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Hao J, Ma J, Wang Y. Understanding viroids, endogenous circular RNAs, and viroid-like RNAs in the context of biogenesis. PLoS Pathog 2024; 20:e1012299. [PMID: 38935625 PMCID: PMC11210808 DOI: 10.1371/journal.ppat.1012299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Affiliation(s)
- Jie Hao
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
| | - Junfei Ma
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
| | - Ying Wang
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
- Plant Molecular and Cell Biology Program, University of Florida, Gainesville, Florida, United States of America
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Mateo R, Xu S, Shornikov A, Yazdi T, Liu Y, May L, Han B, Han D, Martin R, Manhas S, Richards C, Marceau C, Aeschbacher T, Chang S, Manuilov D, Hollnberger J, Urban S, Asselah T, Abdurakhmanov D, Lampertico P, Maiorova E, Mo H. Broad-spectrum activity of bulevirtide against clinical isolates of HDV and recombinant pan-genotypic combinations of HBV/HDV. JHEP Rep 2023; 5:100893. [PMID: 37929228 PMCID: PMC10622701 DOI: 10.1016/j.jhepr.2023.100893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/20/2023] [Accepted: 08/07/2023] [Indexed: 11/07/2023] Open
Abstract
Background & Aims Bulevirtide (BLV) is a small lipopeptide agent that specifically binds to the sodium taurocholate cotransporting polypeptide (NTCP) bile salt transporter and HBV/HDV receptor on the surface of human hepatocytes and inhibits HDV and HBV entry. As a satellite virus of HBV, HDV virions are formed after assembly of HDV RNA with the HBV envelope proteins (HBsAg). Because both viruses exist as eight different genotypes, this creates a potential for high diversity in the HBV/HDV combinations. To investigate the sensitivity of various combinations of HBV/HDV genotypes to BLV, clinical and laboratory strains were assessed. Methods For the laboratory strains, the different envelopes from HBV genotypes A through H were combined with HDV genotypes 1-8 in cotransfection assays. Clinical plasma isolates were obtained from clinical studies and academic collaborations to maximise the diversity of HBV/HDV genotypes tested. Results The mean BLV EC50 against HDV laboratory strains ranged from 0.44 to 0.64 nM. Regardless of HBV and HDV genotypes, the clinical isolates showed similar sensitivities to BLV with mean values that ranged from 0.2 to 0.73 nM. Conclusions These data support the use of BLV in patients infected with any HBV/HDV genotypes. Impact and implications This study describes the potent activity of BLV against multiple laboratory strains spanning all HBV/HDV A-H/1-8 genotype combinations and the most diverse collection of HDV clinical samples tested to date, including HBV/HDV genotype combinations less frequently observed in the clinic. Overall, all isolates and laboratory strains displayed similar in vitro nanomolar sensitivity to BLV. This broad-spectrum antiviral activity of BLV has direct implications on potential simplified treatment for any patient infected with HDV, regardless of genotype, and supports the new 2023 EASL Clinical Practice Guidelines on HDV that recommend antiviral treatment for all patients with CHD.
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Affiliation(s)
| | - Simin Xu
- Gilead Sciences Inc., Foster City, CA, USA
| | | | | | - Yang Liu
- Gilead Sciences Inc., Foster City, CA, USA
| | | | - Bin Han
- Gilead Sciences Inc., Foster City, CA, USA
| | - Dong Han
- Gilead Sciences Inc., Foster City, CA, USA
| | | | | | | | | | | | | | | | - Julius Hollnberger
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg Partner Site, Heidelberg, Germany
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg Partner Site, Heidelberg, Germany
| | - Tarik Asselah
- Université de Paris-Cité, Centre de Recherche sur l'Inflammation, INSERM UMR 1149, Hôpital Beaujon, Department of Hepatology, AP-HP, Clichy, France
| | | | - Pietro Lampertico
- Division of Gastroenterology and Hepatology, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- CRC 'A. M. and A. Migliavacca' Center for Liver Disease, Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | | | - Hongmei Mo
- Gilead Sciences Inc., Foster City, CA, USA
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3
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Hollnberger J, Liu Y, Xu S, Chang S, Martin R, Manhas S, Aeschbacher T, Han B, Yazdi T, May L, Han D, Shornikov A, Flaherty J, Manuilov D, Suri V, Asselah T, Lampertico P, Wedemeyer H, Aleman S, Richards C, Mateo R, Maiorova E, Cihlar T, Mo H, Urban S. No virologic resistance to bulevirtide monotherapy detected in patients through 24 weeks treatment in phase II and III clinical trials for chronic hepatitis delta. J Hepatol 2023; 79:657-665. [PMID: 37120031 DOI: 10.1016/j.jhep.2023.04.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/14/2023] [Accepted: 04/16/2023] [Indexed: 05/01/2023]
Abstract
BACKGROUND & AIMS Bulevirtide (BLV) is a HDV/HBV entry inhibitor that is associated with virologic response (responders, HDV-RNA undetectable or ≥2 log10 IU/ml decrease from baseline) in >50% of patients after a 24-week treatment. However, some patients only achieve a <1 log10 IU/ml decline in HDV-RNA after the 24-week treatment (non-responders). Here, we report a viral resistance analysis in participants receiving BLV monotherapy who were non-responders or experienced virologic breakthrough (VB, i.e., two consecutive increases in HDV-RNA of ≥1 log10 IU/ml from nadir or two consecutive HDV-RNA detectable results if previously undetectable) from the phase II MYR202 and phase III MYR301 study. METHODS Deep-sequencing of the BLV-corresponding region in HBV PreS1 and of the HDV HDAg gene, as well as in vitro phenotypic testing, were performed for the participant with VB (n = 1) and non-responders (n = 20) at baseline (BL) and Week 24 (WK24). RESULTS No amino acid exchanges associated with reduced susceptibility to BLV within the BLV-corresponding region or within HDAg were identified in isolates from any of the 21 participants at BL or at WK24. Although variants (HBV n = 1; HDV n = 13) were detected at BL in some non-responders or in the participant with VB, none were associated with reduced sensitivity to BLV in vitro. Furthermore, the same variant was detected in virologic responders. A comprehensive phenotypic analysis demonstrated that the BLV EC50 values from 116 BL samples were similar across non-responders, partial responders (HDV RNA decline ≥1 but <2 log10 IU/ml), and responders regardless of the presence of HBV and/or HDV polymorphisms. CONCLUSIONS No amino acid substitutions associated with reduced sensitivity to BLV monotherapy were detected at BL or WK24 in non-responders or the participant with VB after 24-week BLV treatment. IMPACT AND IMPLICATIONS This is the first study investigating the development of resistance in patients treated with BLV. Excluding resistance to BLV as an explanation for an insufficient decrease in HDV-RNA levels during BLV therapy is an important finding for patients, clinicians, and researchers. It demonstrates that BLV has a high barrier to resistance, indicating it is safe and suitable for long-term treatment, although long-term surveillance for resistance should be performed. Our results hint at other still unknown mechanisms as an explanation for the persistence of serum HDV-RNA during inhibition of viral entry. CLINICAL TRIAL NUMBERS NCT03546621 and NCT03852719.
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Affiliation(s)
- Julius Hollnberger
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany; German Center for Infection Research (DZIF), Heidelberg Partner Site, Heidelberg, Germany
| | - Yang Liu
- Gilead Sciences Inc., Foster City, California, USA.
| | - Simin Xu
- Gilead Sciences Inc., Foster City, California, USA
| | - Silvia Chang
- Gilead Sciences Inc., Foster City, California, USA
| | - Ross Martin
- Gilead Sciences Inc., Foster City, California, USA
| | | | | | - Bin Han
- Gilead Sciences Inc., Foster City, California, USA
| | | | - Lindsey May
- Gilead Sciences Inc., Foster City, California, USA
| | - Dong Han
- Gilead Sciences Inc., Foster City, California, USA
| | | | | | | | - Vithika Suri
- Gilead Sciences Inc., Foster City, California, USA
| | - Tarik Asselah
- Department of Hepatologi, Hôpital Beaujon, AP-HP, Université de Paris-Cité, INSERM UMR 1149, Clichy, France
| | - Pietro Lampertico
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Italy; "A.M. e A. Migliavacca" Center for the Study of Liver Disease, Università degli Studi di Milano, Milan, Italy
| | | | - Soo Aleman
- Karolinska Universitetssjukhuset, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | - Tomas Cihlar
- Gilead Sciences Inc., Foster City, California, USA
| | - Hongmei Mo
- Gilead Sciences Inc., Foster City, California, USA
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany; German Center for Infection Research (DZIF), Heidelberg Partner Site, Heidelberg, Germany.
