Genetic Characterization and Pathogenicity of a Novel Recombined Porcine Reproductive and Respiratory Syndrome Virus 2 among Nadc30-Like, Jxa1-Like, and Mlv-Like Strains
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and Virus Isolation
2.2. RNA Extraction and Full-Genome Sequencing
2.3. Genome Alignment and Phylogenetic Analysis
2.4. Recombinant Analysis of Strain SCN17
2.5. Pathogenicity Analysis of Strain SCN17
2.6. Statistical Analysis
3. Results
3.1. Full-Genome Characterization and Homology Analysis
3.2. Sequence Analysis of Nsp2, GP5, and 3′-UTR
3.3. Phylogenetic Analysis
3.4. Recombination Analysis of SCN17
3.5. Pathogenicity Analysis of SCN17
3.5.1. Clinical Symptoms
3.5.2. Viremia and PRRSV-Specific Antibodies
3.5.3. Macroscopic and Microscopic Lesions in the Lungs
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of Interest
References
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Genomic Region | NADC30 | VR-2332 | JXA1 | CH-1a | QYYZ | RespPRRS MLV (Vaccine Strain) |
---|---|---|---|---|---|---|
Pairwise % identity (nt/aa) | ||||||
Complete genome | 92.3 | 86.7 | 82.9 | 83.4 | 80.3 | 86.8 |
5′UTR | 93.2 | 96.9 | 91.3 | 94.4 | 90.8 | 96.9 |
nsp1α | 91.9/96.1 | 98.7/98.3 | 91.1/96.1 | 93.9/98.3 | 89.1/95.4 | 98.7/98.3 |
nsp1β | 91.6/91.6 | 79.5/77.3 | 78.8/76.4 | 78.7/73.9 | 67.7/66.8 | 79.1/76.8 |
nsp2 | 93.5/91.5 | 69.5/65.0 | 67.6/62.7 | 67.2/62.4 | 67.4/62.4 | 69.5/64.9 |
nsp3 | 91.6/96.5 | 92.0/96.1 | 84.6/93.0 | 86.5/93.5 | 78.8/88.4 | 92.0/96.1 |
nsp4 | 85.9/92.6 | 98.5/99.0 | 89.2/94.1 | 91.3/96.1 | 82.0/91.3 | 98.5/99.0 |
nsp5 | 90.2/92.9 | 98.0/97.6 | 89.4/93.5 | 91.8/92.9 | 81.2/90.7 | 98.4/98.2 |
nsp6 | 93.8/100 | 100/100 | 95.8/93.8 | 93.8/93.8 | 93.3/93.1 | 100/100 |
nsp7a | 95.7/96.0 | 89.7/96.0 | 85.5/91.9 | 85.9/93.3 | 78.4/90.8 | 89.7/96.0 |
nsp7b | 93.6/95.5 | 81.8/79.1 | 77.0/74.5 | 78.8/75.5 | 72.8/71.5 | 81.8/79.1 |
nsp8 | 94.8/93.3 | 89.6/88.9 | 85.9/88.9 | 86.7/88.9 | 78.6/90.5 | 89.6/88.9 |
nsp9 | 90.9/97.7 | 96.4/98.9 | 90.7/97.3 | 91.1/97.2 | 78.6/95.6 | 96.4/98.9 |
nsp10 | 87.4/67.0 | 98.3/95.5 | 89.6/73.4 | 91.8/79.8 | 87.2/95.6 | 98.3/95.7 |
nsp11 | 92.4/97.3 | 91.6/94.6 | 90.4/96.4 | 91.5/96.4 | 84.1/94.0 | 92.2/96.0 |
nsp12 | 95.2/94.8 | 87.8/91.5 | 87.8/92.8 | 88.5/91.5 | 82.5/90.3 | 88.0/91.5 |
GP2a | 94.7/93.4 | 87.0/88.3 | 86.0/86.8 | 86.3/87.5 | 84.2/89.7 | 86.8/87.9 |
ORF2b | 95.5/93.2 | 91.0/87.8 | 89.6/89.2 | 89.2/86.5 | 90.7/89.9 | 90.5/86.5 |
