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Lago BV, Portilho MM, Mello VM, De Sousa PSF, Angelice GP, Marques BCL, da Silva Andrade LT, Marques VA, Lewis-Ximenez LL, Mello FCDA, Villar LM. Genetic variability of hepatitis B virus in acute and in different phases of chronic infection in Brazil. Sci Rep 2024; 14:10742. [PMID: 38730249 PMCID: PMC11087654 DOI: 10.1038/s41598-024-60900-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
The selection pressure imposed by the host immune system impacts on hepatitis B virus (HBV) variability. This study evaluates HBV genetic diversity, nucleos(t)ide analogs resistance and HBsAg escape mutations in HBV patients under distinct selective pressures. One hundred and thirteen individuals in different phases of HBV infection were included: 13 HBeAg-positive chronic infection, 9 HBeAg-positive chronic hepatitis, 47 HBeAg-negative chronic infection (ENI), 29 HBeAg-negative chronic hepatitis (ENH) and 15 acute infected individuals. Samples were PCR amplified, sequenced and genetically analyzed for the overlapping POL/S genes. Most HBV carriers presented genotype A (84/113; 74.3%), subgenotype A1 (67/84; 79.7%), irrespective of group, followed by genotypes D (20/113; 17.7%), F (8/113; 7.1%) and E (1/113; 0.9%). Clinically relevant mutations in polymerase (tL180M/M204V) and in the Major Hydrophilic Region of HBsAg (sY100C, T118A/M, sM133T, sD144A and sG145R) were observed. Our findings, however, indicated that most polymorphic sites were located in the cytosolic loops (CYL1-2) and transmembrane domain 4 (TMD4) of HBsAg. Lower viral loads and higher HBV genetic diversity were observed in ENI and ENH groups (p < 0.001), suggesting that these groups are subjected to a higher selective pressure. Our results provide information on the molecular characteristics of HBV in a diverse clinical setting, and may guide future studies on the balance of HBV quasispecies at different stages of infection.
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Affiliation(s)
- Barbara Vieira Lago
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil.
- Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Fiocruz, Rio de Janeiro, Brazil.
| | - Moyra Machado Portilho
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Vinicius Motta Mello
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil.
| | - Paulo Sergio Fonseca De Sousa
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Giovana Paula Angelice
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Bianca Cristina Leires Marques
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Larissa Tropiano da Silva Andrade
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Vanessa Alves Marques
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Lia Laura Lewis-Ximenez
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Francisco Campello do Amaral Mello
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
| | - Livia Melo Villar
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fiocruz, Hélio and Peggy Pereira Pavillion, Ground Floor, Office B09, FIOCRUZ Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, 210360-040, Brazil
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2
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Kasianchuk N, Dobrowolska K, Harkava S, Bretcan A, Zarębska-Michaluk D, Jaroszewicz J, Flisiak R, Rzymski P. Gene-Editing and RNA Interference in Treating Hepatitis B: A Review. Viruses 2023; 15:2395. [PMID: 38140636 PMCID: PMC10747710 DOI: 10.3390/v15122395] [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: 10/28/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
The hepatitis B virus (HBV) continues to cause substantial health and economic burdens, and its target of elimination may not be reached in 2030 without further efforts in diagnostics, non-pharmaceutical prevention measures, vaccination, and treatment. Current therapeutic options in chronic HBV, based on interferons and/or nucleos(t)ide analogs, suppress the virus replication but do not eliminate the pathogen and suffer from several constraints. This paper reviews the progress on biotechnological approaches in functional and definitive HBV treatments, including gene-editing tools, i.e., zinc-finger proteins, transcription activator-like effector nucleases, and CRISPR/Cas9, as well as therapeutics based on RNA interference. The advantages and challenges of these approaches are also discussed. Although the safety and efficacy of gene-editing tools in HBV therapies are yet to be demonstrated, they show promise for the revitalization of a much-needed advance in the field and offer viral eradication. Particular hopes are related to CRISPR/Cas9; however, therapeutics employing this system are yet to enter the clinical testing phases. In contrast, a number of candidates based on RNA interference, intending to confer a functional cure, have already been introduced to human studies. However, larger and longer trials are required to assess their efficacy and safety. Considering that prevention is always superior to treatment, it is essential to pursue global efforts in HBV vaccination.