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4
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Brunetto MR, Ricco G, Negro F, Wedemeyer H, Yurdaydin C, Asselah T, Papatheodoridis G, Gheorghe L, Agarwal K, Farci P, Buti M. EASL Clinical Practice Guidelines on hepatitis delta virus. J Hepatol 2023; 79:433-460. [PMID: 37364791 DOI: 10.1016/j.jhep.2023.05.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/01/2023] [Indexed: 06/28/2023]
Abstract
Hepatitis D virus (HDV) is a defective virus that requires the hepatitis B virus to complete its life cycle and cause liver damage in humans. HDV is responsible for rare acute and chronic liver diseases and is considered the most aggressive hepatitis virus. Acute infection can cause acute liver failure, while persistent infection typically causes a severe form of chronic hepatitis which is associated with rapid and frequent progression to cirrhosis and its end-stage complications, hepatic decompensation and hepatocellular carcinoma. Major diagnostic and therapeutic innovations prompted the EASL Governing Board to commission specific Clinical Practice Guidelines on the identification, virologic and clinical characterisation, prognostic assessment, and appropriate clinical and therapeutic management of HDV-infected individuals.
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5
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Hoblos R, Kefalakes H. Immunology of hepatitis D virus infection: General concepts and present evidence. Liver Int 2023; 43 Suppl 1:47-59. [PMID: 36074070 DOI: 10.1111/liv.15424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/27/2022] [Accepted: 09/05/2022] [Indexed: 02/13/2023]
Abstract
Infection with the hepatitis D virus induces the most severe form of chronic viral hepatitis, affecting over 12 million people worldwide. Chronic HDV infection leads to rapid development of liver cirrhosis and hepatocellular carcinoma in ~70% of patients within 15 years of infection. Recent evidence suggests that an interplay of different components of the immune system are contributing to viral control and may even be implicated in liver disease pathogenesis. This review will describe general concepts of antiviral immune response and elicit the present evidence concerning the interplay of the hepatitis D virus with the immune system.
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Affiliation(s)
- Reem Hoblos
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Helenie Kefalakes
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
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6
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Stephenson-Tsoris S, Liang TJ. Hepatitis Delta Virus-Host Protein Interactions: From Entry to Egress. Viruses 2023; 15:1530. [PMID: 37515216 PMCID: PMC10383234 DOI: 10.3390/v15071530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Hepatitis delta virus (HDV) is the smallest known human virus and causes the most severe form of human viral hepatitis, yet it is still not fully understood how the virus replicates and how it interacts with many host proteins during replication. This review aims to provide a systematic review of all the host factors currently known to interact with HDV and their mechanistic involvement in all steps of the HDV replication cycle. Finally, we discuss implications for therapeutic development based on our current knowledge of HDV-host protein interactions.
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Affiliation(s)
- Susannah Stephenson-Tsoris
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD 20892, USA
| | - T Jake Liang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD 20892, USA
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7
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Khalfi P, Kennedy PT, Majzoub K, Asselah T. Hepatitis D virus: Improving virological knowledge to develop new treatments. Antiviral Res 2023; 209:105461. [PMID: 36396025 DOI: 10.1016/j.antiviral.2022.105461] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/21/2022] [Accepted: 11/05/2022] [Indexed: 11/16/2022]
Abstract
Hepatitis delta virus (HDV), a satellite of hepatitis B virus (HBV), possesses the smallest viral genome known to infect animals. HDV needs HBV surface protein for secretion and entry into target liver cells. However, HBV is dispensable for HDV genome amplification, as it relies almost exclusively on cellular host factors for replication. HBV/HDV co-infections affect over 12 million people worldwide and constitute the most severe form of viral hepatitis. Co-infected individuals are at higher risk of developing liver cirrhosis and hepatocellular carcinoma compared to HBV mono-infected patients. Bulevirtide, an entry inhibitor, was conditionally approved in July 2020 in the European Union for adult patients with chronic hepatitis delta (CHD) and compensated liver disease. There are several drugs in development, including lonafarnib and interferon lambda, with different modes of action. In this review, we detail our current fundamental knowledge of HDV lifecycle and review antiviral treatments under development against this virus, outlining their respective mechanisms-of-action. Finally, we describe the antiviral effect these compounds are showing in ongoing clinical trials, discussing their promise and potential pitfalls for managing HDV infected patients.
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Affiliation(s)
- Pierre Khalfi
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier 34293 cedex 5, France
| | - Patrick T Kennedy
- The Blizard Institute, Queen Mary University of London, The Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Karim Majzoub
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS-UMR 5535, Montpellier 34293 cedex 5, France.
| | - Tarik Asselah
- Université de Paris, Cité CRI, INSERM UMR 1149, Department of Hepatology, AP-HP Hôpital Beaujon, Clichy, France.
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8
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Dissanayaka Mudiyanselage SD, Ma J, Pechan T, Pechanova O, Liu B, Wang Y. A remodeled RNA polymerase II complex catalyzing viroid RNA-templated transcription. PLoS Pathog 2022; 18:e1010850. [PMID: 36121876 PMCID: PMC9521916 DOI: 10.1371/journal.ppat.1010850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/29/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022] Open
Abstract
Viroids, a fascinating group of plant pathogens, are subviral agents composed of single-stranded circular noncoding RNAs. It is well-known that nuclear-replicating viroids exploit host DNA-dependent RNA polymerase II (Pol II) activity for transcription from circular RNA genome to minus-strand intermediates, a classic example illustrating the intrinsic RNA-dependent RNA polymerase activity of Pol II. The mechanism for Pol II to accept single-stranded RNAs as templates remains poorly understood. Here, we reconstituted a robust in vitro transcription system and demonstrated that Pol II also accepts minus-strand viroid RNA template to generate plus-strand RNAs. Further, we purified the Pol II complex on RNA templates for nano-liquid chromatography-tandem mass spectrometry analysis and identified a remodeled Pol II missing Rpb4, Rpb5, Rpb6, Rpb7, and Rpb9, contrasting to the canonical 12-subunit Pol II or the 10-subunit Pol II core on DNA templates. Interestingly, the absence of Rpb9, which is responsible for Pol II fidelity, explains the higher mutation rate of viroids in comparison to cellular transcripts. This remodeled Pol II is active for transcription with the aid of TFIIIA-7ZF and appears not to require other canonical general transcription factors (such as TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and TFIIS), suggesting a distinct mechanism/machinery for viroid RNA-templated transcription. Transcription elongation factors, such as FACT complex, PAF1 complex, and SPT6, were also absent in the reconstituted transcription complex. Further analyses of the critical zinc finger domains in TFIIIA-7ZF revealed the first three zinc finger domains pivotal for RNA template binding. Collectively, our data illustrated a distinct organization of Pol II complex on viroid RNA templates, providing new insights into viroid replication, the evolution of transcription machinery, as well as the mechanism of RNA-templated transcription.
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Affiliation(s)
| | - Junfei Ma
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Tibor Pechan
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Olga Pechanova
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Bin Liu
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
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9
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Ma J, Mudiyanselage SDD, Wang Y. Emerging value of the viroid model in molecular biology and beyond. Virus Res 2022; 313:198730. [PMID: 35263622 PMCID: PMC8976779 DOI: 10.1016/j.virusres.2022.198730] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/25/2022] [Accepted: 03/05/2022] [Indexed: 01/21/2023]
Abstract
Viroids are single-stranded circular noncoding RNAs that infect plants. Research in the past five decades has deciphered the viroid genome structures, viroid replication cycles, numerous host factors for viroid infection, viroid motifs for intracellular and intercellular trafficking, interactions with host defense machinery, etc. In this review, we mainly focus on some significant questions that remain to be tackled, centered around (1) how the RNA polymerase II machinery performs transcription on RNA templates of nuclear-replicating viroids, (2) how viroid RNAs coordinate multiple structural elements for diverse functions, and (3) how viroid RNAs activate plant immunity. Research on viroids has led to seminal discoveries in biology, and we expect the research directions outlined in this review to continue providing key knowledge inspiring other areas of biology.
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Affiliation(s)
- Junfei Ma
- Department of Biological Sciences, Mississippi State University, MS 39762, USA
| | | | - Ying Wang
- Department of Biological Sciences, Mississippi State University, MS 39762, USA.
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10
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Zi J, Gao X, Du J, Xu H, Niu J, Chi X. Multiple Regions Drive Hepatitis Delta Virus Proliferation and Are Therapeutic Targets. Front Microbiol 2022; 13:838382. [PMID: 35464929 PMCID: PMC9022428 DOI: 10.3389/fmicb.2022.838382] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/11/2022] [Indexed: 12/02/2022] Open
Abstract
Hepatitis Delta Virus (HDV) is the smallest mammalian single-stranded RNA virus. It requires host cells and hepatitis B virus (HBV) to complete its unique life cycle. The present review summarizes the specific regions on hepatitis D antigen (HDAg) and hepatitis B surface antigen (HBsAg) that drive HDV to utilize host cell machinery system to produce three types of RNA and two forms of HDAg, and hijack HBsAg for its secretion and de novo entry. Previously, interferon-α was the only recommended therapy for HDV infection. In recent years, some new therapies targeting these regions, such as Bulevirtide, Lonafarnib, Nucleic acid polymers have appeared, with better curative effects and fewer adverse reactions.
