1
|
Ding Y, Guo H, Hong X, Li Q, Miao Z, Pan Q, Zheng K, Wang W. The distinct spatiotemporal evolutionary landscape of HBV and HDV largely determines the unique epidemic features of HDV globally. Mol Phylogenet Evol 2024; 197:108114. [PMID: 38825156 DOI: 10.1016/j.ympev.2024.108114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 05/07/2024] [Accepted: 05/26/2024] [Indexed: 06/04/2024]
Abstract
Chronic infection of hepatitis B virus (HBV) and hepatitis D virus (HDV) causes the most severe form of viral hepatitis. Due to the dependence on HBV, HDV was deemed to co-evolve and co-migrate with HBV. However, we previously found that the naturally occurred HDV/HBV combinations do not always reflect the most efficient virological adaptation (Wang et al., 2021). Moreover, regions with heavy HBV burden do not always correlate with high HDV prevalence (e.g., East Asia), and vice versa (e.g., Central Asia). Herein, we systematically elucidated the spatiotemporal evolutionary landscape of HDV to understand the unique epidemic features of HDV. We found that the MRCA of HDV was from South America around the late 13th century, was globally dispersed mainly via Central Asia, and evolved into eight genotypes from the 19th to 20th century. In contrast, the MRCA of HBV was from Europe ∼23.7 thousand years ago (Kya), globally dispersed mainly via Africa and East Asia, and evolved into eight genotypes ∼1100 years ago. When HDV stepped in, all present-day HBV genotypes had already formed and its global genotypic distribution had stayed stable geographically. Nevertheless, regionalized HDV adapted to local HBV genotypes and human lineages, contributing to the global geographical separation of HDV genotypes. Additionally, a sharp increase in HDV infections was observed after the 20th century. In conclusion, HDV exhibited a distinct spatiotemporal distribution path compared with HBV. This unique evolutionary relationship largely fostered the unique epidemic features we observe nowadays. Moreover, HDV infections may continue to ramp up globally, thus more efforts are urgently needed to combat this disease.
Collapse
Affiliation(s)
- Yibo Ding
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China
| | - Hongbo Guo
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.
| | - Xinfang Hong
- Second Medical Center of PLA General Hospital, Beijing, China
| | - Qiudi Li
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China
| | - Zhijiang Miao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands.
| | - Kuiyang Zheng
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.
| | - Wenshi Wang
- Department of Pathogen Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Jiangsu International Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.
| |
Collapse
|
2
|
Brázda V, Valková N, Dobrovolná M, Mergny JL. Abundance of G-Quadruplex Forming Sequences in the Hepatitis Delta Virus Genomes. ACS OMEGA 2024; 9:4096-4101. [PMID: 38284014 PMCID: PMC10809645 DOI: 10.1021/acsomega.3c09288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/30/2024]
Abstract
Hepatitis delta virus (HDV) is a highly unusual RNA satellite virus that depends on the presence of hepatitis B virus (HBV) to be infectious. Its compact and variable single-stranded RNA genome consists of eight major genotypes distributed unevenly across different continents. The significance of noncanonical secondary structures such as G-quadruplexes (G4s) is increasingly recognized at the DNA and RNA levels, particularly for transcription, replication, and translation. G4s are formed from guanine-rich sequences and have been identified in the vast majority of viral, eukaryotic, and prokaryotic genomes. In this study, we analyzed the G4 propensity of HDV genomes by using G4Hunter. Unlike HBV, which has a G4 density similar to that of the human genome, HDV displays a significantly higher number of potential quadruplex-forming sequences (PQS), with a density more than four times greater than that of the human genome. This finding suggests a critical role for G4s in HDV, especially given that the PQS regions are conserved across HDV genotypes. Furthermore, the prevalence of G4-forming sequences may represent a promising target for therapeutic interventions to control HDV replication.
