Background
Methods
RDT sampling
Study size
DNA extraction
PCR-corrected RDT positivity and negativity
Genetic analysis
Controls and duplicates
Library preparation
Quality trimming and base calling
Mixed infections
Statistics
Bias
Results
Evaluation of the applicability of RDTs as source of DNA for NGS-based molecular surveillance
PCR-corrected RDT positivity and negativity
PCR success-rate for single copy genes during library preparation
Molecular markers of anti-malarial resistance
Frequencies of haplotypes | |||||
---|---|---|---|---|---|
Gene | Haplotype | 2014 | 2015 | 2016 | p-value (trend) |
18S success | 76% (n = 228) | 80% (n = 676) | 66% (n = 486) | ||
pfcrt c. 72-76 | CVMNK (wildtype) | 67% (45/67) | 60% (187/311) | 45% (99/219) | 0.006 |
CVIET (mutant) | 33% (22/67) | 40% (124/311) | 55% (120/219) | 0.006 | |
pfmdr1 c. 86 + 184 | NF | 57% (43/75) | 73% (212/290) | 62% (116/187) | 0.052 |
NY | 29% (22/75) | 23% (68/290) | 29% (55/187) | 0.052 | |
YF | 11% (8/75) | 3% (9/290) | 9% (16/187) | 0.084 | |
YY | 3% (2/75) | 0% (1/290) | 0% (0/187) | 0.109 | |
pfdhfr c. 51 + 59 + 108 | NCS (wildtype) | 17% (14/82) | 4% (18/407) | 4% (17/443) | 0.001 |
IRN (triple mutant) | 73% (60/82) | 92% (373/407) | 85% (376/443) | 0.001 | |
pfdhps c. 436 + 437 + 540 + 581 + 613 | AAKAA (wildtype) | 25% (17/68) | 25% (23/93) | 23% (39/170) | 0.956 |
AGKAA (mutant) | 15% (10/68) | 6% (6/93) | 11% (19/170) | 0.439 | |
SAKAA (wildtype) | 26% (18/68) | 29% (27/93) | 21% (36/170) | 0.083 | |
SGKAA (mutant) | 34% (23/68) | 38% (35/93) | 43% (73/170) | 0.448 | |
pfdhfr c. 51 + 59 + 108 + pfdhps c. 437 | IRN + G (quadruple mutant) | 33% (16/49) | 49% (97/199) | 51% (94/185) | 0.072 |
Gene | Codon | Amino acid | 2014 | 2015 | 2016 | |||
---|---|---|---|---|---|---|---|---|
Percentage | Count | Percentage | Count | Percentage | Count | |||
18S | 228 | 676 | 486 | |||||
pfcrt | 74 | M | 74 | 64 | 67 | 267 | 48 | 120 |
I | 43 | 37 | 53 | 209 | 61 | 152 | ||
75 | N | 74 | 64 | 67 | 267 | 48 | 120 | |
E | 43 | 37 | 53 | 209 | 61 | 152 | ||
76 | K | 74 | 64 | 68 | 271 | 48 | 120 | |
T | 43 | 37 | 53 | 210 | 61 | 152 | ||
pfmdr1 | 86 | N | 88 | 70 | 97 | 351 | 92 | 202 |
Y | 14 | 11 | 4 | 13 | 13 | 29 | ||
184 | F | 70 | 56 | 81 | 315 | 74 | 163 | |
Y | 34 | 27 | 42 | 163 | 38 | 84 | ||
1034 | S | 100 | 67 | 100 | 182 | 100 | 202 | |
C | 0 | 0 | 0 | 0 | 0 | 0 | ||
1042 | N | 100 | 67 | 100 | 182 | 100 | 202 | |
D | 0 | 0 | 0 | 0 | 0 | 0 | ||
1246 | D | 96 | 64 | 100 | 182 | 100 | 201 | |
Y | 4 | 3 | 0 | 0 | 0 | 1 | ||
pfdhfr | 51 | N | 28 | 24 | 9 | 40 | 16 | 80 |
I | 76 | 65 | 94 | 408 | 92 | 471 | ||
59 | C | 29 | 25 | 11 | 47 | 19 | 96 | |
R | 76 | 65 | 93 | 403 | 91 | 466 | ||
108 | S | 20 | 17 | 7 | 35 | 7 | 40 | |
N | 84 | 73 | 96 | 449 | 97 | 526 | ||
164 | I | 100 | 86 | 100 | 432 | 100 | 513 | |
L | 0 | 0 | 0 | 0 | 0 | 0 | ||
pfdhps | 436 | S | 73 | 36 | 77 | 157 | 68 | 127 |
A | 31 | 15 | 30 | 62 | 36 | 67 | ||
437 | A | 67 | 33 | 57 | 114 | 47 | 88 | |
G | 33 | 16 | 53 | 107 | 58 | 109 | ||
540 | K | 98 | 52 | 99 | 134 | 99 | 186 | |
E | 2 | 1 | 1 | 2 | 1 | 2 | ||
581 | A | 100 | 53 | 100 | 136 | 100 | 185 | |
G | 0 | 0 | 0 | 0 | 0 | 0 | ||
613 | A | 100 | 52 | 98 | 129 | 99 | 187 | |
S/T | 0 | 0 | 2 | 2 | 1 | 1 |