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

From: Effect of oligonucleotide primers in determining viral variability within hosts

Region Primer namea Nucleotide positionb 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
  1. ag indicates genomic sense and a indicates antigenomic sense.
  2. bNucleotide positions according to sequence accession no. M62321.
  3. cNucleotides in bold indicate differences between primer sets and underlined nucleotides indicate overlapping positions of nested primers.