Use of whole genome sequencing in the Dutch Acute HCV in HIV study: focus on transmitted antiviral resistance

• Published in: Clinical microbiology and infection Vol. 23; no. 2; pp. 123.e1 - 123.e4
• Main Authors: Christiansen, M.T., Hullegie, S.J., Schutten, M., Einer-Jensen, K., Tutill, H.J., Breuer, J., Rijnders, B.J.A.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01-02-2017
• Subjects: Acute hepatitis C; Antiviral Agents - pharmacology; Antiviral Agents - therapeutic use; Coinfection; Drug Resistance, Viral; Genome, Viral; Genotype; Hepacivirus - drug effects; Hepacivirus - genetics; Hepatitis C - drug therapy; Hepatitis C - epidemiology; Hepatitis C - transmission; Hepatitis C - virology; HIV; HIV Infections; Humans; Microbial Sensitivity Tests; Mutation; Netherlands - epidemiology; Protease inhibitors; Resistance; Sequence Analysis, DNA; Treatment; Viral Load; Viral Nonstructural Proteins - genetics; Resistance; Treatment; HIV; Protease inhibitors; Acute hepatitis C
• ISSN: 1198-743X; 1469-0691
• DOI: 10.1016/j.cmi.2016.09.018

Within HIV-positive men having sex with men, the epidemic of hepatitis C virus (HCV) is ongoing. Transmission of resistant variants of HCV after failure of treatment with directly acting antivirals (DAA) could be a major threat to the effectivity of therapy. We determined whether HCV-resistant variants to DAAs were prevalent amongst patients with an acute HCV infection diagnosed in 2013 and 2014 in the Netherlands.
Target enrichment for viral nucleic acid separation and deep sequencing were used to recover whole HCV genomes of 50 patients with an acute HCV infection. The genomes were assembled by de novo assembly and analysed for known DAA resistance mutations.
In acute HCV infected treatment-naive patients, the relevant resistance-associated substitutions were Q80K (40%) in NS3/4a, M28V (24%) and Q30H combined with Y93H (2%) in NS5A and M414T (2%) or S556G (2%) in NS5b. Patients whose HCV infection failed to respond to boceprevir, peginterferon and ribavirin therapy developed mutations in NS3 at position T54A and R155K.
Target enrichment and whole genome sequencing were successfully applied directly on clinical samples from patients with an acute HCV infection.