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Cao X, Tang L, Song J. Circular Single-Stranded DNA: Discovery, Biological Effects, and Applications. ACS Synth Biol 2024; 13:1038-1058. [PMID: 38501391 DOI: 10.1021/acssynbio.4c00040] [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] [Indexed: 03/20/2024]
Abstract
The field of nucleic acid therapeutics has witnessed a significant surge in recent times, as evidenced by the increasing number of approved genetic drugs. However, current platform technologies containing plasmids, lipid nanoparticle-mRNAs, and adeno-associated virus vectors encounter various limitations and challenges. Thus, we are devoted to finding a novel nucleic acid vector and have directed our efforts toward investigating circular single-stranded DNA (CssDNA), an ancient form of nucleic acid. CssDNAs are ubiquitous, but generally ignored. Accumulating evidence suggests that CssDNAs possess exceptional properties as nucleic acid vectors, exhibiting great potential for clinical applications in genetic disorders, gene editing, and immune cell therapy. Here, we comprehensively review the discovery and biological effects of CssDNAs as well as their applications in the field of biomedical research for the first time. Undoubtedly, as an ancient form of DNA, CssDNA holds immense potential and promises novel insights for biomedical research.
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Affiliation(s)
- Xisen Cao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
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2
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Prediction of humoral and cellular immune response to COVID-19 mRNA vaccination by TTV load in kidney transplant recipients and hemodialysis patients. J Clin Virol 2023; 162:105428. [PMID: 36989730 PMCID: PMC10036154 DOI: 10.1016/j.jcv.2023.105428] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/14/2023] [Accepted: 03/19/2023] [Indexed: 03/25/2023]
Abstract
Background Immunosuppressed individuals such as kidney transplant recipients (KTR) and hemodialysis patients (DP) show impaired immune responses to COVID-19 vaccination. Plasma Torque Teno Virus (TTV) DNA load is used as surrogate for the individual degree of immunosuppression. We now assessed the association of TTV load at time of COVID-19 vaccination with humoral and cellular immune response rates to vaccination in KTR, DP, and healthy medical personnel (MP). Methods A total of 100 KTR, 115 DP and 54 MP were included. All were SARS-CoV-2 seronegative at the time of vaccination with either BNT162b2 or mRNA-1273. Plasma TTV loads were assessed at the time of first vaccination. After two-dose vaccination, seroconversion (de novo detection of SARS-CoV-2 S1-IgA and/or IgG) was determined. In addition, cellular responses as assessed by interferon γ release and neutralizing antibodies were assessed in a subset of participants. ROC analyses were performed to define TTV load cut-offs predicting specific immune responses to vaccination. Results Plasma TTV loads at the time of first vaccination were negatively associated with seroconversion after two-dose vaccination in KTR (OR 0.87, 95% CI 0.76-0.99). TTV loads were significantly lower in KTR who developed humoral and cellular immune responses to vaccination compared to non-responders (p=0.0411 and 0.0030, respectively). Of patients with TTV loads above 106 copies/ml, none developed cellular immune responses against SARS-CoV-2, and only 2 of 17 (12%) seroconverted in response to vaccination. Conclusion Plasma TTV loads at the time of first vaccination in immunosuppressed individuals may be useful to predict individual vaccine-specific immune responses.
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3
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Identification and Genomic Characterization of Anelloviruses in Patients with Chronic Lymphocytic Leukemia. J Clin Pharm Ther 2023. [DOI: 10.1155/2023/4125745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Purpose. Metagenomics has revealed that, in addition to the digestive tract, certain viruses are also commonly found in human blood. In order to explore and monitor potential novel viruses, three serum samples of patients with chronic lymphocytic leukemia were collected at the No. 2 People’s Hospital of Changshu City, China. Materials and Methods. We sequenced the virome of serum samples from three patients with chronic lymphocytic leukemia using an unbiased viral metagenomic approach and subsequently performed maximum likelihood phylogenetic analysis using MrBayes v3.2. In addition, pairwise sequence comparison was produced with ORF1 amino acid sequences of anelloviruses within Bayesian consensus tree. Results. Partial genomes of eight different anelloviruses containing the complete ORF1 gene have been identified. BLASTp results showed that the amino acid sequence identity of these viruses with the best match in GenBank was between 56.22% and 95.43%. Phylogenetic analysis based on ORF1 indicated that seven sequences belong to the genus Alphatorquevirus and one sequence belongs to the genus Gammatorquevirus. Conclusions. This virological investigation has increased our understanding of the diversity of anelloviruses in human serum, but further study is needed to verify its potential correlation with disease.
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Stincarelli MA, Baj A, Guidotti B, Spezia PG, Novazzi F, Lucenteforte E, Tillati S, Focosi D, Maggi F, Giannecchini S. Plasma Torquetenovirus (TTV) microRNAs and severity of COVID-19. Virol J 2022; 19:79. [PMID: 35562762 PMCID: PMC9099037 DOI: 10.1186/s12985-022-01812-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/27/2022] [Indexed: 12/03/2022] Open
Abstract
Background Torquetenovirus (TTV), a widespread anellovirus recognized as the main component of the healthy human virome, displays viremia that is highly susceptible to variations in immune competence. TTV possesses microRNA (miRNA)-coding sequences that might be involved in viral immune evasion. Among TTV-encoded miRNAs, miRNA t1a, t3b, and tth8 have been found in biological fluids. Here, the presence of TTV DNA and TTV miRNAs in the plasma of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected subjects was investigated to monitor the possible association with coronavirus disease 2019 (COVID-19) severity. Methods Detection of TTV DNA and miRNA t1a, t3b, and tth8 was investigated in plasma samples of 56 SARS-CoV-2-infected subjects with a spectrum of different COVID-19 outcomes. TTV DNA and TTV miRNAs were assessed with a universal single step real-time TaqMan PCR assay and miRNA quantitative RT-PCR miRNA assay, respectively. Results The TTV DNA prevalence was 59%, whereas at least one TTV miRNA was found in 94% of the patients tested. miRNA tth8 was detected in 91% of subjects, followed by miRNAs t3b (64%) and miRNAt1a (30%). Remarkably, although TTV DNA was unrelated to COVID-19 severity, miRNA tth8 was significantly associated with the degree of disease (adjusted incidence rate ratio (IRR) 2.04, 95% CI 1.14–3.63, for the subjects in the high severity group compared to those in the low severity group). Conclusions Our findings encourage further investigation to understand the potential role of TTV miRNAs in the different outcomes of COVID-19 at early and late stages.
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Affiliation(s)
- Maria Alfreda Stincarelli
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, 50134, Florence, Italy
| | - Andreina Baj
- Department of Medicine and Surgery, University of Insubria, 21100, Varese, Italy
| | - Bernardo Guidotti
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, 50134, Florence, Italy
| | | | - Federica Novazzi
- Department of Medicine and Surgery, University of Insubria, 21100, Varese, Italy
| | - Ersilia Lucenteforte
- Department of Clinical and Experimental Medicine, University of Pisa, 56100, Pisa, Italy
| | - Silvia Tillati
- Department of Clinical and Experimental Medicine, University of Pisa, 56100, Pisa, Italy
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124, Pisa, Italy
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, 21100, Varese, Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, 50134, Florence, Italy.
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5
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Woerner J, Huang Y, Hutter S, Gurnari C, Sánchez JMH, Wang J, Huang Y, Schnabel D, Aaby M, Xu W, Thorat V, Jiang D, Jha BK, Koyuturk M, Maciejewski JP, Haferlach T, LaFramboise T. Circulating microbial content in myeloid malignancy patients is associated with disease subtypes and patient outcomes. Nat Commun 2022; 13:1038. [PMID: 35210415 PMCID: PMC8873459 DOI: 10.1038/s41467-022-28678-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 02/01/2022] [Indexed: 02/06/2023] Open
Abstract
Although recent work has described the microbiome in solid tumors, microbial content in hematological malignancies is not well-characterized. Here we analyze existing deep DNA sequence data from the blood and bone marrow of 1870 patients with myeloid malignancies, along with healthy controls, for bacterial, fungal, and viral content. After strict quality filtering, we find evidence for dysbiosis in disease cases, and distinct microbial signatures among disease subtypes. We also find that microbial content is associated with host gene mutations and with myeloblast cell percentages. In patients with low-risk myelodysplastic syndrome, we provide evidence that Epstein-Barr virus status refines risk stratification into more precise categories than the current standard. Motivated by these observations, we construct machine-learning classifiers that can discriminate among disease subtypes based solely on bacterial content. Our study highlights the association between the circulating microbiome and patient outcome, and its relationship with disease subtype.
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Affiliation(s)
- Jakob Woerner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Yidi Huang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | | | - Carmelo Gurnari
- Department of Translational Hematology & Oncology Research, Cleveland Clinic Foundation, Cleveland, USA
| | | | - Janet Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Yimin Huang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Daniel Schnabel
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Michael Aaby
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Wanying Xu
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Vedant Thorat
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Dongxu Jiang
- Department of Translational Hematology & Oncology Research, Cleveland Clinic Foundation, Cleveland, USA
| | - Babal K Jha
- Department of Translational Hematology & Oncology Research, Cleveland Clinic Foundation, Cleveland, USA
| | - Mehmet Koyuturk
- Department of Computer Science, Case Western Reserve University, Cleveland, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology & Oncology Research, Cleveland Clinic Foundation, Cleveland, USA
| | | | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA.
