Resistance-associated variants in HCV subtypes 1a and 1b detected by Ion Torrent sequencing platform.
As a result of increased understanding of the HCV life cycle, a new generation of drugs known as direct-acting antivirals (DAAs) was developed and is constantly being improved. At baseline, HCV variants resistant to DAA therapy may pre-exist, increasing the likelihood of treatment failure. The aim of this study was to investigate the presence of resistance-associated variants (RAVs) in treatment-naive patients infected with HCV subtypes 1a and 1b.



Next-generation sequencing was used to assess the frequencies of NS3-4A, NS5A and NS5B RAVs in 100 HCV monoinfected DAA-naive patients (HCV-1a: n=51; HCV-1b: n=49).



Complete HCV sequence information was obtained for most samples. RAVs were detected in the NS3-4A (T54S, V55A, Q80K and R155K), NS5A (Q30H/R, H58P and Y93C/H/N) and NS5B (A421V) regions in 10%, 22% and 8%, respectively, of patients infected with HCV subtype-1a. Among the patients infected with HCV subtype-1b, mutations in the NS3-4A (F43I, T54S, Q80H, D168E and M175L), NS5A (L28M, R30Q, L31M, Q54H, A92T and Y93H) and NS5B (L159F, C316N, A421V and S556G) regions were observed in 12%, 53% and 31% of patients, respectively.



High-throughput DNA sequencing allows an easier and more complete analysis of DAA RAVs, including mutations that represent only a minor variant of the whole viral population. RAVs to the three different classes of DAAs were found in our population. The characterization of their profile in the circulating virus is relevant to determine the better treatment option for infected individuals or to guide the implementation of treatment policies.
Laboratory of Tropical Gastroenterology and Hepatology 'João Alves de Queiroz and Castorina Bittencourt Alves', LIM-07, Institute of Tropical Medicine and Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, Brazil.|Graduate Program in Biotechnology Interunits (USP/Butantan/IPT), University of São Paulo, São Paulo, Brazil.
Karine V
KV
Gaspareto
Laboratory of Parasitology, LIM-46, Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil.
Roberto M
RM
Ribeiro
Laboratory of Tropical Gastroenterology and Hepatology 'João Alves de Queiroz and Castorina Bittencourt Alves', LIM-07, Institute of Tropical Medicine and Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, Brazil.
Fernanda
F
de Mello Malta
Laboratory of Tropical Gastroenterology and Hepatology 'João Alves de Queiroz and Castorina Bittencourt Alves', LIM-07, Institute of Tropical Medicine and Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, Brazil.
Michele S
MS
Gomes-Gouvêa
Hospital Israelita Albert Einstein, São Paulo, Brazil.
Nair H
NH
Muto
Laboratory of Virology, LIM-52, Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil.
Camila M
CM
Romano
Laboratory of Virology, LIM-52, Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil.
Maria C
MC
Mendes-Correa
Laboratory of Tropical Gastroenterology and Hepatology 'João Alves de Queiroz and Castorina Bittencourt Alves', LIM-07, Institute of Tropical Medicine and Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, Brazil.
Flair J
FJ
Carrilho
Laboratory of Parasitology, LIM-46, Institute of Tropical Medicine and Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil.
Ester C
EC
Sabino
Laboratory of Tropical Gastroenterology and Hepatology 'João Alves de Queiroz and Castorina Bittencourt Alves', LIM-07, Institute of Tropical Medicine and Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, Brazil.|Graduate Program in Biotechnology Interunits (USP/Butantan/IPT), University of São Paulo, São Paulo, Brazil.|Hospital Israelita Albert Einstein, São Paulo, Brazil.
João R
JR
Rebello Pinho
D000328:Adult; D000998:Antiviral Agents / Q000494:pharmacology; D024882:Drug Resistance, Viral / Q000235:genetics*; D005260:Female; D016174:Hepacivirus / Q000145:classification / Q000187:drug effects / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases; D012324:RNA-Dependent RNA Polymerase
D000998:Antiviral Agents; D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases; C093542:NS4 protein, hepatitis C virus; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase