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

Vanneste, Kevin; Garlant, Linda; Broeders, Sylvia; Van Gucht, Steven; Roosens, Nancy H.

doi:10.1186/s12859-018-2313-0

Table 4 Dengue virus RT-qPCR method performance in terms of interspecies in silico specificity

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
Method name	# genomes analysed	# genomes detected	# genomes not detected	# genomes unknown	% in silico specificity	% average in silico specificity	# genomes detected	# genomes not detected	# genomes unknown	% in silico specificity	% average in silico specificity
Callahan_1_s	927	0	861	66	[100–100]	[100–100]	0	861	66	[100–100]	[100–100]
Callahan_2_s	927	0	834	93	[100–100]		0	834	93	[100–100]
Callahan_3_s	927	0	786	141	[100–100]		0	786	141	[100–100]
Callahan_4_s	927	0	817	110	[100–100]		0	817	110	[100–100]
Callahan_g	927	0	340	587	[100–100]	[100–100]	0	340	587	[100–100]	[100–100]
Cecilia_4_s	927	0	132	795	[100–100]	[100–100]	0	132	795	[100–100]	[100–100]
Chien_1_s	927	0	927	0	[100–100]	[100–100]	0	927	0	[100–100]	[100–100]
Chien_2_s	927	0	927	0	[100–100]		0	927	0	[100–100]
Chien_3_s	927	0	927	0	[100–100]		0	927	0	[100–100]
Chien_4_s	927	0	927	0	[100–100]		0	927	0	[100–100]
Conceicao_g	927	0	3	924	[100–100]	[100–100]	0	3	924	[100–100]	[100–100]
Drosten_g	927	0	7	920	[100–100]	[100–100]	0	7	920	[100–100]	[100–100]
Gurukumar_g	927	0	67	860	[100–100]	[100–100]	0	67	860	[100–100]	[100–100]
Ito_1_s	927	0	0	927	[100–100]	[100–100]	0	0	927	[100–100]	[100–100]
Ito_2_s	927	0	10	917	[100–100]		0	10	917	[100–100]
Ito_3_s	927	0	46	881	[100–100]		0	46	881	[100–100]
Ito_4_s	927	0	10	917	[100–100]		0	10	917	[100–100]
Johnson_1_s	927	0	113	814	[100–100]	[100–100]	0	113	814	[100–100]	[100–100]
Johnson_2_s	927	0	42	885	[100–100]		0	42	885	[100–100]
Johnson_3_s	927	0	121	806	[100–100]		0	121	806	[100–100]
Johnson_4_s	927	0	881	46	[100–100]		0	881	46	[100–100]
Kim_1_s	927	0	52	875	[100–100]	[100–100]	0	52	875	[100–100]	[100–100]
Kim_2_s	927	0	788	139	[100–100]		0	788	139	[100–100]
Kim_3_s	927	0	4	923	[100–100]		0	4	923	[100–100]
Kim_4_s	927	0	871	56	[100–100]		0	871	56	[100–100]
Kong_1_s	927	0	914	13	[100–100]	[100–100]	0	914	13	[100–100]	[100–100]
Kong_2_s	927	0	848	79	[100–100]		0	848	79	[100–100]
Kong_3_s	927	0	913	14	[100–100]		0	913	14	[100–100]
Kong_4_s	927	0	926	1	[100–100]		0	926	1	[100–100]
Laue_1_s	927	0	927	0	[100–100]	[100–100]	0	927	0	[100–100]	[100–100]
Laue_2_s	927	0	927	0	[100–100]		0	927	0	[100–100]
Laue_3_s	927	0	923	4	[100–100]		0	923	4	[100–100]
Laue_4_s	927	0	822	105	[100–100]		0	822	105	[100–100]
Leparc_Goffart_1_s	927	0	139	788	[100–100]	[100–100]	0	139	788	[100–100]	[100–100]
Leparc_Goffart_2_s	927	0	5	922	[100–100]		0	5	922	[100–100]
Leparc_Goffart_3_s	927	0	848	79	[100–100]		0	848	79	[100–100]
Leparc_Goffart_4_s	927	0	2	925	[100–100]		0	2	925	[100–100]
Leparc_Goffart_g	927	0	359	568	[100–100]	[100–100]	0	359	568	[100–100]	[100–100]
Pongsiri_g	927	0	391	536	[100–100]	[100–100]	0	391	536	[100–100]	[100–100]
Sadon_1_s	927	0	3	924	[100–100]	[100–100]	0	3	924	[100–100]	[100–100]
Sadon_2_s	927	0	796	131	[100–100]		0	796	131	[100–100]
Sadon_3_s	927	0	9	918	[100–100]		0	9	918	[100–100]
Sadon_4_s	927	0	45	882	[100–100]		0	45	882	[100–100]
Santiago_1_s	927	0	113	814	[100–100]	[100–100]	0	113	814	[100–100]	[100–100]
Santiago_2_s	927	0	42	885	[100–100]		0	42	885	[100–100]
Santiago_3_s	927	0	121	806	[100–100]		0	121	806	[100–100]
Santiago_4_s	927	0	881	46	[100–100]		0	881	46	[100–100]
Warrilow_g	927	0	353	574	[100–100]	[100–100]	0	353	574	[100–100]	[100–100]

Results were generated according to the workflow presented in Fig. 1. The first column lists the method name (see Table 1). RT-qPCR methods for dengue virus detection (denoted by the extension ‘_g’) were evaluated by challenging them with 927 genomes of West Nile virus. RT-qPCR methods for dengue serotype-specific detection (denoted by the extension ‘_s’) were evaluated by challenging the primers and probe combination for every different serotype independently with 927 genomes of West Nile virus. The second column lists the number of analysed genomes per method. The next five columns list the 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 specificity per serotype per method, and the range between the more and the less conservative score for the in silico specificity 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

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ISSN: 1471-2105

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