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6
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Linthorst J, Welkers MRA, Sistermans EA. Clinically relevant DNA viruses in pregnancy. Prenat Diagn 2022; 43:457-466. [PMID: 35170055 DOI: 10.1002/pd.6116] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/28/2022] [Accepted: 02/11/2022] [Indexed: 11/10/2022]
Abstract
Infections by DNA viruses during pregnancy are associated with increased health risks to both mother and fetus. Although not all DNA viruses are related to an increased risk of complications during pregnancy, several can directly infect the fetus and/or cause placental dysfunction. During NIPT analysis, the presence of viral DNA can be detected, theoretically allowing screening early in pregnancy. Although treatment options are currently limited, this might rapidly change in the near future. It is therefore important to be aware of the potential impact of these viruses on feto-maternal health. In this manuscript we provide a brief introduction into the most commonly detected DNA viruses in human cell-free DNA sequencing experiments and their pathogenic potential during pregnancy. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jasper Linthorst
- Dept of Human Genetics and Amsterdam Reproduction & Development research institute, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands, van der Boechorststraat 7, 1081, BT Amsterdam, The Netherlands
| | - Matthijs R A Welkers
- Dept of Medical Microbiology and Infection Prevention, Amsterdam UMC, Amsterdam, The Netherlands
| | - Erik A Sistermans
- Dept of Human Genetics and Amsterdam Reproduction & Development research institute, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands, van der Boechorststraat 7, 1081, BT Amsterdam, The Netherlands
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7
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Redondo N, Navarro D, Aguado JM, Fernández-Ruiz M. Viruses, friends and foes: The case of Torque Teno virus and the net state of immunosuppression. Transpl Infect Dis 2021; 24:e13778. [PMID: 34933413 DOI: 10.1111/tid.13778] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/16/2021] [Accepted: 12/05/2021] [Indexed: 11/30/2022]
Abstract
New reliable biomarkers are needed to improve individual risk assessment for post-transplant infection, acute graft rejection and other immune-related complications after solid organ transplantation (SOT) and allogeneic hematopoietic stem cell transplantation (allo-HSCT). One promising strategy relies on the monitoring of replication kinetics of virome components as functional surrogate for the net state of immunosuppression. Torque Teno Virus (TTV) is a small, non-enveloped, circular, single-stranded DNA anellovirus with no attributable pathological effects. A major component of the human blood virome, TTV exhibits various features that facilitate its application as immune biomarker: high prevalence rates, nearly ubiquitous distribution, stable viral loads with little intra-individual variability, insensitivity to antiviral drugs, and availability of commercial PCR assays for DNA quantification. The present review summarizes the available studies supporting the use of post-transplant TTV viremia to predict patient and graft outcomes after SOT and allo-HSCT. Taken together, this evidence suggests that high or increasing TTV DNA levels precede the occurrence of infectious complications in the SOT setting, whereas low or decreasing viral loads are associated with the development of acute rejection. The interpretation in allo-HSCT recipients is further complicated by complex interplay with the underlying disease, conditioning regimen and timing of recovery of lymphocyte counts, although TTV kinetics may act as a marker of immunological reconstitution at the early post-transplant period. The standardization of PCR methods and reporting units for TTV DNAemia and the results from ongoing interventional trials evaluating a TTV load-guided strategy to adjust immunosuppressive therapy are achievements expected in the coming years. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Natalia Redondo
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Spain
| | - David Navarro
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Spain.,Department of Microbiology, Hospital Clínico Universitario, Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain.,Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - José María Aguado
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Spain.,Department of Medicine, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Mario Fernández-Ruiz
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Spain.,Department of Medicine, School of Medicine, Universidad Complutense, Madrid, Spain
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8
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Hsiao KL, Wang LY, Cheng JC, Cheng YJ, Lin CL, Liu HF. Detection and genetic characterization of the novel torque teno virus group 6 in Taiwanese general population. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210938. [PMID: 34737877 PMCID: PMC8564604 DOI: 10.1098/rsos.210938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
Torque teno virus (TTV) is one of the most common human viruses and can infect an individual with multiple genotypes chronically and persistently. TTV group 6 is a recently discovered phylogenetic group first isolated from eastern Taiwan indigenes, but whether the TTV group 6 was also prevalent in the general population still unknown. One hundred and three randomly collected blood samples from general population and 66 TTV positive DNA samples extracted from Taiwan indigenes were included. A group-6-specific PCR was developed for re-screen over TTV positive samples. Two TTV group 6 positive samples from general population were cloned and sequenced for identifying mix-infected TTVs and confirming their classification by maximum-likelihood and Bayesian inference phylogeny. TTV group 6 can be detected in 4.5% (4/89) and 7.6% (5/66) of TTV positive samples from Taiwanese general population and eastern Taiwan indigenes, respectively. Sample VC09 was mix-infected with TTV groups 3 and 6. Sample VC99 was mix-infected with TTV groups 3, 4 and 6. A highly diverse triple overlapping region was observed, which may represent a unique phenomenon of TTV. The group-6-specific PCR can successfully detect TTV group 6. TTV group 6 may be prevalent worldwide regardless of the geographic region and/or ethnic groups.
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Affiliation(s)
- Kuang-Liang Hsiao
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Li-Yu Wang
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
| | - Ju-Chien Cheng
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Yu-Jung Cheng
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Chiung-Ling Lin
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Hsin-Fu Liu
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Institute of Biomedical Sciences, MacKay Medical College, New Taipei City, Taiwan
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9
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Iravani Saadi M, Ramzi M, Hesami Z, kheradmand N, Owjfard M, Nabi Abdolyousefi E, Karimi Z. MiR-181a and -b expression in acute lymphoblastic leukemia and its correlation with acute graft-versus-host disease after hematopoietic stem cell transplantation, COVID-19 and torque teno viruses. Virusdisease 2021; 32:727-736. [PMID: 34722832 PMCID: PMC8543773 DOI: 10.1007/s13337-021-00743-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/14/2021] [Indexed: 11/29/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL), a malignant transformation and proliferation of the lymphoid line of blood cells, is characterized by chromosomal abnormalities and genetic changes. The purpose of this research was the evaluation of expression level of miR-181a and -b in patients with ALL compared to the control group. Furthermore, we examined their expression level in hematopoietic stem-cell transplantation (HSCT) patients who developed acute graft-versus-host disease (aGVHD) in comparison with those without aGVHD and explore the relationship between their expression level and cytogenetic abnormalities. In this cross-sectional study, 76 newly diagnosed adult De novo ALL patients were enrolled who were admitted to our referral hospital. All patients received standard chemotherapy, consisting of daunorubicin. A total of 37 patients underwent HSCT from the related human leukocyte antigen-matched donors. ALL patients have been diagnosed with the coronavirus disease 2019 (COVID-19) and Torque teno viruses (TTVs). We assessed the expression levels of miR-181a and -b in the peripheral blood sample of ALL patients at the time of diagnosis prior to chemotherapy, and healthy matched individuals by RT–PCR. TTVs and COVID-19 load were also determined via RT–PCR. In conclusion, the expression level of miR-181a and -b were significantly higher in ALL patients than healthy controls and also increased in patients who developed aGVHD in comparison with those without aGVHD. MiR-181a and -b can be a useful biomarker in ALL and a useful indicator of aGVHD. The expression level of miR-181a in ALL patients with COVID-19 is significantly up-regulated, while it is reduced in these patients with TTV.
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Affiliation(s)
- Mahdiyar Iravani Saadi
- Hematology Research Center and Department of Bone Marrow Transplantation, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mani Ramzi
- Hematology Research Center and Department of Bone Marrow Transplantation, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Hematology, Medical Oncology and Stem Cell Transplantation, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Hesami
- Hematology Research Center and Department of Bone Marrow Transplantation, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nadiya kheradmand
- Hematology Research Center and Department of Bone Marrow Transplantation, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Owjfard
- Clinical Neurology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ehsan Nabi Abdolyousefi
- Hematology Research Center and Department of Bone Marrow Transplantation, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahed Karimi
- Hematology Research Center and Department of Bone Marrow Transplantation, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Hematology, Medical Oncology and Stem Cell Transplantation, Shiraz University of Medical Sciences, Shiraz, Iran
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10
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Leijonhufvud G, Bajalan A, Teixeira Soratto TA, Gustafsson B, Bogdanovic G, Bjerkner A, Allander T, Ljungman G, Andersson B. Better detection of Torque teno virus in children with leukemia by metagenomic sequencing than by quantitative PCR. J Med Virol 2021; 94:634-641. [PMID: 34672369 DOI: 10.1002/jmv.27409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/06/2021] [Accepted: 10/16/2021] [Indexed: 11/11/2022]
Abstract
Torque teno virus (TTV) is a group of chronically persisting viruses with a short circular DNA genome. TTV demonstrates a wide sequence diversity and a large majority of humans are chronically infected by one or more types of TTV. As TTV is ubiquitous, and viral replication correlates with immune status, TTV has been studied as a marker to assess global functional immune competence in transplant recipients. Most studies of the prevalence, amounts, and variation in TTV have been performed using PCR assays. We here present a comparison of the most frequently used quantitative PCR (qPCR) assay for TTV with shotgun metagenomic sequencing for detection and characterization of TTV in a cohort of pediatric cancer patients. The results show that TTV is more common than the qPCR assays indicate, and analysis of the TTV genome sequences indicate that a qPCR with primers and probe designed on a conserved region of the TTV genome may fail to detect some of the TTV strains found in this study.
