Mutations and deletions in core promoter and precore stop codon in relation to viral replication and liver damage in Singaporean hepatitis B virus carriers

Deep sequencing of hepatitis B virus basal core promoter and precore mutants in HBeAg-positive chronic hepatitis B patients

Mutants in the basal core promoter (BCP) and precore (PC) regions of hepatitis B virus (HBV) genome are associated with the progression of chronic hepatitis B (CHB) infection. However, quasispecies characteristics of naturally occurring mutants in those regions in HBeAg-positive CHB patients has not been well described, partly limited by quantitative assay. This study aimed to develop an Ion Torrent deep sequencing assay to determine BCP and PC mutant percentages in HBeAg-positive CHB patients who were treatment naïve and correlate them with different viral and host factors. Our results showed that Ion Torrent deep sequencing could achieve high accuracy (R²>0.99) within a dynamic range between 1% and 100%. Twelve hotspots with prevalence of greater than 20% were observed in EnhII/BCP/PC regions. G1719T, T1753V, A1762T and G1764A were genotype C related. BCP A1762T/G1764A double mutants were generally accompanied with PC 1896 wild type or lower PC G1896A mutant percentage. Lower serum HBeAg and HBsAg levels were associated with higher BCP A1762T/G1764A mutant percentages (≥50%). ALT levels were higher in patients with PC G1896A mutant percentage greater than 10%. In conclusion, deep sequencing such as Ion Torrent sequencing could accurately quantify HBV mutants for providing clinical relevant information during HBV infection.

Quantitative evaluation of hepatitis B virus mutations and hepatocellular carcinoma risk: a meta-analysis of prospective studies

BACKGROUND

The temporal relationship between hepatitis B virus (HBV) mutations and hepatocellular carcinoma (HCC) remains unclear.

METHODS

We conducted a meta-analysis including cohort and nested case-control studies to prospectively examine the HCC risk associated with common variants of HBV in the PreS, Enhancer II, basal core promoter (BCP) and precore regions. Pertinent studies were identified by searching PubMed, Web of Science and the Chinese Biological Medicine databases through to November 2014. Study-specific risk estimates were combined using fixed or random effects models depending on whether significant heterogeneity was detected.

RESULTS

Twenty prospective studies were identified, which included 8 cohort and 12 nested case-control studies. There was an increased risk of HCC associated with any PreS mutations with a pooled relative risk (RR) of 3.82 [95% confidence interval (CI): 2.59-5.61]. The pooled-RR for PreS deletion was 3.98 (95% CI: 2.28-6.95), which was higher than that of PreS2 start codon mutation (pooled-RR=2.63, 95% CI: 1.30-5.34). C1653T in Enhancer II was significantly associated with HCC risk (pooled-RR=1.83; 95% CI: 1.21-2.76). For mutations in BCP, statistically significant pooled-RRs of HCC were obtained for T1753V (pooled-RR=2.09; 95% CI: 1.49-2.94) and A1762T/G1764A double mutations (pooled-RR=3.11; 95% CI: 2.08-4.64). No statistically significant association with HCC risk was observed for G1896A in the precore region (pooled-RR=0.77; 95% CI: 0.47-1.26).

CONCLUSIONS

This study demonstrated that PreS mutations, C1653T, T1753V, and A1762T/G1764A, were associated with an increased risk of HCC. Clinical practices concerning the HCC risk prediction and diagnosis may wish to focus on patients with these mutations.

Lower mutation frequency of BCP/precore regions in e antigen-negative chronic HBV-infected children instead of adults patients

To describe the Hepatitis B e antigen(HBeAg) seroconversion related mutation profiles of the basal core promoter(BCP)/precore regions in e antigen seroconverted child patients, a cohort of 245 child patients with CHB and a control patients group of 92 adult patients with CHB were recruited. The mutation frequencies of six nucleotides or nucleotide combinations including nucleotide (nt)1896, nt1762/1764, nt1752, nt1846, nt1899 and nt1753 showed significant differences between HBeAg positive and HBeAg-negative child patients groups. The frequencies of these HBeAg seroconversion-related mutations were significantly lower in HBeAg-negative children with CHB than in HBeAg-negative adults with CHB, especially for the mutation G1896A (41.1% vs 91.7%, P<0.001), and the average number of BCP/precore region mutations in samples from HBeAg-negative child patients was also obviously lower than in HBeAg-negative adult patients(3.62±3.03 vs 4.89±2.09, P<0.001), suggesting less impact of mutations in the BCP/precore region on HBeAg seroconversion in child patients than adult patients.

