Hepatitis Delta Virus Genotype Research Articles

Development and validation of an efficient in-house real-time reverse transcription polymerase chain reaction assay for the quantitative detection of serum hepatitis delta virus RNA in a diverse South London population

Hepatitis delta virus (HDV) causes both acute and chronic hepatitis, always in the presence of hepatitis B. Analysis of global HDV isolates has shown that at least eight genotypes exist. HDV RNA quantitation and genotyping are important tools in the diagnosis and management of infected individuals. There is, as yet, no commercially available quantitative HDV RNA assay. Several laboratories have developed in-house assays, but equivalent detection and quantitation across all HDV genotypes has not been demonstrated. In this study, the development of an in-house real-time reverse transcription polymerase chain reaction (RT PCR) assay is described to quantify HDV RNA in serum or plasma. Its efficiency was validated by testing 99 samples from patients with known chronic HDV infection, along with 22 samples from individuals without HDV. The assay has a dynamic range of 6.4×10(2) to 6.4×10(8)copies/mL. Amplicons of the quantitative PCR can be directly used for sequence analysis and genotyping. HDV-1, HDV-5 and HDV-6 were identified, reflecting the areas of origin of our cohort of patients. The ability to genotype and to accurately quantify HDV RNA levels in the more recently discovered African genotypes will be important for investigating the natural history of HDV in this group, compared to those with genotype 1 disease.

Standardized One-Step Real-Time Reverse Transcription-PCR Assay for Universal Detection and Quantification of Hepatitis Delta Virus from Clinical Samples in the Presence of a Heterologous Internal-Control RNA

As for other chronic viral diseases, quantification of hepatitis delta virus (HDV) loads may be useful for patient management. We describe a one-step quantitative reverse transcription-PCR assay that is reliable and automatable and meets the regulatory authorities' standards for accurate quantification of the major HDV genotypes. It includes an internal control and uses in vitro-transcribed RNAs as standards. Its linearity range is 500 to 1.7 × 10(11) copies/ml, its sensitivity is around 150 copies/ml, its repeatability is around 15%, and its reproducibility is below 0.25 log(10) copies/ml.

Determination of Hepatitis Delta Virus Genotype among HBV Carriers in Southwest of Iran

Background and Aims: HDV is a defective satellite virus and classified in genus Deltavirus. Its disease is related and limited to HBV-infected patients. Acute infection of delta agent occurs in two different patterns; simultaneous infection with both HBV & HDV or super infection of chronically HBV infected patients that lead to more sever type of hepatitis. According to genetic diversity of genomic RNA of HDV, 8 clades have been classified. The aim of this study was to determine the delta virus genotype among the HBV & HDV infected patients in Ahvaz city. Materials and Methods: Sera sample collected from 31 seropositive HDV patients including 21 male and 9 female mean age 46±13.5 suffering from chronic hepatitis and 1 male patient with acute hepatitis. The encoding region for C terminal half of the Delta anti gene of the HDV’s genomic RNA reverse transcribed and then amplified by nested PCR. The HDV PCR positive samples were sequenced, and the sequences were compared with reference sequences on GenBank. All samples were tested for HBV DNA, HCV RNA and HCV anti body. Results: Only 15(48%) out of 31 anti HDV seropositive patients were positive for HDV RNA by nested RT-PCR. Alignment and phylogenic analysis of the present HDV sequences revealed that all sequences belong to clade 1. Only 1 HDV RNA positive patient was positive for HBV DNA by nested PCR. Conclusion: According to previous studies the clade 1 (genotype 1) is the predominant clade of HDV in our country. However some (2-HDV-R, 4-HDV-R &11-HDV-R) of our isolates show extensive differences from the two previously isolated HDVs from Iran. Most of the our isolates were closely related to the Iranian HDVs, but Egyptian HDV still remains the most relevant foreign isolate. Suppression of HBV replication by delta virus is common but mutual suppression of HDV and HCV remains unclear.

