Newly developed automated-massively parallel sequencing presenting the accuracy of hepatitis C virus genotyping and application on resistance-associated variants detection
DOI:
https://doi.org/10.14456/gag.2017.1Keywords:
, HCV genotyping, mixed-HCV infection, massively parallel sequencing, Sanger sequencingAbstract
Most hepatitis C virus (HCV) infection becomes chronic diseases and predictably develops into liver cirrhosis or hepatocellular carcinoma. HCV can be classified into 7 genotypes (GT) and multiple subtypes (ST). HCV treatment guidelines focus on determining the accuracy of HCV genotyping and subtyping, before starting treatment in all HCV-infected individuals. Efficient HCV genotyping and subtyping have become essential tools for indicating the optimal treatment. Current routine assays for HCV genotyping are easy and quick turnaround, but apparently subtyping is limited to identification. This study evaluated the accuracy of HCV genotyping in a newly developed automated-massively parallel sequencing (MPS) technique of previously identified HCV-infected specimens. The results indicated that by using the reference method, MPS and a bioinformatic pipeline, the genotype and subtype had identical accuracy of 95.65%. Interestingly, MPS could detect the remaining 4.35% as mixed-HCV type infected specimens, while the reference method could not. This result indicated that the MPS technique was highly accurate in identifying the HCV genotype and mixed-type infection. In addition, MPS can detect resistance-associated variants (RAVs) simultaneously with the HCV genotyping, especially in HCV GT1-infected specimens. Since HCV GT1 has a highly frequent presence of pre-existing RAVs, with resistance associated to direct-acting antivirals (DAAs), this study found that up to 60% of HCV GT1 sample were RAVs. This discovery of important RAVs in the patient infected with HCV GT1 could be beneficial in guiding the therapy decisions while avoiding the use of some DAAs. Thereby, the opportunity for patients to access the best treatment is enhanced.
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