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Zanella MC, Vu DL, Hosszu-Fellous K, Neofytos D, Van Delden C, Turin L, Poncet A, Simonetta F, Masouridi-Levrat S, Chalandon Y, Cordey S, Kaiser L. Longitudinal Detection of Twenty DNA and RNA Viruses in Allogeneic Hematopoietic Stem Cell Transplant Recipients Plasma. Viruses 2023; 15:v15040928. [PMID: 37112908 PMCID: PMC10142697 DOI: 10.3390/v15040928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Metagenomics revealed novel and routinely overlooked viruses, representing sources of unrecognized infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT). We aim to describe DNA and RNA virus prevalence and kinetics in allo-HSCT recipients' plasma for one year post HSCT. We included 109 adult patients with first allo-HSCT from 1 March 2017 to 31 January 2019 in this observational cohort study. Seventeen DNA and three RNA viral species were screened with qualitative and/or quantitative r(RT)-PCR assays using plasma samples collected at 0, 1, 3, 6, and 12 months post HSCT. TTV infected 97% of patients, followed by HPgV-1 (prevalence: 26-36%). TTV (median 3.29 × 105 copies/mL) and HPgV-1 (median 1.18 × 106 copies/mL) viral loads peaked at month 3. At least one Polyomaviridae virus (BKPyV, JCPyV, MCPyV, HPyV6/7) was detected in >10% of patients. HPyV6 and HPyV7 prevalence reached 27% and 12% at month 3; CMV prevalence reached 27%. HSV, VZV, EBV, HHV-7, HAdV and B19V prevalence remained <5%. HPyV9, TSPyV, HBoV, EV and HPg-V2 were never detected. At month 3, 72% of patients had co-infections. TTV and HPgV-1 infections were highly prevalent. BKPyV, MCPyV and HPyV6/7 were frequently detected relative to classical culprits. Further investigation is needed into associations between these viral infections and immune reconstitution or clinical outcomes.
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Affiliation(s)
- Marie-Céline Zanella
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Diem-Lan Vu
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Krisztina Hosszu-Fellous
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, 1211 Geneva, Switzerland
| | - Dionysios Neofytos
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Chistian Van Delden
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Lara Turin
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Antoine Poncet
- Center for Clinical Research, Department of Health and Community Medicine, University of Geneva, 1206 Geneva, Switzerland
- Division of Clinical Epidemiology, Department of Health and Community Medicine, University Hospital of Geneva, 1211 Geneva, Switzerland
| | - Federico Simonetta
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Stavroula Masouridi-Levrat
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Yves Chalandon
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Samuel Cordey
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, 1211 Geneva, Switzerland
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Doan MAL, Roczkowsky A, Smith M, Blevins G, van Landeghem FKH, Gelman BB, Branton WG, Stapleton JT, Hobman TC, Power C. Infection of Glia by Human Pegivirus Suppresses Peroxisomal and Antiviral Signaling Pathways. J Virol 2021; 95:e0107421. [PMID: 34524914 DOI: 10.1128/JVI.01074-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Human pegivirus (HPgV) infects peripheral leukocytes but was recently shown to be a neurotropic virus associated with leukoencephalitis in humans. In the present study, we investigated the neural cell tropism of HPgV as well as its effects on host immune responses. HPgV wild type (WT) and a mutant virus with a deletion in the HPgV NS2 gene (ΔNS2) were able to productively infect human astrocytes and microglia but not neurons or an oligodendrocyte-derived cell line. Of note, the ΔNS2 virus replicated better than WT pegivirus in astrocytes, with both viruses being able to subsequently infect and spread in fresh human astrocyte cultures. Infection of human glia by HPgV WT and ΔNS2 viruses resulted in suppression of peroxisome-associated genes, including PEX11B, ABCD1, PEX7, ABCD3, PEX3, and PEX5L, during peak viral production, which was accompanied by reduced expression of IFNB, IRF3, IRF1, and MAVS, particularly in ΔNS2-infected cells. These data were consistent with analyses of brain tissue from patients infected with HPgV in which we observed suppression of peroxisome and type I interferon gene transcripts, including PEX11B, ABCD3, IRF1, and IRF3, with concurrent loss of PMP70 immunoreactivity in glia. Our data indicate that human astrocytes and microglia are permissive to HPgV infection, resulting in peroxisome injury and suppressed antiviral signaling that is influenced by viral diversity. IMPORTANCE Human pegiviruses are detected in 1 to 5% of the general population, principally infecting leukocytes, although their effects on human health remain uncertain. Here, we show that human pegivirus infects specific neural cell types in culture and human brain and, like other neurotropic flaviviruses, causes suppression of peroxisome and antiviral signaling pathways, which could favor ongoing viral infection and perhaps confer susceptibility to the development of neurological disease.
