title: Evolution of multi-drug resistant HCV clones from pre-existing resistant-associated variants during direct-acting antiviral therapy determined by third-generation sequencing.
abstract: Resistance-associated variant (RAV) is one of the most significant clinical challenges in treating HCV-infected patients with direct-acting antivirals (DAAs). We investigated the viral dynamics in patients receiving DAAs using third-generation sequencing technology. Among 283 patients with genotype-1b HCV receiving daclatasvir + asunaprevir (DCV/ASV), 32 (11.3%) failed to achieve sustained virological response (SVR). Conventional ultra-deep sequencing of HCV genome was performed in 104 patients (32 non-SVR, 72 SVR), and detected representative RAVs in all non-SVR patients at baseline, including Y93H in 28 (87.5%). Long contiguous sequences spanning NS3 to NS5A regions of each viral clone in 12 sera from 6 representative non-SVR patients were determined by third-generation sequencing, and showed the concurrent presence of several synonymous mutations linked to resistance-associated substitutions in a subpopulation of pre-existing RAVs and dominant isolates at treatment failure. Phylogenetic analyses revealed close genetic distances between pre-existing RAVs and dominant RAVs at treatment failure. In addition, multiple drug-resistant mutations developed on pre-existing RAVs after DCV/ASV in all non-SVR cases. In conclusion, multi-drug resistant viral clones at treatment failure certainly originated from a subpopulation of pre-existing RAVs in HCV-infected patients. Those RAVs were selected for and became dominant with the acquisition of multiple resistance-associated substitutions under DAA treatment pressure.
authors.affiliation: Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
authors.forename: Haruhiko
authors.initials: H
authors.lastname: Takeda
authors.affiliation: Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Ueda
authors.affiliation: Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
authors.forename: Tadashi
authors.initials: T
authors.lastname: Inuzuka
authors.affiliation: Department of Gastroenterology and Hepatology, Japanese Red Cross Wakayama Medical Center, Wakayama, Japan.
authors.forename: Yukitaka
authors.initials: Y
authors.lastname: Yamashita
authors.affiliation: Department of Gastroenterology and Hepatology, Osaka Red Cross Hospital, Osaka, Japan.
authors.forename: Yukio
authors.initials: Y
authors.lastname: Osaki
authors.affiliation: Department of Gastroenterology and Hepatology, Osaka Red Cross Hospital, Osaka, Japan.
authors.forename: Akihiro
authors.initials: A
authors.lastname: Nasu
authors.affiliation: Department of Gastroenterology and Hepatology, Hyogo Prefectural Amagasaki General Medical Center, Hyogo, Japan.
authors.forename: Makoto
authors.initials: M
authors.lastname: Umeda
authors.affiliation: Clinical Research Center, Chiba University Hospital, Chiba, Japan.
authors.forename: Ryo
authors.initials: R
authors.lastname: Takemura
authors.affiliation: Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Seno
authors.affiliation: Center of Preventive Medical Sciences, Chiba University, Chiba, Japan.|Department of Genomic Medicine Omics Research Center, National Cerebral and Cardiovascular Center, Osaka, Japan.
authors.forename: Akihiro
authors.initials: A
authors.lastname: Sekine
authors.affiliation: Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Marusawa
mesh_terms: D000368:Aged; D000998:Antiviral Agents / Q000627:therapeutic use*; D002219:Carbamates; D018432:Drug Resistance, Multiple / Q000187:drug effects* / Q000235:genetics; D024882:Drug Resistance, Viral / Q000187:drug effects* / Q000235:genetics; D004359:Drug Therapy, Combination / Q000379:methods; D005260:Female; D005838:Genotype; D016174:Hepacivirus / Q000187:drug effects* / Q000235:genetics; D019698:Hepatitis C, Chronic / Q000188:drug therapy*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D007093:Imidazoles / Q000627:therapeutic use; D007546:Isoquinolines / Q000627:therapeutic use; D008297:Male; D011759:Pyrrolidines; D013449:Sulfonamides / Q000627:therapeutic use; D017211:Treatment Failure; D014633:Valine / Q000031:analogs & derivatives; D017361:Viral Nonstructural Proteins / Q000235:genetics
chemical_list: D000998:Antiviral Agents; D002219:Carbamates; D007093:Imidazoles; D007546:Isoquinolines; D011759:Pyrrolidines; D013449:Sulfonamides; D017361:Viral Nonstructural Proteins; D014633:Valine; C549273:daclatasvir; C571889:asunaprevir