Collapse
Affiliation(s)
- Václav Brázda
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 621 00, Czech Republic
- Faculty
of Chemistry, Brno University of Technology, Purkyňova 118, Brno 61200, Czech Republic
| | - Natália Valková
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 621 00, Czech Republic
| | - Michaela Dobrovolná
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 621 00, Czech Republic
- Faculty
of Chemistry, Brno University of Technology, Purkyňova 118, Brno 61200, Czech Republic
| | - Jean-Louis Mergny
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 621 00, Czech Republic
- Laboratoire
d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau 91120, France
| |
Collapse
|
3
|
Tian Y, Fan Z, Zhang X, Xu L, Cao Y, Pan Z, Mo Y, Gao Y, Zheng S, Huang J, Zou H, Duan Z, Li H, Ren F. CRISPR/Cas13a-Assisted accurate and portable hepatitis D virus RNA detection. Emerg Microbes Infect 2023; 12:2276337. [PMID: 37882492 PMCID: PMC10796118 DOI: 10.1080/22221751.2023.2276337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/23/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND & AIMS Hepatitis delta virus (HDV) infection accelerates the progression of chronic hepatitis B virus (HBV) infection, posing a large economic and health burden to patients. At present, there remains a lack of accurate and portable detection methods for HDV RNA. Here, we aim to establish a convenient, rapid, highly sensitive and specific method to detect HDV RNA using CRISPR-Cas13a technology. METHODS We established fluorescence (F) and lateral flow strip (L) assays based on CRISPR-Cas13a combined with RT-PCR and RT-RAA for HDV RNA detection, respectively. we conducted a cohort study of 144 patients with HDV-IgG positive to evaluate the CRISPR-Cas13a diagnostic performance for identifying HDV in clinical samples, compared to RT-qPCR and RT-ddPCR. RESULTS For synthetic HDV RNA plasmids, the sensitivity of RT-PCR-CRISPR-based fluorescence assays was 1 copy/μL, higher than that of RT-qPCR (10 copies/μL) and RT-ddPCR (10 copies/μL); for HDV RNA-positive samples, the sensitivity of RT-RAA-CRISPR-based fluorescence and lateral flow strip assays was 10 copies/μL, as low as that of RT-qPCR and RT-ddPCR, and the assay took only approximately 85 min. Additionally, the positivity rates of anti-HDV IgG-positive samples detected by the RT-qPCR, RT-ddPCR, RT-PCR-CRISPR fluorescence and RT-RAA-CRISPR lateral flow strip methods were 66.7% (96/144), 76.4% (110/144), 81.9% (118/144), and 72.2% (104/144), respectively. CONCLUSIONS We developed a highly sensitive and specific, as well as a portable and easy CRISPR-based assay for the detection of HDV RNA, which could be a prospective measure for monitoring the development of HDV infection and evaluating the therapeutic effect.
Collapse
Affiliation(s)
- Yuan Tian
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Zihao Fan
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Xiangying Zhang
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Ling Xu
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Yaling Cao
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Zhenzhen Pan
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Yinkang Mo
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Yao Gao
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Sujun Zheng
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Jing Huang
- Department of Infection Control, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Huaibin Zou
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Zhongping Duan
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Hao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Feng Ren
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| |
Collapse
|
4
|
Umukoro E, Alukal JJ, Pak K, Gutierrez J. State of the Art: Test all for Anti-Hepatitis D Virus and Reflex to Hepatitis D Virus RNA Polymerase Chain Reaction Quantification. Clin Liver Dis 2023; 27:937-954. [PMID: 37778778 DOI: 10.1016/j.cld.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Diagnosis of HDV exposure is based on clinical assays of anti-hepatitis D antibody and current infection with hepatitis D RNA PCR. The role of hepatitis D antigen testing is not yet defined. RT-qPCR is the gold standard for measuring HDV RNA viral load, which is used to assess response to the treatment of HDV infection. Gaps in testing include poor sensitivity of antigen testing and quantitative HDV RNA accuracy can be affected by the genotypic variability of the virus and variation in laboratory techniques. There is also a limitation in HDV testing due to access, cost, and limited knowledge of testing indications. Droplet digital PCR promises to be a more accurate method to quantify HDV RNA. Also, the recent development of a rapid HDV detection test could prove useful in resource-limited areas.
