Genetic Polymorphism and Natural Selection of Apical Membrane Antigen-1 in Plasmodium falciparum Isolates from Vietnam
Abstract
:1. Introduction
2. Materials and Methods
2.1. Blood Samples and Ethics
2.2. Amplification and Sequence Analysis of pfama-1
2.3. Nucleotide Sequence Polymorphism and Neutrality Test
2.4. Population Diversity of pfama-1 among Global P. falciparum Isolates
3. Results
3.1. Sequence Polymorphism of Vietnamese pfama-1
3.2. Amino Acid Polymorphisms in Vietnamese pfama-1 Compared with Global pfama-1
3.3. Nucleotide Diversity and Natural Selection of Vietnamese pfama-1
3.4. Nucleotide Diversity and Natural Selection of Global pfama-1
3.5. Recombination and Linkage Disequilibrium
3.6. Haplotype Network Analysis
3.7. Nucleotide Differentiation among Global pfama-1
3.8. Association between Natural Selection and Host Immune Pressure
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Fragment | Segregating Sites (S) | Singleton Variable Sites | Parsimony Informative Sites | Total No. of Mutations | K | H | Hd ± SD | π ± SD | dN−dS | Tajima’s D |
---|---|---|---|---|---|---|---|---|---|---|
5′-Terminal | 21 | 12 | 9 | 21 | 0.485 | 20 | 0.358 ± 0.055 | 0.0011 ± 0.0002 | −0.0018 | −2.4673 (p < 0.01) |
Domain I | 41 | 12 | 29 | 42 | 4.198 | 30 | 0.575 ± 0.052 | 0.0091 ± 0.0014 | 0.0084 | −1.3889 (p > 0.1) |
Domain II | 17 | 4 | 13 | 18 | 0.915 | 21 | 0.465 ± 0.053 | 0.0031 ± 0.0004 | 0.0020 | −1.9940 (p < 0.05) |
Domain III | 14 | 5 | 9 | 14 | 1.526 | 16 | 0.455 ± 0.053 | 0.0076 ± 0.0012 | −0.0003 | −1.0724 (p > 0.1) |
3′-Terminal | 14 | 9 | 5 | 14 | 0.772 | 17 | 0.432 ± 0.053 | 0.0023 ± 0.0003 | −0.0052 | −1.8470 (p < 0.05) |
Full | 114 | 47 | 67 | 116 | 8.062 | 73 | 0.837 ± 0.034 | 0.0043 ± 0.0006 | 0.0009 | −2.0046 (p < 0.05) |
Isolates | Segregating Sites (S) | Singleton Variable Sites | Parsimony Informative Sites | Total No. of Mutations | K | H | Hd ± SD | π ± SD | dN/dS | Tajima’s D | Fu and Li’s D | Fu and Li’s F |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Vietnam (n = 131) | 114 | 47 | 67 | 116 | 8.062 | 73 | 0.837 ± 0.034 | 0.0043 ± 0.0006 | 1.250 | −2.0046 (p < 0.05) | −3.1913 (p < 0.05) | −3.1959 (p < 0.02) |
Myanmar # (n = 58) | 78 | 16 | 62 | 79 | 19.886 | 37 | 0.948 ± 0.019 | 0.0106 ± 0.0005 | 6.524 | 0.5719 (p > 0.1) | 0.1677 (p > 0.1) | 0.3851 (p > 0.1) |
Thailand # (n = 80) | 58 | 5 | 53 | 61 | 20.621 | 21 | 0.920 ± 0.013 | 0.0110 ± 0.0002 | 6.698 | 2.2222 (p < 0.05) | 0.9572 (p > 0.1) | 1.7516 (p < 0.05) |
Philippines # (n = 55) | 61 | 3 | 58 | 62 | 21.232 | 19 | 0.916 ± 0.019 | 0.0114 ± 0.0003 | 7.200 | 1.9545 (0.1 > p > 0.05) | 1.6123 (p < 0.05) | 2.07960 (p < 0.02) |
PNG # (n = 90) | 68 | 2 | 66 | 75 | 22.923 | 28 | 0.954 ± 0.007 | 0.0123 ± 0.0002 | 7.497 | 1.8082 (0.1 > p > 0.05) | 1.6759 (p < 0.05) | 2.0760 (p < 0.02) |
Solomon Islands # (n = 50) | 56 | 3 | 53 | 57 | 22.044 | 9 | 0.862 ± 0.021 | 0.0118 ± 0.0003 | 7.023 | 2.5455 (p < 0.05) | 1.5447 (p < 0.05) | 2.2804 (p < 0.02) |