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Affiliation(s)
- Gustaf Leijonhufvud
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden.,Department of Pediatric Hematology/Oncology, Children's University Hospital, Uppsala, Sweden
| | - Amanj Bajalan
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tatiany Aparecida Teixeira Soratto
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Britt Gustafsson
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Gordana Bogdanovic
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Annelie Bjerkner
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Tobias Allander
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gustaf Ljungman
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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11
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The Relationship between Torque teno Virus and TLR2 rs5743708 Polymorphism with Breast Cancer. JOURNAL OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASES 2021. [DOI: 10.52547/jommid.9.3.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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12
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Dodi G, Attanasi M, Di Filippo P, Di Pillo S, Chiarelli F. Virome in the Lungs: The Role of Anelloviruses in Childhood Respiratory Diseases. Microorganisms 2021; 9:microorganisms9071357. [PMID: 34201449 PMCID: PMC8307813 DOI: 10.3390/microorganisms9071357] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022] Open
Abstract
More recently, increasing attention has been directed to exploring the function of the global virome in health and disease. Currently, by new molecular techniques, such as metagenomic DNA sequencing, the virome has been better unveiled. By investigating the human lung virome, we could provide novel insights into respiratory diseases. The virome, as a part of the microbiome, is characterized by a constant change in composition related to the type of diet, environment, and our genetic code, and other incalculable factors. The virome plays a substantial role in modulating human immune defenses and contributing to the inflammatory processes. Anelloviruses (AVs) are new components of the virome. AVs are already present during early life and reproduce without apparently causing harm to the host. The role of AVs is still unknown, but several reports have shown that AVs could activate the inflammasomes, intracellular multiprotein oligomers of the innate immune system, which show a crucial role in the host defense to several pathogens. In this narrative revision, we summarize the epidemiological data related to the possible link between microbial alterations and chronic respiratory diseases in children. Briefly, we also describe the characteristics of the most frequent viral family present in the lung virome, Anelloviridae. Furthermore, we discuss how AVs could modulate the immune system in children, affecting the development of chronic respiratory diseases, particularly asthma, the most common chronic inflammatory disease in childhood.
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13
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Lapa D, Del Porto P, Minosse C, D’Offizi G, Antinori A, Capobianchi MR, Visco-Comandini U, McPhee F, Garbuglia AR, Zaccarelli M. Clinical Relevance of Torque Teno Virus (TTV) in HIV/HCV Coinfected and HCV Monoinfected Patients Treated with Direct-Acting Antiviral Therapy. J Clin Med 2021; 10:jcm10102092. [PMID: 34068071 PMCID: PMC8152458 DOI: 10.3390/jcm10102092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023] Open
Abstract
Torque Teno virus (TTV) is a ubiquitous virus that causes chronic infection in humans with unknown clinical consequences. Here, we investigated the influence of TTV infection on HCV direct-acting antiviral (DAA) efficacy in HIV/HCV coinfected and HCV monoinfected patients as controls. Of 92 study patients, 79.3% were TTV DNA positive; untreated patients exhibited a significantly higher proportion of TTV DNA-positivity vs. sustained virological response (SVR) patients (100.0% vs. 65.2%, p < 0.001), while TTV positivity was not significant in DAA failure patients vs. SVR patients despite HIV/HCV coinfection. TTV DNA viral load was higher among HCV monoinfected patients vs. HIV/HCV coinfected, although marginally significant (p = 0.074) and no significant viral load difference was detected between DAA failures and SVR patients, while untreated vs. SVR patients had a significantly higher viral load (19,884, IQR 5977–333,534, vs. 469, IQR 10–4124, p = 0.004). Alpha-genogroup 3 TTV was the most prevalent genetic group, and no specific strain or genogroup was observed in relapser patients. Among HIV/HCV patients with HCV RNA detectable at end of treatment (EOT), TTV DNA was detected in 9/17 treatment responder patients and 3/5 relapser patients, thus, TTV infection does not appear to influence the control HCV viremia after EOT. Levels of IL-6 IL-4, and CD14 were not significantly different between TTV PCR-positive and -negative patients. These results suggest no association between TTV DNA positivity or viral load and HCV DAA failure whether patients were HIV/HCV coinfected or HCV monoinfected.
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Affiliation(s)
- Daniele Lapa
- Laboratory of Virology, “Lazzaro Spallanzani” National Institute for Infectious Diseases, IRCCS, 00149 Rome, Italy; (D.L.); (C.M.); (M.R.C.)
| | - Paola Del Porto
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University, 00185 Rome, Italy;
| | - Claudia Minosse
- Laboratory of Virology, “Lazzaro Spallanzani” National Institute for Infectious Diseases, IRCCS, 00149 Rome, Italy; (D.L.); (C.M.); (M.R.C.)
| | - Gianpiero D’Offizi
- Hepatology and Infectious Diseases Unit, “Lazzaro Spallanzani” National Institute for Infectious Diseases IRCCS, 00149 Rome, Italy; (G.D.); (U.V.-C.)
| | - Andrea Antinori
- Clinical Department, “Lazzaro Spallanzani ” National Institute for Infectious Diseases, IRCCS, 00149 Rome, Italy; (A.A.); (M.Z.)
| | - Maria Rosaria Capobianchi
- Laboratory of Virology, “Lazzaro Spallanzani” National Institute for Infectious Diseases, IRCCS, 00149 Rome, Italy; (D.L.); (C.M.); (M.R.C.)
| | - Ubaldo Visco-Comandini
- Hepatology and Infectious Diseases Unit, “Lazzaro Spallanzani” National Institute for Infectious Diseases IRCCS, 00149 Rome, Italy; (G.D.); (U.V.-C.)
| | | | - Anna Rosa Garbuglia
- Laboratory of Virology, “Lazzaro Spallanzani” National Institute for Infectious Diseases, IRCCS, 00149 Rome, Italy; (D.L.); (C.M.); (M.R.C.)
- Correspondence: ; Tel.: +39-06-5517-0692; Fax: +39-06-559-455
| | - Mauro Zaccarelli
- Clinical Department, “Lazzaro Spallanzani ” National Institute for Infectious Diseases, IRCCS, 00149 Rome, Italy; (A.A.); (M.Z.)
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Li Y, Handley SA, Baldridge MT. The dark side of the gut: Virome-host interactions in intestinal homeostasis and disease. J Exp Med 2021; 218:211916. [PMID: 33760921 PMCID: PMC8006857 DOI: 10.1084/jem.20201044] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022] Open
Abstract
The diverse enteric viral communities that infect microbes and the animal host collectively constitute the gut virome. Although recent advances in sequencing and analysis of metaviromes have revealed the complexity of the virome and facilitated discovery of new viruses, our understanding of the enteric virome is still incomplete. Recent studies have uncovered how virome–host interactions can contribute to beneficial or detrimental outcomes for the host. Understanding the complex interactions between enteric viruses and the intestinal immune system is a prerequisite for elucidating their role in intestinal diseases. In this review, we provide an overview of the enteric virome composition and summarize recent findings about how enteric viruses are sensed by and, in turn, modulate host immune responses during homeostasis and disease.
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Affiliation(s)
- Yuhao Li
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO.,Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Scott A Handley
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO.,Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - Megan T Baldridge
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO.,Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO
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15
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Torque Teno Virus plasma level as novel biomarker of retained immunocompetence in HIV-infected patients. Infection 2021; 49:501-509. [PMID: 33537915 PMCID: PMC8159784 DOI: 10.1007/s15010-020-01573-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023]
Abstract
PURPOSE To predict the course of immune recovery (IR) in HIV-1-infected patients after initiation of combined antiretroviral therapy (cART) by determination of the plasma concentration of Torque Teno Virus (TTV). TTV has been identified as marker for risk assessment in immunosuppressed patients after transplantation procedures. Here, TTV was analyzed in HIV-1-infected therapy-naïve patients to evaluate its use as predictor of the course of IR for guidance of individualized treatment. METHODS TTV DNA was quantified in plasma samples of 301 therapy-naïve HIV-1-infected patients and correlated to CD4+ cell count, HIV viral load, presence of the herpes viruses CMV, EBV and HHV-8, age and sex. Patients were classified according to their initial CD4+ cell count and to the extent of CD4+ T-cell increase within the first year of cART. RESULTS TTV DNA was detectable in 96% of the patients' plasma samples with a median TTV plasma concentration of 5.37 log10 cop/ml. The baseline CD4+ cell count was negatively correlated with TTV plasma concentration (p = 0.003). In patients with a CD4+ cell recovery < 50 cells/µl, the median TTV plasma concentration was significantly higher compared to patients with a CD4+ cell recovery of > 200 CD4+ cells/µl (5.68 log10 cop/ml versus 4.99 log10 cop/ml; p = 0.011). TTV plasma concentration in combination with baseline CD4+ cell count were significantly correlated to CD4+ cell recovery (p = 0.004). For all other parameters considered, no significant correlation for CD4+ cell recovery was found. CONCLUSION Within the cohort, the significantly elevated TTV plasma concentration in patients with diminished CD4+ cell recovery indicates a more profound immune defect. Baseline TTV plasma concentrations and CD4+ cell count are predictive for the course of immune recovery in HIV-1-infected patients with severe immunodeficiency.
