Table 2.
Mutations and haplotypes
| Gene | Haplotype | Total | Year 2016 | Year 2017 | |||
|---|---|---|---|---|---|---|---|
| Number | Percentage | Number | Percentage | Number | Percentage | ||
| PfKelch | A578S | 1 | 0.3 | 0 | 0 | 1 | 0.5 |
| Total n = 349 | K189N | 7 | 2 | 6 | 3.8 | 1 | 0.5 |
| K189N/K | 2 | 0.6 | 0 | 0 | 2 | 1 | |
| K189T | 159 | 45.6 | 76 | 48.4 | 83 | 43.2 | |
| K189T, N197D/N | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| K189T, V636A/V | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| K189T, W660C | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| K189T/K | 25 | 7.2 | 8 | 5.1 | 17 | 8.9 | |
| K189T/K, N197D/N | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| K189T, I354V | 1 | 0.3 | 1 | 0.6 | 0 | 0 | |
| K189T, N197D | 1 | 0.3 | 1 | 0.6 | 0 | 0 | |
| L258M | 1 | 0.3 | 1 | 0.6 | 0 | 0 | |
| N195D/N | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| N195K/N | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| N197D | 1 | 0.3 | 1 | 0.6 | 0 | 0 | |
| Q633R | 1 | 0.3 | 1 | 0.6 | 0 | 0 | |
| R255K | 11 | 3.2 | 6 | 3.8 | 5 | 2.6 | |
| S213G/S | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| WT | 132 | 37.8 | 56 | 35.7 | 76 | 39.6 | |
| Pfcrt | CVMNK | 296 | 84.8 | 129 | 83.8 | 167 | 85.6 |
| Total n = 353 | CVIET | 19 | 5.4 | 11 | 7.1 | 8 | 4.1 |
| Positions | CVMN/DK/T | 3 | 0.9 | 0 | 0 | 7 | 3.6 |
| 72–76 | CVMNK/T | 10 | 2.9 | 10 | 6.5 | 0 | 0 |
| CVM/INK/T | 5 | 1.4 | 4 | 2.6 | 1 | 0.5 | |
| CVM/IN/DK | 2 | 0.6 | 0 | 0 | 2 | 1 | |
| CVM/IN/DK/T | 14 | 4 | 3 | 1.9 | 11 | 5.6 | |
| CVM/IET, CVM/IDT, CVIDK, CVM/IN/DT | 4 | 1.1 | 1 | 0.6 | 3 | 1.5 | |
| Pfmdr1 | NYSND | 134 | 39.9 | 54 | 36.7 | 80 | 42.3 |
| Total n = 336 | NFSND | 160 | 47.6 | 71 | 48.3 | 89 | 47.1 |
| Positions | NY/FSND | 22 | 6.5 | 11 | 7.5 | 11 | 5.8 |
| 86, 184, 1034, | N/YFSND | 1 | 0.3 | 0 | 0 | 1 | 0.5 |
| 1042, 1246 | N/YYSND | 3 | 0.9 | 1 | 0.7 | 2 | 1.1 |
| N/YY/FSND | 1 | 0.3 | 1 | 0.7 | 0 | 0 | |
| YFSND | 13 | 3.9 | 8 | 5.4 | 5 | 2.6 | |
| YYSND | 2 | 0.6 | 1 | 0.7 | 1 | 0.5 | |
| Pfmdr1_Pfcrt | NFD + K | 134 | 40.5 | 58 | 39.5 | 76 | 41.3 |
| Total n = 331 | NFD + K/T | 15 | 4.5 | 8 | 5.4 | 7 | 3.8 |
| Pfmdr1 | NFD + T | 9 | 2.7 | 5 | 3.4 | 4 | 2.2 |
| positions | NYD + K | 112 | 33.8 | 44 | 29.9 | 68 | 37 |
|
86, 184, 1246 Pfcrt position |
NYD + K/T | 11 | 3.3 | 6 | 4.1 | 5 | 2.7 |
