|
1
|
Abdul Majeed N, Zehnder B, Koh C, Heller T, Urban S. Hepatitis delta: Epidemiology to recent advances in therapeutic agents. Hepatology 2023; 78:1306-1321. [PMID: 36738087 DOI: 10.1097/hep.0000000000000331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/19/2022] [Indexed: 02/05/2023]
Abstract
Hepatitis D virus (HDV) was first described in 1977 and is dependent on the presence of hepatitis B surface antigen (HBsAg) for its entry into cells and on the human host for replication. Due to the envelopment with the hepatitis B virus (HBV) envelope, early phases of HDV entry resemble HBV infection. Unlike HBV, HDV activates innate immune responses. The global prevalence of HDV is estimated to be about 5% of HBsAg positive individuals. However, recent studies have described a wide range of prevalence between 12 to 72 million individuals. Infection can occur as super-infection or co-infection. The diagnosis of active HDV infection involves screening with anti HDV antibodies followed by quantitative PCR testing for HDV RNA in those who are HBsAg positive. The diagnostic studies have evolved over the years improving the validity and reliability of the tests performed. HDV infection is considered the most severe form of viral hepatitis and the HDV genotype may influence the disease course. There are eight major HDV genotypes with prevalence varying by geographic region. HDV treatment has been challenging as HDV strongly depends on the host cell for replication and provides few, if any viral targets. Better understanding of HDV virology has led to the development of several therapeutic agents currently being studied in different phase II and III clinical trials. There is increasing promise of effective therapies that will ameliorate the course of this devastating disease.
Collapse
Affiliation(s)
- Nehna Abdul Majeed
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Benno Zehnder
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christopher Koh
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Theo Heller
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 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
| |
Collapse
|
|
2
|
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.
Collapse
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
| |
Collapse
|
|
3
|
Pacin-Ruiz B, Cortese MF, Tabernero D, Sopena S, Gregori J, García-García S, Casillas R, Najarro A, Aldama U, Palom A, Rando-Segura A, Galán A, Vila M, Riveiro-Barciela M, Quer J, González-Aseguinolaza G, Buti M, Rodríguez-Frías F. Inspecting the Ribozyme Region of Hepatitis Delta Virus Genotype 1: Conservation and Variability. Viruses 2022; 14:v14020215. [PMID: 35215809 PMCID: PMC8877431 DOI: 10.3390/v14020215] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/07/2023] Open
Abstract
The hepatitis delta virus (HDV) genome has an autocatalytic region called the ribozyme, which is essential for viral replication. The aim of this study was to use next-generation sequencing (NGS) to analyze the ribozyme quasispecies (QS) in order to study its evolution and identify highly conserved regions potentially suitable for a gene-silencing strategy. HDV RNA was extracted from 2 longitudinal samples of chronic HDV patients and the ribozyme (nucleotide, nt 688-771) was analyzed using NGS. QS conservation, variability and genetic distance were analyzed. Mutations were identified by aligning sequences with their specific genotype consensus. The main relevant mutations were tested in vitro. The ribozyme was conserved overall, with a hyper-conserved region between nt 715-745. No difference in QS was observed over time. The most variable region was between nt 739-769. Thirteen mutations were observed, with three showing a higher frequency: T23C, T69C and C64 deletion. This last strongly reduced HDV replication by more than 1 log in vitro. HDV Ribozyme QS was generally highly conserved and was maintained during follow-up. The most conserved portion may be a valuable target for a gene-silencing strategy. The presence of the C64 deletion may strongly impair viral replication, as it is a potential mechanism of viral persistence.
Collapse
Affiliation(s)
- Beatriz Pacin-Ruiz
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
| | - María Francesca Cortese
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
- Correspondence: (M.F.C.); (D.T.)
| | - David Tabernero
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
- Correspondence: (M.F.C.); (D.T.)
| | - Sara Sopena
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Josep Gregori
- Liver Unit, Liver Disease, Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (J.G.); (J.Q.)
| | - Selene García-García
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
| | - Rosario Casillas
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Adrián Najarro
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Unai Aldama
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Adriana Palom
- Liver Unit, Department of Internal Medicine, Vall d’Hebron University Hospital, 08035 Barcelona, Spain;
| | - Ariadna Rando-Segura
- Department of Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain;
| | - Anna Galán
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Marta Vila
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
| | - Mar Riveiro-Barciela
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
- Liver Unit, Department of Internal Medicine, Vall d’Hebron University Hospital, 08035 Barcelona, Spain;
| | - Josep Quer
- Liver Unit, Liver Disease, Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (J.G.); (J.Q.)
| | | | - María Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
- Liver Unit, Department of Internal Medicine, Vall d’Hebron University Hospital, 08035 Barcelona, Spain;
| | - Francisco Rodríguez-Frías
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (B.P.-R.); (S.S.); (S.G.-G.); (R.C.); (A.N.); (U.A.); (A.G.); (M.V.); (F.R.-F.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, 28029 Madrid, Spain; (M.R.-B.); (M.B.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), Plaça Cívica, 08193 Bellaterra, Spain
| |
Collapse
|
|
4
|
Lu W, Yu K, Li X, Ge Q, Liang G, Bai Y. Identification of full-length circular nucleic acids using long-read sequencing technologies. Analyst 2021; 146:6102-6113. [PMID: 34549740 DOI: 10.1039/d1an01147b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unlike the traditional perception in genomic DNA or linear RNA, circular nucleic acids are a class of functional biomolecules with a circular configuration and are often observed in nature. These circular molecules encompass the full spectrum of size and play an important role in organisms, making circular nucleic acids research worthy. Due to the low abundance of most types of circular nucleic acids and the disadvantages of short-read sequencing platforms, accurate and full-length circular nucleic acid sequencing and identification is difficult. In this review, we have provided insights into full-length circular nucleic acid detection methods using long-read sequencing technologies, with a focus on the experimental and bioinformatics strategies to obtain accurate sequences.
Collapse
Affiliation(s)
- Wenxiang Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Kequan Yu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Xiaohan Li
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Qinyu Ge
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Geyu Liang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Yunfei Bai
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| |
Collapse
|
|
5
|
Dziri S, Rodriguez C, Gerber A, Brichler S, Alloui C, Roulot D, Dény P, Pawlotsky JM, Gordien E, Le Gal F. Variable In Vivo Hepatitis D Virus (HDV) RNA Editing Rates According to the HDV Genotype. Viruses 2021; 13:v13081572. [PMID: 34452437 PMCID: PMC8402866 DOI: 10.3390/v13081572] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/26/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022] Open
Abstract
Human hepatitis delta virus (HDV) is a small defective RNA satellite virus that requires hepatitis B virus (HBV) envelope proteins to form its own virions. The HDV genome possesses a single coding open reading frame (ORF), located on a replicative intermediate, the antigenome, encoding the small (s) and the large (L) isoforms of the delta antigen (s-HDAg and L-HDAg). The latter is produced following an editing process, changing the amber/stop codon on the s-HDAg-ORF into a tryptophan codon, allowing L-HDAg synthesis by the addition of 19 (or 20) C-terminal amino acids. The two delta proteins play different roles in the viral cell cycle: s-HDAg activates genome replication, while L-HDAg blocks replication and favors virion morphogenesis and propagation. L-HDAg has also been involved in HDV pathogenicity. Understanding the kinetics of viral editing rates in vivo is key to unravel the biology of the virus and understand its spread and natural history. We developed and validated a new assay based on next-generation sequencing and aimed at quantifying HDV RNA editing in plasma. We analyzed plasma samples from 219 patients infected with different HDV genotypes and showed that HDV editing capacity strongly depends on the genotype of the strain.
Collapse
Affiliation(s)
- Samira Dziri
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
| | - Christophe Rodriguez
- Centre National de référence des Hépatites Virales B, C et Delta, Département de Virologie, Hôpital Henri Mondor, Assistance Publique-Hôpitaux de Paris, Université Paris-Est, 94000 Créteil, France; (C.R.); (J.M.P.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
| | - Athenaïs Gerber
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
| | - Ségolène Brichler
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
| | - Chakib Alloui
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
| | - Dominique Roulot
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
- Unité d’hépatologie, Hôpital Avicenne, Assistance Publique-Hôpitaux de Paris, Université Sorbonne-Paris-Cité, 93000 Bobigny, France
| | - Paul Dény
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052-UMR CNRS 5286, 69001 Lyon, France
| | - Jean Michel Pawlotsky
- Centre National de référence des Hépatites Virales B, C et Delta, Département de Virologie, Hôpital Henri Mondor, Assistance Publique-Hôpitaux de Paris, Université Paris-Est, 94000 Créteil, France; (C.R.); (J.M.P.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
| | - Emmanuel Gordien
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
| | - Frédéric Le Gal
- Centre National de Référence des Hépatites Virales B, C et Delta, Laboratoire de Microbiologie Clinique, Hôpital-Avicenne, Assistance Publique Hôpitaux de Paris, Université Sorbonne Paris Cité, 93000 Bobigny, France; (S.D.); (A.G.); (S.B.); (C.A.); (P.D.); (E.G.)
