TY - JOUR
T1 - Genotyping Hepatitis B virus by Next-Generation Sequencing :
T2 - Detection of Mixed Infections and Analysis of Sequence Conservation
AU - Dopico, Eva
AU - Vila, Marta
AU - Tabernero, David
AU - Gregori i Font, Josep
AU - Rando Segura, Ariadna
AU - Pacín Ruiz, Beatriz
AU - Guerrero, Laura
AU - Ubillos, Itziar
AU - Martínez, Miguel J.
AU - Costa, Josep
AU - Quer, Josep
AU - Pérez Garreta, Javier
AU - González-Sánchez, Alejandra
AU - Antón, Andrés
AU - Pumarola Suñé, Tomàs
AU - Riveiro Barciela, Mar
AU - Ferrer Costa, Roser
AU - Buti, Maria
AU - Rodríguez Frías, Francisco
AU - Cortese, Maria Francesca
N1 - Publisher Copyright:
© 2024 by the authors.
PY - 2024/5/17
Y1 - 2024/5/17
N2 - 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.
AB - 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.
KW - Distance-Based discrimination method
KW - RNA interference
KW - conservation
KW - genotypes
KW - hepatitis B X gene
KW - hepatitis B virus
KW - information content
KW - next-generation sequencing
KW - preS
KW - quasispecies
KW - Haplotypes
KW - Humans
KW - Male
KW - Phylogeny
KW - High-Throughput Nucleotide Sequencing/methods
KW - Conserved Sequence
KW - Adult
KW - Female
KW - Genome, Viral
KW - Hepatitis B/virology
KW - DNA, Viral/genetics
KW - Genotype
KW - Coinfection/virology
KW - Genotyping Techniques/methods
KW - Hepatitis B virus/genetics
UR - http://www.scopus.com/inward/record.url?scp=85194219695&partnerID=8YFLogxK
UR - https://www.mendeley.com/catalogue/4fc2031d-27cc-30ca-ae2f-1ec6f0bb1369/
U2 - 10.3390/ijms25105481
DO - 10.3390/ijms25105481
M3 - Article
C2 - 38791519
SN - 1422-0067
VL - 25
JO - International Journal of Molecular Sciences
JF - International Journal of Molecular Sciences
IS - 10
M1 - 5481
ER -