| 76 | NYD + T | 9 | 2.7 | 4 | 2.7 | 5 | 2.7 |
| NY/FD + K | 18 | 5.4 | 9 | 6.1 | 9 | 4.9 | |
| NY/FD + K/T | 4 | 1.2 | 2 | 1.4 | 2 | 1.1 | |
| N/YYD + K | 2 | 0.6 | 1 | 0.7 | 1 | 0.5 | |
| YFD + K | 10 | 3 | 6 | 4.1 | 4 | 2.2 | |
| YFD + T | 2 | 0.6 | 2 | 1.4 | 0 | 0 | |
| YFD + K/T, YYD + K, YYD + T, N/YFD + K, N/YY/FD + K | 5 | 1.5 | 2 | 1.4 | 3 | 1.6 | |
| Pfdhfr | AICNI | 13 | 3.8 | 7 | 4.5 | 6 | 3.2 |
| Total n = 346 | AIC/RNI | 6 | 1.7 | 0 | 0 | 6 | 3.2 |
| Positions | AIRNI | 275 | 79.5 | 125 | 80.1 | 150 | 78.9 |
| 16, 51, 59, | ANCSI | 5 | 1.4 | 1 | 0.6 | 4 | 2.1 |
| 108, 164 | ANRNI | 31 | 9 | 12 | 7.7 | 19 | 10 |
| AN/IRNI | 13 | 3.8 | 8 | 5.1 | 5 | 2.6 | |
| ANC/RNI, AN/ICS/NI, AN/IC/RS/NI | 3 | 0.9 | 3 | 1.9 | 0 | 0 | |
| Pfdhps | AAKAA | 185 | 53.2 | 76 | 50.3 | 109 | 55.3 |
| Total n = 348 | AA/GKAA | 11 | 3.2 | 2 | 1.3 | 9 | 4.6 |
| Positions | AGKAA | 24 | 6.9 | 13 | 8.6 | 11 | 5.6 |
| 436, 437, 540, | AGKGS | 12 | 3.4 | 4 | 2.6 | 8 | 4.1 |
| 581, 613 | SAKAA | 5 | 1.4 | 3 | 2.0 | 2 | 1.0 |
| SGEAA | 5 | 1.4 | 2 | 1.3 | 3 | 1.5 | |
| SGEGA | 10 | 2.9 | 3 | 2.0 | 7 | 3.6 | |
| SGKAA | 62 | 17.8 | 30 | 19.9 | 32 | 16.2 | |
| S/AAKAA | 9 | 2.6 | 8 | 5.3 | 1 | 0.5 | |
| S/AA/GKAA | 13 | 3.7 | 4 | 2.6 | 9 | 4.6 | |
| S/AGKAA | 4 | 1.1 | 3 | 2.0 | 1 | 0.5 | |
| AA/GKAS, AGKAS, AGK/EAA, CAKAA, SAK/EGA, SA/GKAA, SGKA/GA, S/AA/GKA/GA | 8 | 2.3 | 3 | 2 | 5 | 2.5 | |
| Pfdhfr_Pfdhps | AICNI + AAKAA | 8 | 2.4 | 3 | 2 | 5 | 2.7 |
| Total n = 336 | AICNI + AGKAA | 1 | 0.3 | 1 | 0.7 | 0 | 0 |
| Pfdhfr | AICNI + SGEAA | 2 | 0.6 | 1 | 0.7 | 1 | 0.5 |
| positions | AICNI + SGKAA | 1 | 0.3 | 1 | 0.7 | 0 | 0 |
| 16, 51, 59, | AICNI + S/AAKAA | 1 | 0.3 | 1 | 0.7 | 0 | 0 |
| 108, 164 | AIC/RNI + AAKAA | 3 | 0.9 | 0 | 0 | 3 | 1.6 |
| Pfdhps | AIC/RNI + S/AA/GKAA | 2 | 0.6 | 0 | 0 | 2 | 1.1 |
| positions | AIC/RNI + S/AGKAA | 1 | 0.3 | 0 | 0 | 1 | 0.5 |
| 436, 437, 540, | AIRNI + AAKAA | 135 | 40.2 | 58 | 38.9 | 77 | 41.2 |
| 581, 613 | AIRNI + AA/GKAA | 10 | 3 | 2 | 1.3 | 8 | 4.3 |
| AIRNI + AA/GKAS | 1 | 0.3 | 1 | 0.7 | 0 | 0 | |
| AIRNI + AGKAA | 20 | 6 | 10 | 6.7 | 10 | 5.3 | |
| AIRNI + AGKAS | 1 | 0.3 | 1 | 0.7 | 0 | 0 | |
| AIRNI + AGKGS | 10 | 3 | 4 | 2.7 | 6 | 3.2 | |
| AIRNI + AGK/EAA | 1 | 0.3 | 1 | 0.7 | 0 | 0 | |
| AIRNI + CAKAA | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| AIRNI + SAKAA | 4 | 1.2 | 3 | 2 | 1 | 0.5 | |