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Affiliation(s)
- Jun Zi
- Gene Therapy Laboratory, Center for Pathogen Biology and Infectious Diseases, First Hospital of Jilin University, Changchun, China
| | - Xiuzhu Gao
- Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, First Hospital of Jilin University, Changchun, China
| | - Juan Du
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, China
| | - Hongqin Xu
- Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, First Hospital of Jilin University, Changchun, China
| | - Junqi Niu
- Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, First Hospital of Jilin University, Changchun, China
| | - Xiumei Chi
- Gene Therapy Laboratory, Center for Pathogen Biology and Infectious Diseases, First Hospital of Jilin University, Changchun, China
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11
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Szirovicza L, Hetzel U, Kipar A, Hepojoki J. Short '1.2× Genome' Infectious Clone Initiates Kolmiovirid Replication in Boa constrictor Cells. Viruses 2022; 14:107. [PMID: 35062311 PMCID: PMC8778117 DOI: 10.3390/v14010107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 11/29/2022] Open
Abstract
Human hepatitis D virus (HDV) depends on hepatitis B virus co-infection and its glycoproteins for infectious particle formation. HDV was the sole known deltavirus for decades and believed to be a human-only pathogen. However, since 2018, several groups reported finding HDV-like agents from various hosts but without co-infecting hepadnaviruses. In vitro systems enabling helper virus-independent replication are key for studying the newly discovered deltaviruses. Others and we have successfully used constructs containing multimers of the deltavirus genome for the replication of various deltaviruses via transfection in cell culture. Here, we report the establishment of deltavirus infectious clones with 1.2× genome inserts bearing two copies of the genomic and antigenomic ribozymes. We used Swiss snake colony virus 1 as the model to compare the ability of the previously reported "2× genome" and the "1.2× genome" infectious clones to initiate replication in cell culture. Using immunofluorescence, qRT-PCR, immuno- and northern blotting, we found the 2× and 1.2× genome clones to similarly initiate deltavirus replication in vitro and both induced a persistent infection of snake cells. The 1.2× genome constructs enable easier introduction of modifications required for studying deltavirus replication and cellular interactions.
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Affiliation(s)
- Leonora Szirovicza
- Medicum, Department of Virology, University of Helsinki, 00290 Helsinki, Finland;
| | - Udo Hetzel
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zürich, 8057 Zürich, Switzerland; (U.H.); (A.K.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland
| | - Anja Kipar
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zürich, 8057 Zürich, Switzerland; (U.H.); (A.K.)
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00790 Helsinki, Finland
| | - Jussi Hepojoki
- Medicum, Department of Virology, University of Helsinki, 00290 Helsinki, Finland;
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zürich, 8057 Zürich, Switzerland; (U.H.); (A.K.)
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Abstract
HDV is a small, defective RNA virus that requires the HBsAg of HBV for its assembly, release, and transmission. Chronic HBV/HDV infection often has a severe clinical outcome and is difficult to treat. The important role of a robust virus-specific T cell response for natural viral control has been established for many other chronic viral infections, but the exact role of the T cell response in the control and progression of chronic HDV infection is far less clear. Several recent studies have characterised HDV-specific CD4+ and CD8+ T cell responses on a peptide level. This review comprehensively summarises all HDV-specific T cell epitopes described to date and describes our current knowledge of the role of T cells in HDV infection. While we now have better tools to study the adaptive anti-HDV-specific T cell response, further efforts are needed to define the HLA restriction of additional HDV-specific T cell epitopes, establish additional HDV-specific MHC tetramers, understand the degree of cross HDV genotype reactivity of individual epitopes and understand the correlation of the HBV- and HDV-specific T cell response, as well as the breadth and specificity of the intrahepatic HDV-specific T cell response.
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Key Words
- ADAR1, adenosine deaminases acting on RNA
- ALT, alanine aminotransferase
- AST, aspartate aminotransferase
- CD4+
- CD8+
- ELISpot, enzyme-linked immune spot assay
- HBV
- HDAg, hepatitis delta antigen
- HDV
- Hepatitis Delta
- ICS, intracellular cytokine staining
- IFN-, interferon-
- L-HDAg, large hepatitis delta antigen
- MAIT, mucosa-associated invariant T cells
- NK cells, natural killer cells
- NTCP, sodium taurocholate co-transporting polypeptide
- PBMCs, peripheral blood mononuclear cells
- PD-1, programmed cell death protein 1
- PTM, post-translational modification
- Peg-IFN-α, pegylated interferon alpha
- S-HDAg, small hepatitis delta antigen
- T cell
- TCF, T cell-specific transcription factor
- TNFα, tumour necrosis factor-α
- Th1, T helper 1
- aa, amino acid(s)
- cccDNA, covalently closed circular DNA
- epitope
- viral escape
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Fearns R. Negative‐strand RNA Viruses. Virology 2021. [DOI: 10.1002/9781119818526.ch3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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Girardi E, Pfeffer S, Baumert TF, Majzoub K. Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell. Semin Cell Dev Biol 2021; 111:86-100. [PMID: 32847707 PMCID: PMC7443355 DOI: 10.1016/j.semcdb.2020.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022]
Abstract
As obligate intracellular parasites with limited coding capacity, RNA viruses rely on host cells to complete their multiplication cycle. Viral RNAs (vRNAs) are central to infection. They carry all the necessary information for a virus to synthesize its proteins, replicate and spread and could also play essential non-coding roles. Regardless of its origin or tropism, vRNA has by definition evolved in the presence of host RNA Binding Proteins (RBPs), which resulted in intricate and complicated interactions with these factors. While on one hand some host RBPs recognize vRNA as non-self and mobilize host antiviral defenses, vRNA must also co-opt other host RBPs to promote viral infection. Focusing on pathogenic RNA viruses, we will review important scenarios of RBP-vRNA interactions during which host RBPs recognize, modify or degrade vRNAs. We will then focus on how vRNA hijacks the largest ribonucleoprotein complex (RNP) in the cell, the ribosome, to selectively promote the synthesis of its proteins. We will finally reflect on how novel technologies are helping in deepening our understanding of vRNA-host RBPs interactions, which can be ultimately leveraged to combat everlasting viral threats.
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Affiliation(s)
- Erika Girardi
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | - Sebastien Pfeffer
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | - Thomas F Baumert
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg, 67000, Strasbourg, France; Pole Hépatodigestif, Institut Hopitalo-universitaire, Hopitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Karim Majzoub
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg, 67000, Strasbourg, France.
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15
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Wang Y. Current view and perspectives in viroid replication. Curr Opin Virol 2021; 47:32-37. [PMID: 33460914 DOI: 10.1016/j.coviro.2020.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 11/16/2022]
Abstract
Viroids are single-stranded circular noncoding RNAs that infect plants. The noncoding nature indicates that viroids must harness their RNA genomes to redirect host machinery for infection. Therefore, the viroid model provides invaluable opportunities for delineating fundamental principles of RNA structure-function relationships and for dissecting the composition and mechanism of RNA-related cellular machinery. There are two viroid families, Pospiviroidae and Avsunviroidae. Members of both families replicate via the RNA-based rolling-circle mechanism with some variations. Viroid replication is generally divided into three steps: transcription, cleavage, and ligation. Decades of studies have uncovered numerous viroid RNA structures with a regulatory role in replication and multiple enzymes critical for the three replication steps. This review discusses these findings and highlights the latest discoveries. Future studies will continue to elucidate regulatory factors and mechanism of host machinery exploited by viroids and provide new insights into host-viroid interactions in the context of pathogenesis.
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Affiliation(s)
- Ying Wang
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39759, USA.
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16
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Wu J, Bisaro DM. Biased Pol II fidelity contributes to conservation of functional domains in the Potato spindle tuber viroid genome. PLoS Pathog 2020; 16:e1009144. [PMID: 33351860 PMCID: PMC7787683 DOI: 10.1371/journal.ppat.1009144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 01/06/2021] [Accepted: 11/10/2020] [Indexed: 01/25/2023] Open
Abstract
Accurate calculation of mutation rates for viruses and viroids is necessary for evolutionary studies and to evaluate adaptation potential. However, estimation of in vivo mutation rates is complicated by selection, which leads to loss or proliferation of certain mutations. To minimize this concern, lethal mutations, including nonsense and non-synonymous mutations, have been used to determine mutation rates for several viruses and viroids, including Potato spindle tuber viroid (PSTVd). However, this approach has limitations, including focus on a relatively small number of genome sites and the possibility that mutations may not actually be lethal or may be maintained by wild type individuals. To avoid selection bias altogether, we sequenced minus-strand PSTVd dimers from concatemeric replication intermediates. The underlying rationale is that mutations found in only one of the monomers were likely generated de novo during RNA polymerase II (Pol II) transcription of the circular plus-strand RNA genome. This approach yielded an apparent Pol II error rate of ~1/1837 nucleotides per transcription cycle, and an estimated mutation rate of ~1/919 nucleotides for a single replication cycle. Remarkably, de novo mutations were nearly absent from the most conserved, replication-critical regions of the PSTVd genome, suggesting that sequence conservation is a consequence of both essential function and template optimization for greater Pol II fidelity. Such biased fidelity may constitute a novel strategy to ensure population success while allowing abundant sampling of sequence space in other genome regions. Comparison with variants in progeny populations derived from a cloned, wild type PSTVd master sequence revealed that most de novo mutations were lost through selection. Polymerase errors are the major source of variation in virus and viroid genomes, and as a consequence polymerase error rates are major determinants of adaptation potential. Accurate calculation of in vivo mutation rates is complicated by selection. To circumvent this issue, dimeric PSTVd minus-strand replication intermediates generated in vivo by host RNA polymerase II (Pol II) were sequenced to identify de novo mutations. This analysis revealed a very high error rate for Pol II transcribing genomic PSTVd RNA, leading to an extremely high mutation rate. Remarkably, however, de novo mutations were rare in the most highly conserved, replication-critical genome regions, suggesting these sequences are selected for both function and enhanced transcription fidelity. This biased fidelity may reveal a novel strategy to ensure population survival while maximizing adaptation potential. Further, comparison of mutations identified by minus-strand dimer sequencing with mutations observed in progeny variants derived from wild type PSTVd showed that most de novo mutations were lost through selection.
