Evolution and Genetic Diversity of Porcine Circovirus 3 in China
Abstract
:1. Introduction
2. Material and Methods
2.1. Tissue Samples, DNA Extraction, PCR Amplification, and Sequencing
2.2. Sequence Collection, Alignment, and Phylogenetic Analysis
2.3. Selection Model Analysis
3. Results
3.1. Characterization of PCV3 Strains Circulating in Fujian
3.2. Phylogenetic and Evolution Analysis of PCV3 in China and Worldwide
3.3. Selection and Amino Acid Function Analysis
4. Discussion
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Primers | Amplicon Length (bp) | |
---|---|---|
PCV3-D-F | ACTTAGAGAACGGACTTGTAACGAA | 649 |
PCV3-D-R | AAATGAGACACAGAGCTATATTCAG | |
PCV3-1-F | ATTATGGATGCTCCTCATCGTG | 553 |
PCV3-1-R | CATCTTCTCCGCAACTTCAGTC | |
PCV3-2-F | GACTGAAGTTGCGGAGAAGATG | 789 |
PCV3-2-R | CGGCACGAAAGAAGTTTGGATT | |
PCV3-3-F | CCCACATGCGAGGGCGTTTACC | 895 |
PCV3-4-R | CGAGGCCGCTTCATCATCCACT | |
PCV2-D-F | AGAAGCTCTCTATCGGAG | 569 |
PCV2-D-R | AAGGTTGAATTCTGGCCC | |
CSFV-D-F | TAGGGTGGACGGGTGTCATAGAGT | 566 |
CSFV-D-R | AAGCATATATTGCTGGAAGTAGCT | |
PRRSV-D-F | GCCTCGTGTTGGGTGGCAGAA | 532 |
PRRSV-D-R | CGCCCTAATTGAATAGGTGACTT |
Isolated Strains | Sequence Similarity among Isolated Strains | Sequence Similarity between Isolated Strains and Reference Strain |
---|---|---|
Rep gene (nt) | 99.0–100% | 98.2–100% |
Rep gene (aa) | 99.3–100% | 97.2–100% |
Cap gene (nt) | 98.6–99.8% | 97.8–100% |
Cap gene (aa) | 98.1–100% | 96.7–100% |
Full-length (nt) | 98.85–99.80% | 97.26–99.90% |
AA | FEL | SLAC | FUBAR | MEME | ||||
---|---|---|---|---|---|---|---|---|
dN-dS | p-Value | dN-dS | p-Value | dN-dS | Post.Pro | w+ | p-Value | |
122 | 6.515 | 0.002 | 13.8 | 0.00217 | 11.731 | 0.999 | >100 | 0 |
320(24) | 2.784 | 0.027 | 6.29 | 0.0585 | 4.93 | 0.993 | >100 | 0.02 |
373(77) | 3.44 | 0.039 | 5.02 | 0.285 | 4.164 | 0.982 | >100 | 0.1 |
352(56) | 3.739 | 0.055 | 5.66 | 0.265 | 5.578 | 0.987 | >100 | 0.12 |
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Chen, Y.; Xu, Q.; Chen, H.; Luo, X.; Wu, Q.; Tan, C.; Pan, Q.; Chen, J.-L. Evolution and Genetic Diversity of Porcine Circovirus 3 in China. Viruses 2019, 11, 786. https://doi.org/10.3390/v11090786
Chen Y, Xu Q, Chen H, Luo X, Wu Q, Tan C, Pan Q, Chen J-L. Evolution and Genetic Diversity of Porcine Circovirus 3 in China. Viruses. 2019; 11(9):786. https://doi.org/10.3390/v11090786
Chicago/Turabian StyleChen, Ye, Quanming Xu, Hong Chen, Xian Luo, Qi Wu, Chen Tan, Qidong Pan, and Ji-Long Chen. 2019. "Evolution and Genetic Diversity of Porcine Circovirus 3 in China" Viruses 11, no. 9: 786. https://doi.org/10.3390/v11090786