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Fama A, Larson MC, Link BK, Habermann TM, Feldman AL, Call TG, Ansell SM, Liebow M, Xiang J, Maurer MJ, Slager SL, Nowakowski GS, Stapleton JT, Cerhan JR. Human Pegivirus Infection and Lymphoma Risk: A Systematic Review and Meta-analysis. Clin Infect Dis 2021; 71:1221-1228. [PMID: 31671178 DOI: 10.1093/cid/ciz940] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 09/20/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Human pegivirus (HPgV) is a single-strand RNA virus belonging to the Flaviviridae. Although no definitive association between HPgV infection and disease has been identified, previous studies have suggested an association of HPgV viremia with risk of lymphomas. METHODS We conducted a systematic review and meta-analysis, including 1 cohort study and 14 case-control studies, assessing the association of HPgV viremia with adult lymphomas. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using a random-effects model, overall and by geographic region and lymphoma subtype. RESULTS The overall OR for lymphoma was 2.85 (95% CI, 1.98-4.11), with statistically significantly elevated ORs observed in 8 of 15 studies. There was a small amount of heterogeneity among studies (I2 = 28.9%; Q = 18.27, P = .16), and the funnel plot provided no evidence for publication bias. The strongest association with lymphoma risk was observed for studies from Southern Europe (OR, 5.68 [95% CI, 1.98-16.3]), whereas weaker ORs (with 95% CIs) were observed for studies from North America (2.24 [1.76-2.85]), Northern Europe (2.90 [.45-18.7), and the Middle East (2.51 [.87-7.27]), but all of similar magnitude. Participants with HPgV viremia had statistically significantly increased risks (OR [95% CI]) for developing diffuse large B-cell (3.29 [1.63-6.62]), follicular (3.01 [1.95-4.63]), marginal zone (1.90 [1.13-3.18]), and T-cell (2.11 [1.17-3.89]) lymphomas, while the risk for Hodgkin lymphoma (3.53 [.48-25.9]) and chronic lymphocytic leukemia (1.45 [.45-4.66]) were increased but did not achieve statistical significance. CONCLUSIONS This meta-analysis supports a positive association of HPgV viremia with lymphoma risk, overall and for the major lymphoma subtypes.
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Affiliation(s)
- Angelo Fama
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Ematologia, Azienda Unità Sanitaria Locale, Istituto di Ricovero e Cura a Carattere Scientifico di Reggio Emilia, Reggio Emilia, Italy
| | - Melissa C Larson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Brian K Link
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Thomas M Habermann
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Timothy G Call
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Stephen M Ansell
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Mark Liebow
- Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Jinhua Xiang
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA.,Iowa City Veterans Affairs Medical Center, Iowa City, Iowa, USA
| | - Matthew J Maurer
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Grzegorz S Nowakowski
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Jack T Stapleton
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA.,Iowa City Veterans Affairs Medical Center, Iowa City, Iowa, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
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Cai HZ, Zhang H, Yang J, Zeng J, Wang H. Preliminary assessment of viral metagenome from cancer tissue and blood from patients with lung adenocarcinoma. J Med Virol 2021; 93:5126-5133. [PMID: 33595122 DOI: 10.1002/jmv.26887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/30/2021] [Accepted: 02/15/2021] [Indexed: 12/18/2022]
Abstract
In this study, using a viral metagenomic method, we investigated the composition of virome in blood and cancer tissue samples that were collected from 25 patients with lung adenocarcinoma. Results indicated that virus sequences showing similarity to human pegivirus (HPgV), anellovirus, human endogenous retrovirus (HERV), and polyomavirus were recovered from this cohort. Three different complete genomes of HPgV were acquired from the blood samples and one complete genome of polyomavirus was determined from the cancer tissue sample. Phylogenetic analysis indicated that the three HPgV strains belonged to genotype 3 and the polyomavirus showed the highest sequence identity (99.73%) to trichodysplasia spinulosa-associated polyomavirus. PCR screening results indicated that the three HPgVs were present in 5 out of the 25 blood samples and the polyomavirus only existed in a cancer tissue sample pool. Whether infections with viruses have an association with lung cancer needs further study with a larger size of sampling.