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Affiliation(s)
- Jian Wu
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - David M. Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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17
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Awan FM, Yang BB, Naz A, Hanif A, Ikram A, Obaid A, Malik A, Janjua HA, Ali A, Sharif S. The emerging role and significance of circular RNAs in viral infections and antiviral immune responses: possible implication as theranostic agents. RNA Biol 2020; 18:1-15. [PMID: 32615049 DOI: 10.1080/15476286.2020.1790198] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Circular RNAs (circRNAs) are ubiquitously expressed, covalently closed rings, produced by pre-mRNA splicing in a reversed order during post-transcriptional processing. Circularity endows 3'-5'-linked circRNAs with stability and resistance to exonucleolytic degradation which raises the question whether circRNAs may be relevant as potential therapeutic targets or agents. High stability in biological systems is the most remarkable property and a major criterion for why circRNAs could be exploited for a range of RNA-centred medical applications. Even though various biological roles and regulatory functions of circRNAs have been reported, their in-depth study is challenging because of their circular structure and sequence-overlap with linear mRNA counterparts. Moreover, little is known about their role in viral infections and in antiviral immune responses. We believe that an in-depth and detailed understanding of circRNA mediated viral protein regulations will increase our knowledge of the biology of these novel molecules. In this review, we aimed to provide a comprehensive basis and overview on the biogenesis, significance and regulatory roles of circRNAs in the context of antiviral immune responses and viral infections including hepatitis C virus infection, hepatitis B virus infection, hepatitis delta virus infection, influenza A virus infection, Epstein-Barr virus infection, kaposi's sarcoma herpesvirus infection, human cytomegalovirus infection, herpes simplex virus infection, human immunodeficiency virus infection, porcine epidemic diarrhoea virus infection, ORF virus infection, avian leukosis virus infection, simian vacuolating virus 40 infection, transmissible gastroenteritis coronavirus infection, and bovine viral diarrhoea virus infection. We have also discussed the critical regulatory role of circRNAs in provoking antiviral immunity, providing evidence for implications as therapeutic agents and as diagnostic markers.
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Affiliation(s)
- Faryal Mehwish Awan
- Institute of Molecular Biology and Biotechnology (IMBB), the University of Lahore (UOL) , Lahore, Pakistan
| | - Burton B Yang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre , Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto , Toronto, Canada.,Institute of Medical Sciences, University of Toronto , Toronto, Canada
| | - Anam Naz
- Institute of Molecular Biology and Biotechnology (IMBB), the University of Lahore (UOL) , Lahore, Pakistan
| | - Aneeqa Hanif
- Institute of Molecular Biology and Biotechnology (IMBB), the University of Lahore (UOL) , Lahore, Pakistan
| | - Aqsa Ikram
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) , Pakistan
| | - Ayesha Obaid
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) , Pakistan
| | - Arif Malik
- Institute of Molecular Biology and Biotechnology (IMBB), the University of Lahore (UOL) , Lahore, Pakistan
| | - Hussnain Ahmed Janjua
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) , Pakistan
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST) , Pakistan
| | - Sumaira Sharif
- Institute of Molecular Biology and Biotechnology (IMBB), the University of Lahore (UOL) , Lahore, Pakistan
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18
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Lin GY, Wu YL, Wang CS, Ko CY, Chen CH, Chen PJ, Peng PH, Hsu CW. Performance of commercially available anti-HDV enzyme-linked immunosorbent assays in Taiwan. Virol J 2020; 17:76. [PMID: 32546164 PMCID: PMC7298757 DOI: 10.1186/s12985-020-01355-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023] Open
Abstract
Background Hepatitis D virus (HDV) infection is a major global health issue around the world. There are approximately 15–20 million individuals infected with HDV worldwide. HDV infection usually causes increased mortality compared with infection with hepatitis B virus (HBV) alone. However, testing for the detection of HDV is not widely available in Taiwan. Therefore, the General Biologicals Corporation (GB) HDV Ab kit was developed for detecting anti-HDV antibodies. Methods A total of 913 serum and 462 EDTA-treated plasma samples were obtained from HBsAg-positive individuals in three hospitals in Taiwan from June 2014 to November 2017. We used three commercially available ELISA kits, DiaPro HDV Ab, DiaSorin ETI-AB-DELTAK-2 and GB HDV Ab, which were utilized strictly according to the instructions of the manufacturers. Results A comparative study of the results from the GB HDV Ab kit and the other commercial ELISA kits (DiaPro and DiaSorin) was performed to determine their efficacy for anti-HDV detection. The results indicated that the sensitivity of the GB HDV Ab kit for serum and EDTA samples was 100% compared to that of the DiaPro and DiaSorin kits, whereas the specificity for serum and EDTA samples was 99.3 and 98.1%, respectively. In addition, the overall agreement of the results of the GB HDV Ab kit for the serum and EDTA samples was 99.3 and 98.3%, respectively. It is worth noting that the performance of the GB HDV Ab kit was not affected by interference from triglyceride, bilirubin, hemoglobin, or human anti-mouse antibody. The limit of detection of the GB HDV Ab kit is approximately 100-fold lower than that of the other two commercial kits. Conclusions The GB HDV Ab kit, which presented equivalent sensitivity and specificity compared to both certified anti-HDV kits, would be a suitable kit for HDV diagnosis in Taiwan.
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Affiliation(s)
- Guan-Yu Lin
- General Biologicals Corporation, Hsinchu, 30076, Taiwan
| | - Yi-Le Wu
- General Biologicals Corporation, Hsinchu, 30076, Taiwan
| | - Cheng-Si Wang
- General Biologicals Corporation, Hsinchu, 30076, Taiwan
| | - Chia-Yun Ko
- General Biologicals Corporation, Hsinchu, 30076, Taiwan
| | - Chien-Hung Chen
- Division of Hepato-Gastroenterology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Pei-Jer Chen
- Hepatitis Research Center, National Taiwan University, Taipei, 10002, Taiwan
| | - Po-Hsin Peng
- General Biologicals Corporation, Hsinchu, 30076, Taiwan.
| | - Chao-Wei Hsu
- Department of Gastroenterology and Hepatology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, 33305, Taiwan.
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19
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Evidence Supporting That RNA Polymerase II Catalyzes De Novo Transcription Using Potato Spindle Tuber Viroid Circular RNA Templates. Viruses 2020; 12:v12040371. [PMID: 32230827 PMCID: PMC7232335 DOI: 10.3390/v12040371] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/22/2020] [Accepted: 03/25/2020] [Indexed: 12/11/2022] Open
Abstract
Transcription is a fundamental process that mediates the interplay between genetic information and phenotype. Emerging evidence indicates that RNA polymerase II (Pol II) can catalyze transcription using both DNA and RNA templates. It is well established that Pol II initiates de novo transcription on DNA templates. However, it is unclear whether Pol II performs de novo transcription or relies on primers for initiation (primed transcription) on RNA templates. Using potato spindle tuber viroid (PSTVd) as a model, we presented evidence showing that circular PSTVd templates are critical for the synthesis of longer-than-unit-length (-)-strand products, which supports the de novo transcription based on the asymmetric rolling circle model of PSTVd replication. We further showed that the crucial factor for primed transcription, transcription factor IIS (TFIIS), is dispensable for PSTVd replication in cells. Together, our data support the de novo transcription on PSTVd RNA templates catalyzed by Pol II. This result has significant implications in understanding the mechanism and machinery underlying Pol II-catalyzed transcription using other RNA templates.
