1
|
Zaiets I, Gunewardena S, Menne S, Weinman SA, Gudima SO. Sera of Individuals Chronically Infected with Hepatitis B Virus (HBV) Contain Diverse RNA Types Produced by HBV Replication or Derived from Integrated HBV DNA. J Virol 2023; 97:e0195022. [PMID: 36877036 PMCID: PMC10062156 DOI: 10.1128/jvi.01950-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/11/2023] [Indexed: 03/07/2023] Open
Abstract
This study aimed to better characterize the repertoire of serum hepatitis B virus (HBV) RNAs during chronic HBV infection in humans, which remains understudied. Using reverse transcription-PCR (RT-PCR), real-time quantitative PCR (RT-qPCR), RNA-sequencing, and immunoprecipitation, we found that (i) >50% of serum samples bore different amounts of HBV replication-derived RNAs (rd-RNAs); (ii) a few samples contained RNAs transcribed from integrated HBV DNA, including 5'-HBV-human-3' RNAs (integrant-derived RNAs [id-RNAs]) and 5'-human-HBV-3' transcripts, as a minority of serum HBV RNAs; (iii) spliced HBV RNAs were abundant in <50% of analyzed samples; (iv) most serum rd-RNAs were polyadenylated via conventional HBV polyadenylation signal; (v) pregenomic RNA (pgRNA) was the major component of the pool of serum RNAs; (vi) the area of HBV positions 1531 to 1739 had very high RNA read coverage and thus should be used as a target for detecting serum HBV RNAs; (vii) the vast majority of rd-RNAs and pgRNA were associated with HBV virions but not with unenveloped capsids, exosomes, classic microvesicles, or apoptotic vesicles and bodies; (viii) considerable rd-RNAs presence in the circulating immune complexes was found in a few samples; and (ix) serum relaxed circular DNA (rcDNA) and rd-RNAs should be quantified simultaneously to evaluate HBV replication status and efficacy of anti-HBV therapy with nucleos(t)ide analogs. In summary, sera contain various HBV RNA types of different origin, which are likely secreted via different mechanisms. In addition, since we previously showed that id-RNAs were abundant or predominant HBV RNAs in many of liver and hepatocellular carcinoma tissues as compared to rd-RNAs, there is likely a mechanism favoring the egress of replication-derived RNAs. IMPORTANCE The presence of integrant-derived RNAs (id-RNAs) and 5'-human-HBV-3' transcripts derived from integrated hepatitis B virus (HBV) DNA in sera was demonstrated for the first time. Thus, sera of individuals chronically infected with HBV contained both replication-derived and integrant-transcribed HBV RNAs. The majority of serum HBV RNAs were the transcripts produced by HBV genome replication, which were associated with HBV virions and not with other types of extracellular vesicles. These and other above-mentioned findings advanced our understanding of the HBV life cycle. In addition, the study suggested a promising target area on the HBV genome to increase sensitivity of the detection of serum HBV RNAs and supported the idea that simultaneous detection of replication-derived RNAs (rd-RNAs) and relaxed circular DNA (rcDNA) in serum provides more adequate evaluation of (i) the HBV genome replication status and (ii) the durability and efficiency of the therapy with anti-HBV nucleos(t)ide analogs, which could be useful for improvement of the diagnostics and treatment of HBV-infected individuals.
