Effect of oligonucleotide primers in determining viral variability within hosts

Table 1 List of primers for the E1E2 and NS5A regions of HCV

Region	Primer name^a	Nucleotide position^b	Primer set	Sequence 5'-3'^c	Primer degeneracy
E1E2	1-Eg1	1290–1309	1	CGCATGGCA TGG R A T ATGAT	2
	2-Eg1	1290–1309	2	CGCATGGCY TGG G A Y ATGAT	4
	1-Eg2	1300–1321	1	GG R ATATGAT G ATGAAC TGGTC	2
	2-Eg2	1300–1321	2	GG G ATATGAT R ATGAAY TGGTC	4
	1-Ea	1873–1854	1	GGA GTGAAG CAR TAT ACT GG	2
	2-Ea	1873–1854	2	GGG GTGAAR CAR TAY ACY GG	16
NS5A	1-Ng1	6715–6739	1	TGGAY GGGGTGC GC CTA CAT AGGT W	4
	2-Ng1	6715–6739	2	TGGAC GGGGTGY GM CTR CAY AGGT T	16
	1-Ng2	6734–6753	1	TAGGT W YGCS CCCCCYTGCA	16
	2-Ng2	6734–6753	2	TAGGT T YGCG CCCCCYTGCA	4
	1-Na	7519–7503	1	CCC TCSAGR GGG GGCAT	4
	2-Na	7519–7503	2	CCY TCSARG GGR GGCAT	16

^ag indicates genomic sense and a indicates antigenomic sense.
^bNucleotide positions according to sequence accession no. M62321.
^cNucleotides in bold indicate differences between primer sets and underlined nucleotides indicate overlapping positions of nested primers.

ISSN: 1743-422X