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20
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Bigogno CM, Falahieh RR, Ho KMA, Jeffrey-Smith A, Jones M, Usai C, Battisti A, Gill U, Kennedy P. The genetic landscape of hepatitis delta virus infection. Clin Med (Lond) 2020; 20:s101. [DOI: 10.7861/clinmed.20-2-s101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Abeywickrama-Samarakoon N, Cortay JC, Sureau C, Müller S, Alfaiate D, Guerrieri F, Chaikuad A, Schröder M, Merle P, Levrero M, Dény P. Hepatitis Delta Virus histone mimicry drives the recruitment of chromatin remodelers for viral RNA replication. Nat Commun 2020; 11:419. [PMID: 31964889 PMCID: PMC6972770 DOI: 10.1038/s41467-020-14299-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/21/2019] [Indexed: 12/26/2022] Open
Abstract
Hepatitis Delta virus (HDV) is a satellite of Hepatitis B virus with a single-stranded circular RNA genome. HDV RNA genome synthesis is carried out in infected cells by cellular RNA polymerases with the assistance of the small hepatitis delta antigen (S-HDAg). Here we show that S-HDAg binds the bromodomain (BRD) adjacent to zinc finger domain 2B (BAZ2B) protein, a regulatory subunit of BAZ2B-associated remodeling factor (BRF) ISWI chromatin remodeling complexes. shRNA-mediated silencing of BAZ2B or its inactivation with the BAZ2B BRD inhibitor GSK2801 impairs HDV replication in HDV-infected human hepatocytes. S-HDAg contains a short linear interacting motif (SLiM) KacXXR, similar to the one recognized by BAZ2B BRD in histone H3. We found that the integrity of the S-HDAg SLiM sequence is required for S-HDAg interaction with BAZ2B BRD and for HDV RNA replication. Our results suggest that S-HDAg uses a histone mimicry strategy to co-activate the RNA polymerase II-dependent synthesis of HDV RNA and sustain HDV replication. Histone mimicry of viral components is a strategy to subvert host factors for virus replication. Here, the authors show that an acetylated histone-like motif of the small Hepatitis Delta Antigen (S-HDAg) interacts with the chromatin remodeler BAZ2B to recruit the DNA-dependent RNA polymerase II for HDV RNA replication.
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Affiliation(s)
| | - Jean-Claude Cortay
- INSERM, U1052 UMR CNRS 5286, Cancer Research Center of Lyon (CRCL), 151 cours Albert Thomas, 69424, Lyon, France
| | - Camille Sureau
- Laboratoire de Virologie Moléculaire, INSERM U1134, Institut National de la Transfusion Sanguine, 6 rue Alexandre Cabanel, 75739, Paris, France
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, D-60438, Frankfurt am Main, Germany
| | - Dulce Alfaiate
- INSERM, U1052 UMR CNRS 5286, Cancer Research Center of Lyon (CRCL), 151 cours Albert Thomas, 69424, Lyon, France.,Département de Pathologie et Immunologie, Université de Genève, avenue de Champel 41, 1206, Genève, Switzerland.,Department of Infectious and Tropical Diseases, Hôpital de la Croix Rousse, Hospices Civils de Lyon and Université Lyon I, 103 Grande Rue de la Croix-Rousse, 69004, Lyon, France
| | - Francesca Guerrieri
- INSERM, U1052 UMR CNRS 5286, Cancer Research Center of Lyon (CRCL), 151 cours Albert Thomas, 69424, Lyon, France.,Italian Institute of Technology (IIT) - Center for Life Nanoscience (CLNS), Sapienza University, Viale Regina Elena, 291, 00161, Rome, Italy
| | - Apirat Chaikuad
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, D-60438, Frankfurt am Main, Germany
| | - Martin Schröder
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, D-60438, Frankfurt am Main, Germany
| | - Philippe Merle
- INSERM, U1052 UMR CNRS 5286, Cancer Research Center of Lyon (CRCL), 151 cours Albert Thomas, 69424, Lyon, France.,Department of Hepatology, Hôpital de la Croix Rousse, Hospices Civils de Lyon and Université Lyon I, 103 Grande Rue de la Croix-Rousse, 69004, Lyon, France
| | - Massimo Levrero
- INSERM, U1052 UMR CNRS 5286, Cancer Research Center of Lyon (CRCL), 151 cours Albert Thomas, 69424, Lyon, France. .,Italian Institute of Technology (IIT) - Center for Life Nanoscience (CLNS), Sapienza University, Viale Regina Elena, 291, 00161, Rome, Italy. .,Department of Hepatology, Hôpital de la Croix Rousse, Hospices Civils de Lyon and Université Lyon I, 103 Grande Rue de la Croix-Rousse, 69004, Lyon, France.
| | - Paul Dény
- INSERM, U1052 UMR CNRS 5286, Cancer Research Center of Lyon (CRCL), 151 cours Albert Thomas, 69424, Lyon, France. .,Laboratoire de Microbiologie Clinique, Groupe des Hôpitaux Universitaires de Paris - Seine Saint Denis, UFR Santé Médecine, Biologie Humaine, Université Paris 13, 125 Rue de Stalingrad, 93009, Bobigny, France.
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22
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Ifeorah IM, Faleye TOC, Bakarey AS, Adewumi OM, Gerber A, Le Gal F, Adeniji JA, Gordien E, Onyemelukwe NF. Characterization of hepatitis delta virus strains spreading in Abuja, Nigeria. J Med Virol 2019; 91:1688-1692. [PMID: 31081541 DOI: 10.1002/jmv.25503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/20/2019] [Accepted: 05/06/2019] [Indexed: 11/08/2022]
Abstract
Hepatitis delta virus (HDV) is responsible for the most severe form of liver disease in humans. So far, eight genotypes (HDV-1 to -8) have been individualized worldwide. Little is known about HDV strains that spread in Nigeria. HDV genotyping was performed in 15 anti-HDV positive samples from a cohort of 306 hepatitis B virus (HBV)-infected patients in Abuja (Nigeria). Phylogenetic analyses revealed 90% were HDV-1, two among them clustering with European/Asian HDV-1, the remaining one being HDV-6. It was also found that two members of a couple superinfected with the same HDV strain, were enveloped by two different HBV strains of genotype E.
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Affiliation(s)
- Ijeoma M Ifeorah
- Department of Medical Laboratory Sciences, Faculty of Health Science and Technology, College of Medicine, University of Nigeria Enugu Campus, Enugu, Nigeria
| | - Temitope O C Faleye
- Department of Microbiology, Faculty of Science, Ekiti State University, Ado Ekiti, Nigeria.,Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeleye S Bakarey
- Institute for Advanced Medical Research & Training, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olubusuyi M Adewumi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Athenais Gerber
- French National Reference Center for Hepatitis B, C, and Delta, Bobigny, France.,Laboratory of Clinical Microbiology, Avicenne Hospital, Bobigny, France
| | - Frédéric Le Gal
- French National Reference Center for Hepatitis B, C, and Delta, Bobigny, France.,Laboratory of Clinical Microbiology, Avicenne Hospital, Bobigny, France
| | - Johnson A Adeniji
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Emmanuel Gordien
- French National Reference Center for Hepatitis B, C, and Delta, Bobigny, France.,Laboratory of Clinical Microbiology, Avicenne Hospital, Bobigny, France
| | - Ngozi F Onyemelukwe
- Department of Medical Laboratory Sciences, Faculty of Health Science and Technology, College of Medicine, University of Nigeria Enugu Campus, Enugu, Nigeria
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23
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Holdt LM, Kohlmaier A, Teupser D. Circular RNAs as Therapeutic Agents and Targets. Front Physiol 2018; 9:1262. [PMID: 30356745 PMCID: PMC6189416 DOI: 10.3389/fphys.2018.01262] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/21/2018] [Indexed: 12/26/2022] Open
Abstract
It has recently been reported that thousands of covalently linked circular RNAs (circRNAs) are expressed from human genomes. circRNAs emerge during RNA splicing. circRNAs are circularized in a reaction termed "backsplicing," whereby the spliceosome fuses a splice donor site in a downstream exon to a splice acceptor site in an upstream exon. Although a young field of research, first studies indicate that backsplicing is not an erroneous reaction of the spliceosome. Instead, circRNAs are produced in cells with high cell-type specificity and can exert biologically meaningful and specific functions. These observations and the finding that circRNAs are stable against exonucleolytic decay are raising the question whether circRNAs may be relevant as therapeutic agents and targets. In this review, we start out with a short introduction into classification, biogenesis and general molecular mechanisms of circRNAs. We then describe reports, where manipulating circRNA abundance has been shown to have therapeutic value in animal disease models in vivo, with a focus on cardiovascular disease (CVD). Starting from existing approaches, we outline particular challenges and opportunities for future circRNA-based therapeutic approaches that exploit stability and molecular effector functions of native circRNAs. We end with considerations which designer functions could be engineered into artificial therapeutic circular RNAs.
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Affiliation(s)
| | | | - Daniel Teupser
- Institute of Laboratory Medicine, University Hospital, Ludwig Maximilian University of Munich (LMU), Munich, Germany
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24
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Le Gal F, Brichler S, Drugan T, Alloui C, Roulot D, Pawlotsky JM, Dény P, Gordien E. Genetic diversity and worldwide distribution of the deltavirus genus: A study of 2,152 clinical strains. Hepatology 2017; 66:1826-1841. [PMID: 28992360 DOI: 10.1002/hep.29574] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/29/2017] [Indexed: 12/12/2022]
Abstract
UNLABELLED Hepatitis delta virus (HDV) is responsible for the most severe form of acute and chronic viral hepatitis. We previously proposed that the Deltavirus genus is composed of eight major clades. However, few sequences were available to confirm this classification. Moreover, little is known about the structural and functional consequences of HDV variability. One practical consequence is the failure of most quantification assays to properly detect or quantify plasmatic HDV RNA. Between 2001 and 2014, 2,152 HDV strains were prospectively collected and genotyped in our reference laboratory by means of nucleotide sequencing and extensive phylogenetic analyses of a 400-nucleotide region of the genome (R0) from nucleotides 889 to 1289 encompassing the 3' end of the delta protein-coding gene. In addition, the full-length genome sequence was generated for 116 strains selected from the different clusters, allowing for in-depth characterization of the HDV genotypes and subgenotypes. This study confirms that the HDV genus is composed of eight genotypes (HDV-1 to HDV-8) defined by an intergenotype similarity >85% or >80%, according to the partial or full-length genome sequence, respectively. Furthermore, genotypes can be segregated into two to four subgenotypes, characterized by an intersubgenotype similarity >90% (>84% for HDV-1) over the whole genome sequence. Systematic analysis of genome and protein sequences revealed highly conserved functional nucleotide and amino acid motifs and positions across all (sub)genotypes, indicating strong conservatory constraints on the structure and function of the genome and the protein. CONCLUSION This study provides insight into the genetic diversity of HDV and a clear view of its geographical localization and allows speculation as to the worldwide spread of the virus, very likely from an initial African origin. (Hepatology 2017;66:1826-1841).