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Affiliation(s)
- Hua-Zhong Cai
- Department of Emergency, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Heteng Zhang
- Department of Clinical Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jie Yang
- Department of Clinical Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jian Zeng
- Department of Clinical Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hao Wang
- Department of Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu, China
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Hoffmann R, Ruegamer T, Schaubächer J, Rohrhofer A, Kirmeß P, Fiebig KM, Schmidt B, Eichler J. Exploring Viral Interference Using Peptides: Molecular Determinants of HIV-1 Inhibition by a Peptide Derived from Human Pegivirus-1 Envelope Protein E2. ChemMedChem 2021; 16:1290-1296. [PMID: 33378104 PMCID: PMC8248410 DOI: 10.1002/cmdc.202000892] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/29/2020] [Indexed: 01/13/2023]
Abstract
Co-infection with the human pegivirus 1 (HPgV-1) often has a beneficial effect on disease progression in HIV-1-infected individuals. Several HPgV-1 proteins and peptides, including a 20-mer peptide (P6-2) derived from the N-terminal region of the HPgV-1 surface protein E2, have been associated with this phenomenon, which is referred to as viral interference. We identified the cysteine residues, the hydrophobic core tetrapeptide, as well as the C-terminal negative charge as key factors for the HIV-1 inhibitory activity of P6-2. Analysis of mutations in P6-2-resistant HIV-1 indicated a binding site for the peptide in the HIV-1 envelope glycoprotein gp120. In fact, P6-2 was shown to bind to soluble gp120, as well as to a peptide presenting the gp120 V3 loop. Furthermore, the HIV-1 inhibitory activity of P6-2 could be revoked by the V3 loop peptide, thus indicating a molecular mechanism that involves interaction of P6-2 with the gp120 V3 loop.
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Affiliation(s)
- Rebecca Hoffmann
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Tamara Ruegamer
- Institute of Clinical Microbiology and Hygiene, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Johanna Schaubächer
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Anette Rohrhofer
- Institute of Clinical Microbiology and Hygiene, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Peter Kirmeß
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Karen M Fiebig
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Barbara Schmidt
- Institute of Clinical Microbiology and Hygiene, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany.,Institute of Medical Microbiology and Hygiene, University of Regensburg, Franz-Josef-Strauß-Allee 11, 93053, Regensburg, Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
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6
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Greenhalgh S, Schmidt R, Day T. Fighting the Public Health Burden of AIDS With the Human Pegivirus. Am J Epidemiol 2019; 188:1586-1594. [PMID: 31145443 DOI: 10.1093/aje/kwz139] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 12/17/2022] Open
Abstract
Highly active antiretroviral therapy has revolutionized the battle against human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS). From its current global rollout, HIV/AIDS morbidity and mortality has been greatly reduced, yet there exists substantial interest in the development of new therapies to further mitigate the HIV/AIDS health burden and to inhibit any fallout from the development of antiretroviral drug resistance. One potential intervention is the human pegivirus (HPgV). HPgV is not known to cause disease, and most remarkably it is shown to delay the progression of HIV to AIDS. However, the health benefit of increasing HPgV prevalence in the community of HIV-infected men remains unknown at the public health level. We evaluated the utility of HPgV biovaccination for mitigating the HIV/AIDS health burden using mathematical models. Importantly, our work considers the potential concern that HPgV will, itself, evolve to become disease-causing by permitting mutant disease-causing HPgV strains to potentially arise during treatment. Our findings show that HPgV biovaccination rates of 12.5%-50% annually could prevent 4.2-23.6 AIDS incidences and 3.3-18.8 AIDS deaths, and could save 2.9-18.6 disability-adjusted life years per 1,000 people. Together, these findings indicate that HPgV biovaccination could be an effective therapy for reducing HIV/AIDS morbidity and mortality, and thus warrants further exploration.