Collapse
Affiliation(s)
| | - Joseph J Alukal
- University of California, School of Medicine, 3390 University Avenue, Riverside, CA 92501, USA
| | - Kevin Pak
- Naval Medical Center, 34800 Bob Wilson Drive, San Diego, CA 92134, USA
| | - Julio Gutierrez
- Center for Organ Transplant, Scripps Clinic, Scripps MD Anderson Center, Scripps Green Hospital, 10666 N. Torrey Pines Road (N-200), La Jolla, CA 92037, USA.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Nemteanu R, Clim A, Hincu CE, Gheorghe L, Ciortescu I, Plesa A. Interferon-Free Regimens and Direct-Acting Antiviral Agents for Delta Hepatitis: Are We There Yet? Curr Issues Mol Biol 2023; 45:7878-7890. [PMID: 37886941 PMCID: PMC10605217 DOI: 10.3390/cimb45100498] [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: 09/07/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Chronic delta hepatitis is a global health problem. Although a smaller percentage of chronic HBV-infected patients are coinfected with the hepatitis delta virus, these patients have a higher risk of an accelerated progression to fulminant "delta hepatitis", cirrhosis, hepatic decompensation, and hepatocellular carcinoma, putting a financial strain on the healthcare system and increasing the need for a liver transplant. Since its discovery, tremendous efforts have been directed toward understanding the intricate pathogenic mechanisms, discovering the complex viral replication process, the essential replicative intermediates, and cell division-mediated viral spread, which enables virion viability. The consideration of the interaction between HBV and HDV is crucial in the process of developing novel pharmaceuticals. Until just recently, interferon-based therapy was the only treatment available worldwide. This review aims to present the recent advancements in understanding the life cycle of HDV, which have consequently facilitated the development of innovative drug classes. Additionally, we will examine the antiviral strategies currently in phases II and III of development, including bulevirtide (an entry inhibitor), lonafarnib (a prenylation inhibitor), and REP 2139 (an HBsAg release inhibitor).
Collapse
Affiliation(s)
- Roxana Nemteanu
- Medical I Department, Grigore T. Popa University of Medicine and Pharmacy, 700100 Iasi, Romania; (A.C.); (L.G.); (A.P.)
- Institute of Gastroenterology and Hepatology, “Sfantul. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Andreea Clim
- Medical I Department, Grigore T. Popa University of Medicine and Pharmacy, 700100 Iasi, Romania; (A.C.); (L.G.); (A.P.)
| | - Corina Elena Hincu
- Department of Radiology, “Sfantul Spiridon” Hospital, 700111 Iasi, Romania;
| | - Liliana Gheorghe
- Medical I Department, Grigore T. Popa University of Medicine and Pharmacy, 700100 Iasi, Romania; (A.C.); (L.G.); (A.P.)
- Department of Radiology, “Sfantul Spiridon” Hospital, 700111 Iasi, Romania;
| | - Irina Ciortescu
- Medical I Department, Grigore T. Popa University of Medicine and Pharmacy, 700100 Iasi, Romania; (A.C.); (L.G.); (A.P.)
- Institute of Gastroenterology and Hepatology, “Sfantul. Spiridon” University Hospital, 700111 Iasi, Romania
| | - Alina Plesa
- Medical I Department, Grigore T. Popa University of Medicine and Pharmacy, 700100 Iasi, Romania; (A.C.); (L.G.); (A.P.)