High rate of core promoter and precore mutations in patients with chronic hepatitis B

Background

The prevalence of precore (PC) and core promoter (CP) mutations in patients with chronic hepatitis B virus (HBV) infection (CHB) and their impact on liver disease is incompletely defined in the United States.

Methods

A retrospective chart review using a cross-sectional approach of 1,186 CHB patients was conducted.

Results

Of 926 patients tested for HBV e antigen (HBeAg), 37 % were HBeAg+. Of 194 patients tested for mutations, 80 % had PC or CP mutations or both; 89 % of HBeAg-negative and 56 % of HBeAg+ patients had PC or CP mutations or both (p < 0.001). The mean log₁₀ ALT was significantly lower in patients with both mutations compared to patients without mutations. The mean log₁₀ HBV DNA was significantly lower in patients with only PC mutations (4.82) compared to patients without mutations (5.71, p = 0.019). With the study population divided into four subgroups based on ALT level at time of diagnosis, cirrhosis incidence was significantly higher in patients with ALT 1–2 × ULN and ALT > 2 × ULN compared to patients with ALT ≤ 0.5 × ULN.

Conclusions

Our finding that PC and CP mutations may be associated with milder liver disease in some patients could serve as the basis for longitudinal studies to help delineate treatment need and duration in patients with these mutations. If confirmed, the finding of an association between ALT 1–2 × ULN and increased incidence of cirrhosis could call into question guidelines which only recommend treatment with ALT > 2 × ULN.

Genotyping and molecular characterization of hepatitis B virus from human immunodeficiency virus-infected individuals in southern Africa

Hepatitis B virus (HBV) and human immunodeficiency virus (HIV) are hyperendemic in sub-Saharan Africa. The HBV genotypes prevailing in HIV-infected Africans are unknown. Our aim was to determine the HBV genotypes in HIV-infected participants and to identify clinically significant HBV mutations. From 71 HBV DNA^+ve HIV-infected participants, 49 basic core promoter/precore (BCP/PC) and 29 complete S regions were successfully sequenced. Following phylogenetic analysis of 29 specimens in the complete S region, 28 belonged to subgenotype A1 and one to D3. Mutations affecting HBeAg expression at the transcriptional (1762T1764A), translational (Kozak 1809–1812, initiation 1814–1816, G1896A with C1858T), or post translational levels (G1862T), were responsible for the high HBeAg-negativity observed. The G1862T mutation occurred only in subgenotype A1 isolates, which were found in one third (7/21) of HBsAg^−ve participants, but in none of the 18 HBsAg^+ve participants (p<0.05). Pre-S deletion mutants were detected in four HBsAg^+ve and one HBsAg^−ve participant/s. The following mutations occurred significantly more frequently in HBV isolated in this study than in strains of the same cluster of the phylogenetic tree: ps1F25L, ps1V88L/A; ps2Q10R, ps2 R48K/T, ps2A53V and sQ129R/H, sQ164A/V/G/D, sV168A and sS174N (p<0.05). ps1I48V/T occurred more frequently in females than males (p<0.05). Isolates with sV168A occurred more frequently in participants with viral loads >200 IU per ml (p<0.05) and only sS174N occurred more frequently in HBsAg^−ve than in HBsAg^+ve individuals (p<0.05). Prior to initiation of ART, ten percent, 3 of 29 isolates sequenced, had drug resistance mutations rtV173L, rtL180M+rtM204V and rtV214A, respectively. This study has provided important information on the molecular characteristics of HBV in HIV-infected southern Africans prior to ART initiation, which has important clinical relevance in the management of HBV/HIV co-infection in our unique setting.