Current Concept in the Pathophysiology of Hepatitis Delta Infection

Hepatitis delta virus (HDV) is a unique human virus, showing similarities with plant viroids. Although impressive knowledge on virus structure and replication has been achieved, several questions like HBV/HDV interaction and post translational modifications of HD antigens remain to be answered. Potential targets for therapeutic strategies are now emerging. To date, eight major genotypes of the HDV have been identified. The HDV-1 is the prevailing genotype in Europe, but migration phenomena may change this profile. Immune response is likely to play an important role in the pathogenesis of HDV-induced liver disease; few data are available on T cells response either during infection and therapy. HDV usually suppresses HBV replication; recent studies show as viral dominances may change over time. Delta infection leads to severe liver disease, with different patterns of progression to liver fibrosis and decompensation. Beside the association between HDV/HBV and HCC is demonstrated a risk specifically related to HDV remains controversial.

Quantitation of hepatitis delta virus using a single-step internally controlled real-time RT-qPCR and a full-length genomic RNA calibration standard

Quantitation of circulating hepatitis delta virus (HDV) RNA is important for assessing the response to antiviral therapy and for understanding the complex dynamic interactions between hepatitis B virus (HBV) and HDV replication. Although several PCR assays for HDV RNA have been described none of them incorporate an internal control or use a full-length RNA calibration standard for absolute quantitation. This study describes the development and evaluation of a novel single-step real-time RT-qPCR assay for HDV RNA quantitation which incorporates a Brome Mosaic virus internal control to prevent false negatives and under-reporting due to inhibitors or due to inefficient RNA purification, reverse transcription or PCR amplification. The assay has a dynamic range of ≥7log(10) and is designed to detect all HDV genotypes. The 95% detection limit is ∼3800 HDV RNA copies/ml, 700 copies/ml being detectable in 20% of repeats. Both intra-assay and inter-assay variability are low (CV 8% and 17%, respectively). Plasma HDV RNA was detected in 75% of 59 HDV antibody-positive samples with titres ranging from 8.4×10(4) to 4.4×10(8) copies/ml. The assay described provides a reliable and sensitive quantitative system for therapeutic monitoring and for studying the dynamic interplay between hepatitis B virus replication and HDV viral load.

Hepatitis delta in HIV/HBV co-infected patients in Brazil: is it important?

This study was carried out to evaluate the prevalence of hepatitis delta virus (HDV) among human immunodeficiency virus (HIV)/hepatitis B virus (HBV) co-infected patients from São Paulo, in the Southeast Region of Brazil. A total of 3259 HIV patients with serological markers for HBV were initially enrolled in the study. Among these patients, 154 (4.7%) were hepatitis B surface antigen (HBsAg)-reactive. Serum samples were obtained from 86 HBsAg-positive patients and were submitted to anti-HDV serological assay. One (1.2%) HIV/HBV patient was found to be anti-HDV-positive, and the HDV infection was confirmed by PCR. Phylogenetic analysis showed that this HDV sequence grouped with other HDV genotype 1 sequences from Mediterranean European countries, suggesting that this virus has a common ancestor with HDV from that region. This patient was probably infected by sexual transmission, as he reported unprotected sexual intercourse with multiple partners over the course of many years but denied intravenous drug use or any travel to the Brazilian Amazon, an area known to have a high HDV prevalence. HDV infection is infrequent in the Southeast Region of Brazil, however there have been a few cases in this region. HIV/HBV patients are at potential risk for HDV infection, therefore investigations for the presence of HDV infection must be carried out in these patients.

Hepatitis Delta virus genotype 8 infection in Northeast Brazil: Inheritance from African slaves?