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Affiliation(s)
- Nadiia Kasianchuk
- Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland
| | | | - Sofiia Harkava
- Junior Academy of Sciences of Ukraine, Regional Branch in Dnipro, 49000 Dnipro, Ukraine;
| | - Andreea Bretcan
- National College “Ienăchiță Văcărescu”, 130016 Târgoviște, Romania;
| | - Dorota Zarębska-Michaluk
- Department of Infectious Diseases and Allergology, Jan Kochanowski University, 25-317 Kielce, Poland;
| | - Jerzy Jaroszewicz
- Department of Infectious Diseases and Hepatology, Medical University of Silesia in Katowice, 41-902 Bytom, Poland;
| | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Białystok, 15-540 Białystok, Poland;
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznań, Poland
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3
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do Lago BV, Bezerra CS, Moreira DA, Parente TE, Portilho MM, Pessôa R, Sanabani SS, Villar LM. Genetic diversity of hepatitis B virus quasispecies in different biological compartments reveals distinct genotypes. Sci Rep 2023; 13:17023. [PMID: 37813888 PMCID: PMC10562391 DOI: 10.1038/s41598-023-43655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023] Open
Abstract
The selection pressure imposed by the host immune system impacts hepatitis B virus (HBV) quasispecies variability. This study evaluates HBV genetic diversity in different biological fluids. Twenty paired serum, oral fluid, and DBS samples from chronic HBV carriers were analyzed using both Sanger and next generation sequencing (NGS). The mean HBV viral load in serum was 5.19 ± 4.3 log IU/mL (median 5.29, IQR 3.01-7.93). Genotype distribution was: HBV/A1 55% (11/20), A2 15% (3/20), D3 10% (2/20), F2 15% (3/20), and F4 5% (1/20). Genotype agreement between serum and oral fluid was 100% (genetic distances 0.0-0.006), while that between serum and DBS was 80% (genetic distances 0.0-0.115). Two individuals presented discordant genotypes in serum and DBS. Minor population analysis revealed a mixed population. All samples displayed mutations in polymerase and/or surface genes. Major population analysis of the polymerase pointed to positions H122 and M129 as the most polymorphic (≥ 75% variability), followed by V163 (55%) and I253 (50%). Neither Sanger nor NGS detected any antiviral primary resistance mutations in the major populations. Minor population analysis, however, demonstrated the rtM204I resistance mutation in all individuals, ranging from 2.8 to 7.5% in serum, 2.5 to 6.3% in oral fluid, and 3.6 to 7.2% in DBS. This study demonstrated that different fluids can be used to assess HBV diversity, nonetheless, genotypic differences according to biological compartments can be observed.
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Affiliation(s)
- Bárbara Vieira do Lago
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Cristianne Sousa Bezerra
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
- Departamento de Educação, Instituto Federal de Educação, Ciência e Tecnologia do Ceará, Fortaleza, Ceará, Brazil
| | - Daniel Andrade Moreira
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Thiago Estevam Parente
- Laboratório de Genômica Aplicada e Bioinovações, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Rodrigo Pessôa
- Postgraduate Program in Translational Medicine, Department of Medicine, Federal University of Sao Paulo (UNIFESP), São Paulo, Brazil
| | - Sabri Saeed Sanabani
- Laboratory of Medical Investigation (LIM) 03, Clinics Hospital, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Livia Melo Villar
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil.
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Dong C, Song Z, Sun C, Wang K, Chen J, Zhang W, Wu D, Zheng W, Yang Y, Qin H, Han C, Zhang F, Wang Z, Xu M, Zhang G, Xie E, Jiao J, Cao S, Gao W, Shen Z. HBsAg seroconversion in de novo hepatitis B virus-infected paediatric liver transplant recipients with anti-viral therapy. J Viral Hepat 2022; 29:1099-1106. [PMID: 36094676 DOI: 10.1111/jvh.13749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 08/02/2022] [Accepted: 09/07/2022] [Indexed: 12/29/2022]
Abstract
We investigated the clinical characteristics and therapeutic strategies for paediatric liver transplant (PLT) recipients who experienced de novo hepatitis B virus infection and the features of HBsAg seroconversion. A total of 821 PLT were performed in HBV-free recipients between January 2013 and January 2019 in Paediatric Organ Transplant Center, Tianjin First Central Hospital. Twenty-one recipients developed de novo HBV infection, the clinical data were analysed. The overall incidence of de novo HBV infection was 2.5%. Only one recipient received an HBcAb-negative graft, 20 recipients received HBcAb-positive grafts. The incidence of de novo HBV infection in HBcAb-negative and HBcAb-positive graft recipients were 0.2% and 6.3%, respectively. Fifteen de novo HBV-infected recipients showed HBsAg seroconversion, the incidence of HBsAg seroconversion was 71.4%. The median time from the diagnosis of de novo HBV infection to HBsAg seroconversion was 15 (1, 73) months. Recipients with hepatitis B surface antigen (HBsAg) titre <1000 IU/L and negative hepatitis B e antigen (HBeAg) at the time of de novo HBV infection diagnosis were more likely to achieve HBsAg seroconversion. Nucleotide analogues were effective in treating recipients with de novo HBV infection. De novo HBV infection does not impact liver graft function as well as recipient and graft survival rate. De novo HBV infection does not impact PLT recipient outcomes under close monitoring and appropriate treatment. High incidence of HBsAg seroconversion can be achieved after anti-viral therapy.
