Background
Methods
Sample collection
DNA extraction and molecular assays
Statistical analysis
Results
Detection and identification of Plasmodium species
Plasmodium falciparum genetic diversity
Pfmsp2
Neutral STRs loci
n | TA1 | TA102 | ARA2 | TA87 | Pfk2 | TA81 | TA42 | Pfg377 | TA109 | Mean | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Humans
|
TBs
| 299 |
Na
| 13 | 12 | 9 | 15 | 14 | 11 | 14 | 7 | 17 | 12 |
Rs
| 12 | 11 | 8 | 12 | 13 | 10 | 10 | 5 | 13 | 10 | |||
uH
| 0.852 | 0.832 | 0.787 | 0.838 | 0.877 | 0.829 | 0.344 | 0.612 | 0.799 | 0.75 | |||
BsM
| 195 |
Na
| 11 | 11 | 9 | 14 | 12 | 11 | 7 | 7 | 15 | 11 | |
Rs
| 10 | 9 | 8 | 9 | 10 | 9 | 5 | 5 | 9 | 8 | |||
uH
| 0.846 | 0.848 | 0.771 | 0.829 | 0.857 | 0.792 | 0.293 | 0.642 | 0.811 | 0.74 | |||
BsN
| 104 |
Na
| 11 | 8 | 8 | 9 | 11 | 10 | 11 | 5 | 9 | 9 | |
Rs
| 10 | 7 | 8 | 8 | 11 | 10 | 7 | 5 | 7 | 8 | |||
uH
| 0.859 | 0.771 | 0.809 | 0.844 | 0.877 | 0.868 | 0.424 | 0.531 | 0.747 | 0.75 | |||
BsW
| 141 |
Na
| 10 | 11 | 7 | 13 | 12 | 11 | 8 | 5 | 9 | 10 | |
Rs
| 9 | 10 | 7 | 10 | 11 | 10 | 6 | 5 | 8 | 8 | |||
uH
| 0.819 | 0.854 | 0.797 | 0.840 | 0.874 | 0.851 | 0.307 | 0.634 | 0.805 | 0.753 | |||
BsD
| 158 |
Na
| 11 | 10 | 9 | 11 | 12 | 10 | 11 | 7 | 13 | 10 | |
Rs
| 10 | 8 | 8 | 9 | 11 | 9 | 8 | 5 | 9 | 9 | |||
uH
| 0.866 | 0.817 | 0.766 | 0.841 | 0.871 | 0.798 | 0.375 | 0.592 | 0.788 | 0.746 | |||
Mosquitoes
|
TMq
| 228 |
Na
| 13 | 12 | 8 | 11 | 12 | 10 | 6 | 8 | 18 | 11 |
Rs
| 12 | 12 | 8 | 11 | 12 | 10 | 6 | 7 | 16 | 10 | |||
uH
| 0.88 | 0.874 | 0.810 | 0.849 | 0.833 | 0.779 | 0.365 | 0.712 | 0.869 | 0.77 | |||
MqM
| 130 |
Na
| 12 | 11 | 7 | 9 | 12 | 9 | 6 | 6 | 15 | 10 | |
Rs
| 10 | 11 | 7 | 8 | 10 | 8 | 6 | 5 | 13 | 9 | |||
uH
| 0.851 | 0.870 | 0.780 | 0.845 | 0.845 | 0.753 | 0.462 | 0.713 | 0.848 | 0.77 | |||
MqN
| 98 |
Na
| 9 | 7 | 7 | 8 | 8 | 8 | 3 | 6 | 14 | 8 | |
Rs
| 9 | 7 | 7 | 8 | 8 | 8 | 3 | 6 | 11 | 7 | |||
uH
| 0.862 | 0.815 | 0.760 | 0.814 | 0.816 | 0.747 | 0.191 | 0.718 | 0.837 | 0.73 | |||
MqW
| 86 |
Na
| 11 | 11 | 5 | 9 | 12 | 9 | 6 | 7 | 8 | 9 | |
Rs
| 10 | 11 | 5 | 9 | 11 | 9 | 6 | 6 | 8 | 8 | |||
uH
| 0.882 | 0.904 | 0.741 | 0.823 | 0.846 | 0.774 | 0.428 | 0.717 | 0.808 | 0.769 | |||
MqD
| 142 |
Na
| 10 | 7 | 8 | 9 | 10 | 8 | 4 | 5 | 17 | 9 | |
Rs
| 10 | 7 | 8 | 9 | 10 | 8 | 4 | 5 | 14 | 8 | |||
uH
| 0.873 | 0.796 | 0.834 | 0.826 | 0.825 | 0.788 | 0.300 | 0.713 | 0.873 | 0.758 |
Drug resistant associated genes
SNPs: Pfcrt, Pfmdr1, Pfdhfr and Pfdhps
STR loci flanking Pfdhfr and Pfdhps genes
Genetic diversity and linkage disequilibrium
Microsatellites | Sampled populations - Miyobo | Sampled populations - Ngonamanga | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Single mutant | Double mutant | Triple mutant | All samples | Triple mutant | |||||||||
( N=10) | (N=37) | (N=17) | (N=64) | (N=82) | |||||||||
R
s
|
H
e
|
R
s
|
H
e
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R
s
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H
e
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R
s
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H
e
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F
ST
|
P
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R
s
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H
e
| ||
Loci
flanking
dhfr
gene
| Dhfr 0.3 | 3 | 0.51 | 3 | 0.32 | 2 | 0.15 | 3 | 0.33 | 0.02 | NS | 7 | 0.26 |
Dhfr 4.4 | 1 | 0.00 | 2 | 0.14 | 2 | 0.17 | 2 | 0.10 | -0.04 | NS | 3 | 0.10 | |