Vanuatu # (n = 85) | 50 | 6 | 44 | 50 | 18.905 | 5 | 0.633 ± 0.028 | 0.0101 ± 0.0003 | 6.471 | 2.8973 (p < 0.01) | 0.8642 (p > 0.1) | 2.0039 (p < 0.05) |
Ghana # (n = 37) | 75 | 7 | 68 | 85 | 26.261 | 32 | 0.992 ± 0.008 | 0.0141 ± 0.0003 | 7.423 | 1.0674 (p > 0.1) | 1.2179 (p > 0.1) | 1.38500 (p > 0.1) |
Tanzania # (n = 62) | 81 | 8 | 73 | 89 | 25.444 | 47 | 0.989 ± 0.005 | 0.0136 ± 0.0002 | 8.135 | 1.1819 (p > 0.1) | 1.1635 (p > 0.1) | 1.4020 (p > 0.1) |
n | Ra | Rb | Rm | |
---|---|---|---|---|
Vietnam | 131 | 0.0000 | 0.001 | 20 |
Myanmar # | 78 | 0.0141 | 26.3 | 24 |
Thailand # | 38 | 0.0243 | 45.3 | 20 |
Philippines # | 61 | 0.0218 | 40.8 | 17 |
PNG # | 68 | 0.0500 | 93.4 | 28 |
Solomon Islands # | 56 | 0.0120 | 22.5 | 14 |
Vanuatu # | 50 | 0.0010 | 1.8 | 9 |
Ghana # | 75 | 0.0921 | 172 | 27 |
Tanzania # | 81 | 0.0915 | 171 | 28 |
Vietnam | Myanmar # | Thailand # | Philippines # | PNG # | SI # | Vanuatu # | Ghana # | Tanzania # | |
---|---|---|---|---|---|---|---|---|---|
Vietnam | 11.56767 | 12.82408 | 11.95679 | 14.11411 | 11.92480 | 12.32934 | 12.07054 | 13.64608 | |
Myanmar # | 0.40780 | 20.15798 | 20.35295 | 21.58878 | 20.68805 | 19.15425 | 22.14497 | 20.15798 | |
Thailand # | 0.37881 | 0.06073 | 20.87018 | 21.83959 | 21.16846 | 19.73726 | 22.40481 | 22.72679 | |
Philippines # | 0.41382 | 0.08390 | 0.03818 | 22.28146 | 21.61888 | 19.81950 | 23.25483 | 23.46398 | |
PNG # | 0.37343 | 0.05281 | 0.03818 | 0.02319 | 22.60884 | 20.97135 | 23.89528 | 25.95093 | |
SI # | 0.42009 | 0.09605 | 0.06636 | 0.03529 | 0.03529 | 20.06783 | 23.83759 | 23.92600 | |
Vanuatu # | 0.40551 | 0.09740 | 0.10535 | 0.06689 | 0.06689 | 0.04933 | 21.13622 | 21.66300 | |
Ghana # | 0.37955 | 0.07802 | 0.04140 | 0.04167 | 0.03640 | 0.04953 | 0.12425 | 25.74924 | |
Tanzania # | 0.39934 | 0.08139 | 0.05865 | 0.05787 | 0.03662 | 0.05782 | 0.14141 | 0.00019 |
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Kang, J.-M.; Lê, H.G.; Võ, T.C.; Naw, H.; Yoo, W.G.; Sohn, W.-M.; Trinh, N.T.M.; Quang, H.-H.; Na, B.-K. Genetic Polymorphism and Natural Selection of Apical Membrane Antigen-1 in Plasmodium falciparum Isolates from Vietnam. Genes 2021, 12, 1903. https://doi.org/10.3390/genes12121903
Kang J-M, Lê HG, Võ TC, Naw H, Yoo WG, Sohn W-M, Trinh NTM, Quang H-H, Na B-K. Genetic Polymorphism and Natural Selection of Apical Membrane Antigen-1 in Plasmodium falciparum Isolates from Vietnam. Genes. 2021; 12(12):1903. https://doi.org/10.3390/genes12121903
Chicago/Turabian StyleKang, Jung-Mi, Hương Giang Lê, Tuấn Cường Võ, Haung Naw, Won Gi Yoo, Woon-Mok Sohn, Nguyen Thi Minh Trinh, Huynh-Hong Quang, and Byoung-Kuk Na. 2021. "Genetic Polymorphism and Natural Selection of Apical Membrane Antigen-1 in Plasmodium falciparum Isolates from Vietnam" Genes 12, no. 12: 1903. https://doi.org/10.3390/genes12121903