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Maev IV, Karlovich TI, Burmistrov AI, Chekmazov IA, Andreev DN, Reshetnyak VI. Current Views of Torque Teno Virus (TTV) in Liver Diseases. RUSSIAN JOURNAL OF GASTROENTEROLOGY, HEPATOLOGY, COLOPROCTOLOGY 2020; 30:7-22. [DOI: 10.22416/1382-4376-2020-30-4-7-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Affiliation(s)
- I. V. Maev
- Moscow State University of Medicine and Dentistry
| | - T. I. Karlovich
- Central Clinical Hospital with Outpatient Care of the Russian President Administration
| | | | - I. A. Chekmazov
- Central Clinical Hospital with Outpatient Care of the Russian President Administration
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Davis JS, Chu G, Pathinayake P, Jones D, Giffard P, Macera L, Choi P, Bartlett NW. Seroprevalence of Torque Teno Virus in hemodialysis and renal transplant patients in Australia: A cross-sectional study. Transpl Infect Dis 2020; 22:e13400. [PMID: 33462980 DOI: 10.1111/tid.13400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/28/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Torque teno virus (TTV) is a non-pathogenic anellovirus commonly found in the blood of human beings. Emerging data suggest that TTV viral load is proportional to the degree of immunosuppression, but its seroprevalence is unknown in Australia. We aimed to determine the seroprevalence of TTV in an Australian population of renal patients. METHODS We developed a real-time PCR to measure TTV viral load, using the TaqMan platform and previously published primers and probes. Following ethics approval and informed consent, we collected blood from hemodialysis patients not receiving immunosuppression, and renal transplant patients. All patients were recruited from a single teaching hospital in New South Wales. RESULTS We enrolled 50 hemodialysis and 30 renal transplant patients. 56 (70%) were males, and the mean (sd) age was 61 (16) years. TTV was detectable in plasma of 40/50 (80%) of hemodialysis patients and 28/30 (93%) of transplant patients. The mean TTV viral load was higher in transplant patients than in dialysis patients (6.3 log versus 5.0 log copies/ml, P = .001). CONCLUSIONS Torque teno virus is prevalent in Australian renal patients and thus may be a useful novel marker to help tailor immunosuppressive therapy in renal transplant patients. Further work is needed to establish TTV seroprevalence in other regions and patient groups, and to investigate whether there is correlation with clinically important events (infection and rejection episodes) in longitudinal studies.
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Affiliation(s)
- Joshua S Davis
- Department of Immunology and Infectious Diseases, John Hunter Hospital, Newcastle, NSW, Australia.,School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, Australia.,Menzies School of Health Research, Darwin, NT, Australia
| | - Ginger Chu
- Department of Nephrology, John Hunter Hospital, Newcastle, NSW, Australia
| | - Prabuddhua Pathinayake
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, Hunter Medical Research Institute, University of Newcastle, NSW, Australia
| | - Denise Jones
- Department of Nephrology, John Hunter Hospital, Newcastle, NSW, Australia
| | - Phil Giffard
- Menzies School of Health Research, Darwin, NT, Australia
| | - Lisa Macera
- Department of Translational Research, University of Pisa, Pisa, Italy
| | - Peter Choi
- Department of Nephrology, John Hunter Hospital, Newcastle, NSW, Australia
| | - Nathan W Bartlett
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, Hunter Medical Research Institute, University of Newcastle, NSW, Australia
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18
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Reshetnyak VI, Maev IV, Burmistrov AI, Chekmazov IA, Karlovich TI. Torque teno virus in liver diseases: On the way towards unity of view. World J Gastroenterol 2020; 26:1691-1707. [PMID: 32351287 PMCID: PMC7183866 DOI: 10.3748/wjg.v26.i15.1691] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/23/2020] [Accepted: 03/26/2020] [Indexed: 02/06/2023] Open
Abstract
The review presents the data accumulated for more than 20 years of research of torque teno virus (TTV). Its molecular genetic structure, immunobiology, epidemiology, diagnostic methods, possible replication sites, and pathogenicity factors are described. TTV is a virus that is frequently detectable in patients with different viral hepatitides, in cases of hepatitis without an obvious viral agent, as well as in a healthy population. There is evidence suggesting that biochemical and histological changes occur in liver tissue and bile duct epithelium in TTV monoinfection. There are sufficient histological signs of liver damage, which confirm that the virus can undergo a replicative cycle in hepatocytes. Along with this, cytological hybridization in TTV-infected cells has shown no substantial cytopathic (cell-damaging) effects that are characteristic of pathogenic hepatotropic viruses. Studying TTV has led to the evolution of views on its role in the development of human pathology. The first ideas about the hepatotropism of the virus were gradually reformed as new data became available on the prevalence of the virus and its co-infection with other viruses, including the viruses of the known types of hepatitides. The high prevalence of TTV in the human population indicates its persistence in the body as a virome and a non-pathogenic virus. It has recently been proposed that the level of TTV DNA in the blood of patients undergoing organ transplantation should be used as an endogenous marker of the body’s immune status. The available data show the polytropism of the virus and deny the fact that TTV can be assigned exclusively to hepatitis viruses. Fortunately, the rare detection of the damaging effect of TTV on hepatic and bile duct epithelial cells may be indirect evidence of its conditionally pathogenic properties. The ubiquity of the virus and the variability of its existence in humans cannot put an end to its study.
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Affiliation(s)
- Vasiliy I Reshetnyak
- Department of Propaedeutic of Internal Diseases and Gastroenterology, A.I. Yevdokimov Moscow State University of Medicine and Dentistry, Moscow 127473, Russia
| | - Igor V Maev
- Department of Propaedeutic of Internal Diseases and Gastroenterology, A.I. Yevdokimov Moscow State University of Medicine and Dentistry, Moscow 127473, Russia
| | - Alexandr I Burmistrov
- Department of Propaedeutic of Internal Diseases and Gastroenterology, A.I. Yevdokimov Moscow State University of Medicine and Dentistry, Moscow 127473, Russia
| | - Igor A Chekmazov
- Central Clinical Hospital with Polyclinic, Presidential Administration of the Russian Federation, Moscow 121359, Russia
| | - Tatiana I Karlovich
- Central Clinical Hospital with Polyclinic, Presidential Administration of the Russian Federation, Moscow 121359, Russia
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19
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Strassl R, Schiemann M, Doberer K, Görzer I, Puchhammer-Stöckl E, Eskandary F, Kikic Ž, Gualdoni GA, Vossen MG, Rasoul-Rockenschaub S, Herkner H, Böhmig GA, Bond G. Quantification of Torque Teno Virus Viremia as a Prospective Biomarker for Infectious Disease in Kidney Allograft Recipients. J Infect Dis 2019; 218:1191-1199. [PMID: 30007341 PMCID: PMC6490304 DOI: 10.1093/infdis/jiy306] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 05/17/2018] [Indexed: 12/14/2022] Open
Abstract
Background Drug-induced immunosuppression following kidney transplantation is crucial to prevent allograft rejection, but increases risk for infectious disease. Tailoring of drug dosing to prevent both rejection and infection is greatly desirable. The apathogenic and ubiquitous torque teno virus (TTV) reflects immunocompetence of the host and might be a potential candidate for immunologic monitoring. Methods To assess TTV as an infection biomarker, virus load was prospectively quantified in peripheral blood of 169 consecutive renal allograft recipients at the Medical University Vienna. Results Patients with infection showed higher TTV levels compared to patients without infection (4.2 × 108 copies/mL [interquartile range, IQR, 2.7 × 107–1.9 × 109] vs 2.9 × 107 [IQR 1.0 × 106–7.2 × 108]; P = .006). Differences in TTV load became evident almost 3 months before infection (median 77 days, IQR 19–98). Each log level of TTV copies/mL increased the odds ratio for infection by 23% (95% confidence interval 1.04–1.45; P = .014). TTV >3.1 × 109 copies/mL corresponded to 90% sensitivity to predict infections. Logistic regression demonstrated independent association between TTV levels and infection. Conclusions TTV quantification predicts infection after kidney transplantation and might be a potential tool to tailor immunosuppressive drug therapy.
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Affiliation(s)
- Robert Strassl
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
| | - Martin Schiemann
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
| | - Konstantin Doberer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
| | - Irene Görzer
- Department of Virology, Medical University of Vienna, Austria
| | | | - Farsad Eskandary
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
| | - Željko Kikic
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
| | - Guido A Gualdoni
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
| | - Mathias G Vossen
- Division of Infectious Diseases, Department of Medicine I, Medical University of Vienna, Austria
| | | | - Harald Herkner
- Department of Emergency Medicine, Medical University of Vienna, Austria
| | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
| | - Gregor Bond
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Austria
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20
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Rezahosseini O, Drabe CH, Sørensen SS, Rasmussen A, Perch M, Ostrowski SR, Nielsen SD. Torque-Teno virus viral load as a potential endogenous marker of immune function in solid organ transplantation. Transplant Rev (Orlando) 2019; 33:137-144. [PMID: 30981537 DOI: 10.1016/j.trre.2019.03.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/29/2019] [Accepted: 03/31/2019] [Indexed: 12/27/2022]
Abstract
Solid organ transplantation (SOT) recipients receive immunosuppressive therapy to avoid rejection of the transplanted organ. Immunosuppressive therapy increases the risk of infections. However, no existing marker reliably reveals the status of the immune function in SOT recipients. Torque-Teno virus or Transfusion-transmitted virus (TTV) has gained attention as a possible endogenous marker of the immune function. TTV is a non-enveloped, circular single strand DNA virus, and it may be considered a part of the human virome. In a bidirectional relationship, the immune system detects TTV and TTV may also modulate the activity of immune system. These characteristics have made the virus a possible candidate indicator of immune function. In this systematic review, we describe the role and potential function of TTV viral load as an endogenous marker of the immune function and consequently the level of immune suppression in SOT recipients.
