Table 2

NGS analysis of recombinant ED43 viruses harbouring RASs recovered from the second passage culture

HCV genePolyproteinP#SNP frequencies (%)NS5B*
NS3*NS5A*
NT posNT changeAA posAA changeAA posY56H, D168AA156MA156M, I2841VL28VL30P, Y93HL30H, M31VL28M, L30F,M31VL30ƠL30Ơ, T2047IS282TS282T, A1309P
NS33584TC1082YH56
NS33884GA1182AM15699.699.8
NS33885CT99.699.7
NS33921AC1194DA168
NS34265GC1309AP28399.8
NS35268AG1643KR61713.9
NS4B5645AG1769IV5827.5
NS5A6338CG2000LV2899.6
NS5A6338CA2000LM2899.9
NS5A6339TC2000LP287.2
NS5A6344CT2002LF3099.8
NS5A6344CTCdel‡2002Ldel‡3097.097.0
NS5A6345TC2002LP3099.5
NS5A6345TA2002LH3099.6
NS5A6347AG2003MV3199.899.9
NS5A6480CT2047TI757.199.8
NS5A6510AG2057HR855.6
NS5A6533TC2065YH9399.5
NS5A6637CA2099FL1278.6
NS5A6737CT2133HY16123.7
NS5A7266AT2309HL33797.2
NS5A7578GA2413GD4415.5
NS5B8406AG2689DG2725.3
NS5B8435A2699SC28216.9§
NS5B8436GC2699ST28297.499.6
NS5B8861AG2841IV42457.299.9
  • All recombinant viruses harbouring RASs were generated using the ED43-31m_opt backbone as shown in figures 2–4. Shaded background indicates frequencies of mutations that were introduced into this recombinant. Only non-synonymous (coding) mutations that represented >5% of the viral population are shown.

  • *Target proteins in which the recombinants harbouring RASs were numbered.

  • †This recombinant had a deletion at NS5A position 30.

  • ‡Three nucleotides were deleted, resulting in an amino acid deletion.

  • §The linkage analysis showed that this nucleotide was combined with C at position 8436, resulting in the reversion of S282T with a frequency of 16.9%. Therefore, the actual frequency of S282T was ~80%.

  • AA, amino acid; NGS, next-generation sequencing; NT, nucleotide; NT pos and AA pos, nucleotide and amino acid positions; P#, protein specific numbers; RAS, resistance-associated substitution; SNP, single nucleotide polymorphism.