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Affiliation(s)
- Chong Dong
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Zhuolun Song
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Chao Sun
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Kai Wang
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Jing Chen
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Wei Zhang
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Di Wu
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Weiping Zheng
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Yang Yang
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Hong Qin
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Chao Han
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Fubo Zhang
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Zhen Wang
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Min Xu
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Guofeng Zhang
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Enbo Xie
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Junli Jiao
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Shunqi Cao
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Wei Gao
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
| | - Zhongyang Shen
- Department of Paediatric Transplantation, Tianjin First Central Hospital, Tianjin, China.,Tianjin Key Laboratory for Organ Transplantation, Tianjin, China
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5
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Van Poelvoorde LAE, Delcourt T, Vuylsteke M, De Keersmaecker SCJ, Thomas I, Van Gucht S, Saelens X, Roosens N, Vanneste K. A general approach to identify low-frequency variants within influenza samples collected during routine surveillance. Microb Genom 2022; 8. [PMID: 36169645 DOI: 10.1099/mgen.0.000867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Influenza viruses exhibit considerable diversity between hosts. Additionally, different quasispecies can be found within the same host. High-throughput sequencing technologies can be used to sequence a patient-derived virus population at sufficient depths to identify low-frequency variants (LFV) present in a quasispecies, but many challenges remain for reliable LFV detection because of experimental errors introduced during sample preparation and sequencing. High genomic copy numbers and extensive sequencing depths are required to differentiate false positive from real LFV, especially at low allelic frequencies (AFs). This study proposes a general approach for identifying LFV in patient-derived samples obtained during routine surveillance. Firstly, validated thresholds were determined for LFV detection, whilst balancing both the cost and feasibility of reliable LFV detection in clinical samples. Using a genetically well-defined population of influenza A viruses, thresholds of at least 104 genomes per microlitre and AF of ≥5 % were established as detection limits. Secondly, a subset of 59 retained influenza A (H3N2) samples from the 2016-2017 Belgian influenza season was composed. Thirdly, as a proof of concept for the added value of LFV for routine influenza monitoring, potential associations between patient data and whole genome sequencing data were investigated. A significant association was found between a high prevalence of LFV and disease severity. This study provides a general methodology for influenza LFV detection, which can also be adopted by other national influenza reference centres and for other viruses such as SARS-CoV-2. Additionally, this study suggests that the current relevance of LFV for routine influenza surveillance programmes might be undervalued.