Collapse
Affiliation(s)
- Igor Zaiets
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Sumedha Gunewardena
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Stephan Menne
- Department of Microbiology and Immunology, Georgetown University, Washington, DC, USA
| | - Steven A. Weinman
- Department of Internal Medicine, Division of Gastroenterology, Liver Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Severin O. Gudima
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, USA
| |
Collapse
|
2
|
Belaiba Z, Ayouni K, Gdoura M, Kammoun Rebai W, Touzi H, Sadraoui A, Hammemi W, Yacoubi L, Abdelati S, Hamzaoui L, Msaddak Azzouz M, Chouikha A, Triki H. Whole genome analysis of hepatitis B virus before and during long-term therapy in chronic infected patients: Molecular characterization, impact on treatment and liver disease progression. Front Microbiol 2022; 13:1020147. [PMID: 36325017 PMCID: PMC9618822 DOI: 10.3389/fmicb.2022.1020147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/15/2022] [Indexed: 07/23/2023] Open
Abstract
Hepatitis B virus (HBV) infection remains a serious public health concern worldwide despite the availability of an efficient vaccine and the major improvements in antiviral treatments. The aim of the present study is to analyze the mutational profile of the HBV whole genome in ETV non-responder chronic HBV patients, in order to investigate antiviral drug resistance, immune escape, and liver disease progression to Liver Cirrhosis (LC) or Hepatocellular Carcinoma (HCC). Blood samples were collected from five chronic hepatitis B patients. For each patient, two plasma samples were collected, before and during the treatment. Whole genome sequencing was performed using Sanger technology. Phylogenetic analysis comparing the studied sequences with reference ones was used for genotyping. The mutational profile was analyzed by comparison with the reference sequence M32138. Genotyping showed that the studied strains belong to subgenotypes D1, D7, and D8. The mutational analysis showed high genetic variability. In the RT region of the polymerase gene, 28 amino acid (aa) mutations were detected. The most significant mutations were the pattern rtL180M + rtS202G + rtM204V, which confer treatment resistance. In the S gene, 35 mutations were detected namely sP120T, sT126S, sG130R, sY134F, sS193L, sI195M, and sL216stop were previously described to lead to vaccine, immunotherapy, and/or diagnosis escape. In the C gene, 34 mutations were found. In particular, cG1764A, cC1766G/T, cT1768A, and cC1773T in the BCP; cG1896A and cG1899A in the precore region and cT12S, cE64D, cA80T, and cP130Q in the core region were associated with disease progression to LC and/or HCC. Other mutations were associated with viral replication increase including cT1753V, cG1764A/T, cC1766G/T, cT1768A, and cC1788G in the BCP as well as cG1896A and cG1899A in the precore region. In the X gene, 30 aa substitutions were detected, of which substitutions xT36D, xP46S, xA47T, xI88F, xA102V, xI127T, xK130M, xV131I, and xF132Y were previously described to lead to LC and/or HCC disease progression. In conclusion, our results show high genetic variability in the long-term treatment of chronic HBV patients causing several effects. This could contribute to guiding national efforts to optimize relevant HBV treatment management in order to achieve the global hepatitis elimination goal by 2030.
Collapse
Affiliation(s)
- Zeineb Belaiba
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health,” LR20IPT02, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Kaouther Ayouni
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health,” LR20IPT02, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Mariem Gdoura
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health,” LR20IPT02, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Wafa Kammoun Rebai
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Henda Touzi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Amel Sadraoui
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Walid Hammemi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Lamia Yacoubi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Salwa Abdelati
- Department of Gastroenterology, Polyclinic of CNSS, Sousse, Tunisia
| | - Lamine Hamzaoui
- Department of Gastroenterology, Hospital of Tahar Maamouri, Nabeul, Tunisia
| | | | - Anissa Chouikha
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health,” LR20IPT02, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Approach and Technological Innovation for a Better Health,” LR20IPT02, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis, Tunisia
| |
Collapse
|
3
|
Yang ZW, Pham TTH, Hsu CC, Lien CH, Phan QH. Single-Layer-Graphene-Coated and Gold-Film-Based Surface Plasmon Resonance Prism Coupler Sensor for Immunoglobulin G Detection. SENSORS 2022; 22:s22041362. [PMID: 35214258 PMCID: PMC8962983 DOI: 10.3390/s22041362] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 02/07/2023]
Abstract
A graphene-based surface plasmon resonance (SPR) prism coupler sensor is proposed for the rapid detection of immunoglobulin G (IgG) antibodies. The feasibility of the proposed sensor is demonstrated by measuring the IgG concentration in phantom mouse and human serum solutions over the range of 0–250 ng/mL. The results show that the circular dichroism and principal fast axis angle of linear birefringence increase in line with increases in IgG concentration over the considered range. Moreover, the proposed device has a resolution of 5–10 ng/mL and a response time of less than three minutes. In general, the sensor provides a promising approach for IgG detection and has significant potential for rapid infectious viral disease testing applications.
