Table 1

Non-synonymous ORF mutations in ED43 recombinant viruses during culture adaptation

ED43H77SNP frequencies (%)
ED43-20mED43-31mED43-31m_optED43cc*
HCV geneNT posNT changeAA posAA changeAA pos4.1† (4th, 13)5.0†
(10th, 6)
4.3†
(2nd, 8)
5.1†
(2nd, 6)
5.1†
(2nd, 6)
E1923CA195RS1957.16,9
E11152TG271VG27128.189.199.9100100
E21553TC405SP4057.2
E21712TC458CR45826.288.999.9100100
E22534TC732SP7328.6
p72597AG753ND75316.8
p72646TC769IT76910.2
p72730TC797FS79711.5
NS22819AG827TA827100100100100100
NS22883AG848YC8486.588.299.6100100
NS33710AG1124TA112411,3
NS34211AG1291IV1291100100100100100
NS34487GA1383EK138311.7
NS34733AG1465SG1465100100100100100
NS34736TA1466LM146699.8100100100100
NS35054TC1572FL157245.89.8100100100
NS4A5354GT1672AS1672100100100100100
NS4B5697CT1786AV1786100100100100100
NS4B5804AG1822TA1822100100100100100
NS4B5933AG1865TA1865100100100100100
NS4B5949GA1870SN1870100100100100100
NS4B6066GC1909GA190938.087.899.9100100
NS5A6257GA1973AT197325.888.4100100
NS5A7017TC2226LP22267.7
NS5A7109GA2257AT22615.388.499.9100100
NS5A7126CA2262DE226517.8
NS5A7151AG2271IV227446.79.6
NS5A7325AG2329TA23325.488.499.5100100
NS5A7436AG2366TA236945.99.0
NS5A7503TC2388MT238811.27.3
NS5A7578AG2413DG2416100100100100100
NS5B7975CA2545DE2548100100100100100
NS5B7979AG2547ND255011.8
NS5B8033AG2565ND25685.9
NS5B8131AT2597KN260095.899.799.8100100
NS5B8134AC2598KN26018.6
NS5B8365TG2675DE2678100100100100100
NS5B8718TC2793VA27966.188.4100100100
NS5B8730AG2797KR2800100100100100100
NS5B8756GA2806ET2809100100100100100
NS5B8757AC100100100100100
NS5B9087CT2916AV2919100100100100100
NS5B9132AG2931QR293498.197.3100--
NS5B9267AG2976DG2979100100100100100
NS5B9273AT2978YF2981100100100100100
NS5B9281AG2981MV2984100100100100100
NS5B9284TC2982SP298526.090.1100100100
NS5B9289TG2983HQ29866.37.0
NS5B9312TG2991LR2994100100100100100
NS5B9315GA2992CY299599.399.1100100100
  • Only mutations with a frequency of >5% of the viral population in NGS analysis are shown. Shaded background indicates frequencies of engineered mutations.

  • *Nucleotide G at position 38 in 5’UTR was changed to A.

  • †HCV infectivity titres at indicated passage and day (parentheses) are shown as log10FFU/mL.

  • ‡These recombinant viruses had A at position 9132 instead of G, and this nt was maintained.

  • AA, amino acid; NGS, next-generation sequencing; NT, nucleotide; NT pos and AA pos, nucleotide and amino acid positions; SNP, single nucleotide polymorphism.