GP3 | 94.6/91.4 | 82.9/79.2 | 83.5/80.8 | 83.3/80.8 | 79.1/80.0 | 83.0/80.0 |
GP4 | 95.9/96.1 | 87.7/87.2 | 85.8/88.3 | 87.0/88.3 | 83.0/86.8 | 87.7/87.2 |
GP5 | 89.3/89.6 | 86.1/84.2 | 90.4/87.6 | 90.3/88.1 | 81.3/81.9 | 86.1/84.2 |
M | 95.8/97.7 | 89.0/92.6 | 88.4/93.1 | 87.4/92.0 | 88.0/92.9 | 89.1/92.6 |
N | 96.5/96.8 | 90.9/91.1 | 89.8/89.5 | 90.9/91.1 | 85.4/88.8 | 90.9/91.1 |
3′UTR | 89.4 | 92.7 | 84.8 | 85.4 | 85.3 | 89.4 |
Recombinant Event | Breakpoints | Major (Similarity) | Minor (Similarity) | p-Value of the Detection Methods | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Beginning | Ending | RDP | GENECONV | BootScan | MaxChi | Chimaera | SiScan | 3Seq | |||
1 | 15 | 705 | NADC30 (94.3%) | RespPRRS MLV (98.4%) | 4.370 × 10−29 | 6.623 × 10−22 | 1.109 × 10−29 | 5.911 × 10−11 | 5.319 × 10−11 | 5.136 × 10−12 | NS |
2 | 4822 | 6425 | NADC30 (94.2%) | RespPRRS MLV (98.7%) | 2.367 × 10−92 | 4.075 × 10−85 | 1.104 × 10−92 | 5.846 × 10−22 | 2.225 × 10−27 | 2.942 × 10−33 | 8.000 × 10−50 |
3 | 7982 | 10,787 | NADC30 (94.2%) | RespPRRS MLV (98.6%) | 1.451 × 10−113 | 2.545 × 10−115 | 3.212 × 10−116 | 2.761 × 10−30 | 7.540 × 10−38 | 4.304 × 10−51 | 1.183 × 10−111 |
4 | 13,604 | 13,907 | NADC30 (94.2%) | JXA1 (96.4%) | 7.527 × 10−23 | 3.589 × 10−12 | 2.247 × 10−23 | 2.110 × 10−08 | 1.489 × 10−09 | 2.605 × 10−06 | NS |
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Zhou, L.; Kang, R.; Yu, J.; Xie, B.; Chen, C.; Li, X.; Xie, J.; Ye, Y.; Xiao, L.; Zhang, J.; et al. Genetic Characterization and Pathogenicity of a Novel Recombined Porcine Reproductive and Respiratory Syndrome Virus 2 among Nadc30-Like, Jxa1-Like, and Mlv-Like Strains. Viruses 2018, 10, 551. https://doi.org/10.3390/v10100551
Zhou L, Kang R, Yu J, Xie B, Chen C, Li X, Xie J, Ye Y, Xiao L, Zhang J, et al. Genetic Characterization and Pathogenicity of a Novel Recombined Porcine Reproductive and Respiratory Syndrome Virus 2 among Nadc30-Like, Jxa1-Like, and Mlv-Like Strains. Viruses. 2018; 10(10):551. https://doi.org/10.3390/v10100551
Chicago/Turabian StyleZhou, Long, Runmin Kang, Jifeng Yu, Bo Xie, Changying Chen, Xingyu Li, Jing Xie, Yonggang Ye, Lu Xiao, Jinling Zhang, and et al. 2018. "Genetic Characterization and Pathogenicity of a Novel Recombined Porcine Reproductive and Respiratory Syndrome Virus 2 among Nadc30-Like, Jxa1-Like, and Mlv-Like Strains" Viruses 10, no. 10: 551. https://doi.org/10.3390/v10100551