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Affiliation(s)
- Omid Rezahosseini
- Viro-immunology Research Unit, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Camilla Heldbjerg Drabe
- Viro-immunology Research Unit, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Allan Rasmussen
- Department of Surgical Gastroenterology and Transplantation, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Michael Perch
- Department of Cardiology, Section for Lung Transplantation, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Dam Nielsen
- Viro-immunology Research Unit, Department of Infectious Diseases 8632, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
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21
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Fernández-Ruiz M, Albert E, Giménez E, Ruiz-Merlo T, Parra P, López-Medrano F, San Juan R, Polanco N, Andrés A, Navarro D, Aguado JM. Monitoring of alphatorquevirus DNA levels for the prediction of immunosuppression-related complications after kidney transplantation. Am J Transplant 2019; 19:1139-1149. [PMID: 30346659 DOI: 10.1111/ajt.15145] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/10/2018] [Accepted: 09/29/2018] [Indexed: 01/25/2023]
Abstract
The replication kinetics of nonpathogenic anelloviruses belonging to the Alphatorquevirus genus (such as torque teno virus) might reflect the overall state of posttransplant immunosuppression. We analyzed 221 kidney transplant (KT) recipients in whom plasma alphatorquevirus DNA load was quantified by real-time polymerase chain reaction at baseline and regularly through the first 12 posttransplant months. Study outcomes included posttransplant infection and a composite of opportunistic infection and/or de novo malignancy (immunosuppression-related adverse event [iRAE]). Alphatorquevirus DNA loads at month 1 were higher among patients who subsequently developed posttransplant infection (P = .023) or iRAE (P = .009). Likewise, those with iRAE beyond months 3 and 6 also exhibited higher peak viral loads over the preceding periods. Areas under the curve for log10 alphatorquevirus DNAemia estimated by months 1 or 6 were significantly higher in patients experiencing study outcomes. Alphatorquevirus DNA loads above 3.15 and 4.56 log10 copies/mL at month 1 predicted the occurrence of posttransplant infection (adjusted hazard ratio [aHR]: 2.88; 95% confidence interval [CI]: 1.13-7.36; P = .027) and iRAE (aHR: 5.17; 95% CI: 2.01-13.33; P = .001). In conclusion, posttransplant monitoring of plasma alphatorquevirus DNA kinetics may be useful to identify KT recipients at increased risk of immunosuppression-related complications.
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Affiliation(s)
- Mario Fernández-Ruiz
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre," Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Eliseo Albert
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
| | - Estela Giménez
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain
| | - Tamara Ruiz-Merlo
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre," Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Patricia Parra
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre," Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco López-Medrano
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre," Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael San Juan
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre," Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Natalia Polanco
- Department of Nephrology, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain
| | - Amado Andrés
- Department of Nephrology, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain.,Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - José María Aguado
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre," Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), School of Medicine, Universidad Complutense, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
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Kosulin K, Kernbichler S, Pichler H, Lawitschka A, Geyeregger R, Witt V, Lion T. Post-transplant Replication of Torque Teno Virus in Granulocytes. Front Microbiol 2018; 9:2956. [PMID: 30555452 PMCID: PMC6281686 DOI: 10.3389/fmicb.2018.02956] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/16/2018] [Indexed: 12/17/2022] Open
Abstract
Torque Teno virus (TTV) in humans is characterized by ubiquitous occurrence in peripheral blood (PB), without any related disease described to date. Several studies reported a significant increase of TTV plasma DNA levels in allogeneic transplant recipients, and suggested a correlation of elevated virus titers with immunosuppression and transplant-related complications. However, the site of viral replication in this setting has remained unclear. We have studied TTV in serial plasma specimens derived from 43 pediatric allogeneic hematopoietic stem cell transplantation (HSCT) recipients by RQ-PCR, and found increasing TTV-DNA levels in all patients post-transplant, with a peak around day +100 and maximum virus copy numbers reaching 4 × 10E9/ml. To assess whether the virus replicates in PB-cells, leukocyte subsets including granulocytes, monocytes, NK-cells, T- and B-lymphocytes were serially isolated by flow-sorting for TTV analysis in 19 patients. The virus was undetectable in most cell types, but was identified in granulocytes in all instances, revealing a median DNA copy number increase of 1.8 logs between days +30–100 post-transplant. Our data therefore provide evidence for TTV replication in granulocytes in this setting. In a control cohort of immunocompetent children and in HSCT recipients before day +30, TTV positivity in granulocytes was less common (33%), and the copy numbers were considerably lower. However, rising TTV replication about 2 weeks after granulocyte engraftment (>500 cells/μl) was observed suggesting that granulocyte recovery might be required for TTV expansion in severely immunosuppressed transplant recipients.
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Affiliation(s)
- Karin Kosulin
- Children's Cancer Research Institute, Vienna, Austria
| | | | | | | | | | - Volker Witt
- St. Anna Children's Hospital, Vienna, Austria
| | - Thomas Lion
- Children's Cancer Research Institute, Vienna, Austria.,Department of Pediatrics, Medical University of Vienna, Vienna, Austria
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Martelli F, Macera L, Spezia PG, Medici C, Pistello M, Guasti D, Romagnoli P, Maggi F, Giannecchini S. Torquetenovirus detection in exosomes enriched vesicles circulating in human plasma samples. Virol J 2018; 15:145. [PMID: 30236130 PMCID: PMC6149034 DOI: 10.1186/s12985-018-1055-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/13/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Torquetenovirus (TTV) belongs to Anelloviridae family, infects nearly all people indefinitely without causing overt disease establishing a fine and successful interaction with the host. Increasing evidence have shown some human viruses exploit extracellular vesicles thereby helping viral persistence in the host. Here, the presence of TTV in extracellular vesicles circulating in human plasma was investigated. METHODS TTV DNA was quantified in plasma-derived exosomes from 122 samples collected from 97 diseased patients and 25 healthy donors. Exosomes enriched vesicles (EEVs) were extracted from plasma and characterized by Nanoparticle tracking analysis, by western blot for presence of tetraspanin CD63, CD81 and annexin II protein and, finally, by electron microscopy (EM). Presence and quantitation of TTV DNA were assessed with an universal single step real-time TaqMan PCR assay. RESULTS Preliminary investigation showed that the human plasma extracted extracellular vesicles exhibited a main size of 70 nm, had concentration of 2.5 × 109/ml, and scored positive for tetraspanin CD63, CD81 and annexin II, typical characteristic of the exosomes vesicles. EEVs extracted from pooled plasma with TTV DNA viremia of 9.7 × 104 copies/ml showed to contain 6.3 × 102 TTV copies/ml, corresponding to 0.65% of total viral load. Important, TTV yield changed significantly following freezing/thawing, detergents and DNAse treatment of plasma before EEVs extraction. EEVs purified by sucrose-density gradient centrifugation and analysis of gradient fraction positive for exosomes marker CD63 harbored 102 TTV copies/ml. Moreover, EM evidenced the presence of TTV-like particles in EEVs. Successive investigation of plasma EEVs from 122 subjects (37 HIV-positive, 20 HCV infected, 20 HBV infected, 20 kidney transplant recipients, and 25 healthy) reported TTV DNA detection in 42 (34%) of the viremic samples (37 were from diseased patients and 5 from healthy people) at a mean level of 4.8 × 103 copies/ml. The examination of EEVs selected samples reported the presence of TTV genogroup 1, 3, 4 and 5, with genogroup 3 highly observed. CONCLUSIONS Collectively, although these observations should be confirmed by further studies, circulation of TTV particles in EEVs opens new avenues and mechanistic insights on the molecular strategies adopted by anelloviruses to persist in the host.
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Affiliation(s)
- Francesco Martelli
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, I-50134, Florence, Italy
| | - Lisa Macera
- Virology Unit, Pisa University Hospital, Pisa, Italy.,Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy
| | - Pietro Giorgio Spezia
- Virology Unit, Pisa University Hospital, Pisa, Italy.,Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy
| | - Chiara Medici
- Virology Unit, Pisa University Hospital, Pisa, Italy
| | - Mauro Pistello
- Virology Unit, Pisa University Hospital, Pisa, Italy.,Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Pisa, Italy
| | - Daniele Guasti
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, I-50134, Florence, Italy
| | - Paolo Romagnoli
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, I-50134, Florence, Italy
| | | | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, I-50134, Florence, Italy.
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24
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Temporal dynamics of the lung and plasma viromes in lung transplant recipients. PLoS One 2018; 13:e0200428. [PMID: 29979780 PMCID: PMC6034876 DOI: 10.1371/journal.pone.0200428] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/26/2018] [Indexed: 12/31/2022] Open
Abstract
The human virome plays an important role for the clinical outcome of lung transplant recipients (LTRs). While pathogenic viruses may cause severe infections, non-pathogenic viruses may serve as potential markers for the level of immunosuppression. However, neither the complexity of the virome in different compartments nor the dynamics of the virus populations posttransplantation are yet understood. Therefore, in this study the virome was analyzed by metagenomic sequencing in simultaneously withdrawn bronchoalveolar lavage (BAL) and plasma samples of 15 LTRs. In seven patients, also follow-up samples were investigated for abundance and dynamics of virus populations posttransplantation. Five eukaryotic and two prokaryotic virus families were identified in BAL, and nine eukaryotic and two prokaryotic families in plasma. Anelloviruses were the most abundant in both compartments, followed by Herpes- and Coronaviruses. Virus abundance was significantly higher in LTRs than in healthy controls (Kruskal-Wallis test, p<0.001). Up to 48 different anellovirus strains were identified within a single LTR. Analyses in the follow-up patients revealed for the first time a highly complex and unique dynamics of individual anellovirus strains in the posttransplantation period. The abundance of anelloviruses in plasma was inversely correlated with that of other eukaryotic viruses (Pearson correlation coefficient r = -0.605; p<0.05). A broad spectrum of virus strains co-exists in BAL and plasma of LTRs. Especially for the anelloviruses, a high degree of co-infections and a highly individual and complex dynamics after transplantation was observed. The biological impact of these findings and their relation to clinical variables remain to be elucidated by future analyses.
