Skip to main content

Table 2 Dengue virus RT-qPCR method performance in terms of in silico sensitivity

From: Application of whole genome data for in silico evaluation of primers and probes routinely employed for the detection of viral species by RT-qPCR using dengue virus as a case study

Method name

# genomes analysed

One mismatch allowed at 3′ end of primer-template pairs

No mismatches allowed at 3′ end of primer-template pairs

# genomes detected

# genomes not detected

# genomes unknown

% in silico sensitivity

% average in silico sensitivity

# genomes detected

# genomes not detected

# genomes unknown

% in silico sensitivity

% average in silico sensitivity

Callahan_1_g

1359

1209

14

136

[88.96–98.86]

[90.12–98.80]

1206

17

136

[88.74–98.61]

[89.80–98.46]

Callahan_2_g

1164

1055

13

96

[90.64–98.78]

1054

14

96

[90.55–98.69]

Callahan_3_g

777

707

11

59

[90.99–98.47]

704

14

59

[90.60–98.05]

Callahan_4_g

182

167

0

15

[91.76–100]

163

4

15

[89.56–97.60]

Callahan_1_s

1359

1356

3

0

[99.78–99.78]

[99.48–99.48]

1287

72

0

[94.70–94.70]

[81.99–81.99]

Callahan_2_s

1164

1150

14

0

[98.80–98.80]

638

526

0

[54.81–54.81]

Callahan_3_s

777

777

0

0

[100–100]

777

0

0

[100–100]

Callahan_4_s

182

181

1

0

[99.45–99.45]

153

29

0

[84.07–84.07]

Cecilia_4_s

182

153

4

25

[84.07–97.45]

[84.07–97.45]

121

36

25

[66.48–77.07]

[66.48–77.07]

Chien_1_s

1359

1357

2

0

[99.85–99.85]

[99.11–99.11]

4

1355

0

[0.29–0.29]

[6.95–6.95]

Chien_2_s

1164

1138

26

0

[97.77–97.77]

1

1163

0

[0.09–0.09]

Chien_3_s

777

777

0

0

[100–100]

58

719

0

[7.46–7.46]

Chien_4_s

182

179

3

0

[98.35–98.35]

179

3

0

[98.35–98.35]

Conceicao_1_g

1359

1359

0

0

[100–100]

[99.91–99.91]

1354

5

0

[99.63–99.63]

[95.23–95.23]

Conceicao_2_g

1164

1163

1

0

[99.91–99.91]

1159

5

0

[99.57–99.57]

Conceicao_3_g

777

776

1

0

[99.87–99.87]

623

154

0

[80.18–80.18]

Conceicao_4_g

182

181

1

0

[99.45–99.45]

180

2

0

[98.90–98.90]

Drosten_1_g

1359

1088

48

223

[80.06–95.77]

[83.77–98.22]

1082

51

226

[79.62–95.50]

[82.60–97.26]

Drosten_2_g

1164

1012

3

149

[86.94–99.70]

979

28

157

[84.11–97.22]

Drosten_3_g

777

660

1

116

[84.94–99.85]

658

1

118

[84.68–99.85]

Drosten_4_g

182

157

1

24

[86.26–99.37]

157

1

24

[86.26–99.37]

Gurukumar_1_g

1359

1082

48

229

[79.62–95.75]

[79.64–96.35]

1074

53

232

[79.03–95.30]

[77.51–94.27]

Gurukumar_2_g

1164

1003

4

157

[86.17–99.60]

969

31

164

[83.25–96.90]

Gurukumar_3_g

777

655

1

121

[84.30–99.85]

650

1

126

[83.66–99.85]

Gurukumar_4_g

182

33

52

97

[18.13–38.82]

6

79

97

[3.30–7.06]

Ito_1_s

1359

1353

6

0

[99.56–99.56]

[99.43–99.43]

0

1359

0

[0.00–0.00]

[57.18–57.18]

Ito_2_s

1164

1150

14

0

[98.80–98.80]

1075

89

0

[92.35–92.35]

Ito_3_s

777

777

0

0

[100–100]

737

40

0

[94.85–94.85]

Ito_4_s

182

182

0

0

[100–100]

179

3

0

[98.35–98.35]

Johnson_1_s

1359

1357

2

0

[99.85–99.85]

[98.56–98.59]

1125

234

0

[82.78–82.78]

[69.04–69.06]

Johnson_2_s

1164

1150

13

1

[98.80–98.88]

1125

38

1

[96.65–96.73]

Johnson_3_s

777

748

29

0

[96.27–96.27]

10

767

0

[1.29–1.29]

Johnson_4_s

182

177

5

0

[97.25–97.25]

144

38

0

[79.12–79.12]

Kim_1_s

1359

914

445

0

[67.26–67.26]

[86.53–86.53]

528

831

0

[38.85–38.85]

[60.71–60.71]

Kim_2_s

1164

1146

18

0

[98.45–98.45]

