Mutations in the S gene region of hepatitis B virus genotype D in Turkish patients

Mutations in the S gene of hepatitis B virus in three generations of patients with chronic hepatitis B

Failure to neutralize HBsAg and subsequent escape from the host immune system may be caused by HBsAg mutations, particularly in the "a" determinant, which alters the antigenicity of the protein. The purpose of this study was to examine the frequency of S gene mutations in three generations of HBV cases in northeastern Iran. In this study, 90 patients with chronic HBV were assigned to three groups according to the inclusion criteria. The plasma were utilized to extract viral DNA, and the PCR was applied. Direct sequencing and alignment were performed on the S gene, using reference sequence. The results indicated that all HBV genomes were categorized as the genotype D/ayw2. Among 79 point mutations detected, 36.8% were silent, and 56.2% were missense. In the S region, mutations were observed in 88.9% of CHB subjects studied. In the three-generation group, 21.5% of mutations were in the "a" determinant, and 2.6%, 19.5%, and 87.0% of these mutations were observed in antigenic epitopes of CTLs, CD4+, and B cells, respectively. In addition, 56.7% of mutations occurred at Major Hydrophilic Region. S143L and G145R mutations which the most prevalent in the three-generation (36.7%, 20%), and two-generation (42.5%, 20%) groups, related to the failure of HBsAg detection, vaccine, and immunotherapy escape. The findings showed that most of the mutations were concentrated in the B cell epitope. Most CHB cases from the three-generation, especially grandmothers, had HBV S gene mutations and subsequent amino acid mutations, suggesting that these mutations may be critical for pathogenesis and vaccine evasion.

Molecular and Genetic Characterization of Hepatitis B Virus (HBV) among Saudi Chronically HBV-Infected Individuals

The study aimed to characterize the genotype and subgenotypes of HBV circulating in Saudi Arabia, the presence of clinically relevant mutations possibly associated with resistance to antivirals or immune escape phenomena, and the possible impact of mutations in the structural characteristics of HBV polymerase. Plasma samples from 12 Saudi Arabian HBV-infected patients were analyzed using an in-house PCR method and direct sequencing. Saudi patients were infected with mainly subgenotype D1. A number of mutations in the RT gene (correlated to antiviral resistance) and within and outside the major hydrophilic region of the S gene (claimed to influence immunogenicity and be related to immune escape) were observed in almost all patients. Furthermore, the presence of mutations in the S region caused a change in the tertiary structure of the protein compared with the consensus region. Clinical manifestations of HBV infection may change dramatically as a result of viral and host factors: the study of mutations and protein-associated cofactors might define possible aspects relevant for the natural and therapeutic history of HBV infection.

Molecular characterization and phylogenetic analyses of full-length viral genomes from Iranian patients with chronic hepatitis B virus

Aim: Chronic hepatitis B infection is the main cause of liver complications such as hepatic failure, liver cirrhosis and hepatocellular carcinoma (HCC). In this study, we attempted to evaluate molecular characterization and phylogenetic analyses of full-length viral genomes from chronic hepatitis B virus (HBV)-infected patients. Methods: The full-length genomic sequence of the five HBV isolates from Ahvaz (city of Iran) patients was amplified, cloned in pTZ57R/T vector, sequenced and examined. Results: Phylogenetic analyses showed that all isolates belonged to genotype D (D1/D3). Serotyper tool identified ayw2 serotype in all HBV isolates. YMDE mutation was detected in an HBV isolate in the reverse transcriptase domain. Conclusion: In the present study, the analyses of full-length sequence of genome revealed that the HBV genotype D, sub-genotype D1/D3, and subtype ayw2 were predominant among Ahvaz HBV strains. As HBV genome replicates and is mediated via reverse transcription process, periodic investigations of full HBV genome are needed.

In silico functional and structural characterization of hepatitis B virus PreS/S-gene in Iranian patients infected with chronic hepatitis B virus genotype D

Objective

Chronic hepatitis B (CHB) virus infection is the most prevalent chronic liver disease and has become a serious threat to human health. In this study, we attempted to specify and predict several properties including physicochemical, mutation sites, B-cell epitopes, phosphorylation sites, N-link, O-link glycosylation sites, and protein structures of S protein isolated from Ahvaz.

