title: HCV inter-subtype 1a/1b recombinant detected by complete-genome next-generation sequencing.
abstract: Next-generation sequencing (NGS) provides a practical approach to HCV complete-genome sequencing, detecting low-frequency variants and allowing analysis of viral genetic diversity (quasispecies) in the sample, and so far, it is very useful for identifying preexisting drug-resistant mutants and emerging escape mutations, as well as detecting viral recombinants containing genomic regions from different genotypes and subtypes. The aim of this study was to analyze the complete coding region of hepatitis C virus (HCV) genotype 1 (subtypes 1a and 1b) from patients with chronic infection who were direct-acting antiviral (DAA) naïve. Next-generation sequencing (Ion Torrent™ PGM) was used to determine the sequence of the complete coding region of 100 HCV-monoinfected DAA-naïve patients (51 and 49 subtypes 1a and 1b, respectively). We report the first description of nearly complete HCV genome sequences of subtype 1a and 1b isolates from a large population of Brazilian patients with chronic hepatitis C, and HCV-1a grouped in two different clades. Using this methodology, an inter-subtype 1a/1b recombinant was identified in this study.
authors.affiliation: Laboratory of Tropical Gastroenterology and Hepatology "João Alves de Queiroz and Castorina Bittencourt Alves", LIM-07, Institute of Tropical Medicine, University of São Paulo, Av. Dr. Enéas Carvalho Aguiar, 500, 2nd floor IMT-II, São Paulo, SP, 05403-000, Brazil.|Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil.|Graduate Program in Biotechnology Interunits (USP/Butantan/IPT), University of São Paulo, São Paulo, Brazil.
authors.forename: Karine Vieira
authors.initials: KV
authors.lastname: Gaspareto
authors.affiliation: Laboratory of Parasitology, LIM-46, Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, Brazil.|Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, SP, Brazil.
authors.forename: Roberto Marques
authors.initials: RM
authors.lastname: Ribeiro
authors.affiliation: Laboratory of Tropical Gastroenterology and Hepatology "João Alves de Queiroz and Castorina Bittencourt Alves", LIM-07, Institute of Tropical Medicine, University of São Paulo, Av. Dr. Enéas Carvalho Aguiar, 500, 2nd floor IMT-II, São Paulo, SP, 05403-000, Brazil. femalta@yahoo.com.|Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil. femalta@yahoo.com.
authors.forename: Fernanda
authors.initials: F
authors.lastname: de Mello Malta
authors.affiliation: Laboratory of Tropical Gastroenterology and Hepatology "João Alves de Queiroz and Castorina Bittencourt Alves", LIM-07, Institute of Tropical Medicine, University of São Paulo, Av. Dr. Enéas Carvalho Aguiar, 500, 2nd floor IMT-II, São Paulo, SP, 05403-000, Brazil.|Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil.
authors.forename: Michele Soares
authors.initials: MS
authors.lastname: Gomes-Gouvêa
authors.affiliation: Hospital Israelita Albert Einstein, São Paulo, SP, Brazil.
authors.forename: Nair Hideko
authors.initials: NH
authors.lastname: Muto
authors.affiliation: Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, SP, Brazil.|Laboratory of Virology, LIM-52, Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, Brazil.
authors.forename: Maria Cassia
authors.initials: MC
authors.lastname: Mendes-Correa
authors.affiliation: Laboratory of Bioinformatics, Sírio-Libanês Hospital, São Paulo, Brazil.
authors.forename: Andrei
authors.initials: A
authors.lastname: Rozanski
authors.affiliation: Laboratory of Tropical Gastroenterology and Hepatology "João Alves de Queiroz and Castorina Bittencourt Alves", LIM-07, Institute of Tropical Medicine, University of São Paulo, Av. Dr. Enéas Carvalho Aguiar, 500, 2nd floor IMT-II, São Paulo, SP, 05403-000, Brazil.|Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil.
authors.forename: Flair José
authors.initials: FJ
authors.lastname: Carrilho
authors.affiliation: Laboratory of Parasitology, LIM-46, Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, Brazil.|Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, SP, Brazil.
authors.forename: Ester Cerdeira
authors.initials: EC
authors.lastname: Sabino
authors.affiliation: Laboratory of Tropical Gastroenterology and Hepatology "João Alves de Queiroz and Castorina Bittencourt Alves", LIM-07, Institute of Tropical Medicine, University of São Paulo, Av. Dr. Enéas Carvalho Aguiar, 500, 2nd floor IMT-II, São Paulo, SP, 05403-000, Brazil.|Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil.|Graduate Program in Biotechnology Interunits (USP/Butantan/IPT), University of São Paulo, São Paulo, Brazil.|Hospital Israelita Albert Einstein, São Paulo, SP, Brazil.
authors.forename: João Renato Rebello
authors.initials: JR
authors.lastname: Pinho
mesh_terms: D001938:Brazil; D016679:Genome, Viral; D005838:Genotype; D016174:Hepacivirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D019698:Hepatitis C, Chronic / Q000821:virology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D010802:Phylogeny; D011995:Recombination, Genetic; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins