3.1Single PCR/RT–PCR amplification results
200 μL of PRV, PCV2, PRRSV, CSFV and SIV positive viruses were extracted, and PCR products were extracted according to the instructions of the RNA/DNA extraction kit. PCR/ RT-PCR was used to detect the effectiveness of the designed primers for amplification of the target genes. The results showed that the expression levels of PRV, PCV2, PRRSV, CSFV and SIV positive viruses were 200 μL. The specific bands amplified by single pcr/rt-pcr for PRV, PCV2, PRRSV, CSFV and SIV were consistent with the size of the target fragment. The cloning and sequencing results of each amplified fragment showed that the amplified fragment was the expected gene fragment. The enlarged results are shown in Figure 1.
M: DL2000 Marker; N: negative sample; 1: PCR product of PRV; 2: PCR product of PCV2; 3: PCR product of PRRSV; 4: PCR product of CSFV; 5: PCR product of SIV
Fig. 1 Results of the PCR detection of PRV, PCV2, PRRSV, CSFV, and SIV
3.2Identification of the PCR products
The single PCR/RT–PCR products of PRV, PCV2, PRRSV, CSFV, and SIV were purified, cloned, and sequenced. The results showed that the amplified fragments were the specific gene fragments of each virus.
3.3.1 Optimized conditions for single PCR/RT–PCR
The optimal amounts of primers were determined with a series of experiments in which the concentrations of the primers binding the sample templates were altered. The results showed that when the upstream and downstream primers of PRV and PRRSV were added with 1µL each, and the upstream and downstream primers of PCV2, CSFV and SIV were added with 1.5µL each, the detection effect of PCR/RT-PCR was the most obvious. The optimal reaction system of PRV and PCV2 was 50µL: 10 PCR buffer 5µL, dNTPs1µL, upstream and downstream primers of PRV 1µL, upstream and downstream primers of PCV2 1.5µL, template DNA1µL, rTaq2µL, and ddH2O 39µL and 38µL respectively. The optimal reaction system of PRRSV, CSFV and SIV: reaction system was 25µL: 2×1 Step Buffer 12.5µL; PrimeScript One Step Enzyme Mix 1µL; The upstream and downstream primers of PRRSV were 1µL each, and the upstream and downstream primers of CSFV and SIV were 1.5µL each. Templates 1µL each; RNase Free H2O 9µL, 8µL, 8µL, respectively.
The annealing temperatures of the individual PCRs were tested to determine the optimum reaction conditions. PRRSV showed best amplification at an annealing temperature of 55.0 °C; PRV, PCV2, and CSFV at 56.0 °C; and SIV at 57.0 °C. (1) The optimal conditions for PRV and PCV2 were: 95 °C for 5 min; 35 cycles of 95 °C for 30s, 56.0 °C for 30s, and 72 °C for 30s, s; and 72 °C 10 min. (2) The optimal conditions for PRRSV, CSFV, and SIV were PRV (56 °C)、CSFV (56 °C)、SIV 56 (56 °C) for 30s , 72 °C 30s, 35 cycles; 72 °C for 10 min. The optimization of amplification is shown in Figure 2.
M: DL2000 Marker; 1: 51.0 °C; 2: 53 °C; 3: 55 °C; 4: 56 °C; 5: 57 °C: 6: 58 °C; 7: 60.0 °C
Fig. 2 Optimization of annealing temperaturesfor mPCR of PRV, PCV2, PRRSV, CSFV, and SIV
3.3.2 Testing the sensitivity of single PCRs/RT–PCRs
In the PCRs for single viruses, the minimum amounts of each virus detected were PRV 2.5 pg, PCV2 2.2 pg, PRRSV 3.2 pg, CSFV8.3 pg, and SIV 3.7 pg (Figure 3).
M: DL2000 Marker; 1. diluted 10−1; 2. diluted 10−2; 3. diluted 10−3; 4. diluted 10−4; 5. diluted 10−5
Fig. 3 Sensitivity of the single PCRs/RT–PCRs for PRV, PCV2, PRRSV, CSFV, and SIV
3.4 Establishment of the five-plex PCR method
3.4.1 Optimization of the five-plex PCR method
The optimal primer concentrations were determined by varying the concentrations of the primers used to bind the sample templates. The results showed that the optimum reaction conditions for the five-plex PCR in a 50 μL reaction system were: 0.5 μL (PRV, PCV2), 1.5 μL (PRRSV, CSFV), or 1 μL (SIV) of each forward and reverse primer. The result of the multiplex PCR was the best when the number of reaction cycles was 35 and the annealing temperature was 56.5 °C. The optimal reaction system was a 50 μL reaction volume containing 25 μL of 2 × One Step Buffer, 2 μL of PrimeScript One Step Enzyme Mix, 0.5 μL (PRV, PCV2), 1.5 μL (PRRSV, CSFV), or 1 μL (SIV) of each forward and reverse primer, 1 μL of each template (PRV, PCV2, PRRSV, CSFV, and SIV), and 9 μL of RNase-free H2O. The optimal cycling parameters were 50 °C for 40 min; 94 °C for 5 min; 35 cycles of 94 °C for 30s, 56.5 °C for 30 s, and 72 °C for 30 s; and 72 °C for 10 min. The optimization of the amplification results is shown in Figure 4.
M: DL2000 Marker; N: negative control; 1: 51.0 °C; 2: 51.6 °C; 3: 52.7 °C; 4: 54.5 °C; 5: 56.5 °C; 6: 58.2 °C; 7: 59.3 °C; 8: 60.0 °C
Fig. 4 Optimization of the annealing temperaturefor mPCR of PRV, PCV2, PRRSV, CSFV, and SIV
3.4.2 Specificity of the five-plex PCR method
No bands were amplified from the PEDV or PPV template with the five-plex PCR, whereas when the PRV, PCV2, PRRSV, CSFV, and SIV templates were amplified, the target fragments were the sizes of the specific bands expected. The results are shown in Figure 5.
M: DL2000 Marker; 1: PCR products of PRV, PCV2, PRRSV, CSFV, and SIV; 2: PCR products of PRV; 3: PCV2; 4: PRRSV; 5: CSFV; 6: SIV; 7: PPV; and 8: PEDV
Fig. 5 Specificity test of the mPCR for PRV, PCV2, PRRSV, CSFV, and SIV
3.4.3 Sensitivity of the five-plex PCR method
In the multiplex PCR, the minimum amounts of the various viruses detected were PRV 18 pg, PCV 22 pg, PRRSV 26 pg, CSFV 48 pg, and SIV 32 pg. The results are shown in Figure 6.
M: DL2000 Marker; 1. diluted 100; 2. diluted 10−1; 3. diluted 10−2; 4. diluted 10−3; 5. diluted 10−4; 6. diluted 10−5
Fig. 6 Sensitivity of the mPCR for PRV, PCV2, PRRSV, CSFV, and SIV
3.4.4 Five-plex PCR method used for clinical samples
The 48 clinical samples tested showed positive results. The PRV-positive rate was 13% (6/48), the PCV2-positive rate was 42% (20/48), the PRRSV-positive rate was 38% (18/48), the CSFV-positive rate was 21% (10/48), and the SIV-positive rate was 40% (19/48). The rate of double infections was 31% (15/48), the rate of triple infections was 17% (8/48), the rate of quadruple infections was 6% (3/48), and the rate of quintuple infections was 0. The correspondence between the test results and the single RT–PCR results was 100%.