Materials and methods

Initially, hepatitis B virus DNA (HBV DNA) was extracted from five sera samples of untreated chronic hepatitis B patients. The full-length HBV genomes were amplified and then cloned in pTZ57 R/T vector. The full sequences of HBV were registered in the GenBank with accessions numbers (MK355500), (MK355501) and (MK693107-9). PROTSCALE, Expasy's ProtParam, immuneepitope, ABCpred, BcePred, Bepipred, Algpred, VaxiJen, SCRATCH, DiANNA, plus a number of online analytical processing tools were used to analyse and predict the preS/S gene of genotype D sequences. The present study is the first analytical research on samples obtained from Ahvaz.

Results

We found major hydrophilic region (MHR) mutations at "a" determining region that included K122R, N131T, F134Y, P142L, and T126N mutations. Moreover, Ahvaz sequences revealed four sites (4, 112, 166, and 309) in the preS/S gene for N-glycosylation that could possibly be a potential target for anti-HBV therapy.

Conclusion

In the present study, mutations were identified at positions T113S and N131T within the MHR region of S protein; these mutations can potentially decrease the effect of hepatitis B vaccination in vaccine recipients.

Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus

Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected "by eye" prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to result in more differences among trees. Therefore, differences between the trees could be best explained by phylogenetic uncertainty unrelated to the MSA method used. Nevertheless, automated alignment approaches did not require human intervention and were therefore considerably less time-intensive than traditional approaches. Because of this, we conclude that fully automated algorithms for MSA are fully compatible with older methods even in extremely difficult to align data sets. Additionally, we found that most HBV diagnostic genotypes did not correspond to evolutionarily-sound groups, regardless of alignment type and support threshold. This suggests there may be errors in genotype classification in the database or that HBV genotypes may need a revision.

Could resistant and escape variants of hepatitis B virus be a problem in the future?

Aim: Nucleos(t)ide analogs have a risk for the development of Polymerase gene mutations and they can cause compensatory mutations in the HBV surface gene. Alteration in the ‘a determinant’ of the s gene predispose for escape mutants. We aimed to evaluate primary, compensatory and escape mutations in chronic hepatitis B. Materials & methods: Two hundred nineteen specimens were obtained and HBV pol gene region was sequenced and amplified and HBV pol/s gene mutations were determined. Results: We detected primary mutation in 29.8% patients. Compensatory mutations were detected in 50.3%patients. Hepatitis B Immunoglobulin escape mutations, vaccine escape mutations, Hepatitis B diagnosis-escape and immunoselected amino acid substitutions were observed in 9.6%, 6.9%, 5.2% and 11.9% of patients, respectively. Antiviral drug-associated potential vaccine-escape mutants were detected in 17.9% patients. Conclusion: Therefore, epidemiological and demographical changes may be possible. Therefore, the typical HBsAg mutants and antiviral drug-associated potential vaccine-escape mutants should be monitored carefully.

Entecavir as a first-line treatment for hepatitis B virus reactivation following polychemotherapy for chronic lymphocytic leukemia and invasive ductal carcinoma: a report of two cases and review of the literature

OBJECTIVE

Hepatitis B reactivation has been reported in chronic carriers of hepatitis B [hepatitis B surface antigen (HBsAg)] or in patients with prior hepatitis B virus (HBV) infection who are HBsAg-negative and have antibodies against hepatitis B core antigen (anti-HBc) with or without antibodies to HBsAg (anti-HBs). Lamivudine has been the first and commonly used nucleoside analog to inhibit HBV replication; however, prolonged therapy has been associated with an increased risk for drug-resistant mutations and mortality rates. Entecavir, a deoxyguanosine analog, offers several advantages over lamivudine for the treatment of HBV reactivation following chemotherapy while exhibiting more potent antiviral activity and a lower resistance rate.

METHODS

Herein, we report rapid and sustained suppression of polychemotherapy-related HBV reactivation by entecavir administered as a prompt antiviral therapy in the cases of two patients with chronic lymphocytic leukemia and invasive ductal carcinoma. A review of the literature is discussed.

RESULTS

Entecavir produced a rapid and sustained suppression of polychemotherapy-related HBV reactivation as a prompt antiviral therapy in the cases of two patients with chronic lymphocytic leukemia and invasive ductal carcinoma.

CONCLUSION

Allowing a rapid and sustained control of HBV replication, entecavir seems to be a promising drug for first-line prompt treatment of HBV reactivation in patients undergoing chemotherapy for hematological as well as solid organ malignancies, with safe long-term use enabling maintenance of resolved hepatitis.

Partial virological response to three different nucleotide analogues in naive patients with chronic hepatitis B

BACKGROUND

The definition of partial virological response (PVR) was proposed because of its clinical relevance. PVR relates to subsequent therapeutic failure which results in the modification of the regimen. Whether this rationale can be applied to all nucleotide analogues (NA) is not clear. This study was undertaken to analyze PVR influence on therapeutic outcomes during lamivudine, entecavir or tenofovir monotherapy in NA-naive patients with chronic hepatitis B in routine clinical practice.

