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Table 2 Mutations and haplotypes

From: Molecular surveillance for operationally relevant genetic polymorphisms in Plasmodium falciparum in Southern Chad, 2016–2017

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

  1. 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
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Malaria Journal

ISSN: 1475-2875

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