- Unité INSERM U955, équipe 18, 94000 Créteil, France;
- Correspondence:
| |
Collapse
|
|
6
|
Maestro S, Gómez-Echarte N, Camps G, Usai C, Suárez L, Vales Á, Olagüe C, Aldabe R, González-Aseguinolaza G. AAV-HDV: An Attractive Platform for the In Vivo Study of HDV Biology and the Mechanism of Disease Pathogenesis. Viruses 2021; 13:v13050788. [PMID: 33925087 PMCID: PMC8145145 DOI: 10.3390/v13050788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023] Open
Abstract
Hepatitis delta virus (HDV) infection causes the most severe form of viral hepatitis, but little is known about the molecular mechanisms involved. We have recently developed an HDV mouse model based on the delivery of HDV replication-competent genomes using adeno-associated vectors (AAV), which developed a liver pathology very similar to the human disease and allowed us to perform mechanistic studies. We have generated different AAV-HDV mutants to eliminate the expression of HDV antigens (HDAgs), and we have characterized them both in vitro and in vivo. We confirmed that S-HDAg is essential for HDV replication and cannot be replaced by L-HDAg or host cellular proteins, and that L-HDAg is essential to produce the HDV infectious particle and inhibits its replication. We have also found that lack of L-HDAg resulted in the increase of S-HDAg expression levels and the exacerbation of liver damage, which was associated with an increment in liver inflammation but did not require T cells. Interestingly, early expression of L-HDAg significantly ameliorated the liver damage induced by the mutant expressing only S-HDAg. In summary, the use of AAV-HDV represents a very attractive platform to interrogate in vivo the role of viral components in the HDV life cycle and to better understand the mechanism of HDV-induced liver pathology.
Collapse
Affiliation(s)
- Sheila Maestro
- Programa de Terapia Génica y Regulación de la Expresión Génica, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Avenida Pío XII, 31080 Pamplona, Spain; (S.M.); (N.G.-E.); (G.C.); (C.U.); (Á.V.); (C.O.)
- Instituto de Investigación Sanitaria de Navarra, IdiSNA, 31080 Pamplona, Spain
| | - Nahia Gómez-Echarte
- Programa de Terapia Génica y Regulación de la Expresión Génica, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Avenida Pío XII, 31080 Pamplona, Spain; (S.M.); (N.G.-E.); (G.C.); (C.U.); (Á.V.); (C.O.)
- Instituto de Investigación Sanitaria de Navarra, IdiSNA, 31080 Pamplona, Spain
| | - Gracián Camps
- Programa de Terapia Génica y Regulación de la Expresión Génica, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Avenida Pío XII, 31080 Pamplona, Spain; (S.M.); (N.G.-E.); (G.C.); (C.U.); (Á.V.); (C.O.)
- Instituto de Investigación Sanitaria de Navarra, IdiSNA, 31080 Pamplona, Spain
| | - Carla Usai
- Programa de Terapia Génica y Regulación de la Expresión Génica, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Avenida Pío XII, 31080 Pamplona, Spain; (S.M.); (N.G.-E.); (G.C.); (C.U.); (Á.V.); (C.O.)
- Instituto de Investigación Sanitaria de Navarra, IdiSNA, 31080 Pamplona, Spain
| | - Lester Suárez
- Suite 110 Research Triangle Park, 20 TW Alexander Drive, AskBio, NC 27709, USA;
| | - África Vales
- Programa de Terapia Génica y Regulación de la Expresión Génica, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Avenida Pío XII, 31080 Pamplona, Spain; (S.M.); (N.G.-E.); (G.C.); (C.U.); (Á.V.); (C.O.)
- Instituto de Investigación Sanitaria de Navarra, IdiSNA, 31080 Pamplona, Spain
| | - Cristina Olagüe
- Programa de Terapia Génica y Regulación de la Expresión Génica, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Avenida Pío XII, 31080 Pamplona, Spain; (S.M.); (N.G.-E.); (G.C.); (C.U.); (Á.V.); (C.O.)
- Instituto de Investigación Sanitaria de Navarra, IdiSNA, 31080 Pamplona, Spain
| | - Rafael Aldabe
- Programa de Terapia Génica y Regulación de la Expresión Génica, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Avenida Pío XII, 31080 Pamplona, Spain; (S.M.); (N.G.-E.); (G.C.); (C.U.); (Á.V.); (C.O.)