METHODS

We retrospectively analyzed 150 NA-naive patients with chronic hepatitis B. These subjects received lamivudine, entecavir or tenofovir monotherapy between February 2001 and July 2013.

RESULTS

Sixty-nine patients were treated with lamivudine, 35 with entecavir, and 46 with tenofovir. The median therapeutic duration was 19.5 (6-147) months. PVR rates at 24 weeks were similar among three NAs (lamivudine 33.3%, entecavir 35.0%, tenofovir 32.4%, P=0.981). For all three NAs, patients with a higher baseline viral load or HBeAg-positive status had a higher serum viral positive rate tested by polymerase chain reaction at week 24 and 48. Cumulative probability of virological breakthrough (VBR) for patients treated with lamivudine was 67% at 5 years, and PVR at 24 weeks was the independent risk factor for VBR (HR: 3.09; 95% CI: 1.09-8.74; P=0.034); also lamivudine treated patients older than 50 years seemed to have a tendency for VBR (HR: 2.80; 95% CI: 0.99-8.18; P=0.052). A majority of entecavir and tenofovir partial responders achieved and maintained virological response with prolonged monotherapy, except one entecavir treated patient who experienced VBR due to resistance mutations.

CONCLUSIONS

Management strategy for lamivudine treatment should include adaptation of regimen according to PVR as an on-treatment response parameter due to its relation with unacceptably high VBR probability. Similar conclusion should not be directly related to entecavir or tenofovir treatment.

Isolated anti-hbc and occult HBV infection in dialysis patients

Background:

Occult Hepatitis B virus (HBV) infection (OBI) is defined as the presence of HBV-DNA in the liver or serum with undetectable hepatitis B surface antigen (HBsAg). Hemodialysis (HD) patients are at risk of acquiring parenterally transmitted infections.

Objectives:

The aim of this study was to assess the prevalence of OBI in HD patients.

Patients and Methods:

A hundred HBsAg negative HD patients were included in this study from main dialysis units in Tehran, Iran. HBsAg, hepatitis B surface antibody (anti-HBs), hepatitis B core antibody (anti-HBc) and liver enzymes levels were examined in all subjects. The presence of HBV-DNA was determined in plasma samples using real-time PCR.

Results:

A hundredpatients with a mean age of 58.5 ± 16.1 years were enrolled in this study. In total, 56.7% were male and 43.3% female. Anti-HBs, anti-HBc, anti-HCV and anti-HIV were detected in 56.7%, 2%, 5.2% and 1% of patients, respectively. Isolated anti-HBc was detected in 2% of cases. HBV-DNA was detected in 1% of HBsAg negative patients.

Conclusions:

This study showed a low rate of isolated anti-HBc and occult HBV infection in HD patients. It can be due to improvement of people’s knowledge about HBV transmission routes, HBV vaccination of HD patients and regular surveillance of HBV infection.

Viral hepatitis induces hepatocellular cancer: what can we learn from epidemiology comparing iran and worldwide findings?

CONTEXT

Several risk factors play the role in the development of hepatocellular carcinoma (HCC) from which chronic hepatitis B and C infections are the most important ones. DNA integration of hepatitis viruses alters the function of critical genes promoting malignant transformation of virus-infected liver cells.

EVIDENCE ACQUISITION

There are remarkable geographic differences in prevalence of chronic viral hepatitis and incidence of HCC. Middle Eastern countries are characterized by a moderate to high prevalence rate of chronic viral hepatitis in the population. This review discusses about epidemiologic findings of hepatitis B and C infections, and HCC, as well as focuses on Middle East countries, particularly Iran. We provide an overview about risk factors, prevention and treatment, and bring up the role of HCC induced by chronic viral hepatitis.

RESULTS

Vaccination against hepatitis B virus (HBV) in the early childhood is highly effective to lower infection rates, substantially. For hepatitis C, adequate hygiene when dealing with human blood and screening programs for blood donors can mainly reduce infection rates. As HCC is strongly associated with chronic viral hepatitis, prevention against the infection is crucial for preventing against HCC too.

CONCLUSIONS

Although prevention and treatment of chronic hepatitis B and C have improved within the last decades even in high-risk countries, effective and sustainable reduction of these infections still needs more actions.