- Institute of Gastroenterology and Hepatology, “Sfantul. Spiridon” University Hospital, 700111 Iasi, Romania
| |
Collapse
|
7
|
Salichos L, Minosse C, Visco-Comandini U, Taibi C, Zulian V, D’Offizi G, Pallothu N, McPhee F, Garbuglia AR. Phylogenetic and Phylodynamic Analysis of Delta Strains Circulating in Italy. Viruses 2023; 15:1791. [PMID: 37766200 PMCID: PMC10537423 DOI: 10.3390/v15091791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
The hepatitis delta virus (HDV) exhibits high genetic and evolutionary variability and is classified into eight genotypes (HDV-1 to -8). HDV-1 is the most widespread genotype worldwide and includes several subtypes. It predominates mainly in Europe, the Middle East, North America, and Northern Africa, and is associated with both severe and mild forms of liver disease. In this study, we performed phylogenetic and phylodynamic analyses of HDV strains circulating in Regione Lazio, Italy, to understand when these strains were introduced into the Lazio region and to define their genetic variability in Italy. Fifty HDV RNA positive patient samples were amplified using a nested RT-PCR approach targeting the HDV R0 region and sequenced. A phylogenetic tree of patient-derived sequences and reference sequences representing HDV-1 to -8 was constructed using the GTRGAMMA model in RAxML v8. The results indicated that HDV-1 was the predominant genotype with HDV-1d being the most frequently inferred subtype. HDV-1 sequences clustering with subtypes 1b and 1e were also identified. A phylodynamic analysis of HDV-1 sequences employing a Bayesian birth-death model inferred a clock rate of 3.04 × 10-4 substitutions per site per million years, with a 95% Highest Posterior Density (HPD) interval of 3.45 × 10-5 to 5.72 × 10-4. A Bayesian birth-death analysis with tree calibration based on a sample dating approach indicated multiple original sources of infection (from the late 1950s to late 1980s). Overall, these results suggest that HDV sequences from the native Italian and non-Italian patients analyzed in this study represent multiple lineages introduced across a wide period. A common ancestral origin should be excluded.
Collapse
Affiliation(s)
- Leonidas Salichos
- Biological and Chemical Sciences, New York Institute of Technology, Manhattan, NY 10023, USA; (L.S.); (N.P.)
| | - Claudia Minosse
- Virology Laboratory, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (C.M.); (V.Z.)
| | - Ubaldo Visco-Comandini
- Infectious Diseases and Hepatology Unit, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (U.V.-C.); (C.T.); (G.D.)
| | - Chiara Taibi
- Infectious Diseases and Hepatology Unit, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (U.V.-C.); (C.T.); (G.D.)
| | - Verdiana Zulian
- Virology Laboratory, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (C.M.); (V.Z.)
| | - Gianpiero D’Offizi
- Infectious Diseases and Hepatology Unit, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (U.V.-C.); (C.T.); (G.D.)
| | - Nayan Pallothu
- Biological and Chemical Sciences, New York Institute of Technology, Manhattan, NY 10023, USA; (L.S.); (N.P.)
| | | | - Anna Rosa Garbuglia
- Virology Laboratory, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (C.M.); (V.Z.)