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Affiliation(s)
- Scott Greenhalgh
- Department of Mathematics, Siena College, Loudonville, New York
- Department of Mathematics and Statistics, Queen’s University, Kingston, Ontario, Canada
| | - Rebecca Schmidt
- Department of Mathematics and Statistics, Queen’s University, Kingston, Ontario, Canada
| | - Troy Day
- Department of Mathematics and Statistics, Queen’s University, Kingston, Ontario, Canada
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Bukowska-Ośko I, Perlejewski K, Pawełczyk A, Rydzanicz M, Pollak A, Popiel M, Cortés KC, Paciorek M, Horban A, Dzieciątkowski T, Radkowski M, Laskus T. Human Pegivirus in Patients with Encephalitis of Unclear Etiology, Poland. Emerg Infect Dis 2019; 24:1785-1794. [PMID: 30226156 PMCID: PMC6154136 DOI: 10.3201/eid2410.180161] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Sequence analysis of human pegivirus from 3 patients indicates that the central nervous system constitutes a separate viral compartment from serum. Human pegivirus (HPgV), previously called hepatitis G virus or GB virus C, is a lymphotropic virus with undefined pathology. Because many viruses from the family Flaviviridae, to which HPgV belongs, are neurotropic, we studied whether HPgV could infect the central nervous system. We tested serum and cerebrospinal fluid samples from 96 patients with a diagnosis of encephalitis for a variety of pathogens by molecular methods and serology; we also tested for autoantibodies against neuronal antigens. We found HPgV in serum and cerebrospinal fluid from 3 patients who had encephalitis of unclear origin; that is, all the markers that had been tested were negative. Single-strand confirmation polymorphism and next-generation sequencing analysis revealed differences between the serum and cerebrospinal fluid–derived viral sequences, which is compatible with the presence of a separate HPgV compartment in the central nervous system. It is unclear whether HPgV was directly responsible for encephalitis in these patients.
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Jordier F, Deligny ML, Barré R, Robert C, Galicher V, Uch R, Fournier PE, Raoult D, Biagini P. Human pegivirus isolates characterized by deep sequencing from hepatitis C virus-RNA and human immunodeficiency virus-RNA-positive blood donations, France. J Med Virol 2018; 91:38-44. [PMID: 30133782 DOI: 10.1002/jmv.25290] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/14/2018] [Indexed: 01/18/2023]
Abstract
Human pegivirus (HPgV, formerly GBV-C) is a member of the genus Pegivirus, family Flaviviridae. Despite its identification more than 20 years ago, both natural history and distribution of this viral group in human hosts remain under exploration. Analysis of HPgV genomes characterized up to now points out the scarcity of French pegivirus sequences in databases. To bring new data regarding HPgV genomic diversity, we investigated 16 French isolates obtained from hepatitis C virus-RNA and human immunodeficiency virus-RNA-positive blood donations following deep sequencing and coupled molecular protocols. Initial phylogenetic analysis of 5'-untranslated region (5'-UTR)/E2 partial sequences permitted to assign HPgV isolates to genotypes 2 (n = 15) and 1 (n = 1), with up to 16% genetic diversity observed for both regions considered. Seven nearly full-length representative genomes were characterized subsequently, with complete polyprotein coding sequences exhibiting up to 13% genetic diversity; closest nucleotide (nt) divergence with available HPgV sequences was in the range 7% to 11%. A 36 nts deletion located on the NS4B coding region (N-terminal part, 12 amino acids) of the genotype 1 HPgV genome characterized was identified, along with single nucleotide deletions in two genotype 2, 5'-UTR sequences.
