Search Results (16)

Human viral infections remain a significant global health challenge, contributing to a substantial number of cancer cases worldwide. Among them, infections with oncoviruses such as hepatitis B virus (HBV) and hepatitis C virus (HCV) are key drivers of hepatocellular carcinoma (HCC). Despite the availability of an effective HBV vaccine since the 1980s, millions remain chronically infected due to the persistence of covalently closed circular DNA (cccDNA) as a reservoir in hepatocytes. Current antiviral therapies, including nucleos(t)ide analogs and interferon, effectively suppress viral replication but fail to eliminate cccDNA, underscoring the urgent need for innovative therapeutic strategies. Direct-acting antiviral agents (DAAs), which have revolutionized HCV treatment with high cure rates, offer a promising model for HBV therapy. A particularly attractive target is the intrinsically disordered region (IDR) of the HBx protein, which regulates cccDNA transcription, viral replication, and oncogenesis by interacting with key host proteins. DAAs targeting these interactions could inhibit viral persistence, suppress oncogenic signaling, and overcome treatment resistance. This review highlights the potential of HBx-directed DAAs to complement existing therapies, offering renewed hope for a functional HBV cure and reduced cancer risk. Full article

Microbial communities in wastewater treatment plants (WWTPs) play a crucial role in the decontamination of polluted water. An uncultured order-level lineage AKYH767 of the phylum Bacteroidota has been consistently detected in microbial consortia of activated sludge at WWTPs worldwide, but its functional role remains elusive. Representatives of AKYH767 were also detected in soils and freshwater bodies, which may be their natural reservoirs. Here, we obtained ten high-quality metagenome-assembled genomes, including one closed circular genome, of AKYH767 bacteria from metagenomes of the wastewater and activated sludge and used genomic data to uncover the metabolic potential of these bacteria and to predict their functional role. The cells of the AKYH767 bacteria were inferred to be rod-shaped and non-motile. Genome-based metabolic reconstruction predicted the Embden–Meyerhof pathway, the non-oxidative stage of the pentose phosphate pathway, and the complete tricarboxylic acid cycle. A facultatively anaerobic chemoheterotrophic lifestyle with the capacity to oxidize low organic substrates through aerobic respiration was suggested. Under anaerobic conditions AKYH767 bacteria can perform different steps of denitrification. They have limited capacities to hydrolyze carbohydrates and proteinaceous substrates but can utilize fatty acids. A peculiar property of AKYH767 bacteria is the presence of the phenylacetyl-CoA pathway for the utilization of phenylacetate, and about half of the genomes encoded the benzoate degradation pathway. Apparently, in bioreactors at WWTPs, the AKYH767 bacteria could be involved in the denitrification and biodegradation of aromatic compounds. Based on phylogenetic and genomic analyses, the novel AKYH767 bacterium is proposed to be classified as Candidatus Pollutiaquabacter aromativorans, within the candidate order Pollutiaquabacterales. Full article

Hepatitis B virus (HBV) is a major global health issue, with an estimated 254 million people living with chronic HBV infection worldwide as of 2022. Chronic HBV infection is the leading cause of cirrhosis and liver cancer. Current treatment with nucleos(t)ide analogs is effective in the suppression of viral activity but generally requires lifelong treatment. They fail to eradicate the HBV viral reservoir, called covalently closed circular DNA (cccDNA), which replicates in the nucleus of liver cells. The cccDNA serves as the sole template for viral replication, as it generates the pregenomic RNA (pgRNA) necessary for producing new viral genomes. This stable form of viral DNA can reactivate the virus when treatment is stopped. HBV cccDNA is therefore one of the main challenges in curing chronic HBV infections. By targeting steps such as cccDNA formation, capsid assembly, or particle secretion, researchers continue to seek ways to interfere with HBV replication and to reduce its persistence, ultimately to eradicate HBV as a global health problem. This review provides an overview of what is currently known about cccDNA formation and biogenesis and the ongoing efforts to target and eradicate it to cure chronic HBV infections. Full article

