Internally Controlled, Generic Real-Time PCR for Quantification and Multiplex Real-Time PCR with Serotype-Specific Probes for Serotyping of Dengue Virus Infections

Table 1

Primers and fluorescence-labeled probes of DENV and noncompetitive IC (MS2 RNA).

Primer or probe	Sequence (5′–3′)	5′ reporter	3′ quencher
DENV-F (10546)-generic	GGTTAGAGGAGACCCCTCCC
DENV-R (10711)-generic	GAGACAGCAGGATCTCTGGTCT
MS2-F	CATAAGTTAGATGGCCGTCTGT
MS2-R	TAGAGACGACAACCATGCCAAAC
DENV-generic-MGB probe	AAACAGCATATTGACGCTGGGA	FAM	BHQ1
MS2 probe	TCCAGACAACGTGCAACATATCGCGACGTATCGTGATATGG	HEX	BHQ1
DENV-1-MGB probe	AACACCATGGGAAGCTGTACCCTG	FAM	BHQ1
DENV-2-MGB probe	GAGATGAAGCTGTAGTCTCACTGG	HEX	BHQ1
DENV-3-MGB probe	TGAGGGAAGCTGTACCTCCTTGCA	Texas Red	BHQ2
DENV-4-MGB probe	CCCGAAGCCAGGAGGAAGCTGTACTCC	CY5	BHQ2

Nucleotide numbering for generic primers DENV-F and -R is relative to DENV-1 (reference strain AF226685).
F: forward primer; R: reverse primer; MGB: minor groove binding; BHQ1 or 2: black hole quencher 1 or 2.