- Instituto de Investigación Sanitaria de Navarra, IdiSNA, 31080 Pamplona, Spain
- Correspondence: (R.A.); (G.G.-A.); Tel.: +34-948194700 (ext 4024) (R.A.); +34-948194700 (ext 4024) (G.G.-A.)
| | - Gloria González-Aseguinolaza
- Programa de Terapia Génica y Regulación de la Expresión Génica, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Avenida Pío XII, 31080 Pamplona, Spain; (S.M.); (N.G.-E.); (G.C.); (C.U.); (Á.V.); (C.O.)
- Instituto de Investigación Sanitaria de Navarra, IdiSNA, 31080 Pamplona, Spain
- Correspondence: (R.A.); (G.G.-A.); Tel.: +34-948194700 (ext 4024) (R.A.); +34-948194700 (ext 4024) (G.G.-A.)
| |
Collapse
|
|
7
|
Lu IN, Muller CP, He FQ. Applying next-generation sequencing to unravel the mutational landscape in viral quasispecies. Virus Res 2020; 283:197963. [PMID: 32278821 PMCID: PMC7144618 DOI: 10.1016/j.virusres.2020.197963] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized the scale and depth of biomedical sciences. Because of its unique ability for the detection of sub-clonal variants within genetically diverse populations, NGS has been successfully applied to analyze and quantify the exceptionally-high diversity within viral quasispecies, and many low-frequency drug- or vaccine-resistant mutations of therapeutic importance have been discovered. Although many works have intensively discussed the latest NGS approaches and applications in general, none of them has focused on applying NGS in viral quasispecies studies, mostly due to the limited ability of current NGS technologies to accurately detect and quantify rare viral variants. Here, we summarize several error-correction strategies that have been developed to enhance the detection accuracy of minority variants. We also discuss critical considerations for preparing a sequencing library from viral RNAs and for analyzing NGS data to unravel the mutational landscape.
Collapse
Affiliation(s)
- I-Na Lu
- DKFZ-Division Translational Neurooncology at the WTZ, DKTK partner site, University Hospital Essen, D-45147 Essen, Germany; Department of Infectious Diseases, Aarhus University Hospital, DK-8200 Aarhus N, Denmark.
| | - Claude P Muller
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-Sur-Alzette, Luxembourg; Laboratoire National de Santé, L-3583 Dudelange, Luxembourg
| | - Feng Q He
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-Sur-Alzette, Luxembourg; Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
| |
Collapse
|
|
8
|
Godoy C, Tabernero D, Sopena S, Gregori J, Cortese MF, González C, Casillas R, Yll M, Rando A, López-Martínez R, Quer J, González-Aseguinolaza G, Esteban R, Riveiro-Barciela M, Buti M, Rodríguez-Frías F. Characterization of hepatitis B virus X gene quasispecies complexity in mono-infection and hepatitis delta virus superinfection. World J Gastroenterol 2019; 25:1566-1579. [PMID: 30983817 PMCID: PMC6452231 DOI: 10.3748/wjg.v25.i13.1566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/25/2019] [Accepted: 03/02/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatitis delta virus (HDV) seems to strongly suppress hepatitis B virus (HBV) replication, although little is known about the mechanism of this interaction. Both these viruses show a dynamic distribution of mutants, resulting in viral quasispecies. Next-generation sequencing is a viable approach for analyzing the composition of these mutant spectra. As the regulatory hepatitis B X protein (HBx) is essential for HBV replication, determination of HBV X gene (HBX) quasispecies complexity in HBV/HDV infection compared to HBV mono-infection may provide information on the interactions between these two viruses.
AIM To compare HBV quasispecies complexity in the HBX 5’ region between chronic hepatitis delta (CHD) and chronic HBV mono-infected patients.
METHODS Twenty-four untreated patients were included: 7/24 (29.2%) with HBeAg-negative chronic HBV infection (CI, previously termed inactive carriers), 8/24 (33.3%) with HBeAg-negative chronic hepatitis B (CHB) and 9/24 (37.5%) with CHD. A serum sample from each patient was first tested for HBV DNA levels. The HBX 5’ region [nucleotides (nt) 1255-1611] was then PCR-amplified for subsequent next-generation sequencing (MiSeq, Illumina, United States). HBV quasispecies complexity in the region analyzed was evaluated using incidence-based indices (number of haplotypes and number of mutations), abundance-based indices (Hill numbers of order 1 and 2), and functional indices (mutation frequency and nucleotide diversity). We also evaluated the pattern of nucleotide changes to investigate which of them could be the cause of the quasispecies complexity.
