Genomic Analysis of Porcine Reproductive and Respiratory Syndrome Virus 1 Revealed Extensive Recombination and Potential Introduction Events in China
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Processing and Sequencing
2.2. Virus Isolation
2.3. Dataset
2.4. Recombination Analysis
2.5. NSP2 Polymorphic Patterns
2.6. Phylogenetic Analysis
2.7. Quantitative Reverse-Transcription PCR (RT-qPCR)
2.7.1. Design of Primers and Probe
2.7.2. RT-qPCR Assay
2.7.3. Generation of the Standard Curve
2.7.4. Sensitivity Analysis, Specificity Analysis, Reproducibility, and Repeatability Analysis
2.8. Nucleotide Sequence Accession Numbers
3. Results
3.1. Identification of PRRSV-1 Samples in Mainland China
3.2. Genomic Sequence Analysis of Three PRRSV-1 Samples
3.3. Deletion and Mutations of the Three PRRSV-1 Samples
3.4. Recombination Analysis of PRRSV-1 Samples
3.5. Comparison of NSP2 at the Amino Acid Level
3.6. Phylogenetic Analysis of Three Samples Based on the Complete Genome Sequences
3.7. Phylogenetic Analysis of Three Samples Based on the ORF5 Genome Sequences
3.8. Establishment of RT-qPCR for PRRSV-1 Samples
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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% of Identity to Lelystad Virus | |||
---|---|---|---|
HeB3 | HeB47 | HL85 | |
Complete genome (nt) | 91.3 | 93.8 | 88.4 |
pp1a (aa) | 89.8 | 92.3 | 78.7 |
pp1ab (aa) | 97.5 | 98.4 | 96.6 |
GP2 (aa) | 94 | 94.8 | 90.4 |
GP3 (aa) | 90.6 | 92.9 | 78.9 |
GP4 (aa) | 91.2 | 90.7 | 89.5 |
GP5 (aa) | 89.6 | 91.6 | 87.6 |
M (aa) | 96.5 | 98.3 | 96.5 |
N (aa) | 95.3 | 96.1 | 91.5 |
Standard Plasmid (Copies/μL) | Reproducibility (Inter-Assay) | Repeatability (Intra-Assay) | ||
---|---|---|---|---|
Mean ± SD | CV | Mean ± SD | CV | |
High (2.5 × 106) | 19.01 ± 0.03 | 0.16 | 19.15 ± 0.11 | 0.49 |
Medium (2.5 × 104) | 25.59 ± 0.16 | 0.63 | 25.67 ± 0.06 | 0.23 |
Low (2.5 × 102) | 32.51 ± 0.04 | 0.12 | 32.35 ± 0.09 | 0.28 |
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Yu, F.; Liu, L.; Tian, X.; Chen, L.; Huang, X.; Sun, Y.; Yan, Y.; Tian, Z.; Cai, X.; Liu, D.; et al. Genomic Analysis of Porcine Reproductive and Respiratory Syndrome Virus 1 Revealed Extensive Recombination and Potential Introduction Events in China. Vet. Sci. 2022, 9, 450. https://doi.org/10.3390/vetsci9090450
Yu F, Liu L, Tian X, Chen L, Huang X, Sun Y, Yan Y, Tian Z, Cai X, Liu D, et al. Genomic Analysis of Porcine Reproductive and Respiratory Syndrome Virus 1 Revealed Extensive Recombination and Potential Introduction Events in China. Veterinary Sciences. 2022; 9(9):450. https://doi.org/10.3390/vetsci9090450
Chicago/Turabian StyleYu, Fang, Liqiang Liu, Xiaoxiao Tian, Ligong Chen, Xinyi Huang, Yue Sun, Yi Yan, Zhijun Tian, Xuehui Cai, Di Liu, and et al. 2022. "Genomic Analysis of Porcine Reproductive and Respiratory Syndrome Virus 1 Revealed Extensive Recombination and Potential Introduction Events in China" Veterinary Sciences 9, no. 9: 450. https://doi.org/10.3390/vetsci9090450