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Table 1 List of evaluated RT-qPCR methods for dengue virus detection

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

Targeted genomic region

Reference publication

Callahan_1_g

3’UTR

[31]

Callahan_2_g

3’UTR

Callahan_3_g

3’UTR

Callahan_4_g

3’UTR

Callahan_1_s

NS5

[31]

Callahan_2_s

capsid

Callahan_3_s

capsid

Callahan_4_s

capsid

Cecilia_4_s

3’ UTR

[25]

Chien_1_s

NS5

[26]

Chien_2_s

NS5

Chien_3_s

NS5

Chien_4_s

NS5

Conceicao_1_g

5’UTR

[20]

Conceicao_2_g

5’UTR

Conceicao_3_g

5’UTR

Conceicao_4_g

5’UTR

Drosten_1_g

3’ UTR

[21]

Drosten_2_g

3’ UTR

Drosten_3_g

3’ UTR

Drosten_4_g

3’ UTR

Gurukumar_1_g

3’ UTR

[22]

Gurukumar_2_g

3’ UTR

Gurukumar_3_g

3’ UTR

Gurukumar_4_g

3’ UTR

Ito_1_s

E

[27]

Ito_2_s

E

Ito_3_s

E

Ito_4_s

E

Johnson_1_s

N5S

[7]

Johnson_2_s

E

Johnson_3_s

prM

Johnson_4_s

prM

Kim_1_s

NS1

[33]

Kim_2_s

NS1

Kim_3_s

NS1

Kim_4_s

NS1

Kong_1_s

NS5

[28]

Kong_2_s

NS5

Kong_3_s

NS5

Kong_4_s

NS5

Laue_1_s

3’ UTR

[34]

Laue_2_s

3’ UTR

Laue_3_s

3’ UTR

Laue_4_s

3’ UTR

Leparc_Goffart_1_g

3’UTR

[32]

Leparc_Goffart_2_g

3’UTR

Leparc_Goffart_3_g

3’UTR

Leparc_Goffart_4_g

3’UTR

Leparc_Goffart_1_s

capsid

[32]

Leparc_Goffart_2_s

capsid

Leparc_Goffart_3_s

capsid

Leparc_Goffart_4_s

capsid

Pongsiri_1_g

3’UTR

[23]

Pongsiri_2_g

3’UTR

Pongsiri_3_g

3’UTR

Pongsiri_4_g

3’UTR

Sadon_1_s

capsid

[29]

Sadon_2_s

capsid

Sadon_3_s

capsid

Sadon_4_s

capsid

Santiago_1_s

NS5

[30]

Santiago_2_s

E

Santiago_3_s

prM

Santiago_4_s

prM

Warrilow_1_g

3’UTR

[24]

Warrilow_2_g

3’UTR

Warrilow_3_g

3’UTR

Warrilow_4_g

3’UTR

  1. The first column lists the adapted method name. Methods for dengue virus and serotype-specific detection are labelled with the extensions ‘_g’ and ‘_s’, respectively. Each method is subdivided in the four dengue virus serotypes to evaluate each serotype individually, even for methods designed to detect the entire species. The method ‘Cecilia_4_s’ was only evaluated for the fourth serotype as it was specifically designed towards this purpose [25]. The second column lists the targeted genomic region. The third column lists the reference publication for each method. See also Additional file 1: Table S1 for detailed sequence information for primers, probe and reference template, for every method
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BMC Bioinformatics

ISSN: 1471-2105

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