| AIRNI + SAK/EGA | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| AIRNI + SA/GKAA | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| AIRNI + SGEAA | 2 | 0.6 | 0 | 0 | 2 | 1.1 | |
| AIRNI + SGEGA | 8 | 2.4 | 3 | 2 | 5 | 2.7 | |
| AIRNI + SGKAA | 53 | 15.8 | 27 | 18.1 | 26 | 13.9 | |
| AIRNI + SGKA/GA | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| AIRNI + S/AAKAA | 7 | 2.1 | 6 | 4 | 1 | 0.5 | |
| AIRNI + S/AA/GKAA | 7 | 2.1 | 1 | 0.7 | 6 | 3.2 | |
| AIRNI + S/AA/GKA/GA | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| AIRNI + S/AGKAA | 1 | 0.3 | 1 | 0.7 | 0 | 0 | |
| ANCSI + AAKAA | 3 | 0.9 | 1 | 0.7 | 2 | 1.1 | |
| ANCSI + AGKGS | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| ANCSI + S/AA/GKAA | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| ANC/RNI + S/AGKAA | 1 | 0.3 | 1 | 0.7 | 0 | 0 | |
| ANRNI + AAKAA | 20 | 6 | 7 | 4.7 | 13 | 7 | |
| ANRNI + AGKGS | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| ANRNI + SAKAA | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| ANRNI + SGEAA | 1 | 0.3 | 1 | 0.7 | 0 | 0 | |
| ANRNI + SGEGA | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| ANRNI + SGKAA | 5 | 1.5 | 2 | 1.3 | 3 | 1.6 | |
| ANRNI + S/AAKAA | 1 | 0.3 | 1 | 0.7 | 0 | 0 | |
| ANRNI + S/AGKAA | 1 | 0.3 | 1 | 0.7 | 0 | 0 | |
| AN/ICS/NI + AAKAA | 1 | 0.3 | 1 | 0.7 | 0 | 0 | |
| AN/IC/RS/NI + S/AA/GKAA | 1 | 0.3 | 1 | 0.7 | 0 | 0 | |
| AN/IRNI + AAKAA | 10 | 3 | 6 | 4 | 4 | 2.1 | |
| AN/IRNI + AGKAA | 1 | 0.3 | 0 | 0 | 1 | 0.5 | |
| AN/IRNI + S/AA/GKAA | 2 | 0.6 | 2 | 1.3 | 0 | 0 | |
| CytB (Y268S) | Y258 | 347 | 100 | 149 | 100 | 198 | 100 |
| Total n = 347 | Y268S | 0 | 0 | 0 | 0 | 0 | 0 |
| Pfmdr1 CNV | Single copy | 335 | 99.7 | 151 | 100 | 184 | 99.5 |
| Total n = 335 | Multiple copies | 1 | 0.3 | 0 | 0 | 1 | 0.5 |
| Pfpm2 CNV | Single copy | 339 | 100 | 152 | 100 | 187 | 100 |
| Total n = 340 | Multiple copies | 0 | 0 | 0 | 0 | 0 | 0 |
Mutants are shown as AxxxB where ‘A’ refers to the amino acid in single-letter code encoded by the wild type codon, the number ‘xxx’ indicates the codon position and ‘B’ is the amino acid encoded by the mutant allele. Mixed infections are indicated as A/B. Similarly for haplotypes, amino acids encoded by the wild type codons are shown in black and mutants are in underlined bold