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HCV inter-subtype 1a/1b recombinant detected by complete-genome next-generation sequencing

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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.

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Acknowledgments

Special thanks to the patients, to Dr Maria C. M. Correa for providing samples, and to Dr Ester C. Sabino for allowing the use of next-generation sequencing.

Author information

Authors and Affiliations

  1. 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

    Karine Vieira Gaspareto, Fernanda de Mello Malta, Michele Soares Gomes-Gouvêa, Flair José Carrilho & João Renato Rebello Pinho

  2. Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil

    Karine Vieira Gaspareto, Fernanda de Mello Malta, Michele Soares Gomes-Gouvêa, Flair José Carrilho & João Renato Rebello Pinho

  3. Graduate Program in Biotechnology Interunits (USP/Butantan/IPT), University of São Paulo, São Paulo, Brazil

    Karine Vieira Gaspareto & João Renato Rebello Pinho

  4. Laboratory of Parasitology, LIM-46, Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, Brazil

    Roberto Marques Ribeiro & Ester Cerdeira Sabino

  5. Department of Infectious and Parasitic Diseases, School of Medicine, University of São Paulo, São Paulo, SP, Brazil

    Roberto Marques Ribeiro, Maria Cassia Mendes-Correa & Ester Cerdeira Sabino

  6. Hospital Israelita Albert Einstein, São Paulo, SP, Brazil

    Nair Hideko Muto & João Renato Rebello Pinho

  7. Laboratory of Virology, LIM-52, Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, Brazil

    Maria Cassia Mendes-Correa

  8. Laboratory of Bioinformatics, Sírio-Libanês Hospital, São Paulo, Brazil

    Andrei Rozanski

Authors
  1. Karine Vieira Gaspareto
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  2. Roberto Marques Ribeiro
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  6. Maria Cassia Mendes-Correa
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  7. Andrei Rozanski
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  8. Flair José Carrilho
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  9. Ester Cerdeira Sabino
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  10. João Renato Rebello Pinho
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Corresponding author

Correspondence to Fernanda de Mello Malta.

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Conflict of interest

The authors declare that they have no conflict of interest.

Financial support

This project was supported by grant 443152/2014-4 (CNPq) and Alves de Queiroz Family Fund for Research. Karine Vieira Gaspareto is a graduate student from Programa de Pós-Graduação em Biotecnologia, USP, and received a fellowship from CAPES. João Renato Rebello Pinho, Ester Cerdeira Sabino and Maria Cassia Mendes Correa received a fellowship from CNPq (Bolsista de Produtividade).

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Gaspareto, K.V., Ribeiro, R.M., de Mello Malta, F. et al. HCV inter-subtype 1a/1b recombinant detected by complete-genome next-generation sequencing. Arch Virol 161, 2161–2168 (2016). https://doi.org/10.1007/s00705-016-2889-5

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  • DOI: https://doi.org/10.1007/s00705-016-2889-5

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