Cells and virus
Human embryo kidney (HEK) 293 T (ATCC CRL-1573) and Vero 76 (ATCC CRL-1587) cells were cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 50 μg/mL gentamycin and 10 % fetal bovine serum. PichiaPink Strain 1 (Invitrogen) was grown in YPD medium. Insect Sf9 cells (Gibco) were grown in Sf-900 serum-free medium (ThermoFisher Scientific).
PEDV strain USA/Colorado/2013 (GeneBank accession no. KF272920) was provided by Diagnostic Virology Laboratory (NVLS, Ames, USA), and the virus was propagated on Vero 76 cells in DMEM containing 50 μg/mL gentamycin, 2 μg/mL TPCK-trypsin and 0.2 % bovine serum albumin.
Expression of recombinant S1 protein in yeast cells
Yeast codon optimized PEDV S1 gene (coding animo acids 1–734) with the 3’-end polyhistidine coding sequence was synthesized by GenScript. Synthetic S1 gene was digested with restriction enzymes MlyI-KpnI and cloned into the pPinkα-HC vector (ThermoFisher Scientific) into StuI-KpnI sites. Expression of the recombinant protein was performed as recommended by manufacturers (ThermoFisher Scientific). Briefly, PichiaPink strain 1 (ade2
−) was electroporated with pPinkα-S1 linearized plasmid DNA and plated on PAD (Pichia Adenine Dropout) agar plates for selecting transformants. After incubation at 30 °C for 5 days, white colonies were screened for expression of S1. Recombinant yeast cells were grown in buffered glycerol-complex medium (BMGY) and induction was performed in buffered methanol-complex medium (BMMY) with 0.5 % methanol. To prevent non-specific cleavage of S1 protein by yeast cell proteases, aprotinin and phenylmethylsulfonyl fluoride (PMSF) were added during the induction phase at 1 μg/mL each. Yeast cells were grown at 30 °C for 4 days and centrifuged at 3000 g for 5 min at room temperature and supernatant was collected for protein purification.
Expression of recombinant S1 protein in insect cells
S1 coding region of PEDV genome was PCR amplified using primers (5’-TCCGATGAATTCGCCACCATGAAGTCACTCACCTATTTTTGG-3’ and 5’- CTAGATCTCGAGTCAGTGGTGATGATGGTGGTGGAAGCCAGGGAGTTCGCGG-3’). The resulting PCR product was cloned into the XhoI, EcoRI sites of pFastBac vector (ThermoFisher Scientific). Cellfectin® II Reagent (ThermoFisher Scientific) was used for transfecting Sf9 cells in Grace’s insect cell culture medium (ThermoFisher Scientific) for generating recombinant baculovirus. All the steps of generating the recombinant baculovirus full length genome, screening, rescue of recombinant baculovirus and large scale production of S1 protein in Sf9 cells was performed according to manufacturer’s recommendations for Bac-to-Bac Baculovirus Expression System (ThermoFisher Scientific). Briefly, the Sf9 cells were grown at 30 °C for 24 h in the Sf-900 II SFM (ThermoFisher Scientific) at an orbital shaker incubator in two 1 L flasks (500 mL culture volume). Sf9 cells were infected with the recombinant baculovirus at an MOI of 1 and kept for 7 days in the incubator for secretion of the recombinant S1 protein. The supernatant was collected by centrifuging the insect cells at 500 g for 5 min at room temperature.
Expression of recombinant S1 protein in mammalian cells
The S1 ORF plus C-terminal his10 tag (codon optimized for mammalian expression) together with a proceeding Kozak sequence, was cloned downstream of a human CMV promoter plus intron, contained within an in-house episomal vector; elements downstream of the S1 ORF included a woodchuck hepatitis post-transcriptional regulatory element and bovine growth hormone poly-adenylation site (DNA sequence of constructs are available upon request). Constructs were transfected into HEK293T cells using Turbofect (ThermoFisher Scientific) according to the manufacturer’s instructions. Cells stably maintaining the episomal constructs were selected by puromycin. For protein production, stably transfected cells were grown in SFM4HEK293 medium (ThermoFisher Scientific) with shaking at 370C and 5 % CO2. Supernatant was harvested and processed for purification.
Purification of recombinant S1 protein
Purifications of supernatants from the recombinant yeast cells and recombinant baculovirus infected cells were performed in the same way. First, equal volume of wash buffer was added to the samples (50 mM sodium phosphate, 0.3 M sodium chloride, 10 mM imidazole pH 8.0) and then pH was adjusted to 8.0. Next, the samples were passed through 0.2 μm filters to remove cellular debris and applyed to the HisSelect Ni Affinity (Sigma Aldrich) column. The column was washed with three sample volumes of wash buffer, followed by protein elution in one sample volume of elution buffer (50 mM sodium phosphate, 0.3 M sodium chloride, 250 mM imidazole pH 8.0). The eluate was concentrated using the Amicon Ultra-15 (EMD Millipore) filters and protein concentration was determined by a Bradford assay, and the protein quality was analysed by Western blotting.
Supernatants from HEK293T cultures were concentrated 5-fold by tangential flow and protein was purified using His60 Ni Superflow (Clontech) in accordance with the manufacturer’s instructions. Purified protein was dialysed against PBS and quantified using a Bradford assay.
PNGase F and O-Glycosidase was purchased from NEB. Briefly, 2 μg of purified S1 protein was added with 1 μL of 10X glycoprotein denaturing buffer (NEB) in total of 10 μL of reaction volume and denatured at 95 °C for 5 min. Then, the mixture was chilled on ice for 30 s followed by centrifugation for 10 s at 10,000 X g. Reaction volume was increased to 20 μL by adding 2 μL 10X GlycoBuffer (NEB), 2 μL 10 % NP40, water and 1 μL of enzyme PNGase F or 2 μL of O-glycosidase and incubated at 37 °C for 1 h. The extent of glycosylation was analyzed by mobility shift on SDS-PAGE followed by Western blotting.
Protein samples were heated in the SDS sample loading buffer (0.375 M Tris pH 6.8, 12 % SDS, 60 % glycerol, 0.6 M DTT, 0.06 % bromophenol blue) at 95 °C for 5 min. Samples were separated by electrophoresis in 10 % SDS-PAGE followed by transfer of proteins onto nitrocellulose membrane in Towbin’s buffer (0.025 M Tris, 0.192 M glycine, 20 % methanol) at 4 °C for 1 h at 100 V. The membrane was blocked with Blocker Blotto (Thermo Scientific) at room temperature for 1 h. The membrane was incubated in anti-His rabbit antibody (1:2000) in Tris-buffered saline (0.1 M Tris, 0.9 % NaCl) added with 0.1 % Tween-20 and 1 % skim milk at 4 °C on orbital shaker overnight. Membrane was washed three times in TBST, and alkaline phosphate goat anti-rabbit IgG antibody (1:5000) was added and incubated at room temperature for 1 h on orbital shaker. Unbound antibody was washed by three TBST washes and bands were visualized using an AP Conjugate Substrate Kit (BioRad).
All the animal experiments were performed in the animal containment level 3 laboratories of VIDO-InterVac. All pigs were maintained and euthanized as per the protocol, approved by the University of Saskatchewan’s Animal Research Ethics Board and adhered to the Canadian Council on Animal Care guidelines for humane animal use. Two commercial crossbred pregnant sows were used in this study. The sows were vaccinated intramuscularly on both sides of neck with either purified S1 protein (400 μg per dose) or saline mixed with TriAdj adjuvant  three times, 14 days apart (days 0, 14 and 28). Blood samples were collected for serum on days 0, 11, 28 and 35. Farrowing was induced at 16 days after the last vaccination. Colostrum samples were collected on the day of farrowing. Piglets were allowed to suckle their dams, and on the 4th day of their life they were orally challenged with live PEDV (3×102 TCID50 per piglet). Clinical signs, diarrhea, death and weight of challenged piglets were monitored daily throughout the study. Blood samples of all the piglets were collected on the day of challenge for analysis. Rectal swabs were collected from each of the piglets daily for analyzing the presence of viral RNA by qRT-PCR.
Immulon 2 HB 96-well plates (ThermoFisher Scientific) were coated overnight with 0.1 ml/well of 0.5 μg/ml purified recombinant S1 protein. The plates were washed five times in phosphate buffer saline (PBS) containing 0.05 % Tween 20. Sera serially diluted in assay diluent buffer (0.1 M PBST, 0.05 % Tween-20, 1 % fish gelatin) were added to respective wells. After a 2 h incubation, the plates were washed, and 1/3000 diluted HRP-conjugated anti-pig IgG antibodies were added. After 1 h incubation, the plates were washed, and developed with 1-Step Ultra TMB-ELISA substrate solution (ThermoFisher Scientific). The reaction was stopped by adding 30 μL of 2 M sulphuric acid to each well, and optical density values were measured at 450 nm using an ELISA plate reader.
A colostrum sample (1 mL) collected on the day of farrowing was treated with 30 μL rennet (5 mg/mL, Sigma-Aldrich). The colostrum was then incubated at 37 °C for 1 h. Once solidified, the whey was separated by centrifugation at 6000 x g for 20 min. Whey samples were diluted in PBS containing 0.05 % Tween 20 and 1 % casein and applied at four-fold dilution on ELISA plate coated with the purified S1 protein. Plate was incubated at room temperature for 2 h. The plates were washed six times with water between each step. Mouse anti-pig IgA (AbD Serotec) was applied to the plate at 1:300 dilution and incubated for 1 h. Donkey anti-mouse HRP conjugate (Jackson Immunoresearch) was applied at 1:5000 dilution and incubated for 1 h, and 1-Step Ultra TMB-ELISA substrate solution (ThermoFisher Scientific) was applied to the plates to develop the reaction. Then, the reaction was stopped and red as described above.
The presence of PEDV-specific neutralizing antibodies in serum of sows and piglets was determined using a serum neutralizing (SN) test. Briefly, serum samples were diluted 2-fold and mixed with an equal volume of 200 TCID50 of PEDV in each well. After a 1 h incubation at 37 °C, 100 μL of virus-serum mix was added to 96-well microtiter plate with a confluent monolayer of Vero 76 cells. The cells were incubated for 3 h at 37 °C in 5 % CO2 and unbound virus particles were removed with two washes of DMEM. Then, 100 μL DMEM supplemented with trypsin (2 μg/mL) was added to the cells and incubated for 1 h at 37 °C in 5 % CO2. Thereafter, 100 μL DMEM containing trypsin (2 μg/mL) and albumin (0.2 %) were added to each well and the cells were incubated for the period of 7 days at 37 °C in 5 % CO2. The virus neutralizing antibody titers were expressed as the reciprocal of the highest serum dilution that showed no CPE in the cells. PEDV positive and negative control sera were also included in the tests.
Viral RNA isolation and qRT-PCR
Piglet fecal swabs were collected in 0.5 ml DMEM on every day post-infection and stored at -80 °C. RNeasy Plus Kit (Qiagen) was used for RNA isolation from the faecal swab samples. qRT-PCR was conducted in two steps: cDNA synthesis and PCR reactions. cDNA synthesis was performed with 1 μL (50 ng/μL) random hexamers, 1 μL of 10 mM dNTPs, and RNA in 13 μL volume and heated at 65 °C for 5 min and chilled on ice followed by addition of 4 μL of 5X First-strand buffer, 1 μL of 0.1 M DTT and 1 μL of RNaseOUT (ThermoFisher Scientific) and 1 μL of SuperScript III enzyme (ThermoFisher Scientific) in final volume of 20 μL. The reaction conditions include 25 °C for 5 min, 50 °C for 60 min and 70 °C for 15 min. The PCR reaction was performed in a total volume of 20 μL with 2 μl cDNA using Power SYBR green Master Mix (Qiagen); primers (5’-GCAACAACAGGTCCAGATCTC-3’ and 5’-CTCCACGACCCTGGTTATTTC-3’) were present at 0.5 μM. PCR cycling conditions were: 95 °C for 10 min and 41 cycles of 95 °C for 15 s, 60 °C for 1 min.
All data were analyzed using the GraphPad Prism (Version 6) software. Differences between two groups were assessed using unpaired two-tailed t-test. Differences were considered significant if P < 0.05. Survival curves were created using the product limit method of Kaplan and Meier, and comparison of the curves was done using the logrank test.