Hepatitis B virus (HBV) can cause chronic infections, significantly increasing the risk of death from cirrhosis and hepatocellular carcinoma (HCC). A key player in chronic HBV infection is covalently closed circular DNA (cccDNA), a stable episomal form of viral DNA that acts as a persistent reservoir in infected hepatocytes and drives continuous viral replication. Despite the development of several animal models, few adequately replicate cccDNA formation and maintenance, limiting our understanding of its dynamics and the evaluation of potential therapeutic interventions targeting cccDNA. In this study, we aimed to develop a mouse model to investigate cccDNA formation and maintenance. We infected C57BL/6 mice with recombinant adeno-associated virus (rAAV) carrying a 1.3-overlength HBV genome (genotype C) and collected liver tissue at various time points to assess cccDNA levels and viral replication. Our results demonstrated the successful establishment of a chronic hepatitis B mouse model using rAAV-HBV1.3, which supported persistent HBV infection with sustained cccDNA expression in hepatocytes. Serum levels of HBsAg and HBeAg were elevated for up to 12 weeks, while alanine transaminase (ALT) levels remained within the normal range, indicating limited liver damage during this period. We confirmed HBV DNA expression in hepatocytes, and importantly, cccDNA was detected using qPCR after Plasmid-Safe ATP-Dependent DNase treatment, which selectively removes non-cccDNA forms. Additionally, Southern blot analysis confirmed the presence of cccDNA isolated using the Hirt extraction method. This established model provides a valuable platform for studying the long-term maintenance of cccDNA in chronic HBV infection and offers an important tool for testing novel therapeutic strategies aimed at targeting cccDNA. Full article

Cells have developed various mechanisms to counteract viral infections. In an evolutionary arms race, cells mobilize cellular restriction factors to fight off viruses, targeted by viral factors to facilitate their own replication. The hepatitis B virus (HBV) is a small dsDNA virus that causes acute and chronic infections of the liver. Its genome persists in the nuclei of infected hepatocytes as a covalently closed circular DNA (cccDNA) minichromosome, thus building up an episomal persistence reservoir. The chromosomal maintenance complex SMC5/6 acts as a restriction factor hindering cccDNA transcription, whereas the viral regulatory protein HBx targets SMC5/6 for proteasomal degradation, thus relieving transcriptional suppression of the HBV minichromosome. To date, no curative therapies are available for chronic HBV carriers. Knowledge of the factors regulating the cccDNA and the development of therapies involving silencing the minichromosome or specifically interfering with the HBx-SMC5/6 axis holds promise in achieving sustained viral control. Here, we summarize the current knowledge of the mechanism of SMC5/6-mediated HBV restriction. We also give an overview of SMC5/6 cellular functions and how this compares to the restriction of other DNA viruses. We further discuss the therapeutic potential of available and investigational drugs interfering with the HBx-SMC5/6 axis. Full article

There has been over half a century since the discovery of hepatitis B virus (HBV) to now, but approximately 300 million patients with chronic hepatitis B (CHB) still live in the world, resulting in about one million deaths every year. Although currently approved antivirals (e.g., nucleoside analogues) are effective at reducing HBV replication, they have almost no impact on the existing HBV covalently closed circular DNA (cccDNA) reservoir. HBV cccDNA is a critical obstacle to the complete elimination of the virus via antiviral therapy. The true cure of HBV infection requires the eradication of viral cccDNA from HBV-infected cells; thus, the development of new agents directly or indirectly targeting HBV cccDNA is urgently needed due to the limitations of current available drugs against HBV infection. In this regard, it is the major focus of current anti-HBV research worldwide via different mechanisms to either inactivate/inhibit (functional cure) or eliminate (complete cure) HBV cccDNA. Therefore, this review discussed and summarized recent advances and challenges in efforts to inactivate/silence or eliminate viral cccDNA using anti-HBV agents from different sources, such as small molecules (including epigenetic drugs) and polypeptides/proteins, and siRNA or gene-editing approaches targeting/attenuating HBV cccDNA via different mechanisms, as well as future directions that may be considered in efforts to truly cure chronic HBV infection. In conclusion, no breakthrough has been made yet in attenuating HBV cccDNA, although a number of candidates have advanced into the phase of clinical trials. Furthermore, the overwhelming majority of the candidates function to indirectly target HBV cccDNA. No outstanding candidate directly targets HBV cccDNA. Relatively speaking, CCC_R08 and nitazoxanide may be some of the most promising agents to clear HBV infection in small molecule compounds. Additionally, CRISPR-Cas9 systems can directly target HBV cccDNA for decay and demonstrate significant anti-HBV activity. Consequently, gene-editing approaches targeting HBV cccDNA may be one of the most promising means to achieve the core goal of anti-HBV therapeutic strategies. In short, more basic studies on HBV infection need to be carried out to overcome these challenges. Full article

The Hepatitis B virus (HBV) HBx and HBc proteins play a crucial role in associating with covalently closed circular DNA (cccDNA), the primary factor contributing to intrahepatic viral persistence and a major obstacle in achieving a cure for HBV. The cccDNA serves as a reservoir for viral persistence. Targeting the viral HBc and HBx proteins’ interaction with cccDNA could potentially limit HBV replication. In this study, we present epitopes identified from global consensus sequences of HBx and HBc proteins that have the potential to serve as targets for the development of effective vaccine candidates. Furthermore, conserved residues identified through this analysis can be utilized in designing novel, site-specific anti-HBV agents capable of targeting all major genotypes of HBV. Our approach involved designing global consensus sequences for HBx and HBc proteins, enabling the analysis of variable regions and highly conserved motifs. These identified motifs and regions offer potent sites for the development of peptide vaccines, the design of site-specific RNA interference, and the creation of anti-HBV inhibitors. The epitopes derived from global consensus sequences of HBx and HBc proteins emerge as promising targets for the development of effective vaccine candidates. Additionally, the conserved residues identified provide valuable insights for the development of innovative, site-specific anti-HBV agents capable of targeting all major genotypes of HBV from A to J. Full article

Pigeon circovirus (PiCV) is considered to be genetically diverse, with a relatively small circular single-stranded DNA genome of 2 kb that encodes for a capsid protein (Cap) and a replication initiator protein (Rep). Australasia is known to be the origin of diverse species of the Order Columbiformes, but limited data on the PiCV genome sequence has hindered phylogeographic studies in this species. To fill this gap, this study was conducted to investigate PiCV in 118 characteristic samples from different birds across Australia using PCR and sequencing. Eighteen partial PiCV Rep sequences and one complete PiCV genome sequence were recovered from reservoir and aberrant hosts. Phylogenetic analyses revealed that PiCV circulating in Australia was scattered across three different subclades. Importantly, one subclade dominated within the PiCV sequenced from Australia and Poland, whereas other PiCV sequenced in this study were more closely related to the PiCV sequenced from China, USA and Japan. In addition, PiCV Rep sequences obtained from clinically affected plumed whistling duck, blue billed duck and Australian magpie demonstrated natural spillover of PiCV unveiled host generalist characteristics of the pigeon circovirus. These findings indicate that PiCV genomes circulating in Australia lack host adapted population structure but demonstrate natural spillover infection. Full article

Hepatitis B virus (HBV) is a major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Despite the advent of vaccines and potent antiviral agents able to suppress viral replication, recovery from chronic HBV infection is still an extremely difficult goal to achieve. Complex interactions between virus and host are responsible for HBV persistence and the risk of oncogenesis. Through multiple pathways, HBV is able to silence both innate and adaptive immunological responses and become out of control. Furthermore, the integration of the viral genome into that of the host and the production of covalently closed circular DNA (cccDNA) represent reservoirs of viral persistence and account for the difficult eradication of the infection. An adequate knowledge of the virus–host interaction mechanisms responsible for viral persistence and the risk of hepatocarcinogenesis is necessary for the development of functional cures for chronic HBV infection. The purpose of this review is, therefore, to analyze how interactions between HBV and host concur in the mechanisms of infection, persistence, and oncogenesis and what are the implications and the therapeutic perspectives that follow. Full article

Hydraulic fracturing for oil-gas and geothermal reservoir stimulation is closely related to the propagation of Mode I crack. Nonlinear deformation due to rock heterogeneity occurs at such crack tips, which causes the fracture process zone (FPZ) to form before the crack propagates unsteadily. However, the relationship between the FPZ characteristics and rock heterogeneity still remains elusive. We used three rock types common in reservoirs for experimental investigation, and each of them includes two subtypes with different heterogeneity due to grain size or microstructural characteristics. Drawing on the experiment results, we calculated the FPZ size (represented by the radius of an assumed circular FPZ) in each cracked chevron-notched Brazilian disk, and we reproduced the formation process of the FPZ in marble using the discrete element method. We showed that strong heterogeneity is favorable to large FPZ size, can enhance the ability of crack generation and make crack morphology complex. Coupling the Weibull distribution with fracture mechanics, the dependence of the FPZ size on heterogeneity degree can be theoretically explained, which suggests that the inherent heterogeneity of rocks sets the physical foundation for formation of FPZs. These findings can improve our recognition of propagation mechanisms of Mode I cracking and provide useful guidelines for evaluating reservoir fracability. Full article

The dolomitization of carbonate rocks has always been a hot topic in the study of the dolomite reservoir. In this study, the genesis of Cambrian dolomite in the Bachu area, Tarim Basin, was assessed through petrographic examinations, isotope compositions (C, O, and Sr), trace and rare earth elements, and fluid inclusion microthermometry. Microscopic analysis revealed three types of dolomites: very fine-crystalline, nonplanar dolomite (D1); fine-crystalline, nonplanar to planar-s dolomite (D2); and medium- to coarse-crystalline, planar-e to planar-s dolomite (D3). D1 dolomite exhibits well-preserved original sedimentary features, such as algal laminae, stromatolite, and evaporite streak, and is characterized by the ⁸⁷Sr/⁸⁶Sr value and δ¹⁸O value in equilibrium with the coeval seawater, its high Sr and Na content, and its low Mn content. This indicates that D1 dolomite is primarily a penecontemporaneous dolomite in tidal flat or lagoon environments, and its dolomitizing fluid is mainly evaporated mesosaline to penesaline seawater. D2 dolomite shows ghosts of precursor particles; features δ¹³C values in equilibrium with the coeval seawater, high ⁸⁷Sr/⁸⁶Sr values, low Sr content, and positive Eu anomaly; and is widely distributed close to stylolite. This illustrates that D2 dolomite was principally formed by seepage–reflux dolomitization, and is closely related to hydrothermal activity and pressure dissolution. D3 dolomite displays a crystal texture with a cloudy core and compositional zoning, and the original sedimentary fabrics cannot be identified. It has similar δ¹³C values and REE patterns to the calcite precipitated from coeval seawater, high ⁸⁷Sr/⁸⁶Sr values, low Sr contents and high Mn/Sr ratios, which suggests that D3 dolomite is chiefly related to the recrystallization of the precursor dolomite during the deep burial stage, and the deep circular brine provides Mg ions through the fluid–rock reaction. This study shows that the Cambrian dolomite in the Bachu area is mainly formed in the coeval seawater environment during the penecontemporaneous and shallow burial stages, and has extensively suffered from recrystallization and burial diagenesis due to long-term deep burial, which was further strengthened in the fracture-enriched area. Full article

Shale gas is a promising new energy source stored in shale. This research aims to study the laws of rock crack initiation and propagation under the low-temperature fracturing of liquid nitrogen, explore the influencing factors of the shale reservoir fracturing effect, and identify the method that achieves the best fracturing effect and obtains the highest economic benefits. Herein, a visualized physical experiment of the liquid nitrogen effect is carried out, and the fracture process of a numerical model under cold shock is simulated to analyze the effect of homogeneity on shale crack propagation. The results show that two different crack development modes could be observed in the field test. The first one was the horizontal plane radial crack caused by longitudinal thermal shrinkage, and the other one was the vertical tensile crack caused by circumferential shrinkage. A certain interval length was frequently found between the horizontal cracks. The crack propagation of the specimens with different homogenization degrees was basically distributed in the direction perpendicular to the liquid nitrogen contact surface. When the homogenization degrees were m = 2 and 5, the crack surface was rough and the microfracture was disordered and dotted around the crack tip. When m ≥ 10, the dotted damage around the crack tip did not appear, and the crack propagation was close to the results obtained from using the homogeneous materials. Finally, this work simulates the fracture process of a circular hole plane model under cold shock, analyzes the influences of heat transfer coefficient, in situ stress and other parameters on shale temperature, minimum principal stress distribution, and crack propagation, and discusses the optimal method to improve the heat transfer coefficient. The results show that increasing the heat transfer coefficient can increase the tensile stress value and influence the range of the contact boundary, making the rock more prone to cracking and resulting in greater crack development and a better crack initiation effect. The lateral stress coefficient affects the propagation direction of the cracks, and the propagation depths of low-temperature cracks were found to be deeper in the direction of larger principal stress. Full article