Collapse
Affiliation(s)
- Zhe-Wei Yang
- Department of Mechanical Engineering, National United University, Miaoli 36063, Taiwan; (Z.-W.Y.); (C.-C.H.)
| | - Thi-Thu-Hien Pham
- Department of Biomedical Engineering, International University-Vietnam National University, Ho Chi Minh City 700000, Vietnam;
| | - Chin-Chi Hsu
- Department of Mechanical Engineering, National United University, Miaoli 36063, Taiwan; (Z.-W.Y.); (C.-C.H.)
| | - Chi-Hsiang Lien
- Department of Mechanical Engineering, National United University, Miaoli 36063, Taiwan; (Z.-W.Y.); (C.-C.H.)
- Correspondence: (C.-H.L.); (Q.-H.P.)
| | - Quoc-Hung Phan
- Department of Mechanical Engineering, National United University, Miaoli 36063, Taiwan; (Z.-W.Y.); (C.-C.H.)
- Correspondence: (C.-H.L.); (Q.-H.P.)
| |
Collapse
|
4
|
Phinius BB, Anderson M, Bhebhe L, Baruti K, Manowe G, Choga WT, Mupfumi L, Mbangiwa T, Mudanga M, Moyo S, Marlink R, Blackard JT, Gaseitsiwe S. Increased Prevalence of Liver Fibrosis and HIV Viremia among Patients with HIV, HBV, and Tuberculosis in Botswana. Pathogens 2020; 9:pathogens9110950. [PMID: 33202597 PMCID: PMC7696587 DOI: 10.3390/pathogens9110950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 11/16/2022] Open
Abstract
People with concomitant human immunodeficiency virus (HIV) and tuberculosis (TB) have an increased risk of hepatotoxic reactions due to antiretroviral therapy (ART) and anti-TB therapy (ATT). Concomitant hepatitis B virus (HBV) in these patients may lead to poorer health outcomes. To assess liver enzyme levels and immune response in adults with HIV, HBV, and TB, data from 300 antiretroviral-naïve people living with HIV (PLWHIV) were analyzed. The prevalence of HIV/HBV (cHIV/HBV) and HIV/TB (cHIV/TB) was 28% (95% CI: 23.0–33.4) and 10% (95% CI: 6.8–14.0), respectively. HIV/HBV/TB (cHIV/HBV/TB) prevalence was 5.3% (95% CI: 3.1–8.5). There was a statistically significant difference between the groups of participants in HIV viral load (p = 0.004), hemoglobin levels (p = 0.025), and body mass index (p = 0.011). A larger proportion of cHIV/HBV/TB participants (37.5%) had an aspartate aminotransferase to platelet ratio index (APRI) score ≥0.5 (p = 0.013), a lower cutoff for significant liver fibrosis. Immunological non-responders (CD4+ T-cell count <20% gain and HIV viral load <400 copies/mL at 6 months) were observed in all groups except those with cHIV/TB. Our findings support the need to screen for infections that could cause excessive liver damage prior to ATT or ART initiation, such as HBV.
Collapse
Affiliation(s)
- Bonolo B. Phinius
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (B.B.P.); (M.A.); (L.B.); (K.B.); (G.M.); (W.T.C.); (L.M.); (T.M.); (M.M.); (S.M.)
| | - Motswedi Anderson
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (B.B.P.); (M.A.); (L.B.); (K.B.); (G.M.); (W.T.C.); (L.M.); (T.M.); (M.M.); (S.M.)
| | - Lynnette Bhebhe
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (B.B.P.); (M.A.); (L.B.); (K.B.); (G.M.); (W.T.C.); (L.M.); (T.M.); (M.M.); (S.M.)
| | - Kabo Baruti
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (B.B.P.); (M.A.); (L.B.); (K.B.); (G.M.); (W.T.C.); (L.M.); (T.M.); (M.M.); (S.M.)