Hepatitis Delta virus (HDV) is endemic worldwide, but its prevalence varies in different geographical areas. While in the Brazilian Amazon, HDV is known to be endemic and to represent a significant public health problem, few studies have assessed its prevalence in other regions in the country. This study evaluated the seroprevalence of HDV among HBsAg chronic carriers from Maranhão state, a region located in the Northeast of Brazil. Among 133 patients, 5 had anti-HD, of whom 3 had HDV RNA. HDV genotypes were characterized by Bayesian phylogenetic analysis of nucleotide sequences from the HDAg coding region. HDV-3 was identified in one patient who lives in Maranhão, but was born in Amazonas state (Western Amazon basin). Phylogenetic analysis shows that this HDV-3 sequence grouped with other HDV-3 sequences isolated in this state, which suggests that the patient probably contracted HDV infection there. Surprisingly, the other two patients were infected with HDV-8, an African genotype. These patients were born and have always lived in Urbano Santos, a rural county of Maranhão state, moreover they had never been to Africa and denied any contact with people from that continent. This is the first description of the HDV-8 in non-native African populations. This genotype may have been introduced to Brazil through the slaves brought to the country from the West Africa regions during the 16–18th centuries. Our results indicate that the need of clinical and epidemiological studies to investigate the presence of this infection in other areas in Brazil.

Dynamics of Hepatitis D (delta) virus genotype 3 in the Amazon region of South America

Hepatitis delta virus (HDV) is widely distributed and associated with fulminant hepatitis epidemics in areas with high prevalence of HBV. Several studies performed in the 1980s showed data on HDV infection in South America, but there are no studies on the viral dynamics of this virus. The aim of this study was to conduct an evolutionary analysis of hepatitis delta genotype 3 (HDV/3) prevalent in South America: estimate its nucleotide substitution rate, determine the time of most recent ancestor (TMRCA) and characterize the epidemic history and evolutionary dynamics. Furthermore, we characterized the presence of HBV/HDV infection in seven samples collected from patients who died due to fulminant hepatitis from Amazon region in Colombia and included them in the evolutionary analysis. This is the first study reporting HBV and HDV sequences from the Amazon region of Colombia. Of the seven Colombian patients, five were positive for HBV-DNA and HDV-RNA. Of them, two samples were successfully sequenced for HBV (subgenotypes F3 and F1b) and the five samples HDV positive were classified as HDV/3. By using all HDV/3 available reference sequences with sampling dates (n=36), we estimated the HDV/3 substitution rate in 1.07×10−3 substitutions per site per year (s/s/y), which resulted in a time to the most recent common ancestor (TMRCA) of 85years. Also, it was determined that HDV/3 spread exponentially from early 1950s to the 1970s in South America. This work discusses for the first time the viral dynamics for the HDV/3 circulating in South America. We suggest that the measures implemented to control HBV transmission resulted in the control of HDV/3 spreading in South America, especially after the important raise in this infection associated with a huge mortality during the 1950s up to the 1970s. The differences found among HDV/3 and the other HDV genotypes concerning its diversity raises the hypothesis of a different origin and/or a different transmission route.

Differential Regulations of Clathrin Heavy Chain Among the Assembly of Hepatitis Delta Virus Genotypes

Differential Regulations of Clathrin Heavy Chain Among the Assembly of Hepatitis Delta Virus Genotypes

High Prevalence and Predominance of Hepatitis Delta Virus Genotype 1 Infection in Cameroon

Antibodies to the hepatitis delta virus (HDV) were found in 17.6% of 233 hepatitis B virus surface antigen-positive subjects in Cameroon. Phylogenetic analyses showed the presence of HDV-1, HDV-5, HDV-6, and HDV-7 genotypes. These results enrich the limited data on HDV prevalence and molecular diversity in Cameroon.

Hepatitis delta virus infection: Open issues

Hepatitis delta virus (HDV) consists of a circular single-stranded RNA genome which assembles two viral proteins and acquires a lipid envelope in which the hepatitis B surface antigens (HBsAg) are embedded. HDV does not encode its own polymerase, but exploits a cellular enzyme for its replication. A better understanding of the mechanisms of HDV replication mechanism would provide new insights for antiviral strategies. Based on genomic variability, eight major genotypes of HDV have been identified, which differ as much as 40% in the nucleotide sequence. The cloning of HDV-RNA has provided genetic probes for the measurement of HDV-RNA in serum and liver; the sensitivity of HDV-RNA detection improved significantly when the reverse transcriptase-polymerase chain reaction (PCR) technique was introduced. As no commercial test is standardized for viral load detection, home-made assays have been developed in the different referral centers, which may not be comparable. Quantification of HDV in serum by real-time PCR has been recently proposed in the management of chronically infected patients. No specific inhibitors of HDV are available at present and, in spite of the crucial relationship between HDV and HBV, drugs that block HBV have only a theoretical but no sound effect on HDV replication.