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Affiliation(s)
- Laura A E Van Poelvoorde
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Thomas Delcourt
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | | | | | - Isabelle Thomas
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Steven Van Gucht
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Xavier Saelens
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Nancy Roosens
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
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Huo S, Hai Y, Guo Y, Nie L, Li H, Qiao P, Zong K, Li X, Guo Y, Song J, Zhao H, Lei W, Lan Y, Liu WJ, Gao GF. Intra-host variation and evolutionary dynamics of adenoviruses correlate to neutrophils in infected patients. J Med Virol 2022; 94:3863-3875. [PMID: 35355288 DOI: 10.1002/jmv.27744] [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: 01/08/2022] [Revised: 03/26/2022] [Accepted: 03/30/2022] [Indexed: 11/10/2022]
Abstract
With deep sequencing of virus genomes within the hosts, intra-host single nucleotide variations (iSNVs) have been used for analyses of virus genome variation and evolution, which is indicated to correlate with viral pathogenesis and disease severity. Little is known about the features of iSNVs among DNA viruses. We performed the epidemiological and laboratory investigation of one outbreak of adenovirus. The whole genomes of viruses in both original oral swabs and cell-cultured virus isolates were deeply sequenced. We identified 737 iSNVs in the viral genomes sequenced from original samples and 46 viral iSNVs in cell cultured isolates, with 33 iSNVs shared by original samples and cultured isolates. Meanwhile, we found these 33 iSNVs were shared by different patients, among which, three hot-spot areas 6367-6401, 9213-9247 and 10584-10606 within the functional genes of the adenovirus genome were found. Notably, the substitution rates of iSNVs were closely correlated with the clinical and immune indicators of the patients. Especially a positive correlation to neutrophils was found, indicating a predictable biomarker of iSNV dynamics. Our findings demonstrated the neutrophil-correlated dynamic evolution features of the iSNVs within adenoviruses, which indicates a virus-host interaction during human infection of a DNA virus. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shuting Huo
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.,NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Yan Hai
- Inner Mongolia Center for Disease Control and Prevention, Hohhot, 010031, China
| | - Yaxin Guo
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Li Nie
- Tongliao Center for Disease Control and Prevention, Tongliao, 028000, China
| | - Hongmei Li
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.,NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Peiwen Qiao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Kexin Zong
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.,NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Xin Li
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.,NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Yuanyuan Guo
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China.,School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, China
| | - Jingdong Song
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Honglan Zhao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Wenwen Lei
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - Yu Lan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - William J Liu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.,NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China
| | - George F Gao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.,NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 100052, China.,CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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7
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Wang Y, Xiao X, Chen S, Huang C, Zhou J, Dai E, Li Y, Liu L, Huang X, Gao Z, Wu C, Fang M, Gao C. The Impact of HBV Quasispecies Features on Immune Status in HBsAg+/HBsAb+ Patients With HBV Genotype C Using Next-Generation Sequencing. Front Immunol 2021; 12:775461. [PMID: 34899733 PMCID: PMC8656693 DOI: 10.3389/fimmu.2021.775461] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/08/2021] [Indexed: 12/15/2022] Open
Abstract
Background This study aimed to explore the molecular mechanism of the coexistence of hepatitis B surface antigen (HBsAg) and hepatitis B surface antibody (HBsAb) serological pattern via intensive characterization of HBV s gene in both chronic hepatitis B (CHB) and hepatocellular carcinoma (HCC) patients. Method A total of 73 HBsAg+/HBsAb+ patients (CHB = 36, HCC = 37) and 96 HBsAg+/HBsAb− patients (CHB = 47, HCC = 49) were enrolled from 13 medical centers in China. The sequence features were elaborated based on the combination of next-generation sequencing (NGS) and multidimensional bioinformatics analysis. Results The 16 high-frequency missense mutations, changes of stop codon mutation, clustering, and random forest models based on quasispecies features demonstrated the significant discrepancy power between HBsAg+/HBsAb+ and HBsAg+/HBsAb− in CHB and HCC, respectively. The immunogenicity for cytotoxic T lymphocyte (CTL) epitope Se and antigenicity for the major hydrophilic region (MHR) were both reduced in HBsAg+/HBsAb+ patients (CTL Se: p < 0.0001; MHR: p = 0.0216). Different mutation patterns were observed between HBsAg+/HBsAb+ patients with CHB and with HCC. Especially, mutations in antigenic epitopes, such as I126S in CHB and I126T in HCC, could impact the conformational structure and alter the antigenicity/immunogenicity of HBsAg. Conclusion Based on NGS and bioinformatics analysis, this study indicates for the first time that point mutations and quasispecies diversities of HBV s gene could alter the MHR antigenicity and CTL Se immunogenicity and could contribute to the concurrent HBsAg+/HBsAb+ with different features in HCC and CHB. Our findings might renew the understanding of this special serological profile and benefit the clinical management in HBV-related diseases.
