Swine Industry Technology System (CARS-36).

Funding

The funding organizations played no role in the design of the study and decision to submit the manuscript for publication.

Availability of data and materials

The datasets used and analyzed in the current study are available from the corresponding author upon reasonable request.

Ethics approval and consent to participate

This work complied with the Ethical Standards of the Committee on Publication Ethics (COPE).

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

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