Clathrin-Mediated Post-Golgi Membrane Trafficking in the Morphogenesis of Hepatitis Delta Virus

Clathrin is involved in the endocytosis and exocytosis of cellular proteins and the process of virus infection. We have previously demonstrated that large hepatitis delta antigen (HDAg-L) functions as a clathrin adaptor, but the detailed mechanisms of clathrin involvement in the morphogenesis of hepatitis delta virus (HDV) are not clear. In this study, we found that clathrin heavy chain (CHC) is a key determinant in the morphogenesis of HDV. HDAg-L with a single amino acid substitution at the clathrin box retained nuclear export activity but failed to interact with CHC and to assemble into virus-like particles. Downregulation of CHC function by a dominant-negative mutant or by short hairpin RNA reduced the efficiency of HDV assembly, but not the secretion of hepatitis B virus subviral particles. In addition, the coexistence of a cell-permeable peptide derived from the C terminus of HDAg-L significantly interfered with the intracellular transport of HDAg-L. HDAg-L, small HBsAg, and CHC were found to colocalize with the trans-Golgi network and were highly enriched on clathrin-coated vesicles. Furthermore, genotype II HDV, which assembles less efficiently than genotype I HDV does, has a putative clathrin box in its HDAg-L but interacted only weakly with CHC. The assembly efficiency of the various HDV genotypes correlates well with the CHC-binding activity of their HDAg-Ls and coincides with the severity of disease outcome. Thus, the clathrin box and the nuclear export signal at the C terminus of HDAg-L are potential new molecular targets for HDV therapy.

Hepatitis B virus and hepatitis delta virus genotypes in outbreaks of fulminant hepatitis (Labrea black fever) in the western Brazilian Amazon region

The genotypes of hepatitis B (HBV) and delta (HDV) viruses circulating among fulminant hepatitis cases from the western Amazon Basin of Brazil were characterized in this study. HBV and HDV isolates were obtained from liver samples from 14 patients who developed fulminant hepatitis and died during 1978-1989. HBV DNA and HDV RNA were detected in all samples. Phylogenetic analyses of HDV sequences showed that they all clustered with previously characterized sequences of HDV genotype 3 (HDV-3). HBV genotypes F, A and D were found in 50.0, 28.6 and 21.4 % of cases, respectively. These results confirm the predominance of HDV-3 in South America and its association with the severe form of hepatitis, and the finding of the co-infection of HDV-3 with different genotypes of HBV suggests that the association between HDV-3 and HBV-F is not necessarily causally related to a more severe clinical course of infection.

Influence of Hepatitis B Virus (HBV) Genotype on the Clinical Course of Disease in Patients Coinfected with HBV and Hepatitis Delta Virus

We evaluated the influence of hepatitis B virus (HBV) genotype on the course of disease in patients coinfected with HBV and hepatitis delta virus (HDV). We evaluated HBV genotypes in 190 patients, 140 of whom had chronic HBV monoinfection and 50 of whom had chronic HBV-HDV coinfection. Real-time polymerase chain reactions for the amplification of HBV DNA and HDV RNA were developed, and we compared the patient groups with respect to HBV genotype, viral load, alanine aminotransferase (ALT) and bilirubin levels, and disease severity. Coinfected patients had higher ALT and bilirubin levels as well as a higher prevalence of liver cirrhosis and liver carcinoma. ALT levels were higher among individuals coinfected with HDV and HBV genotype F than among individuals infected only with HBV genotype F. Among HDV-HBV-coinfected patients, HDV load was lower among those infected with HBV genotype A than among those infected with HBV genotype D or genotype F. Liver inflammation and HDV load are influenced by HBV genotype in individuals coinfected with HBV and HDV.

