Genotype Shift of Malaysian Porcine Circovirus 2 (PCV2) from PCV2b to PCV2d within a Decade
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Animals
2.2. Molecular Detection of PCV2
2.3. Pairwise Sequence Comparison (PASC) Analysis
2.4. Phylogenetic Analysis and Genotyping
2.5. Nucleotide Sequence Polymorphism Analysis
2.6. Rates of Substitution
3. Results
3.1. Molecular Detection of PCV2
3.2. Pairwise Sequence Comparison (PASC)
3.3. Phylogenetic Analysis and Genotyping
3.4. Nucleotide Sequence Polymorphism Analysis
3.5. Nucleotide Sequence Polymorphism Analysis
3.6. Rates of Substitution
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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PCV2 PCR Detection Rate | Domestic Pig | Abattoir | Wild Boar | |||
---|---|---|---|---|---|---|
Northern Malaysia | Central Malaysia | Southern Malaysia | Overall | |||
% PCR Positive (Animals) | 93.10% (27/29) | 82.76% (24/29) | 71.43% (15/21) | 83.54% (66/79) | 94.74% (18/19) | 100.00% (28/28) |
% PCR Positive (Farms) | 92.86% (13/14) | 85.71% (12/14) | 66.67% (6/9) | 83.78% (31/37) | - | - |
Production Age Group | % PCR Positive (Number of Positive Animals/Tested Animal) |
---|---|
Fetus | 100% (7/7) |
Piglet | 100% (2/2) |
Weaner | 80.36% (45/56) |
Grower | 83.33% (10/12) |
Sow | 100% (2/2) |
Detection Status of Tested Pig (Number of Individuals) | PCV2 Positive | PCV2 Negative |
---|---|---|
PCV3 Positive | 21 | 1 |
PCV3 Negative | 39 | 12 |
Marker Nucleotide Position | 157 A | 162 T | 513 C | 585 T | 643 A | |
---|---|---|---|---|---|---|
Malaysian PCV2d Sequences | ||||||
KL44/OM524605 | A | T | A | T | A | |
SL37/OM524602 | A | T | A | T | A | |
PG201L/OM524626 | A | T | A | T | A | |
PG242L/OM524638 | A | T | A | T | A | |
PG39L/OM524603 | A | T | A | T | A | |
PW199L/OM524625 | A | T | A | T | A | |
WB2/OM524650 | T | A | C | T | A | |
WB5/OM524653 | A | T | A | T | A | |
WB10/OM524657 | T | T | C | T | A | |
% Sequences not matching marker nucleotides | 2.63% (2/76) | 1.32% (1/76) | 9.21% (7/76) | 0.00% | 0.00% |
PCV2 Genotype | Tests of Neutrality | |||||
---|---|---|---|---|---|---|
Tajima’s D | Fu and Li’s D | Fu and Li’s F | ||||
Test Statistic | Statistical Significance, p-Value | Test Statistic | Statistical Significance, p-Value | Test Statistic | Statistical Significance, p-Value | |
PCV2a | −1.2028 | >0.10 | −2.2422 | 0.10 > p > 0.05 | −2.2331 | 0.10 > p > 0.05 |
PCV2b | −2.1293 | <0.05 | −3.3600 | <0.05 | −3.4549 | <0.02 |
PCV2d | −2.5171 | <0.001 | −5.8800 | <0.02 | −5.2945 | <0.02 |
PCV2 Genotype | Positive Selection | Negative Selection | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Total Positively Selected Codon | Selection Pressure Inference Methods | Statistical Consensus across Methods | Total Negatively Selected Codons | Selection Pressure Inference Methods | Statistical Consensus across Methods | |||||||||||
FUBAR | FEL | SLAC | MEME | n = 1 | n = 2 | n = 3 | n = 4 | FUBAR | FEL | SLAC | n = 1 | n = 2 | n = 3 | |||
PCV2a | 3.86% (9/233) | 3 | 1 | 0 | 7 | 8 | 0 | 1 | 0 | 13.73% (32/233) | 29 | 31 | 14 | 4 | 14 | 14 |
PCV2b | 1.72% (4/233) | 3 | 0 | 0 | 1 | 4 | 0 | 0 | 0 | 13.73% (32/233) | 30 | 22 | 9 | 12 | 11 | 9 |
PCV2d | 3.00% (7/233) | 3 | 1 | 1 | 6 | 5 | 1 | 0 | 1 | 13.30% (31/233) | 27 | 26 | 9 | 9 | 13 | 9 |
PCV2 Genotype | ORF2 aa Site with Hx Values > 0.0 | Lowest Hx Value | Highest Hx Value | Standard Deviation, σ |
---|---|---|---|---|
PCV2a (36) | 23.61% (55/233) | 0.127 | 1.192 | 0.208 |
PCV2b (58) | 15.02% (35/233) | 0.087 | 0.743 | 0.111 |
PCV2d (103) | 31.76% (74/233) | 0.055 | 0.898 | 0.108 |
PCV2 Genotype | Mean Rate of Substitution (Substitution per Site per Year) | 95% Highest Posterior Density (HPD) | Effective Sample Size (ESS) |
---|---|---|---|
PCV2a | 4.746 × 10−4 | 8.463 × 10−4 | 246,638 |
PCV2b | 6.571 × 10−4 | 1.024 × 10−3 | 255,628 |
PCV2d | 2.111 × 10−3 | 2.925 × 10−3 | 68,174 |
Combined analysis for all genotypes | 1.102 × 10−3 | 1.374 × 10−3 | 82,401 |
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Tan, C.Y.; Thanawongnuwech, R.; Arshad, S.S.; Hassan, L.; Fong, M.W.C.; Ooi, P.T. Genotype Shift of Malaysian Porcine Circovirus 2 (PCV2) from PCV2b to PCV2d within a Decade. Animals 2022, 12, 1849. https://doi.org/10.3390/ani12141849
Tan CY, Thanawongnuwech R, Arshad SS, Hassan L, Fong MWC, Ooi PT. Genotype Shift of Malaysian Porcine Circovirus 2 (PCV2) from PCV2b to PCV2d within a Decade. Animals. 2022; 12(14):1849. https://doi.org/10.3390/ani12141849
Chicago/Turabian StyleTan, Chew Yee, Roongroje Thanawongnuwech, Siti Suri Arshad, Latiffah Hassan, Michelle Wai Cheng Fong, and Peck Toung Ooi. 2022. "Genotype Shift of Malaysian Porcine Circovirus 2 (PCV2) from PCV2b to PCV2d within a Decade" Animals 12, no. 14: 1849. https://doi.org/10.3390/ani12141849