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Published on: November 7, 2018
Establishment of reference sequences of hepatitis B virus genotype C subgenotypes
1Virology Laboratory, Department of Infectious Diseases, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China.
Insights
This study establishes crucial reference sequences for Hepatitis B virus genotype C (HBV/C) subgenotypes, aiding global research. These new references enhance the accuracy of HBV/C subtyping and phylogenetic analysis.
Area of Science:
- Virology
- Genetics
- Molecular Biology
Background:
- Hepatitis B virus genotype C (HBV/C) exhibits extensive subgenotypic diversity (C1-C16), geographically distributed worldwide.
- The scarcity of reliable reference strains hinders comprehensive research and accurate subtyping of HBV/C isolates.
- Understanding HBV/C subgenotype variations is critical for epidemiological studies and therapeutic development.
Purpose of the Study:
- To establish and validate reference sequences for various HBV/C subgenotypes.
- To facilitate accurate subtyping and phylogenetic analysis of HBV/C.
- To provide essential resources for researchers studying HBV/C diversity and evolution.
Main Methods:
- Phylogenetic analysis of 974 retrieved HBV/C full-length sequences from GenBank.
- Construction of reference sequences using the most frequent nucleotide at each position for each subgenotype.
- Validation through homology and phylogenetic tree analyses, including bootstrap values.
Main Results:
- Successfully established and deposited reference sequences for HBV/C subgenotypes C1, C2, C5, and C6 (GenBank accession numbers KM999990-KM999993).
- Reference sequences demonstrated high homology (>96%) with corresponding subgenotype isolates and significant heterogeneity with other genotypes/subgenotypes.
- Sequence analysis revealed distinct mutation rates in the basal core promoter (BCP) and pre-core (Pre-C) regions across different subgenotypes, with HBV/C5 and C6 being evolutionarily older.
Conclusions:
- The established HBV/C reference sequences are highly reliable for accurate subtyping and phylogenetic studies.
- These references will significantly advance research into HBV/C epidemiology, evolution, and pathogenesis.
- The findings highlight significant genetic diversity and evolutionary patterns within HBV/C subgenotypes.
Abstract:
Hepatitis B virus genotype C (HBV/C) has the largest number of subgenotypes (C1-C16) that vary with geography and isolates. HBV/C prevails in Southeast Asia (C1, C5-C16), East Asia (C2), Oceania (C3), and Australia (C4). Suitable reference strains for different subgenotypes could greatly facilitate research into HBV/C, but unfortunately they are scarce. We retrieved 974 HBV/C full-length sequences from the GenBank database and subgenotyped them by phylogenetic analysis. Reference sequences of each subgenotype from different locations were established with the most frequent nucleotide present at each position of the isolates that belonged to the same subgenotype. The reference sequences of subgenotypes C1, C2, C5, and C6 have been constructed and deposited in GenBank (KM999990-KM999993). The homology between the reference sequences and almost all the isolates belonging to the corresponding subgenotype was higher than 96%. Similarly, bootstrap values in phylogenetic trees supported clustering of reference strains with isolates belonging to the same subgenotypes. Moreover, both homology and phylogeny analyses showed that reference sequences had significant heterogeneity with isolates from other genotypes and subgenotypes. Sequence analysis further revealed that the mutation rate in the basal core promoter (BCP) region was extremely high in HBV/C2, relatively high in HBV/C1, but lower in HBV/C5 and HBV/C6. Mutations in the pre-core (Pre-C) region were common in HBV/C but the mutation rate was lower than in the BCP. HBV/ C5 has the oldest ancestral age, followed by C6, which is much more ancient than C1 and C2. This study successfully established references for HBV/C subgenotypes.
