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Carmona RDCC, Cilli A, da Costa AC, Reis FC, Leal É, dos Santos FCP, Machado BC, Lopes CS, Afonso AMS, Timenetsky MDCST. Pegivirus Detection in Cerebrospinal Fluid from Patients with Central Nervous System Infections of Unknown Etiology in Brazil by Viral Metagenomics. Microorganisms 2023; 12:19. [PMID: 38257846 PMCID: PMC10818654 DOI: 10.3390/microorganisms12010019] [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: 10/25/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 01/24/2024] Open
Abstract
Metagenomic next-generation sequencing (mNGS) methodology serves as an excellent supplement in cases where diagnosis is challenging to establish through conventional laboratory tests, and its usage is increasingly prevalent. Examining the causes of infectious diseases in the central nervous system (CNS) is vital for understanding their spread, managing outbreaks, and effective patient care. In a study conducted in the state of São Paulo, Brazil, cerebrospinal fluid (CSF) samples from 500 patients with CNS diseases of indeterminate etiology, collected between 2017 and 2021, were analyzed. Employing a mNGS approach, we obtained the complete coding sequence of Pegivirus hominis (HPgV) genotype 2 in a sample from a patient with encephalitis (named IAL-425/BRA/SP/2019); no other pathogen was detected. Subsequently, to determine the extent of this virus's presence, both polymerase chain reaction (PCR) and/or real-time PCR assays were utilized on the entire collection. The presence of the virus was identified in 4.0% of the samples analyzed. This research constitutes the first report of HPgV detection in CSF samples in South America. Analysis of the IAL-425 genome (9107 nt) revealed a 90% nucleotide identity with HPgV strains from various countries. Evolutionary analyses suggest that HPgV is both endemic and extensively distributed. The direct involvement of HPgV in CNS infections in these patients remains uncertain.
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Affiliation(s)
| | - Audrey Cilli
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-900, Brazil; (A.C.); (F.C.R.); (B.C.M.)
| | | | - Fabricio Caldeira Reis
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-900, Brazil; (A.C.); (F.C.R.); (B.C.M.)
| | - Élcio Leal
- Institute of Biological Sciences, Federal University of Pará, Belem 66075-000, Brazil;
| | | | - Bráulio Caetano Machado
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-900, Brazil; (A.C.); (F.C.R.); (B.C.M.)
| | - Cristina Santiago Lopes
- Respiratory Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-900, Brazil; (F.C.P.d.S.); (C.S.L.); (A.M.S.A.)
| | - Ana Maria Sardinha Afonso
- Respiratory Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo 01246-900, Brazil; (F.C.P.d.S.); (C.S.L.); (A.M.S.A.)
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Abstract
Two groups identified a novel human flavivirus in the mid-1990s. One group named the virus hepatitis G virus (HGV) and the other named it GB Virus type C (GBV-C). Sequence analyses found these two isolates to be the same virus, and subsequent studies found that the virus does not cause hepatitis despite sharing genome organization with hepatitis C virus. Although HGV/GBV-C infection is common and may cause persistent infection in humans, the virus does not appear to directly cause any other known disease state. Thus, the virus was renamed “human pegivirus 1” (HPgV-1) for “persistent G” virus. HPgV-1 is found primarily in lymphocytes and not hepatocytes, and several studies found HPgV-1 infection associated with prolonged survival in people living with HIV. Co-infection of human lymphocytes with HPgV-1 and HIV inhibits HIV replication. Although three viral proteins directly inhibit HIV replication in vitro, the major effects of HPgV-1 leading to reduced HIV-related mortality appear to result from a global reduction in immune activation. HPgV-1 specifically interferes with T cell receptor signaling (TCR) by reducing proximal activation of the lymphocyte specific Src kinase LCK. Although TCR signaling is reduced, T cell activation is not abolished and with sufficient stimulus, T cell functions are enabled. Consequently, HPgV-1 is not associated with immune suppression. The HPgV-1 immunomodulatory effects are associated with beneficial outcomes in other diseases including Ebola virus infection and possibly graft-versus-host-disease following stem cell transplantation. Better understanding of HPgV-1 immune escape and mechanisms of inflammation may identify novel therapies for immune-based diseases.
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Affiliation(s)
- Jack T. Stapleton
- Medicine Service, Iowa City Veterans Administration Healthcare, Iowa City, IA, United States
- Departments of Internal Medicine, Microbiology & Immunology, University of Iowa, Iowa City, IA, United States
- *Correspondence: Jack T. Stapleton,
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Ludowyke N, Phumiphanjarphak W, Apiwattanakul N, Manopwisedjaroen S, Pakakasama S, Sensorn I, Pasomsub E, Chantratita W, Hongeng S, Aiewsakun P, Thitithanyanont A. Target Enrichment Metagenomics Reveals Human Pegivirus-1 in Pediatric Hematopoietic Stem Cell Transplantation Recipients. Viruses 2022; 14:v14040796. [PMID: 35458526 PMCID: PMC9025367 DOI: 10.3390/v14040796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
Human pegivirus-1 (HPgV-1) is a lymphotropic human virus, typically considered nonpathogenic, but its infection can sometimes cause persistent viremia both in immunocompetent and immunosuppressed individuals. In a viral discovery research program in hematopoietic stem cell transplant (HSCT) pediatric patients, HPgV-1 was detected in 3 out of 14 patients (21.4%) using a target enrichment next-generation sequencing method, and the presence of the viruses was confirmed by agent-specific qRT-PCR assays. For the first time in this patient cohort, complete genomes of HPgV-1 were acquired and characterized. Phylogenetic analyses indicated that two patients had HPgV-1 genotype 2 and one had HPgV-1 genotype 3. Intra-host genomic variations were described and discussed. Our results highlight the necessity to screen HSCT patients and blood and stem cell donors to reduce the potential risk of HPgV-1 transmission.