Current hepatitis delta virus type 1 (HDV1) infections in central and eastern Turkey indicate a wide genetic diversity that is probably linked to different HDV1 origins

Hepatitis delta virus (HDV) is a subviral pathogen of humans, a satellite of hepatitis B virus (HBV) that induces severe acute and chronic liver diseases. The genus Deltavirus consists of eight clades or genotypes, with HDV1 being ubiquitous and frequently characterized. In Turkey, HDV1 infection is highly endemic among HBsAg carriers, especially in the southeastern region. In this study, we analyzed 34 samples from patients who were chronically infected with HBV/HDV, originating from 22 cities of rural regions in the central and eastern parts of Turkey, in order to determine the levels of viral replication and genetic diversity. HDV RNA levels ranged between 3.02 and 8.75 Log copies/mL, and HBV DNA was detected in 25 samples (73.5%), with values ranging from 2.53 to 5.30 Log copies/mL. Analysis of nucleotides 900-1280 of HDV genomes (n = 34) and full-length (n = 17) sequences indicated that all of the strains belonged to genotype HDV1. However, a high genetic diversity was observed among the isolates, with a mean full-length dissimilarity score of 13.05%. HDV sequences clustered with sequences from Western Europe (n = 11), Eastern Europe and Asia (n = 19) or Africa (n = 4). HDV1 isolates related to strains of African origin had a serine residue instead of an alanine at position 202 of the large delta protein. HBV preS1 sequences obtained for 34 isolates indicated an HBV/D genotype in all cases. Taken together, our results indicate that in Turkey, where HBV-HDV dual infection is highly endemic, both viruses have high levels of replication, and HDV strains exhibit wide genetic diversity, which might reflect ancient evolution and/or successive outbreaks.

Lamivudine resistance mutations in European patients with hepatitis B and patients co-infected with HIV and hepatitis B

Evaluation of resistance pattern in patients with chronic hepatitis B. Retrospective study of hepatitis B virus (HBV) resistance mutations in patients found viraemic after first-line treatment. HBV viral load was determined by a real-time polymerase chain reaction and the substitutions in HBV-DNA were studied by polymerase sequencing test. First line treatment had failed in 12 out of 33 patients (36%) receiving anti-HBV drugs. The 12 patients with persistent viraemia were all lamivudine (LAM) experienced and 7 had a polymerase sequencing test available. LAM substitution mutations L180M + M204V/I were found in six out of seven cases, with an accompanying V173L mutation in three cases. These mutations were also related with changes in HBsAg. The use of potent drugs in the first line anti-HBV therapy may reduce the resistance mutations in the future.

Antiviral drug-associated potential vaccine-escape hepatitis B virus mutants in Turkish patients with chronic hepatitis B

BACKGROUND

The hepatitis B virus (HBV) polymerase (pol) gene completely overlaps with the envelope (S) gene. Mutations in the pol gene of HBV, either from selection of primary or secondary resistance mutations, typically result in changes in the overlapping hepatitis B surface antigen (HBsAg). Recent studies have conferred a new acronym to these HBV pol/S gene overlap mutants: ADAPVEMs, for antiviral drug-associated potential vaccine-escape mutants. The present study aimed to assess the prevalence and pattern of ADAPVEMs in Turkish patients with chronic hepatitis B (CHB).

METHODS

The investigation was conducted between March 2007 and July 2010 and involved a total of 442 patients. These patients were in the following phases of HBV infection: immune tolerant (n=50), immune reactive (n=37), inactive carrier (n=90), HBeAg-negative CHB (n=217), and HBsAg-negative (n=12), or were hemodialysis patients (n=36). One hundred eighty-six patients were receiving nucleos(t)ide analogue (NUC) therapy and 256 patients had treatment-naïve CHB.

RESULTS

Seven types of ADAPVEM were detected in the total CHB patients: rtM204V/sI195M, rtM204I/sW196S, rtM204I/sW196L, rtV173L/sE164D, rtA181T/sW172*, rtA181T/sW172L, and rtA181V/sL173F. The ADAPVEMs were associated with lamivudine, telbivudine, and adefovir. The prevalence of ADAPVEMs in all CHB patients was found to be 10% (46/442). The difference in the prevalence of ADAPVEMs across the different CHB clinical phases was not significant (Pearson Chi-square, p=0.112). The prevalence of ADAPVEMs was 24% (44/186) in those undergoing NUC therapy and 0.7% (2/256) in the treatment-naïve group; this difference was significant (Pearson Chi-square, p=0.00).

