**5. Conclusions**

In conclusion, the genotyping results of the Vela NGS were found to be highly concordant with those of the LiPA method. Vela NGS refined the ST assignment in GT 6 and resolved previously indeterminate GTs reported by LiPA. Technically, the HCV Vela NGS was found to have consistent intra- and inter-run reproducibility in terms of GT and ST calling and RAVs identification. Detection of infections with multiple HCV GTs or STs is feasible by Vela NGS. Due to the assay design which relies on investigating the HCV sub-genomic regions, HCV recombinant strains may still be potentially missed. Deep sequencing allows sensitive identification of RAVs in the GT1a and 1b NS3, NS5A and NS5B regions, but the list of target RAVs is not exhaustive. We would also suggest the RAVs detection spectrum should be extended to cover GTs other than HCV 1a and 1b, namely GTs 2-6.
