Table 1.

The list of primers tested during LRP optimization

	Primer	Polarity	Sequence (5′–3′)	Position	Tm (°C)
RT	QR1	Anti-sense	Cggttggggaggaggtag	9356–9373	60.5
	QR2	Anti-sense	Tagccagccgtgaaccag	9248–9265	61
	QR268	Anti-sense	Gctgtagccagccgtgaaccag	9248–9269	68.5
	QR274	Anti-sense	Ccgctgtagccagccgtgaaccag	9248–9271	74.4
	QR3*	Anti-sense	Cagccctgcctcctctgg	9139–9156	64.5
	QR4	Anti-sense	Ggttggggaggaggtagatg	9353–9372	60.7
	QR5	Anti-sense	Tgcagcaagcaggagtagg	9326–9344	60.3
	QR6	Anti-sense	Atcggttggggaggaggtag	9356–9375	62.5
	QR7*	Anti-sense	Atcagtatcatcctcgcccac	8858–8878	61.3
	Q5BR1	Anti-sense	Gcagcaagcaggagtaggcaa	9323–9343	65.1
	Q5BR2	Anti-sense	Tatcggagtgagtttgagct	9199–9218	55.1
	Q5BR3	Anti-sense	Tttgagctttgttcttactg	9187–9206	50.9
PCR	QUF1	Sense	Ggcgacactccaccatagatc	18–38	61.8
	QUF2	Sense	Gccgagtagtgttgggtc	253–270	56.5
	QUF3	Sense	Ctgtgaggaactactgtcttc	45–65	51.5
	QUF4	Sense	Ctgcctgatagggtgcttg	289–307	59.4
	QUF5	Sense	Actcccctgtgaggaactac	39–58	55.7
	WF1	Sense	Actcccctgtgaggaactactgtcttcac	39–67	67.8
	WF2	Sense	Actgtcttcacgcagaaagcgtctagc	57–83	68.9
	WF3	Sense	Agaaagcgtctagccatggcgttag	70–94	67.6
	WF33	Sense	Acgcagaaagcgtctagccat	66–86	63.5
	WF4	Sense	Tagtatgagtgtcgtgcagcctcca	92–116	67.2
	WF5**	Sense	ggatctgacgttaattaacatagtggtctgcggaaccggt	139–160	67.5
	WF6	Sense	Gactgctagccgagtagtgttgggtc	245–270	67.4
	WF7	Sense	Tggtactgcctgatagggtgcttg	284–307	66.5
	WR1*	Anti-sense	Ctattratttcacctggagagtaactgtggag	9021–9052	67.6
	WR2*	Anti-sense	Ctgaggcatgcggccacc	9053–9070	68.7
	WR3*	Anti-sense	Cggtgtctccaagctcgcaa	9090–9109	67.1
	WR4*	Anti-sense	Agaagyctagcgcggacgctc	9116–9136	65.5
	WR5	Anti-sense	Gcagccctgcctcctctgg	9139–9157	68.0
	WTR5	Anti-sense	Gcagccctacctcctctgg	9139–9157	62.3
	WR55**	Anti-sense	atagctgggtggccggccatggcagccctacctcctctgg	9139–9160	67.9
	WR6	Anti-sense	Ttggagtgagtttgagctttgttcttactg	9187–9216	66.7
	WR7	Anti-sense	Gccgctattggagtgagtttgagc	9200–9223	67.3
	HCV6	Anti-sense	Ggtaccccaagtttrctgaggca	9063–9085	63.5
	HCV7	Anti-sense	Gagtaactgtggagtgaaaaygcg	9011–9034	62.2
5′UTR	QUF3	Sense	Ctgtgaggaactactgtcttc	45–65	257 bp
	QUR3	Anti-sense	Ccctatcaggcagtaccacaa	281–301
Core	CoreF2	Sense	Tactgcctgatagggtgcttg	287–307	709 bp
	CoreR3	Anti-sense	Atcggccgyctcgtacacaat	975–995
E1/E2	QRAF2	Sense	Aactgttcaccttctctccca	1207–1227	496 bp
	Q6AR1	Anti-sense	Tcgggacagcctgaagagttg	1682–1702
NS3	NS3AF2	Sense	Tgtggagaacctagagacaac	3933–3953	316 bp
	NS3AR2	Anti-sense	Cgtcggcaaggaacttgccrt	4228–4248
NS5a	Q5AF2	Sense	Atccctcccatataacagcag	6871–6891	251 bp
	Q5AR2	Anti-sense	Acaagcggatcgaaggagtcca	7099–7121
NS5b	Q5BF2	Sense	Atccgtacggaggaggcaat	8298–8317	921 bp
	Q5BR2	Anti-sense	Tatcggagtgagtttgagct	9199–9218

We also show the T_m values for all LRP primers as well as the primer sequences used for monitoring HCV cDNA synthesis. Star indicates that primer sequences are involved within putative stem loops [4], [5], [6]. Double stars indicate that primers contain restriction sites in their 5′ ends. Primer numbering is according to HCV H77 strain (GenBank Accession No. NC_004102). All primers were designed with software Eugene version 1.01. Degenerate bases are matched with standard International Union of Pure and Applied Chemistry (IUPAC) codes.