| |
Collapse
|
8
|
Magvan B, Kloeble AA, Ptok J, Hoffmann D, Habermann D, Gantumur A, Paluschinski M, Enebish G, Balz V, Fischer JC, Chimeddorj B, Walker A, Timm J. Sequence diversity of hepatitis D virus in Mongolia. Front Med (Lausanne) 2023; 10:1108543. [PMID: 37035318 PMCID: PMC10077969 DOI: 10.3389/fmed.2023.1108543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/06/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction The Hepatitis Delta Virus (HDV) is a defective, single-stranded RNA virusoid encoding for a single protein, the Hepatitis Delta Antigen (HDAg), which requires the hepatitis B virus (HBV) envelope protein (HBsAg) for its transmission. Currently, hepatitis D is the most aggressive form of viral hepatitis and treatment options are limited. Worldwide 12 million people are chronically infected with HDV being at high risk for progression to cirrhosis and development of liver cancer. Objectives Although it is well established that Mongolia is the country with the highest prevalence of HDV infections, the information on the molecular epidemiology and factors contributing to HDV sequence diversity are largely unclear. The aim of the study was to characterize the sequence diversity of HDV in rural areas from Mongolia and to determine the extent of HLA class I-associated selection pressure. Patients and methods From the HepMongolia cohort from rural areas in Mongolia, 451 HBsAg-positive individuals were selected and anti-HDV, HDV-RNA and the sequence of the large HDAg was determined. For all individuals the HLA class I locus was genotyped. Residues under selection pressure in the presence of individual HLA class I types were identified with the recently published analysis tool HAMdetector. Results Of 431 HBsAg positive patients, 281 were anti-HDV positive (65%), and HDV-RNA could be detected in 207 of 281 (74%) of patients. The complete large HDAg was successfully sequenced from 131 samples. Phylogenetic analysis revealed that all Mongolian HDV isolates belong to genotype 1, however, they separate into several different clusters without clear regional association. In turn, from phylogeny there is strong evidence for recent local transmission events. Importantly, we found multiple residues with strong support for HLA class I-associated selection pressure consistent with a functional CD8+ T cell response directed against HDV. Conclusion HDV isolates from Mongolia are highly diverse. The molecular epidemiology suggests circulation of multiple subtypes and provides evidence for ongoing recent transmissions.
Collapse
Affiliation(s)
- Battur Magvan
- Department of Microbiology and Infection Prevention and Control, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Anne Alina Kloeble
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Johannes Ptok
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Daniel Habermann
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Anuujin Gantumur
- Department of Microbiology and Infection Prevention and Control, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | | | - Gerelmaa Enebish
- Department of Microbiology and Infection Prevention and Control, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Vera Balz
- Institute for Transplant Diagnostics and Cell Therapeutics, University Hospital Dusseldorf, Dusseldorf, Germany
| | - Johannes C. Fischer
- Institute for Transplant Diagnostics and Cell Therapeutics, University Hospital Dusseldorf, Dusseldorf, Germany
| | - Battogtokh Chimeddorj
- Department of Microbiology and Infection Prevention and Control, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
- Institute of Biomedical Sciences, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Andreas Walker
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
- *Correspondence: Andreas Walker,
| | - Jörg Timm
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
- Jörg Timm,
| |
Collapse
|
9
|
Wang X, Wu T, Oliveira LFS, Zhang D. Sheet, Surveillance, Strategy, Salvage and Shield in global biodefense system to protect the public health and tackle the incoming pandemics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153469. [PMID: 35093353 PMCID: PMC8799268 DOI: 10.1016/j.scitotenv.2022.153469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/23/2022] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
The pandemic of COVID-19 challenges the global health system and raises our concerns on the next waves of other emerging infectious diseases. Considering the lessons from the failure of world's pandemic warning system against COVID-19, many scientists and politicians have mentioned different strategies to improve global biodefense system, among which Sheet, Surveillance, Strategy, Salvage and Shield (5S) are frequently discussed. Nevertheless, the current focus is mainly on the optimization and management of individual strategy, and there are limited attempts to combine the five strategies as an integral global biodefense system. Sheet represents the biosafety datasheet for biohazards in natural environment and human society, which helps our deeper understanding on the geographical pattern, transmission routes and infection mechanism of pathogens. Online surveillance and prognostication network is an environmental Surveillance tool for monitoring the outbreak of pandemic diseases and alarming the risks to take emergency actions, targeting aerosols, waters, soils and animals. Strategy is policies and legislations for social distancing, lockdown and personal protective equipment to block the spread of infectious diseases in communities. Clinical measures are Salvage on patients by innovating appropriate medicines and therapies. The ultimate defensive Shield is vaccine development to protect healthy crowds from infection. Fighting against COVID-19 and other emerging infectious diseases is a long rocky journey, requiring the common endeavors of scientists and politicians from all countries around the world. 5S in global biodefense system bring a ray of light to the current darkest and future road from environmental and geographical perspectives.