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Affiliation(s)
- Natali Ludowyke
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
| | - Worakorn Phumiphanjarphak
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Nopporn Apiwattanakul
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.A.); (S.P.); (S.H.)
| | - Suwimon Manopwisedjaroen
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
| | - Samart Pakakasama
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.A.); (S.P.); (S.H.)
| | - Insee Sensorn
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (I.S.); (W.C.)
| | - Ekawat Pasomsub
- Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (I.S.); (W.C.)
| | - Suradej Hongeng
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.A.); (S.P.); (S.H.)
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (P.A.); (A.T.); Tel.: +66-22015676 (P.A.); +66-22015528 (A.T.)
| | - Arunee Thitithanyanont
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (P.A.); (A.T.); Tel.: +66-22015676 (P.A.); +66-22015528 (A.T.)
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Pradier A, Cordey S, Zanella MC, Melotti A, Wang S, Mamez AC, Chalandon Y, Masouridi-Levrat S, Kaiser L, Simonetta F, Vu DL. Human pegivirus-1 replication influences NK cell reconstitution after allogeneic haematopoietic stem cell transplantation. Front Immunol 2022; 13:1060886. [PMID: 36713419 PMCID: PMC9876574 DOI: 10.3389/fimmu.2022.1060886] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/15/2022] [Indexed: 01/12/2023] Open
Abstract
Introduction Human pegivirus-1 (HPgV-1) is a so-called commensal virus for which no known associated organ disease has been found to date. Yet, it affects immune-reconstitution as previously studied in the HIV population, in whom active co-infection with HPgV-1 can modulate T and NK cell activation and differentiation leading to a protective effect against the evolution of the disease. Little is known on the effect of HPgV-1 on immune-reconstitution in allogeneic hematopoietic stem cell transplant (allo-HSCT) recipients, a patient population in which we and others have previously reported high prevalence of HPgV-1 replication. The aim of this study was to compare the immune reconstitution after allo-HSCT among HPgV-1-viremic and HPgV-1-non-viremic patients. Methods Within a cohort study of 40 allo-HSCT patients, 20 allo-HSCT recipients positive in plasma sample for HPgV-1 by rRT-PCR during the first year (1, 3, 6, 12 months) after transplantation were matched with 20 allo-HSCT recipients negative for HPgV-1. T and NK cell reconstitution was monitored by flow cytometry in peripheral blood samples from allo-HSCT recipients at the same time points. Results We observed no significant difference in the absolute number and subsets proportions of CD4 and CD8 T cells between patient groups at any analysed timepoint. We observed a significantly higher absolute number of NK cells at 3 months among HPgV-1-viremic patients. Immunophenotypic analysis showed a significantly higher proportion of CD56bright NK cells mirrored by a reduced percentage of CD56dim NK cells in HPgV-1-positive patients during the first 6 months after allo-HSCT. At 6 months post-allo-HSCT, NK cell phenotype significantly differed depending on HPgV-1, HPgV-1-viremic patients displaying NK cells with lower CD16 and CD57 expression compared with HPgV-1-negative patients. In accordance with their less differentiated phenotype, we detected a significantly reduced expression of granzyme B in NK cells in HPgV-1-viremic patients at 6 months. Discussion Our study shows that HPgV-1-viremic allo-HSCT recipients displayed an impaired NK cell, but not T cell, immune-reconstitution compared with HPgV-1-non-viremic patients, revealing for the first time a potential association between replication of the non-pathogenic HPgV-1 virus and immunomodulation after allo-HSCT.
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Affiliation(s)
- Amandine Pradier
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Haematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine and Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Samuel Cordey
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Laboratory of virology, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Marie-Céline Zanella
- Laboratory of virology, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
- Division of Infectious diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Astrid Melotti
- Translational Research Center for Oncohematology, Department of Medicine and Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sisi Wang
- Translational Research Center for Oncohematology, Department of Medicine and Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Anne-Claire Mamez
- Division of Haematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
| | - Yves Chalandon
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Haematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine and Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Laurent Kaiser
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Laboratory of virology, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
- Division of Infectious diseases, Geneva University Hospitals, Geneva, Switzerland
- Center for emerging viruses, Geneva University Hospitals, Geneva, Switzerland
| | - Federico Simonetta
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Haematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine and Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Diem-Lan Vu
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Laboratory of virology, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
- Division of Infectious diseases, Geneva University Hospitals, Geneva, Switzerland
- *Correspondence: Diem-Lan Vu, ;
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