Phylodynamic and Genetic Diversity of Canine Parvovirus Type 2c in Taiwan
Abstract
:1. Introduction
2. Results
2.1. Sequence Comparison and Amino Acid Sequence Analysis
2.2. Evolutionary Rates and the Most Recent Common Ancestor of CPV-2 and CPV-2c
2.3. Phylodynamics of CPV-2c
2.4. Selection Pressures in the CPV-2 VP2 Protein
3. Discussion
4. Materials and Methods
4.1. Ethics Statement and Study Design
4.2. Complete VP2 Gene Amplification and Sequencing
4.3. Phylodynamic Analysis
4.4. Selection Pressure of CPV2 VP2 Protein Genes
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Country | Year | Amino Acid at Position | Accession Numbers | ||||||
---|---|---|---|---|---|---|---|---|---|
5 | 267 | 324 | 370 | 383 | 410 | 440 | |||
Taiwan | 2015 | A | Y a | I a | R a | R a | L a | T | KU244254 |
2015 | A | Y a | I a | R a | R a | P | T | KX421787 | |
2015 | G a | Y a | I a | R a | Q | P | T | KX421786 | |
2016 | G a | Y a | I a | R a | Q | P | T | KX421788, KX421789 | |
China | 2009 | A | Y | I | Q | Q | P | T | GU380303 |
2009 | A | F | Y | Q | Q | P | T | GU380305 | |
2014 | G | Y | I | R | Q | P | T | KR611522, KT162005 | |
Argentina | 2008–2009 | A | F | Y | Q | Q | P | T | JF414818–JF414820 |
2009–2010 | A | F | Y | Q | Q | P | A | JF414821–JF414825 | |
2010 | A | F | Y | Q | Q | P | T | JF414826 | |
Belgium | 2008 | A | F | Y | Q | Q | P | T | FJ005247 |
Ecuador | 2012 | A | F | Y | Q | Q | P | T | KF149962–KF149965, KF149967–KF149971, KF149984, |
2012 | A | F | Y | Q | Q | P | S | KF149966 | |
Germany | 1997–1999 | A | F | Y | Q | Q | P | T | FJ005196–FJ005204 |
Greece | 2008–2009 | A | F | Y | Q | Q | P | T | GQ865518, GQ865519 |
Italy | 2000–2010 | A | F | Y | Q | Q | P | T | FJ222821, FJ005195, FJ005205–FJ005213, FJ005215–FJ005234, FJ005237–FJ005245, FJ005248–FJ005251, HQ025913 |
India | 2014 | A | F | Y | Q | Q | P | T | KP071956 |
Spain | 2006–2008 | A | F | Y | Q | Q | P | T | FJ005214, FJ005246 |
Uruguay | 2006–2011 | A | F | Y | Q | Q | P | T | KC196079–KC196093, KC196080–KC196093, KC196095–KC196109, KC196111–KC196114, KM457103–KM457110, KM457115–KM457131, KM457142 |
2010 | A | F | Y | Q | Q | P | A | KC196094 | |
USA | 2007 | A | F | Y | Q | Q | P | T | FJ005235 |
2007 | A | F | Y | Q | Q | P | A | FJ005236 | |
Vietnam | 2004 | A | F | Y | Q | Q | P | T | AB120727 |
TMRCA | Substitution Rates Sub/Site/Year (10−4) | Mean Relative Substitution Rate | SE of Mean | |
---|---|---|---|---|
VP2 gene | 4.586 (3.284~6.076) | |||
CPV-2 | 1973 (1963–1978) a | |||
CPV-2c | 1990 (1984–1996) | 6.071 (4.277~8.132) | ||
CPV-2c Taiwanese strains | 2011 (2010–2013) | |||
1st + 2nd codon position | 0.4 (0.302~0.495) | 5.215 × 10−4 | ||
3rd codon position | 2.199 (2.011~2.396) | 1.043 × 10−3 |
Positively Selected Sites | No. of Negatively Selected Sites | Mean dN/dS | |||||
---|---|---|---|---|---|---|---|
SLAC a | FEL a | FUBA b | SLAC a | FEL a | FUBAR b | ||
CPV-2 VP2 gene | Non | Non | 426 | 8 | 46 | 31 | 0.108 |
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Lin, Y.-C.; Chiang, S.-Y.; Wu, H.-Y.; Lin, J.-H.; Chiou, M.-T.; Liu, H.-F.; Lin, C.-N. Phylodynamic and Genetic Diversity of Canine Parvovirus Type 2c in Taiwan. Int. J. Mol. Sci. 2017, 18, 2703. https://doi.org/10.3390/ijms18122703
Lin Y-C, Chiang S-Y, Wu H-Y, Lin J-H, Chiou M-T, Liu H-F, Lin C-N. Phylodynamic and Genetic Diversity of Canine Parvovirus Type 2c in Taiwan. International Journal of Molecular Sciences. 2017; 18(12):2703. https://doi.org/10.3390/ijms18122703
Chicago/Turabian StyleLin, Yung-Cheng, Shu-Yun Chiang, Hung-Yi Wu, Jih-Hui Lin, Ming-Tang Chiou, Hsin-Fu Liu, and Chao-Nan Lin. 2017. "Phylodynamic and Genetic Diversity of Canine Parvovirus Type 2c in Taiwan" International Journal of Molecular Sciences 18, no. 12: 2703. https://doi.org/10.3390/ijms18122703
APA StyleLin, Y. -C., Chiang, S. -Y., Wu, H. -Y., Lin, J. -H., Chiou, M. -T., Liu, H. -F., & Lin, C. -N. (2017). Phylodynamic and Genetic Diversity of Canine Parvovirus Type 2c in Taiwan. International Journal of Molecular Sciences, 18(12), 2703. https://doi.org/10.3390/ijms18122703