Dhfr 5.3 | 3 | 0.56 | 2 | 0.18 | 1 | 0.00 | 2 | 0.24 | 0.10 | 0.03 | 3 | 0.08 | |
All loci | 2 | 0.36 | 2 | 0.21 | 2 | 0.11 | 2 | 0.22 | 0.03 | 0.05 | 4 | 0.15 | |
Neutral
loci
| TA1 | 4 | 0.82 | 5 | 0.83 | 6 | 0.89 | 6 | 0.85 | 0.04 | 0.04 | 12 | 0.87 |
TA102 | 4 | 0.64 | 7 | 0.88 | 5 | 0.84 | 6 | 0.79 | 0.03 | NS | 8 | 0.78 | |
ARA2 | 4 | 0.69 | 5 | 0.77 | 6 | 0.79 | 5 | 0.75 | -0.03 | NS | 9 | 0.81 | |
TA87 | 4 | 0.87 | 6 | 0.85 | 5 | 0.81 | 6 | 0.84 | 0.01 | NS | 9 | 0.84 | |
PfPK2 | 5 | 0.93 | 6 | 0.86 | 5 | 0.85 | 6 | 0.88 | -0.03 | NS | 12 | 0.87 | |
TA81 | 4 | 0.87 | 5 | 0.81 | 4 | 0.71 | 5 | 0.80 | -0.04 | NS | 10 | 0.87 | |
TA42 | 3 | 0.60 | 2 | 0.11 | 2 | 0.28 | 2 | 0.32 | 0.06 | NS | 8 | 0.36 | |
Pfg377 | 3 | 0.67 | 3 | 0.56 | 3 | 0.65 | 3 | 0.62 | -0.04 | NS | 7 | 0.55 | |
TA109 | 5 | 0.86 | 5 | 0.80 | 4 | 0.79 | 5 | 0.82 | 0.04 | 0.03 | 8 | 0.75 | |
All loci | 4 | 0.77 | 5 | 0.72 | 4 | 0.73 | 5 | 0.74 | <0.01 | NS | 9 | 0.74 |
Microsatellites | Sampled populations - Miyobo | Sampled populations - Ngonamanga | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Single mutant | Double mutant | All samples ( N=60) | Double mutant | Triple mutant | All samples (N=85) | ||||||||||||
(N=63) | (N=22) | ||||||||||||||||
(N=17) | ( N=43) | ||||||||||||||||
R
s
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H
e
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R
s
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H
e
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R
s
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H
e
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F
ST
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P
|
R
s
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H
e
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R
s
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H
e
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R
s
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H
e
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F
ST
|
P
| ||
Loci
flanking
dhps
gene
| Dhps 0.8 | 4 | 0.60 | 5 | 0.75 | 5 | 0.67 | 0.02 | NS | 9 | 0.81 | 5 | 0.64 | 9 | 0.73 | 0.06 | 0.01 |
Dhps 4.3 | 6 | 0.83 | 5 | 0.77 | 6 | 0.80 | <0.01 | NS | 7 | 0.78 | 4 | 0.71 | 7 | 0.75 | 0.13 | <0.01 | |
Dhps 7.7 | 6 | 0.79 | 7 | 0.84 | 8 | 0.82 | 0.09 | <0.01 | 10 | 0.85 | 6 | 0.67 | 10 | 0.76 | 0.14 | <0.01 | |
All loci | 5 | 0.74 | 6 | 0.79 | 6 | 0.76 | 0.04 | <0.01 | 9 | 0.81 | 5 | 0.67 | 9 | 0.74 | 0.11 | <0.01 | |
Neutral
loci
| TA1 | 5 | 0.79 | 8 | 0.87 | 8 | 0.83 | 0.04 | NS | 9 | 086 | 8 | 0.88 | 9 | 0.87 | <0.01 | NS |
TA102 | 5 | 0.78 | 9 | 0.87 | 9 | 0.83 | 0.04 | 0.01 | 6 | 0.75 | 7 | 0.86 | 7 | 0.80 | <-0.01 | NS | |
ARA2 | 6 | 0.79 | 6 | 0.69 | 7 | 0.74 | 0.06 | <0.01 | 7 | 0.80 | 6 | 0.82 | 7 | 0.81 | -0.01 | NS | |
TA87 | 5 | 0.79 | 8 | 0.84 | 7 | 0.82 | 0.05 | 0.02 | 8 | 0.83 | 7 | 0.87 | 8 | 0.85 | 0.02 | NS | |
PfPK2 | 5 | 0.83 | 8 | 0.80 | 8 | 0.81 | 0.11 | 0.02 | 10 | 0.87 | 8 | 0.87 | 11 | 0.87 | 0.02 | <0.05 | |
TA81 | 5 | 0.77 | 6 | 0.78 | 7 | 0.78 | -0.02 | NS | 9 | 0.88 | 8 | 0.83 | 9 | 0.85 | <0.01 | NS | |
TA42 | 1 | 0.00 | 4 | 0.29 | 3 | 0.14 | 0.03 | NS | 5 | 0.44 | 3 | 0.18 | 5 | 0.31 | 0.05 | 0.04 | |
Pfg377 | 3 | 0.56 | 4 | 0.59 | 3 | 0.57 | <-0.01 | NS | 5 | 0.59 | 3 | 0.40 | 5 | 0.50 | 0.01 | NS | |
TA109 | 6 | 0.86 | 6 | 0.81 | 6 | 0.83 | -0.02 | NS | 5 | 0.72 | 5 | 0.60 | 6 | 0.66 | 0.16 | <0.01 | |
All loci | 5 | 0.69 | 6 | 0.73 | 6 | 0.71 | 0.03 | <0.01 | 7 | 0.75 | 6 | 0.70 | 7 | 0.72 | 0.03 | 0.01 |