CONCLUSIONS

We determined the prevalence and pattern of ADAPVEMs in Turkish patients in the different phases of CHB. Preferred drugs in Turkey, such as lamivudine, have the potential to cause the emergence of ADAPVEMs, with the possibility that these will spread to both individuals immunized with the hepatitis B vaccine and nonimmunized individuals. ADAPVEMs should be monitored in infected and treated patients and their public health risks assessed.

Monitoring of hepatitis B virus surface antigen escape mutations and concomitantly nucleos(t)ide analog resistance mutations in Turkish patients with chronic hepatitis B

BACKGROUND

The hepatitis B virus (HBV) polymerase gene completely overlaps with the envelope gene. In the present study we aimed to monitor the prevalence and pattern of the typical mutations for hepatitis B surface antigen (HBsAg) escape, and concomitantly nucleos(t)ide analog (NUC) resistance mutations, in Turkish patients undergoing different antiviral therapies and in treatment-naïve patients with chronic hepatitis B (CHB).

METHODS

The investigation was undertaken between March 2007 and August 2009 and involved a total of 142 patients under NUC therapy (88 males; mean age 42 years (range 13-68); hepatitis B e antigen (HBeAg) negativity in 94 patients; HBV DNA median log 4.3 log(10) IU/ml (range 2.0->6.0); alanine aminotransferase (ALT) median level 76.1 IU/ml (range 12-1082)) and 185 treatment-naïve CHB patients (120 males; mean age 39 years (range 1-76 years); HBeAg negativity in 132 patients; HBV DNA median log 3.5 log(10) IU/ml (range 2.0-6.0); ALT median level 60.7 IU/l (range 8-874)).

RESULTS

The overall prevalence of typical HBsAg escape mutations found in the CHB patients was 8.3% (27/327). In the NUC therapy group the prevalence was 8.5% (12/142), with the following patterns: sY100C+sI110V, sL109I, sP120T, sP127T, sG130R+sG145X, sS132A+sY134N, sY134N+sG145R, sC137G, sD144E, sG145R. In the treatment-naïve group the prevalence was 8.1% (15/185), with the following patterns: sL109I, sI110V, sS117INST, sP120T, sP127T, sM133I, sC137L+sG145R, sS143L. However, NUC resistance mutations were found in 7.7% (11/142) of the patients on NUC therapy and 3.8% (7/185) of the treatment-naïve group patients. Interestingly, the treatment-naïve patients had preexisting drug resistance mutations related to lamivudine (rtL180M+rtM204I), adefovir (rtA181V, rtQ215S, rtI233V), entecavir (intermediate susceptibility with rtL180M+rtM204IHBV variant), telbivudine (rtL180M+rtM204I), and tenofovir (rtA194T).

CONCLUSIONS

The findings of this study show preexisting typical HBsAg escape and NUC resistance mutations are possible. The genetic arrangement of the HBV genome with polymerase and surface genes overlapping has substantial public health and diagnostic implications and relevance.

Geographical and genetic diversity of the human hepatitis B virus

Hepatitis B virus (HBV) is one of the most widely distributed viruses that infect humankind. Distinct clinical and virological characteristics of the HBV-infection have been reported in different geographical parts of the world and are increasingly associated with genetic diversity of the infecting virus. HBV is classified into genotypes and subgenotypes that are associated with ethnicity and geography. The genetic diversity of HBV in its various aspects has been the subject of extensive investigations during the last few decades. Since molecular epidemiology research tools have become widely available, the number of new publications in this field has grown exponentially. This review summarises the recent publications on the geographical distribution of genetic variants of HBV, and proposes updated criteria for the identification of new genotypes and subgenotypes of the virus.

Surface gene mutations of hepatitis B virus among high-risk patients with occult hepatitis B virus infection

Surface gene mutants of hepatitis B virus (HBV) have been reported in a variety of patient groups. Because of limited data regarding these mutations in patients with occult HBV infections; we aimed to determine these mutations among high-risk patients with occult HBV infection. The presence of HBV-DNA was determined in patients with isolated anti-HBc by real-time polymerase chain reaction (PCR). Then, surface gene region was amplified by nested PCR and mutations were analyzed after sequencing. The mutations that resulted in nonfunctional hepatitis B surface antigen (HBsAg) were insertion of single nucleotide in 2 cases, which causes frameshift and single-nucleotide replacement, and premature stop codons at Leu15 and Gly10 in the other 2 cases. Amino acid substitution at amino acid position 207(S207N) was found in the other isolates. Our study suggested that "a" region mutations did not play a major role in HBsAg detection, and other genetic and nongenetic factors may be responsible for failure to detect HBsAg by routine laboratory tests.