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 3 Dengue virus RT-qPCR method performance in terms of intraspecies 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	2123	0	2076	47	[100–100]	[95.43–95.48]	0	2076	47	[100–100]	[100–100]
Callahan_2_s	2318	0	2237	81	[100–100]		0	2237	81	[100–100]
Callahan_3_s	2705	472	2233	0	[82.55–82.55]		0	2705	0	[100–100]
Callahan_4_s	3300	0	3300	0	[100–100]		0	3300	0	[100–100]
Cecilia_4_s	3300	0	1166	2134	[100–100]	[100–100]	0	1166	2134	[100–100]	[100–100]
Chien_1_s	2123	7	2116	0	[99.67–99.67]	[99.93–99.93]	0	2123	0	[100–100]	[100–100]
Chien_2_s	2318	0	2318	0	[100–100]		0	2318	0	[100–100]
Chien_3_s	2705	0	2705	0	[100–100]		0	2705	0	[100–100]
Chien_4_s	3300	0	3300	0	[100–100]		0	3300	0	[100–100]
Ito_1_s	2123	0	1661	462	[100–100]	[99.12–99.46]	0	1661	462	[100–100]	[99.58–99.74]
Ito_2_s	2318	0	1037	1281	[100–100]		0	1037	1281	[100–100]
Ito_3_s	2705	56	1822	827	[97.02–97.93]		27	1851	827	[98.56–99.00]
Ito_4_s	3300	0	1779	1521	[100–100]		0	1779	1521	[100–100]
Johnson_1_s	2123	1	2122	0	[99.95–99.95]	[99.99–99.99]	0	2123	0	[100–100]	[100–100]
Johnson_2_s	2318	0	2224	94	[100–100]		0	2224	94	[100–100]
Johnson_3_s	2705	0	1138	1567	[100–100]		0	1138	1567	[100–100]
Johnson_4_s	3300	0	2613	687	[100–100]		0	2613	687	[100–100]
Kim_1_s	2123	0	1982	141	[100–100]	[100–100]	0	1982	141	[100–100]	[100–100]
Kim_2_s	2318	0	2312	6	[100–100]		0	2312	6	[100–100]
Kim_3_s	2705	0	1488	1217	[100–100]		0	1488	1217	[100–100]
Kim_4_s	3300	0	1060	2240	[100–100]		0	1060	2240	[100–100]
Kong_1_s	2123	0	2123	0	[100–100]	[100–100]	0	2123	0	[100–100]	[100–100]
Kong_2_s	2318	0	2114	204	[100–100]		0	2114	204	[100–100]
Kong_3_s	2705	0	2688	17	[100–100]		0	2688	17	[100–100]
Kong_4_s	3300	0	3269	31	[100–100]		0	3269	31	[100–100]
Laue_1_s	2123	0	1823	300	[100–100]	[100–100]	0	1823	300	[100–100]	[100–100]
Laue_2_s	2318	0	2316	2	[100–100]		0	2316	2	[100–100]
Laue_3_s	2705	0	2695	10	[100–100]		0	2695	10	[100–100]
Laue_4_s	3300	0	3176	124	[100–100]		0	3176	124	[100–100]
Leparc_Goffart_1_s	2123	0	2114	9	[100–100]	[94.67–95.48]	0	2114	9	[100–100]	[100–100]
Leparc_Goffart_2_s	2318	0	742	1576	[100–100]		0	742	1576	[100–100]
Leparc_Goffart_3_s	2705	472	2233	0	[82.55–82.55]		0	2705	0	[100–100]
Leparc_Goffart_4_s	3300	0	3296	4	[100–100]		0	3296	4	[100–100]
Sadon_1_s	2123	3	2119	1	[99.86–99.86]	[99.95–99.97]	3	2119	1	[99.86–99.86]	[99.95–99.97]
Sadon_2_s	2318	0	135	2183	[100–100]		0	135	2183	[100–100]
Sadon_3_s	2705	0	146	2559	[100–100]		0	146	2559	[100–100]
Sadon_4_s	3300	0	3300	0	[100–100]		0	3300	0	[100–100]
Santiago_1_s	2123	0	2123	0	[100–100]	[100–100]	0	2123	0	[100–100]	[100–100]
Santiago_2_s	2318	0	2224	94	[100–100]		0	2224	94	[100–100]
Santiago_3_s	2705	0	1138	1567	[100–100]		0	1138	1567	[100–100]
Santiago_4_s	3300	0	2613	687	[100–100]		0	2613	687	[100–100]

Results were generated according to the workflow presented in Fig. 1. The first column lists the method name (see Table 1). Only RT-qPCR methods for serotype-specific detection were evaluated. 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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