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25
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Elbehery AHA, Feichtmayer J, Singh D, Griebler C, Deng L. The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation. Front Microbiol 2018; 9:1110. [PMID: 29896176 PMCID: PMC5987705 DOI: 10.3389/fmicb.2018.01110] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 05/09/2018] [Indexed: 12/19/2022] Open
Abstract
Human virome, including those of bacteria (bacteriophages) have received an increasing attention recently, owing to the rapid developments in human microbiome research and the awareness of the far-reaching influence of microbiomes on health and disease. Nevertheless, human viromes are still underrepresented in literature making viruses a virtually untapped resource of diversity, functional and physiological information. Here we present the human virome protein cluster database as an effort to improve functional annotation and characterization of human viromes. The database was built out of hundreds of virome datasets from six different body sites. We also show the utility of this database through its use for the characterization of three bronchoalveolar lavage (BAL) viromes from one healthy control in addition to one moderate and one severe chronic obstructive pulmonary disease (COPD) patients. The use of the database allowed for a better functional annotation, which were otherwise poorly characterized when limited to annotation using sequences from full-length viral genomes. In addition, our BAL samples gave a first insight into viral communities of COPD patients and confirm a state of dysbiosis for viruses that increases with disease progression. Moreover, they shed light on the potential role of phages in the horizontal gene transfer of bacterial virulence factors, a phenomenon that highlights a possible contribution of phages to etiopathology.
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Affiliation(s)
- Ali H A Elbehery
- Institute of Virology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
| | - Judith Feichtmayer
- Institute of Groundwater Ecology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
| | - Dave Singh
- EvA Consortium, Manchester, United Kingdom.,Medicines Evaluation Unit, University Hospital of South Manchester Foundation Trust, University of Manchester, Manchester, United Kingdom
| | - Christian Griebler
- Institute of Groundwater Ecology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
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26
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Nordén R, Magnusson J, Lundin A, Tang KW, Nilsson S, Lindh M, Andersson LM, Riise GC, Westin J. Quantification of Torque Teno Virus and Epstein-Barr Virus Is of Limited Value for Predicting the Net State of Immunosuppression After Lung Transplantation. Open Forum Infect Dis 2018; 5:ofy050. [PMID: 29644247 PMCID: PMC5888719 DOI: 10.1093/ofid/ofy050] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/02/2018] [Indexed: 12/13/2022] Open
Abstract
Background Major hurdles for survival after lung transplantation are rejections and infectious complications. Adequate methods for monitoring immune suppression status are lacking. Here, we evaluated quantification of torque teno virus (TTV) and Epstein-Barr virus (EBV) as biomarkers for defining the net state of immunosuppression in lung-transplanted patients. Methods This prospective single-center study included 98 patients followed for 2 years after transplantation. Bacterial infections, fungal infections, viral respiratory infections (VRTI), cytomegalovirus (CMV) viremia, and acute rejections, as well as TTV and EBV levels, were monitored. Results The levels of torque teno virus DNA increased rapidly after transplantation, likely due to immunosuppressive treatment. A modest increase in levels of Epstein-Barr virus DNA was also observed after transplantation. There were no associations between either TTV or EBV and infectious events or acute rejection, respectively, during follow-up. When Tacrolimus was the main immunosuppressive treatment, TTV DNA levels were significantly elevated 6–24 months after transplantation as compared with Cyclosporine treatment. Conclusions Although replication of TTV, but not EBV, appears to reflect the functionality of the immune system, depending on the type of immunosuppressive treatment, quantification of TTV or EBV as biomarkers has limited potential for defining the net state of immune suppression.
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Affiliation(s)
- Rickard Nordén
- Department of Infectious Diseases/Clinical Virology, Institute of Biomedicine, Gothenburg, Sweden
| | - Jesper Magnusson
- Department of Internal Medicine/Respiratory Medicine and Allergology, Institute of Medicine, Gothenburg, Sweden
| | - Anna Lundin
- Department of Infectious Diseases/Clinical Virology, Institute of Biomedicine, Gothenburg, Sweden
| | - Ka-Wei Tang
- Department of Infectious Diseases/Clinical Virology, Institute of Biomedicine, Gothenburg, Sweden
| | - Staffan Nilsson
- Department of Pathology and Genetics, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Sweden
| | - Magnus Lindh
- Department of Infectious Diseases/Clinical Virology, Institute of Biomedicine, Gothenburg, Sweden
| | - Lars-Magnus Andersson
- Department of Infectious Diseases/Clinical Virology, Institute of Biomedicine, Gothenburg, Sweden
| | - Gerdt C Riise
- Department of Internal Medicine/Respiratory Medicine and Allergology, Institute of Medicine, Gothenburg, Sweden
| | - Johan Westin
- Department of Infectious Diseases/Clinical Virology, Institute of Biomedicine, Gothenburg, Sweden
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27
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Somasekar S, Lee D, Rule J, Naccache SN, Stone M, Busch MP, Sanders C, Lee WM, Chiu CY. Viral Surveillance in Serum Samples From Patients With Acute Liver Failure By Metagenomic Next-Generation Sequencing. Clin Infect Dis 2017; 65:1477-1485. [PMID: 29020199 PMCID: PMC5848299 DOI: 10.1093/cid/cix596] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 07/13/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Twelve percent of all acute liver failure (ALF) cases are of unknown origin, often termed indeterminate. A previously unrecognized hepatotropic virus has been suspected as a potential etiologic agent. METHODS We compared the performance of metagenomic next-generation sequencing (mNGS) with confirmatory nucleic acid testing (NAT) to routine clinical diagnostic testing in detection of known or novel viruses associated with ALF. Serum samples from 204 adult ALF patients collected from 1998 to 2010 as part of a nationwide registry were analyzed. One hundred eighty-seven patients (92%) were classified as indeterminate, while the remaining 17 patients (8%) served as controls, with infections by either hepatitis A virus or hepatitis B virus (HBV), or a noninfectious cause for their ALF. RESULTS Eight cases of infection from previously unrecognized viral pathogens were detected by mNGS (4 cases of herpes simplex virus type 1, including 1 case of coinfection with HBV, and 1 case each of HBV, parvovirus B19, cytomegalovirus, and human herpesvirus 7). Several missed dual or triple infections were also identified, and assembled viral genomes provided additional information on genotyping and drug resistance mutations. Importantly, no sequences corresponding to novel viruses were detected. CONCLUSIONS These results suggest that ALF patients should be screened for the presence of uncommon viruses and coinfections, and that most cases of indeterminate ALF in the United States do not appear to be caused by novel viral pathogens. In the future, mNGS testing may be useful for comprehensive diagnosis of viruses associated with ALF, or to exclude infectious etiologies.
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Affiliation(s)
- Sneha Somasekar
- Department of Laboratory Medicine, University of California San Francisco (UCSF) and
| | - Deanna Lee
- Department of Laboratory Medicine, University of California San Francisco (UCSF) and
| | - Jody Rule
- Department of Medicine, Division of Digestive and Liver Diseases, University of Texas Southwestern Medical Center, Dallas; and
| | - Samia N Naccache
- Department of Laboratory Medicine, University of California San Francisco (UCSF) and
| | - Mars Stone
- Blood Systems Research Institute, San Francisco, California
| | - Michael P Busch
- Department of Laboratory Medicine, University of California San Francisco (UCSF) and
- Blood Systems Research Institute, San Francisco, California
| | - Corron Sanders
- Department of Medicine, Division of Digestive and Liver Diseases, University of Texas Southwestern Medical Center, Dallas; and
| | - William M Lee
- Department of Medicine, Division of Digestive and Liver Diseases, University of Texas Southwestern Medical Center, Dallas; and
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco (UCSF) and
- UCSF–Abbott Viral Diagnostics and Discovery Center and
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco
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28
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Bistolas KSI, Rudstam LG, Hewson I. Gene expression of benthic amphipods (genus: Diporeia) in relation to a circular ssDNA virus across two Laurentian Great Lakes. PeerJ 2017; 5:e3810. [PMID: 28966890 PMCID: PMC5621510 DOI: 10.7717/peerj.3810] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/23/2017] [Indexed: 01/15/2023] Open
Abstract
Circular rep-encoding ssDNA (CRESS-DNA) viruses are common constituents of invertebrate viral consortia. Despite their ubiquity and sequence diversity, the effects of CRESS-DNA viruses on invertebrate biology and ecology remain largely unknown. This study assessed the relationship between the transcriptional profile of benthic amphipods of genus Diporeia and the presence of the CRESS-DNA virus, LM29173, in the Laurentian Great Lakes to provide potential insight into the influence of these viruses on invertebrate gene expression. Twelve transcriptomes derived from Diporeia were compared, representing organisms from two amphipod haplotype clades (Great Lakes Michigan and Superior, defined by COI barcode sequencing) with varying viral loads (up to 3 × 106 genome copies organism−1). Read recruitment to de novo assembled transcripts revealed 2,208 significantly over or underexpressed contigs in transcriptomes with above average LM29173 load. Of these contigs, 31.5% were assigned a putative function. The greatest proportion of annotated, differentially expressed transcripts were associated with functions including: (1) replication, recombination, and repair, (2) cell structure/biogenesis, and (3) post-translational modification, protein turnover, and chaperones. Contigs putatively associated with innate immunity displayed no consistent pattern of expression, though several transcripts were significantly overexpressed in amphipods with high viral load. Quantitation (RT-qPCR) of target transcripts, non-muscular myosin heavy chain, β-actin, and ubiquitin-conjugating enzyme E2, corroborated transcriptome analysis and indicated that Lake Michigan and Lake Superior amphipods with high LM29173 load exhibit lake-specific trends in gene expression. While this investigation provides the first comparative survey of the transcriptional profile of invertebrates of variable CRESS-DNA viral load, additional inquiry is required to define the scope of host-specific responses to potential infection.
