Genotyping Hepatitis B virus by Next-Generation Sequencing : Detection of Mixed Infections and Analysis of Sequence Conservation

Eva Dopico, Marta Vila, David Tabernero, Josep Gregori i Font, Ariadna Rando Segura, Beatriz Pacín Ruiz, Laura Guerrero, Itziar Ubillos, Miguel J. Martínez, Josep Costa, Josep Quer, Javier Pérez Garreta, Alejandra González-Sánchez, Andrés Antón, Tomàs Pumarola Suñé, Mar Riveiro Barciela, Roser Ferrer Costa, Maria Buti, Francisco Rodríguez Frías, Maria Francesca Cortese

Research output: Contribution to journalArticleResearchpeer-review

2 Citations (Scopus)

Abstract

Our aim was to develop an accurate, highly sensitive method for HBV genotype determination and detection of genotype mixtures. We examined the preS and 5' end of the HBV X gene (5X) regions of the HBV genome using next-generation sequencing (NGS). The 1852 haplotypes obtained were subjected to genotyping via the Distance-Based discrimination method (DB Rule) using two sets of 95 reference sequences of genotypes A-H. In clinical samples from 125 patients, the main genotypes were A, D, F and H in Caucasian, B and C in Asian and A and E in Sub-Saharan patients. Genotype mixtures were identified in 28 (22.40%) cases, and potential intergenotypic recombination was observed in 29 (23.20%) cases. Furthermore, we evaluated sequence conservation among haplotypes classified into genotypes A, C, D, and E by computing the information content. The preS haplotypes exhibited limited shared conserved regions, whereas the 5X haplotypes revealed two groups of conserved regions across the genotypes assessed. In conclusion, we developed an NGS-based HBV genotyping method utilizing the DB Rule for genotype classification. We identified two regions conserved across different genotypes at 5X, offering promising targets for RNA interference-based antiviral therapies.
Original languageEnglish
Article number5481
Number of pages23
JournalInternational Journal of Molecular Sciences
Volume25
Issue number10
DOIs
Publication statusPublished - 17 May 2024

Keywords

  • Distance-Based discrimination method
  • RNA interference
  • conservation
  • genotypes
  • hepatitis B X gene
  • hepatitis B virus
  • information content
  • next-generation sequencing
  • preS
  • quasispecies
  • Haplotypes
  • Humans
  • Male
  • Phylogeny
  • High-Throughput Nucleotide Sequencing/methods
  • Conserved Sequence
  • Adult
  • Female
  • Genome, Viral
  • Hepatitis B/virology
  • DNA, Viral/genetics
  • Genotype
  • Coinfection/virology
  • Genotyping Techniques/methods
  • Hepatitis B virus/genetics

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