Collapse
Affiliation(s)
- Xinzi Wang
- School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Tianyun Wu
- Research Institute for Environmental Innovation (Tsinghua-Suzhou), Suzhou 215163, PR China
| | - Luis F S Oliveira
- Departamento de Ingeniería Civil y Arquitectura, Universidad de Lima, Avenida Javier Prado Este 4600, Santiago de Surco 1503, Peru; Department of Civil and Environmental, Universidad de la Costa, Calle 58 #55-66, 080002 Barranquilla, Atlántico, Colombia
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, PR China.
| |
Collapse
|
10
|
Databases, Knowledgebases, and Software Tools for Virus Informatics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1368:1-19. [DOI: 10.1007/978-981-16-8969-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
11
|
Hepatitis delta virus genome RNA synthesis initiates at position 1646 with a non-templated guanosine. J Virol 2021; 96:e0201721. [PMID: 34878890 DOI: 10.1128/jvi.02017-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hepatitis delta virus (HDV) is a significant human pathogen that causes acute and chronic liver disease; there is no licensed therapy. HDV is a circular negative-sense ssRNA virus that produces three RNAs in infected cells: genome, antigenome and mRNA; the latter encodes hepatitis delta antigen, the viral protein. These RNAs are synthesized by host DNA-dependent RNA polymerase acting as an RNA-dependent RNA polymerase. Although HDV genome RNA accumulates to high levels in infected cells, the mechanism by which this process occurs remains poorly understood. For example, the nature of the 5' end of the genome, including the synthesis start site and its chemical composition, are not known. Analysis of this process has been challenging because the initiation site is part of an unstable precursor in the rolling circle mechanism by which HDV genome RNA is synthesized. In this study, circular HDV antigenome RNAs synthesized in vitro were used to directly initiate HDV genome RNA synthesis in transfected cells, thus enabling detection of the 5' end of the genome RNA. The 5' end of this RNA is capped, as expected for a Pol II product. Initiation begins at position 1646 on the genome, which is located near the loop end proximal to the start site for HDAg mRNA synthesis. Unexpectedly, synthesis begins with a guanosine that is not conventionally templated by the HDV RNA. IMPORTANCE Hepatitis delta virus (HDV) is a unique virus that causes severe liver disease. It uses host RNA Polymerase II to copy its circular RNA genome in a unique and poorly understood process. Although the virus RNA accumulates to high levels within infected cells, it is not known how synthesis of the viral RNA begins, nor even where on the genome synthesis starts. Here, we identify the start site for the initiation of HDV genome RNA synthesis as position 1646, which is at one end of the closed hairpin-like structure of the viral RNA. The 5' end of the RNA is capped, as expected for Pol II products. However, RNA synthesis begins with a guanosine that is not present in the genome. Thus, although HDV uses Pol II to synthesize the viral genome, some details of the initiation process are different. These differences could be important for successfully targeting virus replication.
Collapse
|
12
|
Nagata S, Kiyohara R, Toh H. Constraint of Base Pairing on HDV Genome Evolution. Viruses 2021; 13:v13122350. [PMID: 34960619 PMCID: PMC8708965 DOI: 10.3390/v13122350] [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: 06/29/2021] [Revised: 10/11/2021] [Accepted: 11/02/2021] [Indexed: 11/17/2022] Open
Abstract
The hepatitis delta virus is a single-stranded circular RNA virus, which is characterized by high self-complementarity. About 70% of the genome sequences can form base-pairs with internal nucleotides. There are many studies on the evolution of the hepatitis delta virus. However, the secondary structure has not been taken into account in these studies. In this study, we developed a method to examine the effect of base pairing as a constraint on the nucleotide substitutions during the evolution of the hepatitis delta virus. The method revealed that the base pairing can reduce the evolutionary rate in the non-coding region of the virus. In addition, it is suggested that the non-coding nucleotides without base pairing may be under some constraint, and that the intensity of the constraint is weaker than that by the base pairing but stronger than that on the synonymous site.