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Affiliation(s)
- Frédéric Le Gal
- Laboratoire de Microbiologie Clinique, Hôpitaux Universitaires de Paris Seine Saint-Denis, Site Avicenne, Université Sorbonne Paris Cité, Bobigny, France.,Centre national de référence des virus des hépatites B, C et Delta, Laboratoire de Virologie, Bobigny, France
| | - Ségolène Brichler
- Laboratoire de Microbiologie Clinique, Hôpitaux Universitaires de Paris Seine Saint-Denis, Site Avicenne, Université Sorbonne Paris Cité, Bobigny, France.,Centre national de référence des virus des hépatites B, C et Delta, Laboratoire de Virologie, Bobigny, France.,Unité INSERM U955, Equipe 18, Créteil, France
| | - Tudor Drugan
- Department of Medical Informatics and Biostatistics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Chakib Alloui
- Laboratoire de Microbiologie Clinique, Hôpitaux Universitaires de Paris Seine Saint-Denis, Site Avicenne, Université Sorbonne Paris Cité, Bobigny, France.,Centre national de référence des virus des hépatites B, C et Delta, Laboratoire de Virologie, Bobigny, France
| | - Dominique Roulot
- Centre national de référence des virus des hépatites B, C et Delta, Laboratoire de Virologie, Bobigny, France.,Unité d'Hépatologie, Hôpitaux Universitaires de Paris Seine Saint-Denis, Site Avicenne, Université Sorbonne Paris Cité, Bobigny, France
| | - Jean-Michel Pawlotsky
- Unité INSERM U955, Equipe 18, Créteil, France.,Centre national de référence des virus des hépatites B, C et Delta, Département de Virologie, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
| | - Paul Dény
- Laboratoire de Microbiologie Clinique, Hôpitaux Universitaires de Paris Seine Saint-Denis, Site Avicenne, Université Sorbonne Paris Cité, Bobigny, France.,Centre de Recherches en Cancérologie de Lyon, INSERM U1052, UMR CNRS 5286, Team Hepatocarcinogenesis and Viral Infection, Lyon, France
| | - Emmanuel Gordien
- Laboratoire de Microbiologie Clinique, Hôpitaux Universitaires de Paris Seine Saint-Denis, Site Avicenne, Université Sorbonne Paris Cité, Bobigny, France.,Centre national de référence des virus des hépatites B, C et Delta, Laboratoire de Virologie, Bobigny, France.,Unité INSERM U955, Equipe 18, Créteil, France
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25
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Solis-Moruno M, de Manuel M, Hernandez-Rodriguez J, Fontsere C, Gomara-Castaño A, Valsera-Naranjo C, Crailsheim D, Navarro A, Llorente M, Riera L, Feliu-Olleta O, Marques-Bonet T. Potential damaging mutation in LRP5 from genome sequencing of the first reported chimpanzee with the Chiari malformation. Sci Rep 2017; 7:15224. [PMID: 29123202 PMCID: PMC5680330 DOI: 10.1038/s41598-017-15544-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/30/2017] [Indexed: 12/29/2022] Open
Abstract
The genus Pan is the closest related to humans (Homo sapiens) and it includes two species: Pan troglodytes (chimpanzees) and Pan paniscus (bonobos). Different characteristics, some of biomedical aspect, separate them from us. For instance, some common human medical conditions are rare in chimpanzees (menopause, Alzheimer disease) although it is unclear to which extent longevity plays an active role in these differences. However, both humans and chimpanzees present similar pathologies, thus, understanding traits in chimpanzees can help unravel the molecular basis of human conditions. Here, we sequenced the genome of Nico, a central chimpanzee diagnosed with a particular biomedical condition, the Chiari malformation. We performed a variant calling analysis comparing his genome to 25 whole genomes from healthy individuals (bonobos and chimpanzees), and after predicting the effects of the genetic variants, we looked for genes within the OMIM database. We found a novel, private, predicted as damaging mutation in Nico in LRP5, a gene related to bone density alteration pathologies, and we suggest a link between this mutation and his Chiari malformation as previously shown in humans. Our results reinforce the idea that a comparison between humans and chimpanzees can be established in this genetic frame of common diseases.
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Affiliation(s)
- Manuel Solis-Moruno
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain.
| | - Marc de Manuel
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Claudia Fontsere
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Alba Gomara-Castaño
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | | | - Dietmar Crailsheim
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Arcadi Navarro
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, Barcelona, 08010, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona, 08028, Spain
| | - Miquel Llorente
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Laura Riera
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Olga Feliu-Olleta
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain.
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, Barcelona, 08010, Spain.
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona, 08028, Spain.
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26
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Moelling K, Broecker F, Russo G, Sunagawa S. RNase H As Gene Modifier, Driver of Evolution and Antiviral Defense. Front Microbiol 2017; 8:1745. [PMID: 28959243 PMCID: PMC5603734 DOI: 10.3389/fmicb.2017.01745] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 08/28/2017] [Indexed: 12/21/2022] Open
Abstract
Retroviral infections are 'mini-symbiotic' events supplying recipient cells with sequences for viral replication, including the reverse transcriptase (RT) and ribonuclease H (RNase H). These proteins and other viral or cellular sequences can provide novel cellular functions including immune defense mechanisms. Their high error rate renders RT-RNases H drivers of evolutionary innovation. Integrated retroviruses and the related transposable elements (TEs) have existed for at least 150 million years, constitute up to 80% of eukaryotic genomes and are also present in prokaryotes. Endogenous retroviruses regulate host genes, have provided novel genes including the syncytins that mediate maternal-fetal immune tolerance and can be experimentally rendered infectious again. The RT and the RNase H are among the most ancient and abundant protein folds. RNases H may have evolved from ribozymes, related to viroids, early in the RNA world, forming ribosomes, RNA replicases and polymerases. Basic RNA-binding peptides enhance ribozyme catalysis. RT and ribozymes or RNases H are present today in bacterial group II introns, the precedents of TEs. Thousands of unique RTs and RNases H are present in eukaryotes, bacteria, and viruses. These enzymes mediate viral and cellular replication and antiviral defense in eukaryotes and prokaryotes, splicing, R-loop resolvation, DNA repair. RNase H-like activities are also required for the activity of small regulatory RNAs. The retroviral replication components share striking similarities with the RNA-induced silencing complex (RISC), the prokaryotic CRISPR-Cas machinery, eukaryotic V(D)J recombination and interferon systems. Viruses supply antiviral defense tools to cellular organisms. TEs are the evolutionary origin of siRNA and miRNA genes that, through RISC, counteract detrimental activities of TEs and chromosomal instability. Moreover, piRNAs, implicated in transgenerational inheritance, suppress TEs in germ cells. Thus, virtually all known immune defense mechanisms against viruses, phages, TEs, and extracellular pathogens require RNase H-like enzymes. Analogous to the prokaryotic CRISPR-Cas anti-phage defense possibly originating from TEs termed casposons, endogenized retroviruses ERVs and amplified TEs can be regarded as related forms of inheritable immunity in eukaryotes. This survey suggests that RNase H-like activities of retroviruses, TEs, and phages, have built up innate and adaptive immune systems throughout all domains of life.
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Affiliation(s)
- Karin Moelling
- Institute of Medical Microbiology, University of ZurichZurich, Switzerland
- Max Planck Institute for Molecular GeneticsBerlin, Germany
| | - Felix Broecker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New YorkNY, United States
| | - Giancarlo Russo
- Functional Genomics Center Zurich, ETH Zurich/University of ZurichZurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology, ETH ZurichZurich, Switzerland
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27
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Botelho-Souza LF, Vasconcelos MPA, Dos Santos ADO, Salcedo JMV, Vieira DS. Hepatitis delta: virological and clinical aspects. Virol J 2017; 14:177. [PMID: 28903779 PMCID: PMC5597996 DOI: 10.1186/s12985-017-0845-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/05/2017] [Indexed: 02/06/2023] Open
Abstract
There are an estimated 400 million chronic carriers of HBV worldwide; between 15 and 20 million have serological evidence of exposure to HDV. Traditionally, regions with high rates of endemicity are central and northern Africa, the Amazon Basin, eastern Europe and the Mediterranean, the Middle East and parts of Asia. There are two types of HDV/HBV infection which are differentiated by the previous status infection by HBV for the individual. Individuals with acute HBV infection contaminated by HDV is an HDV/HBV co-infection, while individuals with chronic HBV infection contaminated by HDV represent an HDV/HBV super-infection. The appropriate treatment for chronic hepatitis delta is still widely discussed since it does not have an effective drug. Alpha interferon is currently the only licensed therapy for the treatment of chronic hepatitis D. The most widely used drug is pegylated interferon but only approximately 25% of patients maintain a sustained viral response after 1 year of treatment. The best marker of therapeutic success would be the clearance of HBsAg, but this data is rare in clinical practice. Therefore, the best way to predict a sustained virologic response is the maintenance of undetectable HDV RNA levels.