The relationship between core promoter mutation of hepatitis B virus, viral load and hepatitis B e antigen status in chronic hepatitis B patients

The aim of this study is to detect the possible association of hepatitis B virus (HBV) core mutation, hepatitis B e antigen (HBeAg) status and the viral load in chronic hepatitis B (CHB) patients. Sixty-six patients with CHB were enrolled. Hepatitis markers and hepatitis C virus antibody (HCV-Ab) were tested using micro particle enzyme immunoassay kits. Viral load was measured by real-time polymerase chain reaction (PCR) and the mutation was analyzed by nested PCR followed by restriction fragment length polymorphism. Most of CHB patients were HBeAg (-ve). The HBeAg status did not have an influence on the presence or absence of T1762/A1764 mutation. HBV-DNA serum level was not significantly different in patients with core mutation and patients without core mutation in HBeAg (-ve) group, while in HBeAg (+ve) group HBV-DNA serum level was significantly higher in patients with core mutation. This study reports the predominance of HBeAg (-ve) and HBV core promoter mutation.

The association of HBV core promoter double mutations (A1762T and G1764A) with viral load differs between HBeAg positive and anti-HBe positive individuals: a longitudinal analysis

BACKGROUND/AIMS

Although there have been a few reports regarding the effect of basal core promoter (BCP) double mutations (A1762T and G1764A) on hepatitis B viral loads, the association remains uncertain. We aim to determine the association after controlling for HBeAg - a strong confounding factor.

METHODS

We selected randomly 190 individuals from a Chinese cohort of 2258 subjects for cross-sectional analysis and 56 of the 190 for longitudinal analysis of viral loads.

RESULTS

In multivariable analysis of the cross-sectional data, BCP double mutations are significantly associated with lower viral loads in HBeAg positive subjects but no difference was found in anti-HBe positive subjects. Triple mutations at nucleotide (nt) 1753, 1762 and 1764 and mutations between nt 1809 and 1817, precore stop mutation (nt 1896) and genotype are not associated with viral loads in either HBeAg or anti-HBe positive subjects. Analysis of the longitudinal data yielded similar results to the cross-sectional data. Viral loads differ significantly between individuals infected with wild-type and BCP double mutations prior to HBeAg seroconversion but this difference is lost after seroconversion.

CONCLUSIONS

BCP double mutations are associated with lower viral loads in HBeAg positive individuals but have no effect on the viral loads of anti-HBe positive individuals.

Cellular transcription modulator SMARCE1 binds to HBV core promoter containing naturally occurring deletions and represses viral replication

Suppression of hepatitis B virus (HBV) replication, a causative agent for chronic hepatitis, is an effective approach to controlling disease progression. Host factors have a significant effect on viral replication efficiency and need to be better characterized. We have reported association between clinical virus load and deletions in HBV viral promoter. We showed here that HBV genome with such deletions led to decreased replication compared with wild type virus. Consistently, the promoter with deletion showed lower activity. A cellular transcription regulator recognizing the promoter with deletion was revealed in gel shift assay and subsequently identified as SMARCE 1 through DNA-protein array assay. The ability of SMARCE 1 in modulating the replication efficiency of HBV was further demonstrated. Taken together, our studies show a direct dependence of HBV on a host factor to modulate its replication efficiency, and provided a new platform for molecular characterization of mechanisms of disease outcome as a result of binding of new transcription factors to rearranged promoter sequences.

Heterogeneity analysis of the hepatitis B virus genome in intrauterine infection

There are many factors leading to intrauterine infection with hepatitis B virus (HBV). These factors include viral structure, HBV mutations, HBV DNA level, placenta barrier, immune status of the mother, and susceptibility of the fetus. The purpose of this study was to investigate the possible relationship between intrauterine infection with and HBV mutations of the genome of the virus. In this study, HBsAg-positive mothers were divided into two groups: intrauterine infection group and non-infection group according to whether the newborn infants were infected or not. The intrauterine infection group included four pairs of mother and their newborn infants infected in utero, and non-infection group included five HBsAg-positive mothers. HBV sequences from the two groups were analyzed and compared. The predominant strains in the mothers and infants from the intrauterine infection group were not completely consistent. This suggested that both HBV predominant strains and minority strains in the mothers could infect their infants through intrauterine transmission. Some HBV mutations probably related to intrauterine infection were examined and it was found that the frequencies of mutations were low in isolates of the virus of infants from the intrauterine infection group and high in the non-infection group. These results suggest that some strains of HBV from the mother may be transmitted selectively to the fetus in utero because of viral heterogeneity. The strains without screened mutations such as P21L in the pre-S1 region may infect the fetus more readily.