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Affiliation(s)
- François Jordier
- Biologie des Groupes Sanguins, Etablissement Français du Sang Provence Alpes Côte d'Azur Corse, Aix Marseille University, CNRS, EFS, ADES, Marseille, France
| | - Marie-Laurence Deligny
- Biologie des Groupes Sanguins, Etablissement Français du Sang Provence Alpes Côte d'Azur Corse, Aix Marseille University, CNRS, EFS, ADES, Marseille, France
| | - Romain Barré
- Biologie des Groupes Sanguins, Etablissement Français du Sang Provence Alpes Côte d'Azur Corse, Aix Marseille University, CNRS, EFS, ADES, Marseille, France
| | - Catherine Robert
- UMR MEPHI, IRD, Aix Marseille University, AP-HM, IHU Méditerranée-Infection, Marseille, France
| | - Vital Galicher
- Biologie des Groupes Sanguins, Etablissement Français du Sang Provence Alpes Côte d'Azur Corse, Aix Marseille University, CNRS, EFS, ADES, Marseille, France
| | - Rathviro Uch
- Biologie des Groupes Sanguins, Etablissement Français du Sang Provence Alpes Côte d'Azur Corse, Aix Marseille University, CNRS, EFS, ADES, Marseille, France
| | - Pierre-Edouard Fournier
- UMR VITROME, IRD, Aix Marseille University, SSA, AP-HM, IHU Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- UMR MEPHI, IRD, Aix Marseille University, AP-HM, IHU Méditerranée-Infection, Marseille, France
| | - Philippe Biagini
- Biologie des Groupes Sanguins, Etablissement Français du Sang Provence Alpes Côte d'Azur Corse, Aix Marseille University, CNRS, EFS, ADES, Marseille, France
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Takeuchi S, Kawada JI, Okuno Y, Horiba K, Suzuki T, Torii Y, Yasuda K, Numaguchi A, Kato T, Takahashi Y, Ito Y. Identification of potential pathogenic viruses in patients with acute myocarditis using next-generation sequencing. J Med Virol 2018; 90:1814-1821. [PMID: 30011073 DOI: 10.1002/jmv.25263] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/30/2018] [Indexed: 12/18/2022]
Abstract
Myocarditis is an inflammatory disease of the myocardium and leads to cardiac dysfunction and heart failure. Although viral infections are considered to be the most common etiology of myocarditis, the identification of the causative virus is still challenging. Recently, next-generation sequencing (NGS) has been applied in the diagnosis of infectious diseases. The aim of the current study was to comprehensively analyze potential pathogenic microorganisms using NGS in the sera of patients with myocarditis. Twelve pediatric and five adult patients hospitalized for acute myocarditis were included. Serum samples in the acute phase were obtained and analyzed using NGS to detect pathogen-derived DNA and RNA. Viral sequence reads were detected in 7 (41%) of the 17 myocarditis patients by NGS. Among these patients, detection of Epstein-Barr virus, human parvovirus B19, torque teno virus, and respiratory syncytial virus reads by NGS was consistent with polymerase chain reaction or antigen test results in one patient each. A large number of human pegivirus reads were detected from one patient by RNA sequencing; however, its pathogenicity to human is unknown. Conversely, the number of detected virus-derived reads was small in most cases, and the pathophysiological role of these viruses remains to be clarified. No significant bacterial or fungal reads other than normal bacterial flora was detected. These data indicate that comprehensive detection of virus-derived DNA and RNA using NGS can be useful for the identification of potential pathogenic viruses in myocarditis.
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Affiliation(s)
- Suguru Takeuchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yusuke Okuno
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazushi Yasuda
- Department of Pediatric Cardiology, Aichi Children's Health and Medical Center, Obu, Japan
| | - Atsushi Numaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taichi Kato
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Abstract
The known genetic diversity of the hepaciviruses and pegiviruses has increased greatly in recent years through the discovery of viruses related to hepatitis C virus and human pegivirus in bats, bovines, equines, primates, and rodents. Analysis of these new species is important for research into animal models of hepatitis C virus infection and into the zoonotic origins of human viruses. Here, we provide the first systematic phylogenetic and evolutionary analysis of these two genera at the whole-genome level. Phylogenies confirmed that hepatitis C virus is most closely related to viruses from horses whereas human pegiviruses clustered with viruses from African primates. Within each genus, several well-supported lineages were identified and viral diversity was structured by both host species and location of sampling. Recombination analyses provided evidence of interspecific recombination in hepaciviruses, but none in the pegiviruses. Putative mosaic genome structures were identified in NS5B gene region and were supported by multiple tests. The identification of interspecific recombination in the hepaciviruses represents an important evolutionary event that could be clarified by future sampling of novel viruses. We also identified parallel amino acid changes shared by distantly related lineages that infect similar types of host. Notable parallel changes were clustered in the NS3 and NS4B genes and provide a useful starting point for experimental studies of the evolution of Hepacivirus host-virus interactions.
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Affiliation(s)
- Julien Thézé
- Department of Zoology, University of Oxford, United Kingdom
| | - Sophia Lowes
- Department of Zoology, University of Oxford, United Kingdom
| | - Joe Parker
- Biodiversity Informatics and Spatial Analysis, The Jodrell Laboratory, Royal Botanic Gardens, Kew, United Kingdom
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, United Kingdom
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