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone 0000, Botswana
| | - Godiraone Manowe
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (B.B.P.); (M.A.); (L.B.); (K.B.); (G.M.); (W.T.C.); (L.M.); (T.M.); (M.M.); (S.M.)
| | - Wonderful T. Choga
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (B.B.P.); (M.A.); (L.B.); (K.B.); (G.M.); (W.T.C.); (L.M.); (T.M.); (M.M.); (S.M.)
- Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lucy Mupfumi
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (B.B.P.); (M.A.); (L.B.); (K.B.); (G.M.); (W.T.C.); (L.M.); (T.M.); (M.M.); (S.M.)
| | - Tshepiso Mbangiwa
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (B.B.P.); (M.A.); (L.B.); (K.B.); (G.M.); (W.T.C.); (L.M.); (T.M.); (M.M.); (S.M.)
- Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Mbatshi Mudanga
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (B.B.P.); (M.A.); (L.B.); (K.B.); (G.M.); (W.T.C.); (L.M.); (T.M.); (M.M.); (S.M.)
- Department of Statistics, Faculty of Sciences, University of Botswana, Gaborone 0000, Botswana
| | - Sikhulile Moyo
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (B.B.P.); (M.A.); (L.B.); (K.B.); (G.M.); (W.T.C.); (L.M.); (T.M.); (M.M.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Richard Marlink
- Rutgers Global Health Institute, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA;
| | - Jason T. Blackard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
| | - Simani Gaseitsiwe
- Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone 0000, Botswana; (B.B.P.); (M.A.); (L.B.); (K.B.); (G.M.); (W.T.C.); (L.M.); (T.M.); (M.M.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Correspondence: ; Tel.: +267-3902671 (ext. 2216)
| |
Collapse
|
5
|
Bai L, Zhang X, Kozlowski M, Li W, Wu M, Liu J, Chen L, Zhang J, Huang Y, Yuan Z. Extracellular Hepatitis B Virus RNAs Are Heterogeneous in Length and Circulate as Capsid-Antibody Complexes in Addition to Virions in Chronic Hepatitis B Patients. J Virol 2018; 92:e00798-18. [PMID: 30282709 PMCID: PMC6258948 DOI: 10.1128/jvi.00798-18] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/04/2018] [Indexed: 12/13/2022] Open
Abstract
Extracellular HBV RNA has been detected in both HBV-replicating cell culture media and sera from chronic hepatitis B (CHB) patients, but its exact origin and composition remain controversial. Here, we demonstrated that extracellular HBV RNA species were of heterogeneous lengths, ranging from the length of pregenomic RNA to a few hundred nucleotides. In cell models, these RNAs were predominantly associated with naked capsids, although virions also harbored a minority of them. Moreover, HBV RNAs in hepatitis B patients' blood circulation were localized in unenveloped capsids in the form of capsid-antibody complexes (CACs) and in virions. Furthermore, we showed that extracellular HBV RNAs could serve as the template for viral DNA synthesis. In conclusion, extracellular HBV RNAs mainly consist of pgRNA or the pgRNA species degraded by the RNase H domain of the polymerase in the process of viral DNA synthesis and circulate as CACs and virions. Their presence in blood circulation of CHB patients may be exploited to develop novel biomarkers for HBV persistence.IMPORTANCE Although increasing evidence suggests the presence of extracellular HBV RNA species, their origin and molecular forms are still under debate. In addition to the infectious virions, HBV is known to secrete several species of incomplete viral particles, including hepatitis B surface antigen (HBsAg) particles, naked capsids, and empty virions, during its replication cycle. Here, we demonstrated that extracellular HBV RNAs were associated with naked capsids and virions in HepAD38 cells. Interestingly, we found that unenveloped capsids circulate in the blood of hepatitis B patients in the form of CACs and, together with virions, serve as vehicles carrying these RNA molecules. Moreover, extracellular HBV RNAs are heterogeneous in length and represent either pregenomic RNA (pgRNA) or products of incomplete reverse transcription during viral replication. These findings provide a conceptual basis for further application of extracellular RNA species as novel biomarkers for HBV persistence.
Collapse
Affiliation(s)
- Lu Bai
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xiaonan Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Maya Kozlowski
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Weixia Li
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Min Wu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jiangxia Liu
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Liang Chen
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jiming Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yuxian Huang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| |
Collapse
|