Hepatitis B virus genotypes and precore mutations in Scottish blood donors

BACKGROUND AND OBJECTIVES

This study was carried out to determine the frequency of hepatitis B virus (HBV) core promoter variants (nucleotide positions 1762, 1764) and precore variants (nucleotide position 1896) in hepatitis B surface antigen (HBsAg)-positive Scottish blood donors. HBV genotypes present in this population were also identified.

MATERIALS AND METHODS

A total of 85 HBsAg-positive blood donor samples were included in the study. Of these, 79 were polymerase chain reaction (PCR) positive and had sequence and mutation information. They were divided into two groups: group 1 (23 individuals) were hepatitis B e antigen (HBeAg)-positive and negative for antibody to HBe (anti-HBe); and group 2 (56 individuals) were HBeAg negative and positive for anti-HBe. A line probe assay was used to detect mutations, and a comparison was made by using direct sequence analysis. A different line probe assay was used to identify HBV genotype.

RESULTS

The frequencies of mutations in group 1 were 22% each for mutations 1762, 1764 and 1896, increasing to 26%, 35% and 55% in group 2, respectively. By contrast, direct sequence analysis failed to identify 70% of wild-type/mutant mixes. The prevalence of viral genotypes was 41% for genotype A, 12% for genotype B, 5% for genotype C, 30% for genotype D and 12% for mixed-genotype infections. Precore mutations were seen in 10%, 88%, 25% and 74% of genotypes A, B, C and D, respectively.

CONCLUSIONS

The results indicate that core promoter and/or precore mutants may be under-reported. The combination of HBV PCR and line probe assays is useful for supplementing HBV serological tests. Non-Caucasian genotypes are present in the UK blood-donating population and will therefore affect the demographics of HBV infection.

Histological spectrum of chronic hepatitis in precore mutants and wild-type hepatitis B virus infection

This study compares the histology of liver biopsies in precore mutant (PCM) and wild-type hepatitis B virus (HBV) infection. Thirty cases of PCM and 60 cases of wild-type HBV infection were included. Patients were diagnosed on the basis of serological profile and HBV DNA assessment. Liver biopsies in each case were assessed for histological activity and stage of fibrosis using a modification of Knodell's scoring system. There was no statistically significant (P=0.14) difference in histological activity in the two groups. The difference in stage of fibrosis in the two groups was statistically significant (P=0.001). Quantitative estimation of viral load did not show any correlation with liver histology. PCM HBV showed greater stage of fibrosis compared with wild-type infection, and this may be related to disease progression and lack of response to therapy.

Paired mutation in core promoter region of HBV in hepatocellular carcinoma by TDI-FP assay

AIM

To detect the A₁₇₆₂ T and G₁₇₆₄ A paired mutations in the core promoter region of the HBV DNA in the hepatocellular carcinoma, to investigate the relationship between them, and to establish a new method for genotyping of mutation patterns.

METHODS

The target DNA fragment of the HBV core promoter region which contains the paired mutations was amplified by polymerase chain reaction and the FP value of the R110- or TAMRA-labeled ddNTP was detected by TDI-FP assay to determine the nt₁₇₆₂ and nt₁₇₆₄ genotype.

RESULTS

Of 20 cases of hepatocellular carcinoma, 18 (90%) was positive for HBV infection. Through TDI-FP assay, there were 13 /20 for T₁₇₆₂ and A₁₇₆₄ paired mutations, 1/20 heterozygous for T₁₇₆₂-A₁₇₆₄/ A₁₇₆₂-G₁₇₆₄ 4/20 negative for the TDI-FP assay. By sequencing, the positive and heterozygous mutations completely accorded with the TDI-FP assay. In the negative results, 2/4 had 8-nucleotide deletion mutation, thus the mutation detection primer could not complement with the template and gave rise to the "false" negative results. The rate of T₁₇₆₂-A₁₇₆₄ positive mutation rate of HBV DNA in heaptocellular carcinoma was 85%, heterozygous 5%, and wild-type 10%.

CONCLUSION

The HBV infection is very high in the heaptocellular carcinoma. The great frequency of the paired mutations in the core promoter indicates that the paired mutations may be significantly related to the pathogenesis of hepatocellular carcinoma. The established TDI-FP is suitable for high throughput and automated genotyping assays due to its rapid and simple manipulation.