One-step real-time RT-PCR assays for serotyping dengue virus in clinical samples

BMC Infectious Diseases

Table 1 Primer and probe sequences

Assay	Primer/probe	Amplicon size (nt)	Target region	Sequences (5’-3’)	Position	Tm
DENV1	DENV1_F	71	NS5	CAATGGATGACAACAGAAGAYATG	9974–9997	56.6
	DENV1_R			TCCATCCATGGGTTTTCCTCTAT	10022–10044	59.5
	DENV1_P			TCAGTGTGGAATAGGGTTT	10001–10019	70.0
DENV2	DENV2_F	199	E protein	GCAGAAACACAACATGGAACRATAGT	1873–1898	56.6
	DENV2_R			TGATGTAGCTGTCTCCRAATGG	2050–2071	59.8
	DENV2_P			TCAACATAGAAGCAGAACC	2030–2048	68.0
DENV3	DENV3_F	167	NS1	ATGGAATGTGTGGGAGGTGG	2860–2879	59.1
	DENV3_R			GGCTTTCTATCCARTAGCCCATG	3004–3026	59.8
	DENV3_P			TATGGCTGAAACTCCGAG	2913–2930	68.0
DENV4	DENV4_F	114	5’ UTR/	GCAGATCTCTGGAAAAATGAACCA	86–109	60.4
	DENV4_R		capsid	GAGAATCTCTTCACCAACCCYTG	177–199	59.8
	DENV4_P		protein	TCAATATGCTGAAACGC	136–152	68.0

Degenerated nucleotides (nt): R: A/G, Y: G/A/C. The MGB-modified probes were labelled with FAM and a non-fluorescence quencher (NFQ)
Genome positions are given according to the NCBI reference sequence for DENV1 [GenBank:NC_001477], DENV2 [GenBank:NC_001474], DENV3 [GenBank:NC_001475], and DENV4 [GenBank:NC_002640]
The mean melting temperatures (Tm) are shown for primers with degenerated nucleotides

ISSN: 1471-2334