Hepatitis B virus (HBV) covalently-closed-circular (ccc)DNA is the key molecule responsible for viral persistence within infected hepatocytes. The evaluation of HBV cccDNA is crucial for the management of patients with chronic HBV infection and for the personalization of treatment. However, the need for liver biopsy is the principal obstacle for the assessment of intrahepatic HBV cccDNA. In the last decade, several studies have investigated the performance of hepatitis B core-related antigen (HBcrAg) as a surrogate of HBV cccDNA amount in the liver. In this meta-analysis, we collected 14 studies (1271 patients) investigating the correlation between serum HBcrAg and intrahepatic HBV cccDNA. Serum HBcrAg showed a high correlation with intrahepatic HBV cccDNA (r = 0.641, 95% confidence interval (CI) 0.510–0.743, p < 0.001). In a head-to-head comparison, we observed that the performance of HBcrAg was significantly superior to that of hepatitis B surface antigen (r = 0.665 vs. r = 0.475, respectively, p < 0.001). Subgroup analysis showed that the correlation between HBcrAg and intrahepatic HBV cccDNA was high, both in hepatitis B e antigen-positive and -negative patients (r = 0.678, 95% CI 0.403–0.840, p < 0.001, and r = 0.578, 95% CI 0.344–0.744, p < 0.001, respectively). In conclusion, the measurement of serum HBcrAg qualifies as a reliable non-invasive surrogate for the assessment of an intrahepatic HBV cccDNA reservoir. Full article

The Pseudo Steady-State (PSS) constant b_Dpss is defined as the difference between the dimensionless wellbore pressure and dimensionless average pressure of a reservoir with a PSS flow regime. As an important parameter, b_Dpss has been widely used for decline curve analysis with Type Curves. For a well with a finite-conductivity fracture, b_Dpss is independent of time and is a function of the penetration ratio of facture and fracture conductivity. In this study, we develop a new semi-analytical solution for b_Dpss calculations using the PSS function of a circular reservoir. Based on the semi-analytical solution, a new conductivity-influence function (CIF) representing the additional pressure drop caused by the effect of fracture conductivity is presented. A normalized conductivity-influence function (NCIF) is also developed to calculate the CIF. Finally, a new approximate solution is proposed to obtain the b_Dpss value. This approximate solution is a fast, accurate, and time-saving calculation. Full article

Chronic infection with the hepatitis B virus (HBV) is a global health concern and accounts for approximately 1 million deaths annually. Amongst other limitations of current anti-HBV treatment, failure to eliminate the viral covalently closed circular DNA (cccDNA) and emergence of resistance remain the most worrisome. Viral rebound from latent episomal cccDNA reservoirs occurs following cessation of therapy, patient non-compliance, or the development of escape mutants. Simultaneous viral co-infections, such as by HIV-1, further complicate therapeutic interventions. These challenges have prompted development of novel targeted hepatitis B therapies. Given the ease with which highly specific and potent nucleic acid therapeutics can be rationally designed, gene therapy has generated interest for antiviral application. Gene therapy strategies developed for HBV include gene silencing by harnessing RNA interference, transcriptional inhibition through epigenetic modification of target DNA, genome editing by designer nucleases, and immune modulation with cytokines. DNA-binding domains and effectors based on the zinc finger (ZF), transcription activator-like effector (TALE), and clustered regularly interspaced short palindromic repeat (CRISPR) systems are remarkably well suited to targeting episomal cccDNA. This review discusses recent developments and challenges facing the field of anti-HBV gene therapy, its potential curative significance and the progress towards clinical application. Full article