Novel Type of Hepatitis B Virus Mutation: Replacement Mutation Involving a Hepatocyte Nuclear Factor 1 Binding Site Tandem Repeat in Chronic Hepatitis B Virus Genotype E

Abstract

The genetic diversity of hepatitis B virus (HBV) strains has evolved through mutations such as point mutations, deletions or insertions, and recombination. We identified and characterized a novel type of mutation which is a complex of external insertion, deletion, and internal duplication in sequences from one of six patients with chronic hepatitis B virus genotype E (HBV/E). We provisionally named this mutation a "replacement mutation"; the core promoter upstream regulatory sequence/basic core promoter was replaced with a part of the S1 promoter covering the hepatocyte nuclear factor 1 (HNF1) binding site, followed by a tandem repeat of the HNF1 site. A longitudinal analysis of the HBV population over 6 years showed the clonal change from wild-type HBV/E to replacement-mutant type, resulting in a lower hepatitis B (HB) e antigen titer, a high HBV DNA level in serum, and progression of liver fibrosis. In an in vitro study using a replication model, the replacement-mutant HBV showed higher replication levels than the wild-type HBV/E replicon, probably mediated by altered transcription factor binding. Additionally, this HNF1 site replacement mutation was associated with excessive HB nucleocapsid protein expression in hepatocytes, in both in vivo and in vitro studies. This novel mutation may be specific to HBV genotype E, and its prevalence requires further investigation.

Influence of hepatitis B virus genotypes on the intra‐ and extracellular expression of viral DNA and antigens†‡

“…Southern and Northern blot hybridizations were performed with a full-length probe of each genotype/subgenotype by previous methods. 37 No significant differences were observed in the detection between internal control HBV DNA and each probe for all genotypes/ subgenotypes.…”

Enhanced hepatitis B virus (HBV) pre-genomic RNA levels and higher transcription efficiency of defective HBV genomes

“…Interestingly, all three sequences (GenBank accession nos AJ344115, AB219534 and GU565217; Fig. 1) with disrupted splice donor/acceptor sites were reported from individuals without detectable HBV surface antigen (HBsAg) (Fujiwara et al, 2005;Jeantet et al, 2002;Zaaijer et al, 2011). While the conservation of nucleotide residues at the splice junction site represents an interesting finding, it is not possible to determine whether this conservation is a result of these nucleotides (GT/AG) encoding a critical amino acid.…”

Characterization of Two Hepatitis B Virus Populations in a Single Korean Hepatocellular Carcinoma Patient with an HBeAg-Negative Serostatus: A Novel X-Gene-Deleted Strain with Inverted Duplication Sequences of Upstream Enhancer Site II

“…An insertion of this type, i.e. an insertion into a region remote from the affected sequences, has been reported previously; examples include a 36-bp insertion in the amino-terminal part of C protein observed in HBV genotype G [19,20] and the insertion of the hepatocyte nuclear factor 1 binding site [21][22][23] . It is noteworthy that insertions of this type are prone to occur at sites close to core upstream regions, such as preC or CURS, which are associated with the excessive production of HBcAg, the aborted production of HBeAg, or the transcription of pregenomic RNA.…”