TABLE 2.

Primers and probes used for DNA sequencing and real-time PCR assays^a

Purpose and target gene	Primer designation	5′-3′ nucleotide sequenced	Amplicon length (bp)	Final concn (nM)
DNA amplification and sequencing primers
purTb	purT Fw1	CACTTGGCACAGCATTAACC	1,145	400
	purT Fw	TAACCCCTAATGCAACCAAAGT	1,130	400
	purT Rv	CTTGTTTTACTTTTTCCAACGC		400
	purT seq	CCAATAGGTCATCGTCAAGAAGA		160
	purT seq1R	TCTTCTTGACGATGACCTATTGG		160
hdg	hdg Fw	TTATGAAATTATGTACCGCACTTG	1,084	400
	hdg Fw1	TGGCGTTTTTTCTGCRTTG	1,125	400
	hdg Rv	TCCTTGATCTTGATTGGCTTG		400
	hdg seq	AACMGTTGCCTATATCATCACTT		160
	hdg seq1R	AAGTGATGATATAGGCAACKGTT		160
sod	sod Fw	GTTAGTGCGGTATGTTCAGTTGGT	502	400
	sod Rv	CCAAGTGGMGCTGGATGATC		400
	sod seq Fw	GTTAGTGCGGTATGTTCAGTTGGT		160
	sod seq Rv	CCAAGTGGMGCTGGATGATC		160
RT-PCR primers and probes
purT 1	purT Fw1	ATTAACCCCTAATGCAACCAAAGT	91	100
	purT Rv1	CTTCAACGCCTAAACGTTGCA		900
	purT pb1c	ATGTTGGGTTCTGGTGAA		300
purT 2	purT Fw2	TTAATGTTGTGCCGACTGCAA	78	100
	purT Rv2	AACTCTTCTGAAGCTAGACGACGAAT		600
	purT pb2c	TCAACTTACGATGAATCGTGA		300

^aAll primers and probes were synthesized at the CDC Biotechnology Core Facility.

^bPrimers for amplification and sequencing of purT.

^cAll probes were labeled with 6-carboxyfluorescein at the 5′ end and black hole quencher at the 3′ end.

^dK = G+T; M = A+C; R = A+G.