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Published on: March 30, 2014
HCV inter-subtype 1a/1b recombinant detected by complete-genome next-generation sequencing
Karine Vieira Gaspareto1,2,3, Roberto Marques Ribeiro4,5, Fernanda de Mello Malta6,7
1Laboratory 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.
Next-generation sequencing enabled complete genome analysis of Hepatitis C Virus (HCV) in Brazilian patients. This study identified viral recombinants and characterized genetic diversity in drug-naïve individuals infected with HCV genotype 1.
Area of Science:
- Virology and Molecular Biology
- Infectious Diseases
- Genomics
Background:
- Hepatitis C Virus (HCV) infection poses a significant global health challenge.
- Understanding HCV genetic diversity, including drug resistance and recombinants, is crucial for effective treatment strategies.
- Next-generation sequencing (NGS) offers advanced capabilities for comprehensive viral genome analysis.
Purpose of the Study:
- To analyze the complete coding region of Hepatitis C Virus (HCV) genotype 1 (subtypes 1a and 1b).
- To investigate viral genetic diversity and identify drug-resistant or escape mutations in direct-acting antiviral (DAA)-naïve patients.
- To detect potential viral recombinants within a Brazilian cohort.
Main Methods:
- Employed Next-generation sequencing (NGS) using the Ion Torrent™ PGM platform.
- Sequenced the complete coding region of 100 HCV-monoinfected, DAA-naïve patients (51 subtype 1a, 49 subtype 1b).
- Analyzed viral genetic diversity, quasispecies, and identified recombinants.
Main Results:
- Generated nearly complete HCV genome sequences for subtype 1a and 1b isolates from a large Brazilian population.
- HCV subtype 1a isolates clustered into two distinct clades.
- Identified a novel inter-subtype 1a/1b recombinant within the study cohort.
Conclusions:
- NGS is a powerful tool for comprehensive HCV genome sequencing, variant detection, and analysis of genetic diversity.
- The study provides valuable insights into the genetic landscape of HCV genotype 1 in Brazil.
- The identification of an inter-subtype recombinant highlights the complex evolutionary dynamics of HCV.