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Affiliation(s)
- Luan Felipo Botelho-Souza
- Laboratório de Virologia Molecular - FIOCRUZ - RONDÔNIA, Rua da Beira, 7671 - BR 364, Km 3,5 Bairro Lagoa, CEP: 76812, Porto Velho, RO, CEP: 76812-329, Brazil.
- Ambulatório de Hepatites Virais, Fundação Oswaldo Cruz Rondônia e Centro de Pesquisa em Medicina Tropical - CEPEM, Avenida Guaporé, 215, anexo Hospital CEMETRON, Agenor M de Carvalho, Porto Velho, RO, CEP: 76812-329, Brazil.
- Programa de Pós-Graduação em Biologia Experimental - PGBioExp, Rodovia Br-364, KM 9, CAMPUS UNIR, Porto Velho, RO, CEP: 76801-974, Brazil.
| | | | - Alcione de Oliveira Dos Santos
- Laboratório de Virologia Molecular - FIOCRUZ - RONDÔNIA, Rua da Beira, 7671 - BR 364, Km 3,5 Bairro Lagoa, CEP: 76812, Porto Velho, RO, CEP: 76812-329, Brazil
- Ambulatório de Hepatites Virais, Fundação Oswaldo Cruz Rondônia e Centro de Pesquisa em Medicina Tropical - CEPEM, Avenida Guaporé, 215, anexo Hospital CEMETRON, Agenor M de Carvalho, Porto Velho, RO, CEP: 76812-329, Brazil
- Programa de Pós-Graduação em Biologia Experimental - PGBioExp, Rodovia Br-364, KM 9, CAMPUS UNIR, Porto Velho, RO, CEP: 76801-974, Brazil
| | - Juan Miguel Villalobos Salcedo
- Laboratório de Virologia Molecular - FIOCRUZ - RONDÔNIA, Rua da Beira, 7671 - BR 364, Km 3,5 Bairro Lagoa, CEP: 76812, Porto Velho, RO, CEP: 76812-329, Brazil
- Ambulatório de Hepatites Virais, Fundação Oswaldo Cruz Rondônia e Centro de Pesquisa em Medicina Tropical - CEPEM, Avenida Guaporé, 215, anexo Hospital CEMETRON, Agenor M de Carvalho, Porto Velho, RO, CEP: 76812-329, Brazil
- Programa de Pós-Graduação em Biologia Experimental - PGBioExp, Rodovia Br-364, KM 9, CAMPUS UNIR, Porto Velho, RO, CEP: 76801-974, Brazil
| | - Deusilene Souza Vieira
- Laboratório de Virologia Molecular - FIOCRUZ - RONDÔNIA, Rua da Beira, 7671 - BR 364, Km 3,5 Bairro Lagoa, CEP: 76812, Porto Velho, RO, CEP: 76812-329, Brazil
- Ambulatório de Hepatites Virais, Fundação Oswaldo Cruz Rondônia e Centro de Pesquisa em Medicina Tropical - CEPEM, Avenida Guaporé, 215, anexo Hospital CEMETRON, Agenor M de Carvalho, Porto Velho, RO, CEP: 76812-329, Brazil
- Programa de Pós-Graduação em Biologia Experimental - PGBioExp, Rodovia Br-364, KM 9, CAMPUS UNIR, Porto Velho, RO, CEP: 76801-974, Brazil
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28
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Chao M, Wang TC, Lin CC, Yung-Liang Wang R, Lin WB, Lee SE, Cheng YY, Yeh CT, Iang SB. Analyses of a whole-genome inter-clade recombination map of hepatitis delta virus suggest a host polymerase-driven and viral RNA structure-promoted template-switching mechanism for viral RNA recombination. Oncotarget 2017; 8:60841-60859. [PMID: 28977829 PMCID: PMC5617389 DOI: 10.18632/oncotarget.18339] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 05/22/2017] [Indexed: 01/05/2023] Open
Abstract
The genome of hepatitis delta virus (HDV) is a 1.7-kb single-stranded circular RNA that folds into an unbranched rod-like structure and has ribozyme activity. HDV redirects host RNA polymerase(s) (RNAP) to perform viral RNA-directed RNA transcription. RNA recombination is known to contribute to the genetic heterogeneity of HDV, but its molecular mechanism is poorly understood. Here, we established a whole-genome HDV-1/HDV-4 recombination map using two cloned sequences coexisting in cultured cells. Our functional analyses of the resulting chimeric delta antigens (the only viral-encoded protein) and recombinant genomes provide insights into how recombination promotes the genotypic and phenotypic diversity of HDV. Our examination of crossover distribution and subsequent mutagenesis analyses demonstrated that ribozyme activity on HDV genome, which is required for viral replication, also contributes to the generation of an inter-clade junction. These data provide circumstantial evidence supporting our contention that HDV RNA recombination occurs via a replication-dependent mechanism. Furthermore, we identify an intrinsic asymmetric bulge on the HDV genome, which appears to promote recombination events in the vicinity. We therefore propose a mammalian RNAP-driven and viral-RNA-structure-promoted template-switching mechanism for HDV genetic recombination. The present findings improve our understanding of the capacities of the host RNAP beyond typical DNA-directed transcription.
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Affiliation(s)
- Mei Chao
- Department of Microbiology and Immunology, Chang Gung University, Guishan, Taoyang, Taiwan.,Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan.,Department of Hepato-Gastroenterology, Liver Research Center, Chang Gung Memorial Hospital, Guishan, Taoyang, Taiwan
| | - Tzu-Chi Wang
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan
| | - Chia-Chi Lin
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan
| | - Robert Yung-Liang Wang
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan.,Department of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan
| | - Wen-Bin Lin
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan
| | - Shang-En Lee
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan
| | - Ying-Yu Cheng
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan
| | - Chau-Ting Yeh
- Department of Hepato-Gastroenterology, Liver Research Center, Chang Gung Memorial Hospital, Guishan, Taoyang, Taiwan
| | - Shan-Bei Iang
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan
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29
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Le Gal F, Brichler S, Sahli R, Chevret S, Gordien E. First international external quality assessment for hepatitis delta virus RNA quantification in plasma. Hepatology 2016; 64:1483-1494. [PMID: 27530084 DOI: 10.1002/hep.28772] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/16/2016] [Indexed: 12/11/2022]
Abstract
UNLABELLED Infection by the hepatitis delta virus (HDV), a satellite of the hepatitis B virus (HBV), increases viral liver disease severity. Its diagnosis is thus vital for HBV-infected patients. HDV-RNA load (HDVL) should be assessed and monitored in plasma using real-time reverse-transcriptase polymerase chain reaction assays. Taking advantage of the recently-developed World Health Organization (WHO) HDV international standard (WHO-HDV-IS), the first international external quality control for HDVL quantification was performed. Two panels of samples were sent to 28 laboratories in 17 countries worldwide. Panel A comprised 20 clinical samples of various genotypes (1, 2, and 5-8) and viral loads, including two negative controls. Panel B, composed of dilutions of the WHO-HDV-IS, allowed the conversion of results from copies/mL into IU/mL for HDVL standardization and interlaboratory comparisons. Comprehensive analysis revealed a very high heterogeneity of assay characteristics, including their technical steps and technologies. Thirteen labs (46.3%) properly quantified all 18 positive samples; 16 (57.1%) failed to detect one to up to 10 samples, and several others underestimated (>3 log IU/mL) HDVL of African genotype strains (1 and 5-8). Discrepancies were mainly attributed to either primers or probe mismatches related to the high genetic variability of HDV and, possibly, to the complex secondary structure of the target genomic RNA. The labs were grouped in four clusters by the statistical analysis of their performances. The best clusters comprised the 17 labs that obtained the expected HDVL values, including five that otherwise failed to quantify one or two samples. CONCLUSION The results of this international quality-control study underline the urgent need to improve methods used to monitor HDV viremia and will be instrumental in achieving that goal. (Hepatology 2016;64:1483-1494).