Collapse
|
13
|
Zakh R, Churkin A, Totzeck F, Parr M, Tuller T, Etzion O, Dahari H, Roggendorf M, Frishman D, Barash D. A Mathematical Analysis of HDV Genotypes: From Molecules to Cells. MATHEMATICS (BASEL, SWITZERLAND) 2021; 9:2063. [PMID: 34540628 PMCID: PMC8445514 DOI: 10.3390/math9172063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hepatitis D virus (HDV) is classified according to eight genotypes. The various genotypes are included in the HDVdb database, where each HDV sequence is specified by its genotype. In this contribution, a mathematical analysis is performed on RNA sequences in HDVdb. The RNA folding predicted structures of the Genbank HDV genome sequences in HDVdb are classified according to their coarse-grain tree-graph representation. The analysis allows discarding in a simple and efficient way the vast majority of the sequences that exhibit a rod-like structure, which is important for the virus replication, to attempt to discover other biological functions by structure consideration. After the filtering, there remain only a small number of sequences that can be checked for their additional stem-loops besides the main one that is known to be responsible for virus replication. It is found that a few sequences contain an additional stem-loop that is responsible for RNA editing or other possible functions. These few sequences are grouped into two main classes, one that is well-known experimentally belonging to genotype 3 for patients from South America associated with RNA editing, and the other that is not known at present belonging to genotype 7 for patients from Cameroon. The possibility that another function besides virus replication reminiscent of the editing mechanism in HDV genotype 3 exists in HDV genotype 7 has not been explored before and is predicted by eigenvalue analysis. Finally, when comparing native and shuffled sequences, it is shown that HDV sequences belonging to all genotypes are accentuated in their mutational robustness and thermodynamic stability as compared to other viruses that were subjected to such an analysis.
Collapse
Affiliation(s)
- Rami Zakh
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel
| | - Alexander Churkin
- Department of Software Engineering, Sami Shamoon College of Engineering, Beer-Sheva 8410501, Israel
| | - Franziska Totzeck
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Marina Parr
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Ohad Etzion
- Soroka University Medical Center, Ben-Gurion University, Beer-Sheva 8410501, Israel
| | - Harel Dahari
- Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Michael Roggendorf
- Institute of Virology, Technische Universität München, 81675 Munich, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel
| |
Collapse
|
14
|
Khoshdel-Rad N, Zahmatkesh E, Bikmulina P, Peshkova M, Kosheleva N, Bezrukov EA, Sukhanov RB, Solovieva A, Shpichka A, Timashev P, Vosough M. Modeling Hepatotropic Viral Infections: Cells vs. Animals. Cells 2021; 10:1726. [PMID: 34359899 PMCID: PMC8305759 DOI: 10.3390/cells10071726] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
The lack of an appropriate platform for a better understanding of the molecular basis of hepatitis viruses and the absence of reliable models to identify novel therapeutic agents for a targeted treatment are the two major obstacles for launching efficient clinical protocols in different types of viral hepatitis. Viruses are obligate intracellular parasites, and the development of model systems for efficient viral replication is necessary for basic and applied studies. Viral hepatitis is a major health issue and a leading cause of morbidity and mortality. Despite the extensive efforts that have been made on fundamental and translational research, traditional models are not effective in representing this viral infection in a laboratory. In this review, we discuss in vitro cell-based models and in vivo animal models, with their strengths and weaknesses. In addition, the most important findings that have been retrieved from each model are described.
Collapse
Affiliation(s)
- Niloofar Khoshdel-Rad
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran; (N.K.-R.); (E.Z.)
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran
| | - Ensieh Zahmatkesh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran; (N.K.-R.); (E.Z.)
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran
| | - Polina Bikmulina
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (P.B.); (M.P.); (A.S.)
- World-Class Research Center “Digital biodesign and personalized healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Maria Peshkova
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (P.B.); (M.P.); (A.S.)