Generation of cytotoxicity against hepatitis delta virus genotypes and quasispecies by epitope modification

Quasispecies are likely responsible for virus escape from host immune surveillance. The aim of this study was to enhance the immune response against varied sequences within the HDV quasispecies in an attempt to control chronic delta hepatitis. The HLA-A2 restricted peptides spanning aa 43-51 of HDAg and three variant peptides bearing single amino acid substitutions were synthesized. Their immunogenicity and capacity to induce effective CTL responses were studied in HHD-2 mice. Native HDV epitope produced limited cytotoxic immune response. Two modified HDV peptides (HDV 43-51 1Y; tyrosine substitution in positive 1, and 43-51 3A; alanine substitution in position 3) could enhance not only the binding affinity with HLA-A2.1 molecules but also the immunogenicity. Ex vivo interferon-gamma ELISPOT and CTL assays revealed that the two modified epitopes-induced CTLs had a higher functional avidity and produced stronger cytotoxicity to lyse constitutively HDAg-expressing Hep-G2 cells. Interestingly, the spectrums of the T cell receptor (TCR) cross-reactivity are broadened and response to multiple HDV variants by the enhanced epitopes immunization. The modified HDV peptides can enhance the immunogenicity and the induced CTLs can cross-react with multiple HDV variants. Combination with the two enhanced epitopes might be a potential immunotherapeutic agent to control HDV quasispecies in HLA-A2 chronic hepatitis D patients.

Chronic delta hepatitis: An overview

Delta hepatitis or hepatitis D leads to acute and chronic liver disease in humans. The causative agent, the hepatitis delta virus (HDV), is a defective virus which leads to hepatitis in humans in the presence of the hepatitis B virus. This helper function of HBV is required for transmission and propagation of HDV infection but not for replication. HDV RNA replication occurs through the double-rolling circle model and does not possess a reverse transcription step. Hepatitis D-induced liver disease is immune-mediated and occurs either as co-infection of both viruses or as superinfection of a hepatitis B carrier with hepatitis D. Based on a sequence variation of 19-38%, to date seven genotypes of HDV have been described. HDV infection has declined significantly in many endemic areas in the last decades, however, due to migration to industrialized countries, this decline appears to have reached a plateau in western countries. The clinical course of delta hepatitis in general is associated with rapid progression. Delta hepatitis may be an additional risk factor for the development of hepatocellular carcinoma. The only established management for delta hepatitis consists of treatment with interferon for a period of at least one year. For those unresponsive to interferon treatment and patients with advanced disease new therapies are an urgent need. Such therapies may be on the horizon but translation of bench work to clinical practice is required.

Current prevalence of hepatitis delta virus (HDV) infection and the range of HDV genotypes in Lebanon

Recently the prevalence of hepatitis B virus (HBV) genotypes and the association between these genotypes and the clinical status of HBV-infected patients were recently investigated in the Lebanese population. The aim of the additional study reported here was to determine the current prevalence of hepatitis delta virus (HDV) infection and the range of HDV genotypes in this Lebanese population. Two hundred and fifty-eight HBsAg-positive patients (107 asymptomatic blood donors, 92 with chronic hepatitis, 24 with cirrhosis, 15 with hepatocellular carcinoma, 20 patients on haemodialysis) from ten medical centers in Lebanon were tested for antibody to hepatitis D virus (anti-HDV). Those testing positive were analysed further for HDV-RNA and for genotyping by reverse transcriptase-polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism (RFLP). Three samples (1.2%) were anti-HDV positive and out of these, only one was HDV-RNA positive (0.6%) and was analysed as HDV genotype I. Our results point to a low endemicity of HDV in the Lebanese population which is in sharp contrast to data reported from Lebanon 20 years ago and to the situation in neighbouring Arab and non-Arab countries in the Mediterranean region. HDV genotype I seems to be the predominant genotype in Lebanon and the Middle East.