RESULTS CHB patients showed higher median HBV-DNA levels [5.4 logIU/mL, interquartile range (IQR) 3.5-7.9] than CHD (3.4 logIU/mL, IQR 3-7.6) (P = n.s.) or CI (3.2 logIU/mL, IQR 2.3-3.5) (P < 0.01) patients. The incidence and abundance indices indicated that HBV quasispecies complexity was significantly greater in CI than CHB. A similar trend was observed in CHD patients, although only Hill numbers of order 2 showed statistically significant differences (CHB 2.81, IQR 1.11-4.57 vs CHD 8.87, 6.56-11.18, P = 0.038). There were no significant differences in the functional indices, but CI and CHD patients also showed a trend towards greater complexity than CHB. No differences were found for any HBV quasispecies complexity indices between CHD and CI patients. G-to-A and C-to-T nucleotide changes, characteristic of APOBEC3G, were higher in CHD and CI than in CHB in genotype A haplotypes, but not in genotype D. The proportion of nt G-to-A vs A-to-G changes and C-to-T vs T-to-C changes in genotype A and D haplotypes in CHD patients showed no significant differences. In CHB and CI the results of these comparisons were dependent on HBV genotype.
CONCLUSION The lower-replication CHD and CI groups show a trend to higher quasispecies complexity than the higher-replication CHB group. The mechanisms associated with this greater complexity require elucidation.
Collapse
Affiliation(s)
- Cristina Godoy
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - David Tabernero
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Sara Sopena
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Josep Gregori
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Roche Diagnostics SL, Sant Cugat del Vallès 08174, Spain
| | - Maria Francesca Cortese
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Carolina González
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Rosario Casillas
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Marçal Yll
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Ariadna Rando
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Rosa López-Martínez
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d’Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
| | | | - Rafael Esteban
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona 08035, Spain
| | - Mar Riveiro-Barciela
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona 08035, Spain
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona 08035, Spain
| | - Francisco Rodríguez-Frías
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
| |
Collapse
|
|
9
|
Tabernero D, Cortese MF, Buti M, Rodriguez-Frias F. HDV evolution-will viral resistance be an issue in HDV infection? Curr Opin Virol 2018; 32:100-107. [PMID: 30415162 DOI: 10.1016/j.coviro.2018.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 10/22/2018] [Accepted: 10/24/2018] [Indexed: 02/07/2023]
Abstract
Hepatitis D virus (HDV) is a hepatotropic subviral infectious agent, obligate satellite of the Hepatitis B virus (HBV) and is highly related to viroids. HDV affects around 5% of the 257 million chronic HBV-carriers worldwide, leading to the most severe form of chronic viral hepatitis. Interferon alpha is the only approved treatment for chronic hepatitis D, albeit with low response rates (around 20%-30%). New antiviral strategies are currently under study. Due to the high viral evolution rates (10-3 to 10-4 substitutions/site/year) HDV forms an extremely complex viral population (quasispecies) that can be studied by Next-Generation Sequencing. Therefore, although specific viral resistance in HDV infection has not been reported, it cannot be completely discarded.
Collapse
Affiliation(s)
- David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Maria Francesca Cortese
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona 08035, Spain
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona 08035, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain.
