Next Generation Sequencing for HCV Genotyping and Optional Identification of Resistance-Associated Variants

Rakhmanaliev, Elian; Zhang, Rui; Huang, Wenpan; Poon, Kok Siong; Cui, Wei-guo; Mui, Jeannie; Koay, Evelyn Siew-Chuan; Passomsub, E.; Chantratita, Wasun; Michel, Gerd

doi:10.1016/s0168-8278(16)01140-5

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“…The detected RAS is reported to confer resistance to simeprevir and to all NS5A inhibitors (15). The Sentosa® SQ NGS (Vela Diagnostics Germany GMBH, Hamburg, Germany) workflow (mean coverage/target > 200 × for genotyping and > 500 × for variant calling) was further performed to analyze both baseline and failure samples (16). In the baseline sample, sequence reads were mapped only to subtype 4d reference genome.…”

Section: Case Presentationmentioning

confidence: 99%

Diagnostic and Therapeutic Implications in a Case of Mixed Hepatitis C Virus (HCV) Infection

Bruzzone

Leo²,

Sticchi

et al. 2017

Hepat Mon

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Introduction: Hepatitis C virus (HCV) multiple infections can influence the course of the disease, either by boosting hepatocellular injury or by increasing the frequency of exacerbations. Their prevalence ranges from 5% to 39% in individuals with HCV infection, with a higher impact on injection drug users (IDUs), or in prison settings. Case Presentation: The current paper reported a case of dual HCV infection in a 31-year-old female, with a referred vertical transmission of HCV infection and also a history of IDU, who harbored a subtype 4d since youth. Treatment failure, after a 24-week course of sofosbuvir/ledipasvir, prompted a reevaluation of present and past HCV status. HCV genotype was determined by INNO-LiPA TM HCV II kit (LiPA II) (Innogenetics, Ghent, Belgium) and sequencing of NS5B region (nucleotide 8281 -8679). Direct-acting antivirals (DAAs) resistance profile was investigated by NS3/4, NS5A and NS5B sequencing with specific primers. The Sentosa® SQ next generation sequencing (NGS) workflow was further performed in the baseline and failure samples. Unexpectedly, a subtype 4d in the pretreatment sample and a subtype 1a in the posttreatment were identified. No resistance associated mutations (RAS) were detected in the subtype 4d, although the 170AV and 174S in the NS3/4 gene, the 30R in the NS5A gene, and the 444D in the NS5B gene were detected in the subtype 1a virus from the failure sample. Conclusions: Two main hypotheses were raised: a reinfection with a new subtype 1a virus during the treatment with a wild type strain, which developed RAS after infection or with an already mutated virus; and a pretreatment hidden dual subtype 4d plus 1a infection.

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Section: Case Presentationmentioning

confidence: 99%