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Affiliation(s)
- Ying Wang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Xiao Xiao
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China.,Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shipeng Chen
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Chenjun Huang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Jun Zhou
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Erhei Dai
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China
| | - Ya Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lijuan Liu
- Department of Laboratory Medicine, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Xianzhang Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhiyuan Gao
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China.,Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chuanyong Wu
- Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Meng Fang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Chunfang Gao
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, China.,Clinical Laboratory Medicine Center, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Goyal A. Modeling reveals no direct role of the extent of HBV DNA integrations on the outcome of infection. J Theor Biol 2021; 526:110793. [PMID: 34087271 DOI: 10.1016/j.jtbi.2021.110793] [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: 03/17/2021] [Revised: 05/15/2021] [Accepted: 05/30/2021] [Indexed: 11/27/2022]
Abstract
Hepatitis B virus (HBV) with its high prevalence and death toll is one of the most important infectious diseases to study. Yet, there is very little progress in the development of within-host models for HBV, which has subsequently hindered our understanding of this virus. The uncertainty around the proliferation of infected hepatocytes has been studied but never in association with other important biological continuous events such as integrations and superinfections. This is despite the fact that these processes affect the diversity and composition of infected cell population in the liver and an improved understanding of the cellular composition will undoubtedly assist in strategizing against this viral infection. Here, we developed novel mathematical models that incorporate these key biological processes and analyzed them both analytically and numerically. Unaffected by the extent of integrated DNA (IDNA), the outcome of HBV infection was primarily dictated by the balance between processes generating and killing infected hepatocytes containing covalent closed circular DNA (cccDNA). The superinfection was found to be a key process in the spread of HBV infection as its exclusion could not reproduce experimentally observed composition of infected hepatocytes at peak of acute HBV infection, a stage where our model predicts that infected hepatocytes most likely carry both cccDNA and IDNA. Our analysis further suggested the existence of some form of selective advantage of infected hepatocytes containing only IDNA to explain the viral dynamics observed during antiviral treatment and the transition from peak to acute infection. Finally, the fine line between liver destruction and resolution of acute HBV infection was found to be highly influenced by the fate of cccDNA during cellular proliferation.
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Affiliation(s)
- Ashish Goyal
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, United States
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Cheng HR, Yang HC, Lin SR, Yang TY, Lin YY, Su TH, Tseng TC, Liu CJ, Kao JH. Combined viral quasispecies diversity and hepatitis B core-related antigen predict off-nucleos(t)ide analog durability in HBeAg-negative patients. Hepatol Int 2021; 15:582-592. [PMID: 33886088 DOI: 10.1007/s12072-021-10186-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/31/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Viral quasispecies dynamics between pre- and post-nucleos(t)ide analog (NA) therapy remains unclear. AIM This study aimed to investigate the HBV quasispecies evolution and its relationship with durability of off-therapy responses in HBeAg-negative chronic hepatitis B (CHB) patients who stopped NA therapy. METHODS Fifty-four HBeAg-negative CHB patients who stopped NAs, including 19 virological controllers (VC) who maintained serum HBV DNA < 2000 IU/mL beyond 1-year off-therapy, and 35 virological relapsers (VR) experiencing virological relapse within 1-year off-therapy were recruited. Viral quasispecies was analyzed by deep sequencing. Hepatitis B core-related antigen (HBcrAg) and HBsAg were also measured. RESULTS VC had significantly higher baseline viral quasispecies diversity of the precore/core gene, measured by nucleotide diversity, than VR. Low baseline viral nucleotide diversity (< 0.01) and high HBcrAg (≧ 2.0 KU/mL), but not HBsAg, at end of treatment (EOT) were significantly associated with higher risk of 1-year virological relapse (hazard ratio [HR] 6.09 and 3.31, respectively). Combination of low baseline viral nucleotide diversity and high HBcrAg at EOT could identify patients at high risk (HR 15.82). Further analysis of the evolution of HBV whole genome showed that HBV nucleotide diversity negatively correlated with serum HBV DNA levels. Notably, the viral quasispecies diversity between pre- and post-NA treatment remained relatively unchanged. CONCLUSION Higher baseline HBV quasispecies diversity associates with more durable off-therapy viral suppression in HBeAg-negative CHB patients. Combination of baseline viral nucleotide diversity and HBcrAg at EOT can identify patients at high risk for virological relapse after stopping NAs.
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Affiliation(s)
- Huei-Ru Cheng
- Department of Internal Medicine, Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, 1 Chang-Te St., Taipei, 10002, Taiwan
| | - Hung-Chih Yang
- Department of Internal Medicine, Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, 1 Chang-Te St., Taipei, 10002, Taiwan
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Su-Ru Lin
- Department of Internal Medicine, Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, 1 Chang-Te St., Taipei, 10002, Taiwan
| | - Ta-Yu Yang
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - You-Yu Lin
- Department of Internal Medicine, Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, 1 Chang-Te St., Taipei, 10002, Taiwan
| | - Tung-Hung Su
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Tai-Chung Tseng
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Jen Liu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Jia-Horng Kao
- Department of Internal Medicine, Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, 1 Chang-Te St., Taipei, 10002, Taiwan.
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
- Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan.
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