HDV GENOTYPES IN THE WESTERN BRAZILIAN AMAZON REGION: A PRELIMINARY REPORT

In Brazil, hepatitis delta virus (HDV) is only reported in Western Amazonia, where severe cases of acute and chronic HDV hepatitis have been described. The study area was chosen in the States of Acre and Rondonia where most cases of hepatitis B virus (HBV)/HDV are reported. From December 2003 to October 2004, 40 HBsAg carriers with anti-HDV IgM were selected. An epidemiologic questionnaire, including demographic and clinical/epidemiologic variables was filled out. HDV amplification and genotyping were performed. Genotype I was detected in 22 patients (55.0%), whereas genotype III was identified in 18 (45.0%). Patients who were infected with genotype I were older (45.1 +/- 17.8 years) than patients infected with genotype III (32.8 +/- 10.9 years; P = 0.01). No symptoms were reported by 21 (52.5%) patients. Otherwise, 19 (47.5%) had symptoms (fatigue, abdominal pain, weight loss, and decompensated liver disease) that motivated them to seek medical care. Genotype III carriers were more symptomatic, but no statistical significance was achieved. Our preliminary results show that HDV genotypes I and III are present in Brazilian Amazonia and that HDV genotype III is not limited to the Amerindian population.

Treatment of chronic hepatitis delta with pegylated interferon‐α2b

Chronic hepatitis D is difficult to treat. The present pilot study investigated the efficacy and tolerability of pegylated (PEG)-interferon (IFN)-alpha2b in chronic hepatitis D. Twelve patients with chronic hepatitis D were prospectively treated with 1.5 microg/kg PEG-IFN-alpha2b for 48 weeks and followed for 24 weeks. Sustained response (SR) was defined as undetectable hepatitis delta virus (HDV) RNA by reverse transcriptase-polymerase chain reaction and normalization of alanine aminotransferase (ALT) at 6 months after treatment. Investigations included HDV RNA kinetics, determination of hepatitis B virus (HBV) and HDV genotypes and histological evaluation. An SR was achieved in two out of 12 of patients (17%). The negative predictive value of a less than 3 log HDV RNA decrease at month 6 was 100%. The positive predictive value of a more than 3 log HDV RNA decrease at month 6 was 67%. A marked ALT reduction at the end of treatment was observed in responders and nonresponders. Ishak histological score was comparable at baseline and significantly improved in responders compared with nonresponders at the end of follow-up (13.5 vs. 8.0; P<0.02). The present study indicates that PEG-IFN-alpha2b is a promising treatment option in chronic hepatitis D. Nonresponders could be identified by a less than 3 log decrease of HDV RNA at 6 months of treatment.

The role of a metastable RNA secondary structure in hepatitis delta virus genotype III RNA editing

RNA editing plays a critical role in the life cycle of hepatitis delta virus (HDV). The host editing enzyme ADAR1 recognizes specific RNA secondary structure features around the amber/W site in the HDV antigenome and deaminates the amber/W adenosine. A previous report suggested that a branched secondary structure is necessary for editing in HDV genotype III. This branched structure, which is distinct from the characteristic unbranched rod structure required for HDV replication, was only partially characterized, and knowledge concerning its formation and stability was limited. Here, we examine the secondary structures, conformational dynamics, and amber/W site editing of HDV genotype III RNA using a miniaturized HDV genotype III RNA in vitro. Computational analysis of this RNA using the MPGAfold algorithm indicated that the RNA has a tendency to form both metastable and stable unbranched secondary structures. Moreover, native polyacrylamide gel electrophoresis demonstrated that this RNA forms both branched and unbranched rod structures when transcribed in vitro. As predicted, the branched structure is a metastable structure that converts readily to the unbranched rod structure. Only branched RNA was edited at the amber/W site by ADAR1 in vitro. The structural heterogeneity of HDV genotype III RNA is significant because not only are both conformations of the RNA functionally important for viral replication, but the ratio of the two forms could modulate editing by determining the amount of substrate RNA available for modification.