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Affiliation(s)
- Frédéric Le Gal
- Laboratory of Bacteriology, Virology and Hygiene, University Hospitals of Paris Seine-Saint-Denis, Avicenne site.,French National Reference Laboratory for hepatitis delta virus, associated to the National Reference Center for Viral Hepatitis B, C and Delta in France
| | - Ségolène Brichler
- Laboratory of Bacteriology, Virology and Hygiene, University Hospitals of Paris Seine-Saint-Denis, Avicenne site.,French National Reference Laboratory for hepatitis delta virus, associated to the National Reference Center for Viral Hepatitis B, C and Delta in France.,INSERM U955, Team 18, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - Roland Sahli
- Institute of Microbiology, Lausanne University Hospital (CHUV), and University of Lausanne, Lausanne, Switzerland
| | - Sylvie Chevret
- Biostatistic Department and Medical Informatics, Saint-Louis Hospital, Paris VII University, Paris, France. .,Biostatistics Department, and Clinical Epidemiology, Saint-Louis Hospital, Paris VII University, Paris, France.
| | - Emmanuel Gordien
- Laboratory of Bacteriology, Virology and Hygiene, University Hospitals of Paris Seine-Saint-Denis, Avicenne site. .,French National Reference Laboratory for hepatitis delta virus, associated to the National Reference Center for Viral Hepatitis B, C and Delta in France. .,INSERM U955, Team 18, Institut Mondor de Recherche Biomédicale, Créteil, France.
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30
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Wranke A, Wedemeyer H. Antiviral therapy of hepatitis delta virus infection - progress and challenges towards cure. Curr Opin Virol 2016; 20:112-118. [PMID: 27792905 DOI: 10.1016/j.coviro.2016.10.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 10/03/2016] [Accepted: 10/10/2016] [Indexed: 12/14/2022]
Abstract
Hepatitis B-/D-virus co-infection causes the most severe form of viral hepatitis, frequently leading to liver cirrhosis, hepatic decompensation and consecutive liver-related mortality. Treatment options for hepatitis delta are limited. The only recommended therapy is pegylated interferon alpha which leads to virological responses in about 25-30% of patients. However, interferon therapy is associated with frequent side-effects and late HDV RNA relapses have been described during long-term follow even in patients who were HDV RNA negative 24 weeks after the end of therapy. Thus, alternative treatment options are urgently needed. Clinical studies have been performed exploring prenylation inhibitors, viral entry inhibitors and nucleic acid polymers to block particle release. We here summarize the progress and challenges towards cure of HDV infection.
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Affiliation(s)
- Anika Wranke
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Heiner Wedemeyer
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; German Center for Infection Research (DZIF), Partner Side HepNet Study-House, Hannover, Germany; HepNet Study-House, Hannover, Germany; Integrated Research and Treatment Center Transplantation, Hannover Medical School, Germany.
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31
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Lempp FA, Ni Y, Urban S. Hepatitis delta virus: insights into a peculiar pathogen and novel treatment options. Nat Rev Gastroenterol Hepatol 2016; 13:580-9. [PMID: 27534692 DOI: 10.1038/nrgastro.2016.126] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chronic hepatitis D is the most severe form of viral hepatitis, affecting ∼20 million HBV-infected people worldwide. The causative agent, hepatitis delta virus (HDV), is a unique human pathogen: it is the smallest known virus; it depends on HBV to disseminate its viroid-like RNA; it encodes only one protein (HDAg), which has both structural and regulatory functions; and it replicates using predominantly host proteins. The failure of HBV-specific nucleoside analogues to suppress the HBV helper function, and the limitations of experimental systems to study the HDV life cycle, have impeded the development of HDV-specific drugs. Thus, the only clinical regimen for HDV is IFNα, which shows some efficacy but long-term virological responses are rare. Insights into the receptor-mediated entry of HDV, and the observation that HDV assembly requires farnesyltransferase, have enabled novel therapeutic strategies to be developed. Interference with entry, for example through blockade of the HBV-HDV-specific receptor sodium/taurocholate cotransporting polypeptide NTCP by Myrcludex B, and inhibition of assembly by blockade of farnesyltransferase using lonafarnib or nucleic acid polymers such as REP 2139-Ca, have shown promising results in phase II studies. In this Review, we summarize our knowledge of HDV epidemiology, pathogenesis and molecular biology, with a particular emphasis on possible future developments.
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Affiliation(s)
- Florian A Lempp
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Yi Ni
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.,German Center for Infection Research (DZIF), Heidelberg Partner Site, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.,German Center for Infection Research (DZIF), Heidelberg Partner Site, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
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32
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New antiviral targets for innovative treatment concepts for hepatitis B virus and hepatitis delta virus. J Hepatol 2016; 64:S117-S131. [PMID: 27084032 DOI: 10.1016/j.jhep.2016.02.016] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/06/2016] [Accepted: 02/08/2016] [Indexed: 02/07/2023]
Abstract
Current therapies of chronic hepatitis B (CHB) remain limited to pegylated-interferon-alpha (PegIFN-α) or any of the five approved nucleos(t)ide analogues (NUC) treatments. While viral suppression can be achieved in the majority of patients with the high-barrier-to-resistance new-generation of NUC, i.e. entecavir and tenofovir, HBsAg loss is achieved by PegIFN-α and/or NUC in only 10% of patients, after a 5-year follow-up. Attempts to improve the response by administering two different NUC or a combination of NUC and PegIFN-α have not provided a dramatic increase in the rate of functional cure. Because of this and the need of long-term NUC administration, there is a renewed interest regarding the understanding of various steps of the HBV replication cycle, as well as specific virus-host cell interactions, in order to define new targets and develop new antiviral drugs. This includes a direct inhibition of viral replication with entry inhibitors, drugs targeting cccDNA, siRNA targeting viral transcripts, capsid assembly modulators, and approaches targeting the secretion of viral envelope proteins. Restoration of immune responses is a complementary approach. The restoration of innate immunity against HBV can be achieved, with TLR agonists or specific antiviral cytokine delivery. Restoration of adaptive immunity may be achieved with inhibitors of negative checkpoint regulators, therapeutic vaccines, or autologous transfer of engineered HBV-specific T cells. Novel targets and compounds will readily be evaluated using both relevant and novel in vitro and in vivo models of HBV infection. The addition of one or several new drugs to current therapies should offer the prospect of a markedly improved response to treatments and an increased rate of functional cure. This should lead to a reduced risk of antiviral drug resistance, and to a decreased incidence of cirrhosis and hepatocellular carcinoma (HCC).
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33
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Flores R, Owens RA, Taylor J. Pathogenesis by subviral agents: viroids and hepatitis delta virus. Curr Opin Virol 2016; 17:87-94. [PMID: 26897654 DOI: 10.1016/j.coviro.2016.01.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 01/21/2016] [Accepted: 01/29/2016] [Indexed: 12/18/2022]
Abstract
The viroids of plants are the simplest known infectious genetic elements. They have RNA genomes of up to 400 nucleotides in length and no protein encoding capacity. Hepatitis delta virus (HDV), an infectious agent found only in humans co-infected with hepatitis B virus (HBV), is just slightly more complex, with an RNA genome of about 1700 nucleotides, and the ability to express just one small protein. Viroid and HDV RNAs share several features that include circular structure, compact folding, and replication via a rolling-circle mechanism. Both agents were detected because of their obvious pathogenic effects. Their simplicity demands a greater need than conventional RNA or DNA viruses to redirect host components for facilitating their infectious cycle, a need that directly and indirectly incites pathogenic effects. The mechanisms by which these pathogenic effects are produced are the topic of this review. In this context, RNA silencing mediates certain aspects of viroid pathogenesis.
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Affiliation(s)
- Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Valencia 46022, Spain.
| | - Robert A Owens
- Molecular Plant Pathology Laboratory, USDA-ARS, Beltsville, MD 20705, USA.
| | - John Taylor
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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34
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Hepatitis B Virus and Hepatitis D Virus Entry, Species Specificity, and Tissue Tropism. Cold Spring Harb Perspect Med 2015; 5:a021378. [PMID: 26238794 DOI: 10.1101/cshperspect.a021378] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Entry of hepatitis B (HBV) and hepatitis D viruses (HDV) into a host cell represents the initial step of infection. This process requires multiple steps, including the low-affinity attachment of the virus to the cell surface, followed by high-affinity attachment to specific receptor(s), and subsequent endocytosis-mediated internalization. Within the viral envelope, the preS1 region is involved in receptor binding. Recently, sodium taurocholate cotransporting polypeptide (NTCP) has been identified as an entry receptor of HBV and HDV by affinity purification using a preS1 peptide. NTCP is mainly or exclusively expressed in the liver, and this membrane protein is at least one of the factors determining the narrow species specificity and hepatotropism of HBV and HDV. However, there are likely other factors that mediate the species and tissue tropism of HBV. This review summarizes the current understanding of the mechanisms of HBV/HDV entry.
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35
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Abstract
Hepatitis D is caused by the hepatitis D virus (HDV), a unique RNA pathogen that requires the hepatitis B surface antigen (HBsAg) to infect. Hepatitis D is transmitted by the parenteral route. The main susceptible group is patients with chronic HBsAg infection who become superinfected with the virus. Hepatitis D occurs throughout the globe, but control of hepatitis B virus (HBV) in the last two decades has consistently diminished the circulation of HDV in industrialized countries. However, hepatitis D remains a medical issue for injecting drug users (IDUs), as well as immigrants from endemic HDV areas, who are reintroducing the infection in Europe.
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Affiliation(s)
- Mario Rizzetto
- Division of Gastroenterology, University of Torino, 10126 Torino, Italy
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