CoronaVIR: Collection and compilation of Computational Resources on Novel Coronavirus (SARS-CoV-2 or COVID-19)

Welcome to Page of Diagnostic Primers

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This page provides the information of Predicted Diagnostic Primers which can be used for the diagnosis of CoVID-19. These primers are predicted by Primer3_Core tool with default parameters. These primers are designated for ORF1ab-RdRP gene of the strain based in template sequences of the genes taken from NCBI Virus Resource.

Note: These primers need experimental Validation.

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Table representing the predicted primers by Primer3_core for ORF1ab-RdRP-gene of nCoV-2019 strain diagnosis

Template Source ID	Template Source country	Gene	Fwd_Primer seq	Rev_Primer seq	oligo seq	Fwd_Primer Start Position	Fwd_Length	Rev_Primer Start Position	Rev_Length	Oligo Start pos	Oligo_Length	Target_Product size	Fwd_Primer Tm	Rev_Primer Tm	Oligo Tm	Fwd (GC%)	Rev (GC%)	Oligo (GC%)
MT066158 and MN970003	Malaysia and Thailand	ORF1ab_RdRP	AGTCGTATTTGTCTTATGGGCA	TCTGAAGCAGTGGAAAAGCAT	CTGAGCGCACCTGTTGTCTA	103	22	228	21	171	20	126	58.653	60.008	60.199	40.909	42.857	55
MT066158 and MN970003	Malaysia and Thailand	ORF1ab_RdRP	TCGTATTTGTCTTATGGGCAC	TCTGAAGCAGTGGAAAAGCAT	CTGAGCGCACCTGTTGTCTA	105	21	228	21	171	20	124	57.647	60.008	60.199	42.857	42.857	55
MT066158 and MN970003	Malaysia and Thailand	ORF1ab_RdRP	GTCGTATTTGTCTTATGGGCA	TCTGAAGCAGTGGAAAAGCAT	CTGAGCGCACCTGTTGTCTA	104	21	228	21	171	20	125	57.647	60.008	60.199	42.857	42.857	55
MT066158 and MN970003	Malaysia and Thailand	ORF1ab_RdRP	GAGTCGTATTTGTCTTATGGGCA	TCTGAAGCAGTGGAAAAGCAT	CTGAGCGCACCTGTTGTCTA	102	23	228	21	171	20	127	60.377	60.008	60.199	43.478	42.857	55
MT066158 and MN970003	Malaysia and Thailand	ORF1ab_RdRP	GTCGTATTTGTCTTATGGGCAC	TCTGAAGCAGTGGAAAAGCAT	CTGAGCGCACCTGTTGTCTA	104	22	228	21	171	20	125	58.517	60.008	60.199	45.455	42.857	55
MT159778	Nigeria	ORF1ab_RdRP	GGAGATGCCACAACTGCTTAT	TGCGTAAAACTCATTCACAAAG	CATTTGTCAAGCTGTCACGG	172	21	366	22	210	20	195	59.212	58.03	60.301	47.619	36.364	50
MT159778	Nigeria	ORF1ab_RdRP	GGAGATGCCACAACTGCTTAT	TGCGTAAAACTCATTCACAAAGT	CATTTGTCAAGCTGTCACGG	172	21	366	23	210	20	195	59.212	58.868	60.301	47.619	34.783	50
MT159778	Nigeria	ORF1ab_RdRP	GGAGATGCCACAACTGCTTAT	TGCGTAAAACTCATTCACAAAGTC	CATTTGTCAAGCTGTCACGG	172	21	366	24	210	20	195	59.212	60.557	60.301	47.619	37.5	50
MT159778	Nigeria	ORF1ab_RdRP	CCTCACTTGTTCTTGCTCGC	CAGTTGTGGCATCTCCTGAT	GTGAAATGGTCATGTGTGGC	26	20	187	20	116	20	162	61.116	58.671	59.819	55	50	50
MT159778	Nigeria	ORF1ab_RdRP	CCTCACTTGTTCTTGCTCGC	GCAGTTGTGGCATCTCCTG	GTGAAATGGTCATGTGTGGC	26	20	188	19	116	20	163	61.116	60.419	59.819	55	50	50
MT050416	Australia	ORF1ab_RdRP	GGAGATGCCACAACTGCTTAT	TGCGTAAAACTCATTCACAAAG	CATTTGTCAAGCTGTCACGG	182	21	376	22	220	20	195	59.212	58.034	60.301	47.619	36.364	50
MT050416	Australia	ORF1ab_RdRP	GGAGATGCCACAACTGCTTAT	TGCGTAAAACTCATTCACAAAGT	CATTTGTCAAGCTGTCACGG	182	21	376	23	220	20	195	59.212	58.034	60.301	47.619	34.783	50
MT050416	Australia	ORF1ab_RdRP	GGAGATGCCACAACTGCTTAT	TGCGTAAAACTCATTCACAAAGTC	CATTTGTCAAGCTGTCACGG	182	21	376	24	220	20	195	59.212	60.557	60.301	47.619	37.5	50
MT050416	Australia	ORF1ab_RdRP	CCTCACTTGTTCTTGCTCGC	CAGTTGTGGCATCTCCTGAT	GTGAAATGGTCATGTGTGGC	36	20	197	20	126	20	162	61.116	58.671	59.819	55	50	50
MT050416	Australia	ORF1ab_RdRP	CCTCACTTGTTCTTGCTCGC	GCAGTTGTGGCATCTCCTG	GTGAAATGGTCATGTGTGGC	36	20	198	19	126	20	163	61.116	60.419	59.819	55	57.895	50
MT072668	Belgium	ORF1ab_RdRP	GGAGATGCCACAACTGCTTAT	TGCGTAAAACTCATTCACAAAG	CATTTGTCAAGCTGTCACGG	470	21	664	22	508	20	195	59.212	58.034	60.301	47.619	36.364	50
MT072668	Belgium	ORF1ab_RdRP	GGAGATGCCACAACTGCTTAT	TGCGTAAAACTCATTCACAAAGT	CATTTGTCAAGCTGTCACGG	470	21	664	23	508	20	195	59.212	58.034	60.301	47.619	34.783	50
MT072668	Belgium	ORF1ab_RdRP	GGAGATGCCACAACTGCTTAT	TGCGTAAAACTCATTCACAAAGTC	CATTTGTCAAGCTGTCACGG	470	21	664	24	508	20	195	59.212	60.557	60.301	47.619	37.5	50
MT072668	Belgium	ORF1ab_RdRP	CCTCACTTGTTCTTGCTCGC	CAGTTGTGGCATCTCCTGAT	GTGAAATGGTCATGTGTGGC	324	20	485	20	414	20	162	61.116	58.671	59.819	55	50	50
MT072668	Belgium	ORF1ab_RdRP	CCTCACTTGTTCTTGCTCGC	GCAGTTGTGGCATCTCCTG	GTGAAATGGTCATGTGTGGC	324	20	486	19	414	20	163	61.116	60.419	59.819	55	57.895	50