- World-Class Research Center “Digital biodesign and personalized healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Nastasia Kosheleva
- World-Class Research Center “Digital biodesign and personalized healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- FSBSI ‘Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia
| | - Evgeny A. Bezrukov
- Department of Urology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.A.B.); (R.B.S.)
| | - Roman B. Sukhanov
- Department of Urology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (E.A.B.); (R.B.S.)
| | - Anna Solovieva
- Department of Polymers and Composites, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Anastasia Shpichka
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (P.B.); (M.P.); (A.S.)
- World-Class Research Center “Digital biodesign and personalized healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Peter Timashev
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (P.B.); (M.P.); (A.S.)
- World-Class Research Center “Digital biodesign and personalized healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Department of Polymers and Composites, N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia;
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Massoud Vosough
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran; (N.K.-R.); (E.Z.)
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran
| |
Collapse
|
15
|
Niro GA, Ferro A, Cicerchia F, Brascugli I, Durazzo M. Hepatitis delta virus: From infection to new therapeutic strategies. World J Gastroenterol 2021; 27:3530-3542. [PMID: 34239267 PMCID: PMC8240063 DOI: 10.3748/wjg.v27.i24.3530] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/07/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023] Open
Abstract
The hepatitis delta virus (HDV) is a small RNA virus that encodes a single protein and which requires the hepatitis B virus (HBV)-encoded hepatitis B surface antigen (HBsAg) for its assembly and transmission. HBV/HDV co-infections exist worldwide and show a higher prevalence among selected groups of HBV-infected populations, specifically intravenous drug users, practitioners of high-risk sexual behaviours, and patients with cirrhosis and hepatocellular carcinoma. The chronic form of HDV-related hepatitis is usually severe and rapidly progressive. Patterns of the viral infection itself, including the status of co-infection or super-infection, virus genotypes (both for HBV and HDV), and persistence of the virus’ replication, influence the outcome of the accompanying and manifested liver disease. Unfortunately, disease severity is burdened by the lack of an effective cure for either virus type. For decades, the main treatment option has been interferon, administered as mono-therapy or in combination with nucleos(t)ide analogues. While its efficacy has been reported for different doses, durations and courses, only a minority of patients achieve a sustained response, which is the foundation of eventual improvement in related liver fibrosis. The need for an efficient therapeutic alternative remains. Research efforts towards this end have led to new treatment options that target specific steps in the HDV life cycle; the most promising among these are myrcludex B, which inhibits virus entry into hepatocytes, lonafarnib, which inhibits farnesylation of the viral-encoded L-HDAg large hepatitis D antigen, and REP-2139, which interferes with HBsAg release and assembly.
Collapse
Affiliation(s)
- Grazia A Niro
- Department of Gastroenterology, IRCCS Casa Sollievo della Sofferenza Hospital Foundation, San Giovanni Rotondo 71013, Italy
| | - Arianna Ferro
- Department of Medical Sciences, University of Turin, Turin 10126, Italy
| | | | | | - Marilena Durazzo
- Department of Medical Sciences, University of Turin, Turin 10126, Italy
| |
Collapse
|
16
|
Comment: Mis-Genotyping of Some Hepatitis D Virus Genotype 2 and 5 Sequences Using HDVdb. Viruses 2020; 12:v12101066. [PMID: 32977660 PMCID: PMC7598266 DOI: 10.3390/v12101066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/16/2020] [Accepted: 09/22/2020] [Indexed: 11/16/2022] Open
Abstract
Evidence that Hepatitis D virus (HDV) genotype is involved in HDV infection pathogenesis is increasing. Indeed, HDV genotypes have been shown to be linked to different outcomes in terms of liver fibrosis and treatment response. Herein, we show that the promising HDVdb genotyping tool available online can lead to wrong genotyping results. The current HDVdb algorithm should be carefully considered as a “beta-version” and warrants algorithm core corrections, as soon as possible, for an optimal and beneficial use.
Collapse
|