1094

70

0

[93.99–93.99]

Kim_3_s

777

774

3

0

[99.61–99.61]

327

450

0

[42.08–42.08]

Kim_4_s

182

179

3

0

[98.35–98.35]

165

17

0

[90.66–90.66]

Kong_1_s

1359

1254

105

0

[92.27–92.27]

[96.12–96.12]

0

1359

0

[0.00–0.00]

[28.12–28.12]

Kong_2_s

1164

1147

17

0

[98.54–98.54]

832

332

0

[71.48–71.48]

Kong_3_s

777

775

2

0

[99.74–99.74]

0

777

0

[0.00–0.00]

Kong_4_s

182

171

11

0

[93.96–93.96]

147

35

0

[80.77–80.77]

Laue_1_s

1359

1358

1

0

[99.93–99.93]

[86.56–86.56]

1027

332

0

[75.57–75.57]

[69.30–69.30]

Laue_2_s

1164

1149

15

0

[98.71–98.71]

1000

164

0

[85.91–85.91]

Laue_3_s

777

327

450

0

[42.08–42.08]

232

545

0

[29.86–29.86]

Laue_4_s

182

180

2

0

[98.90–98.90]

154

28

0

[84.62–84.62]

Leparc_Goffart_1_g

1359

1231

28

100

[90.58–97.78]

[91.07–98.36]

1225

33

101

[90.14–97.38]

[90.67–97.95]

Leparc_Goffart_2_g

1164

1058

14

92

[90.89–98.69]

1057

15

92

[90.81–98.60]

Leparc_Goffart_3_g

777

715

11

51

[92.02–98.48]

712

14

51

[91.63–98.07]

Leparc_Goffart_4_g

182

167

0

15

[91.76–100]

163

4

15

[89.56–97.60]

Leparc_Goffart_1_s

1359

1358

1

0

[99.93–99.93]

[80.18–99.93]

1340

19

0

[98.60–98.60]

[77.83–96.99]

Leparc_Goffart_2_s

1164

475

1

688

[40.81–99.79]

446

30

688

[38.32–93.70]

Leparc_Goffart_3_s

777

777

0

0

[100–100]

775

2

0

[99.74–99.74]

Leparc_Goffart_4_s

182

182

0

0

[100–100]

149

33

0

[81.87–81.87]

Pongsiri_1_g

1359

1291

12

56

[95.00–99.08]

[95.98–99.32]

1287

16

56

[94.70–98.77]

[95.81–99.17]

Pongsiri_2_g

1164

1121

9

34

[96.31–99.20]

1122

8

34

[96.39–99.29]

Pongsiri_3_g

777

750

2

25

[96.53–99.73]

748

4

25

[96.27–99.47]

Pongsiri_4_g

182

180

0

2

[98.90–100]

179

0

3

[98.35–100]

Sadon_1_s

1359

1358

1

0

[99.93–99.93]

[99.66–99.66]

1251

108

0

[92.05–92.05]

[88.91–88.91]

Sadon_2_s

1164

1158

6

0

[99.48–99.48]

1004

160

0

[86.25–86.25]

Sadon_3_s

777

777

0

0

[100–100]

666

111

0

[85.71–85.71]

Sadon_4_s

182

177

5

0

[97.25–97.25]

175

7

0

[96.15–96.15]

Santiago_1_s

1359

1358

1

0

[99.93–99.93]

[99.83–99.86]

1356

3

0

[99.78–99.78]

[97.44–97.47]

Santiago_2_s

1164

1161

2

1

[99.74–99.83]

1135

28

1

[97.51–97.59]

Santiago_3_s

777

777

0

0

[100–100]

735

42

0

[94.59–94.59]

Santiago_4_s

182

180

2

0

[98.90–98.90]

167

15

0

[91.76–91.76]

Warrilow_1_g

1359

1231

20

108

[90.58–98.40]

[91.13–98.63]

1226

24

109

[90.21–98.08]

[90.72–98.26]

Warrilow_2_g

1164

1059

13

92

[90.98–98.79]

1058

14

92

[90.89–98.69]

Warrilow_3_g

777

716

11

50

[92.15–98.49]

712

14

51

[91.63–98.07]

Warrilow_4_g

182

167

0

15

[91.76–100]

163

4

15

[89.56–97.60]

  1. Results were generated according to the workflow presented in Fig. 1. The first column lists the method name (see Table 1). The second column lists the number of analysed genomes per method. The next five columns list he number of genomes detected, the number of genomes not detected, the number of genomes where the outcome is unknown, the range between the more and the less conservative score for the in silico sensitivity per serotype per method, and the range between the more and the less conservative score for the in silico sensitivity averaged over the different serotypes per method (weighted for the different number of analysed genomes per serotype), when one mismatch was allowed at the 3′ end of primer-template pairs. The next five columns list the same information when no single mismatch was allowed at the 3′ end of primer-template pairs