| |
Collapse
|
|
10
|
Colagrossi L, Salpini R, Scutari R, Carioti L, Battisti A, Piermatteo L, Bertoli A, Fabeni L, Minichini C, Trimoulet P, Fleury H, Nebuloso E, De Cristofaro M, Cappiello G, Spanò A, Malagnino V, Mari T, Barlattani A, Iapadre N, Lichtner M, Mastroianni C, Lenci I, Pasquazzi C, De Sanctis GM, Galeota Lanza A, Stanzione M, Stornaiuolo G, Marignani M, Sarmati L, Andreoni M, Angelico M, Ceccherini-Silberstein F, Perno CF, Coppola N, Svicher V. HDV Can Constrain HBV Genetic Evolution in HBsAg: Implications for the Identification of Innovative Pharmacological Targets. Viruses 2018; 10:v10070363. [PMID: 29987240 PMCID: PMC6071122 DOI: 10.3390/v10070363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/06/2018] [Accepted: 07/07/2018] [Indexed: 02/07/2023] Open
Abstract
Chronic HBV + HDV infection is associated with greater risk of liver fibrosis, earlier hepatic decompensation, and liver cirrhosis hepatocellular carcinoma compared to HBV mono-infection. However, to-date no direct anti-HDV drugs are available in clinical practice. Here, we identified conserved and variable regions in HBsAg and HDAg domains in HBV + HDV infection, a critical finding for the design of innovative therapeutic agents. The extent of amino-acid variability was measured by Shannon-Entropy (Sn) in HBsAg genotype-d sequences from 31 HBV + HDV infected and 62 HBV mono-infected patients (comparable for demographics and virological-parameters), and in 47 HDAg genotype-1 sequences. Positions with Sn = 0 were defined as conserved. The percentage of conserved HBsAg-positions was significantly higher in HBV + HDV infection than HBV mono-infection (p = 0.001). Results were confirmed after stratification for HBeAg-status and patients’ age. A Sn = 0 at specific positions in the C-terminus HBsAg were correlated with higher HDV-RNA, suggesting that conservation of these positions can preserve HDV-fitness. Conversely, HDAg was characterized by a lower percentage of conserved-residues than HBsAg (p < 0.001), indicating higher functional plasticity. Furthermore, specific HDAg-mutations were significantly correlated with higher HDV-RNA, suggesting a role in conferring HDV replicative-advantage. Among HDAg-domains, only the virus-assembly signal exhibited a high genetic conservation (75% of conserved-residues). In conclusion, HDV can constrain HBsAg genetic evolution to preserve its fitness. The identification of conserved regions in HDAg poses the basis for designing innovative targets against HDV-infection.
Collapse
Affiliation(s)
- Luna Colagrossi
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Romina Salpini
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Rossana Scutari
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Luca Carioti
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Arianna Battisti
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Lorenzo Piermatteo
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Ada Bertoli
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Lavinia Fabeni
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| | - Carmine Minichini
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania L. Vanvitelli, 81100 Naples, Italy.
| | - Pascale Trimoulet
- Laboratoire de Virologie, Hôpital Pellegrin tripode, 33076 Bordeaux, France.
| | - Hervé Fleury
- Laboratoire de Virologie, Hôpital Pellegrin tripode, 33076 Bordeaux, France.
| | - Elena Nebuloso
- Unit of Microbiology, Sandro Pertini Hospital, 00157 Rome, Italy.
| | | | | | - Alberto Spanò
- Unit of Microbiology, Sandro Pertini Hospital, 00157 Rome, Italy.
| | - Vincenzo Malagnino
- Infectious Diseases Unit, Tor Vergata University Hospital, 00133 Rome, Italy.
| | - Terenzio Mari
- Hepatology Unit, Nuovo Regina Margherita Hospital, 00153 Rome, Italy.
| | - Angelo Barlattani
- Hepatology Unit, Nuovo Regina Margherita Hospital, 00153 Rome, Italy.
| | - Nerio Iapadre
- Infectious Diseases Unit, San Salvatore Hospital, 67100 L'Aquila, Italy.
| | - Miriam Lichtner
- Department of Public Health and Infectious Diseases, Sapienza University, 00185 Rome, Italy.
| | - Claudio Mastroianni
- Department of Public Health and Infectious Diseases, Sapienza University, 00185 Rome, Italy.
| | - Ilaria Lenci
- Hepatology Unit, Tor Vergata University Hospital, 00133 Rome, Italy.
| | | | | | | | - Maria Stanzione
- Department of Internal Medicine, University of Campania L. Vanvitelli, Viral Unit, 81100 Naples, Italy.
| | - Gianfranca Stornaiuolo
- Department of Internal Medicine, University of Campania L. Vanvitelli, Viral Unit, 81100 Naples, Italy.
| | | | - Loredana Sarmati
- Infectious Diseases Unit, Tor Vergata University Hospital, 00133 Rome, Italy.
| | - Massimo Andreoni
- Infectious Diseases Unit, Tor Vergata University Hospital, 00133 Rome, Italy.
| | - Mario Angelico
- Hepatology Unit, Tor Vergata University Hospital, 00133 Rome, Italy.
| | | | - Carlo-Federico Perno
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
- Haematology and Oncohematology, University of Milan, 20122 Milan, Italy.
| | - Nicola Coppola
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania L. Vanvitelli, 81100 Naples, Italy.
| | - Valentina Svicher
- Department of Experimental Medicine and Surgery, Tor Vergata University, 00133 Rome, Italy.
| |
Collapse
|