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Affiliation(s)
| | - Lars G Rudstam
- Department of Natural Resources and the Cornell Biological Field Station, Cornell University, Bridgeport, NY, USA
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY, USA
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29
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Detection of a new species of torque teno mini virus from the gingival epithelium of patients with periodontitis. Virus Genes 2017; 53:823-830. [PMID: 28866831 DOI: 10.1007/s11262-017-1505-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 08/16/2017] [Indexed: 12/12/2022]
Abstract
We describe a novel species of torque teno mini virus called TTMV-204, which was isolated from the gingival epithelium of patients with periodontitis and characterized using viral metagenomics. The sequence of the full genome is 2824 nt in length. Phylogenetic analysis and genetic analyses show classic Betatorquevirus species organization with less than 40% amino acid similarity in ORF1. The prevalence of TTMV-204 in the periodontitis patient population was 18.75% (15/80), which was higher than in periodontally healthy individuals (10.00%, 10/80). However, the difference of the TTMV-204 prevalence between two groups was not statistically significant (p = 0.115). Further investigation is required to determine whether this new virus is associated with inflammation.
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30
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Abstract
Circular single-stranded DNA viruses infect archaea, bacteria, and eukaryotic organisms. The relatively recent emergence of single-stranded DNA viruses, such as chicken anemia virus (CAV) and porcine circovirus 2 (PCV2), as serious pathogens of eukaryotes is due more to growing awareness than to the appearance of new pathogens or alteration of existing pathogens. In the case of the ubiquitous human circular single-stranded DNA virus family Anelloviridae, there is still no convincing direct causal relation to any specific disease. However, infections may play a role in autoimmunity by changing the homeostatic balance of proinflammatory cytokines and the human immune system, indirectly affecting the severity of diseases caused by other pathogens. Infections with CAV (family Anelloviridae, genus Gyrovirus) and PCV2 (family Circoviridae, genus Circovirus) are presented here because they are immunosuppressive and affect health in domesticated animals. CAV shares genomic organization, genomic orientation, and common features of major proteins with human anelloviruses, and PCV2 DNA may be present in human food and vaccines.
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Affiliation(s)
- L M Shulman
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel; .,Laboratory of Environmental Virology, Central Virology Laboratory, Sheba Medical Center Public Health Services, Israel Ministry of Health, Tel Hashomer, 52621, Israel
| | - I Davidson
- Division of Avian Diseases, Kimron Veterinary Institute, Bet Dagan, 50250, Israel;
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31
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Torque Teno Virus Load-Inverse Association With Antibody-Mediated Rejection After Kidney Transplantation. Transplantation 2017; 101:360-367. [PMID: 27525643 DOI: 10.1097/tp.0000000000001455] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Antibody-mediated rejection (AMR) represents one of the cardinal causes of late allograft loss after kidney transplantation, and there is great need for noninvasive tools improving early diagnosis of this rejection type. One promising strategy might be the quantification of peripheral blood DNA levels of the highly prevalent and apathogenic Torque Teno virus (TTV), which might mirror the overall level of immunosuppression and thus help determine the risk of alloimmune response. METHODS To assess the association between TTV load in the peripheral blood and AMR, 715 kidney transplant recipients (median, 6.3 years posttransplantation) were subjected to a systematical cross-sectional AMR screening and, in parallel, TTV quantification. RESULTS Eighty-six of these recipients had donor-specific antibodies and underwent protocol biopsy, AMR-positive patients (n = 46) showed only 25% of the TTV levels measured in patients without AMR (P = 0.003). In a generalized linear model, higher TTV levels were associated with a decreased risk for AMR after adjustment for potential confounders (risk ratio 0.94 per TTV log level; 95% confidence interval 0.90-0.99; P = 0.02). CONCLUSIONS Future studies will have to clarify whether longitudinal assessment of TTV load might predict AMR risk and help guide the type and intensity of immunosuppression to prevent antibody-mediated graft injury.
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33
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Ngoi CN, Siqueira J, Li L, Deng X, Mugo P, Graham SM, Price MA, Sanders EJ, Delwart E. The plasma virome of febrile adult Kenyans shows frequent parvovirus B19 infections and a novel arbovirus (Kadipiro virus). J Gen Virol 2016; 97:3359-3367. [PMID: 27902331 DOI: 10.1099/jgv.0.000644] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Viral nucleic acids present in the plasma of 498 Kenyan adults with unexplained fever were characterized by metagenomics analysis of 51 sample pools. The highest to lowest fraction of plasma pools was positive for parvovirus B19 (75 %), pegivirus C (GBV-C) (67 %), alpha anellovirus (59 %), gamma anellovirus (55 %), beta anellovirus (41 %), dengue virus genotype 2 (DENV-2) (16 %), human immunodeficiency virus type 1 (6 %), human herpesvirus 6 (6 %), HBV (4 %), rotavirus (4 %), hepatitis B virus (4 %), rhinovirus C (2 %), Merkel cell polyomavirus (MCPyV; 2 %) and Kadipiro virus (2 %). Ranking by overall percentage of viral reads yielded similar results. Characterization of viral nucleic acids in the plasma of a febrile East African population showed a high frequency of parvovirus B19 and DENV infections and detected a reovirus (Kadipiro virus) previously reported only in Asian Culex mosquitoes, providing a baseline to compare with future virome studies to detect emerging viruses in this region.
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Affiliation(s)
- Carolyne N Ngoi
- Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, Kilifi, Kenya
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Juliana Siqueira
- Blood Systems Research Institute, San Francisco, CA, USA
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Peter Mugo
- Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, Kilifi, Kenya
| | - Susan M Graham
- Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, Kilifi, Kenya
- University of Washington, Seattle, WA, USA
| | - Matt A Price
- International AIDS Vaccine Initiative, New York, NY, USA
- Department of Epidemiology and Biostatistics, University of California at San Francisco, CA, USA
| | - Eduard J Sanders
- Centre for Geographic Medicine Research - Coast, Kenya Medical Research Institute, Kilifi, Kenya
- Nuffield Department of Medicine, University of Oxford, Headington, UK
| | - Eric Delwart
- Department of Laboratory Medicine, University of California at San Francisco, CA, USA
- Blood Systems Research Institute, San Francisco, CA, USA
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34
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Yang Y, Ju A, Xu X, Cao X, Tao Y. A novel type of cosavirus from children with nonpolio acute flaccid paralysis. Virol J 2016; 13:169. [PMID: 27729038 PMCID: PMC5059993 DOI: 10.1186/s12985-016-0630-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/03/2016] [Indexed: 11/10/2022] Open
Abstract
Human cosavirus (HCoSV) is a genus recently identified in the family Picornaviridae, which contains important pathogens to human health. Here, a novel type of HCoSV strain, cosavirus-zj-1 (GenBank no. KX545380), was identified in the fecal sample of a child with nonpolio acute flaccid paralysis (AFP) in China. Phylogenetic and sequence analyses suggested that this virus strain belonged to a new genotype in HCoSV B species. Our data show that surveillance of HCoSV is necessary for detecting viral agents in children with AFP, despite being the low detection rate.
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Affiliation(s)
- Yan Yang
- The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, China.
| | - Aiping Ju
- Department of Clinical Laboratory, Women and Children's Hospital of Huadu District, Guangzhou, Guangdong, 510800, China
| | - Xiaofen Xu
- The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, China
| | - Xinyu Cao
- The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, China
| | - Ying Tao
- The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, China
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35
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Kawada JI, Okuno Y, Torii Y, Okada R, Hayano S, Ando S, Kamiya Y, Kojima S, Ito Y. Identification of Viruses in Cases of Pediatric Acute Encephalitis and Encephalopathy Using Next-Generation Sequencing. Sci Rep 2016; 6:33452. [PMID: 27625312 PMCID: PMC5022051 DOI: 10.1038/srep33452] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 08/22/2016] [Indexed: 12/27/2022] Open
Abstract
Acute encephalitis/encephalopathy is a severe neurological syndrome that is occasionally associated with viral infection. Comprehensive virus detection assays are desirable because viral pathogens have not been identified in many cases. We evaluated the utility of next-generation sequencing (NGS) for detecting viruses in clinical samples of encephalitis/encephalopathy patients. We first determined the sensitivity and quantitative performance of NGS by comparing the NGS-determined number of sequences of human herpesvirus-6 (HHV-6) in clinical serum samples with the HHV-6 load measured using real-time PCR. HHV-6 was measured as it occasionally causes neurologic disorders in children. The sensitivity of NGS for detection of HHV-6 sequences was equivalent to that of real-time PCR, and the number of HHV-6 reads was significantly correlated with HHV-6 load. Next, we investigated the ability of NGS to detect viral sequences in 18 pediatric patients with acute encephalitis/encephalopathy of unknown etiology. A large number of Coxsackievirus A9 and mumps viral sequences were detected in the cerebrospinal fluid of 2 and 1 patients, respectively. In addition, Torque teno virus and Pepper mild mottle viral sequences were detected in the sera of one patient each. These data indicate that NGS is useful for detection of causative viruses in patients with pediatric encephalitis/encephalopathy.
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Affiliation(s)
- Jun-Ichi Kawada
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Yusuke Okuno
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Yuka Torii
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Ryo Okada
- Horticultural Research Institute, Ibaraki Agricultural Center, 3165-1 Ago, Kasama, 319-0292, Japan
| | - Satoshi Hayano
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Shotaro Ando
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Yasuko Kamiya
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Seiji Kojima
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Yoshinori Ito
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
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Virome characterisation from Guthrie cards in children who later developed acute lymphoblastic leukaemia. Br J Cancer 2016; 115:1008-1014. [PMID: 27552439 PMCID: PMC5061901 DOI: 10.1038/bjc.2016.261] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 07/22/2016] [Accepted: 07/29/2016] [Indexed: 12/17/2022] Open
Abstract
Background: Some childhood acute lymphoblastic leukaemias (ALL) can be traced back to a prenatal origin, where a virus infection could be involved in the first pre-leukaemic clone development. The DNA virome of 95 children who later developed ALL was characterised from neonatal blood spots (NBS) using unbiased next-generation sequencing (NGS) and compared with the virome of 95 non-ALL controls. Methods: DNA was individually extracted from the ALL-patients and controls, pooled, randomly amplified and sequenced using the Illumina MiSeq Sequencing System. Results: Virus-like sequences identified in both groups mapped to human endogenous retroviruses and propionibacterium phage, considered a part of the normal microbial flora. Potential pathogens human herpesvirus type 6 (HHV-6) and parvovirus B19 were also identified, but only few samples in both ALL and controls tested positive by PCR follow-up. Conclusions: Unbiased NGS was employed to search for DNA from potential infectious agents in neonatal samples of children who later developed ALL. Although several viral candidates were identified in the NBS samples, further investigation by PCR suggested that these viruses did not have a major role in ALL development.
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Zhang W, Li L, Deng X, Blümel J, Nübling CM, Hunfeld A, Baylis SA, Delwart E. Viral nucleic acids in human plasma pools. Transfusion 2016; 56:2248-55. [PMID: 27306718 DOI: 10.1111/trf.13692] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/06/2016] [Accepted: 04/21/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND The identification of viruses in human blood is required for epidemiologic surveillance and to detect potentially emerging threats to blood transfusion safety. STUDY DESIGN AND METHODS Viral nucleic acids in plasma fractionation pools assembled from blood donors in the United States and Europe were analyzed by viral metagenomics. RESULTS Anelloviruses were detected in each of the 10 plasma pools. Human pegivirus A (HPgV; GB virus type C) sequences were identified in eight of the 10 pools, more than 90% of which belong to Genotype 2. The recently described human HPgV2 in Flaviviridae was not detected. A small number of sequence reads of human papillomavirus were also detected in three pools. In one pool, two different gemycircularvirus genomes were identified and fully sequenced. The capsid protein of one gemycircularvirus shared 83% to 84% identity to those of genomes from human serum and sewage. The presence of the gemycircularvirus genomes in the plasma pool was independently confirmed and the viral concentration estimated by digital PCR at more than 10(6) copies/mL assuming their origin from single donors. CONCLUSION Further research is required to elucidate whether gemycircularviruses can infect humans or are indicative of contamination occurring during phlebotomy, plasma pool processing, or ongoing donor fungal infections.
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Affiliation(s)
- Wen Zhang
- Blood Systems Research Institute, San Francisco, California.,Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
| | - Linlin Li
- Blood Systems Research Institute, San Francisco, California.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
| | | | | | | | | | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California. .,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California.
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Identification of heterologous Torque Teno Viruses in humans and swine. Sci Rep 2016; 6:26655. [PMID: 27222164 PMCID: PMC4879562 DOI: 10.1038/srep26655] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/22/2016] [Indexed: 12/13/2022] Open
Abstract
Torque Teno Viruses (TTVs) are ubiquitous viruses which are highly prevalent in several mammalian species. Human TTV’s are epidemiologically associated with several human disease conditions such as respiratory illnesses, auto-immune disorders and hepatitis. Recently it was found that swine TTV’s (TTSuVs) can act as primary pathogens. The common occurrence of TTVs as environmental contaminants and the increasing interest in the use of swine organs for xenotransplantation lend importance to the question of whether TTV’s can cross-infect across species. In this study, we examined human and swine sera by swine or human TTV-specific PCRs, to determine whether swine TTVs (TTSuV) DNA can be detected in humans and vice versa. Surprisingly, both human and TTSuV DNA were present in a majority of the samples tested. Transfection of human PBMC’s with TTSuV1 genomic DNA resulted in productive viral infection which was sustained for the three serial passages tested. Lymphoproliferative responses in infected human PBMCs were diminished when compared to the controls. Furthermore, mild to moderate antibody responses against the TTSuV1 ORF2 protein was detected in 16 of the 40 human sera by ELISA. Therefore, these study findings provide initial and fundamental evidence for possible cross-species transmission of TTVs.
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Lack of strong anti-viral immune gene stimulation in Torque Teno Sus Virus1 infected macrophage cells. Virology 2016; 495:63-70. [PMID: 27179346 DOI: 10.1016/j.virol.2016.04.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 04/06/2016] [Accepted: 04/28/2016] [Indexed: 12/30/2022]
Abstract
While recent findings suggest that swine TTVs (TTSuVs) can act as primary or co-infecting pathogens, very little is known about viral immunity. To determine whether TTSuVs downregulate key host immune responses to facilitate their own survival, a swine macrophage cell line, 3D4/31, was used to over-express recombinant TTSuV1 viral particles or the ORF3 protein. Immune gene expression profiles were assessed by a quantitative PCR panel consisting of 22 immune genes, in cell samples collected at 6, 12, 24 and 48h post-transfection. Despite the upregulation of IFN-β and TLR9, interferon stimulated innate genes and pro-inflammatory genes were not upregulated in virally infected cells. The adaptive immune genes, IL-4 and IL-13, were significantly downregulated at 6h post-transfection. The ORF3 protein did not appear do not have a major immuno-suppressive effect, nor did it stimulate anti-viral immunity. Data from this study warrants further investigation into the mechanisms of TTV related immuno-pathogenesis.
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40
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Immune gene expression in swine macrophages expressing the Torque Teno Sus Virus1 (TTSuV1) ORF-1 and 2 proteins. Virus Res 2016; 220:33-8. [PMID: 27059616 DOI: 10.1016/j.virusres.2016.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/03/2016] [Accepted: 04/04/2016] [Indexed: 12/30/2022]
Abstract
Torque Teno viruses (TTVs) are small DNA viruses which are ubiquitous in nature. Recent reports indicate that swine torque teno viruses (TTSuVs) can act as primary pathogens or play a role in exacerbating co-infections. However, very little is known about the TTSuV host-viral interaction or how they so successfully establish chronic infections in the host. To determine whether the major viral proteins can modulate host immunity, recombinant TTSuV1 ORF1 and 2 proteins were expressed in a swine macrophage cell line (3D4/31). The differential expression of a panel of innate, adaptive, regulatory and inflammatory immune genes was studied by quantitative PCR; using cDNA samples collected at 6, 12, 24 and 48h post-transfection. The ORF1 protein induced an early anti-viral response. However, at 6h post-transfection it also upregulated IL-10, PD-1 and SOCS-1, the suppressors of T cell mediated immunity. An ensuing diminishment of the early protective response was noted. The TTSuV1 ORF2 protein suppressed IFN-β and IL-13 responses but did not significantly influence anti-viral immunity otherwise. These findings indicate that the TTSuV1 ORF1 protein plays a significant but dual role in viral immunity.
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41
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Hsiao KL, Wang LY, Lin CL, Liu HF. New Phylogenetic Groups of Torque Teno Virus Identified in Eastern Taiwan Indigenes. PLoS One 2016; 11:e0149901. [PMID: 26901643 PMCID: PMC4762681 DOI: 10.1371/journal.pone.0149901] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/06/2016] [Indexed: 11/18/2022] Open
Abstract
Torque teno virus (TTV) is a single-stranded DNA virus highly prevalent in the world. It has been detected in eastern Taiwan indigenes with a low prevalence of 11% by using N22 region of which known to underestimate TTV prevalence excessively. In order to clarify their realistic epidemiology, we re-analyzed TTV prevalence with UTR region. One hundred and forty serum samples from eastern Taiwanese indigenous population were collected and TTV DNA was detected in 133 (95%) samples. Direct sequencing revealed an extensive mix-infection of different TTV strains within the infected individual. Entire TTV open reading frame 1 was amplified and cloned from a TTV positive individual to distinguish mix-infected strains. Phylogenetic analysis showed eleven isolates were clustered into a monophyletic group that is distinct from all known groups. In addition, another our isolate was clustered with recently described Hebei-1 strain and formed an independent clade. Based on the distribution pattern of pairwise distances, both new clusters were placed at phylogenetic group level, designed as the 6th and 7th phylogenetic group. In present study, we showed a very high prevalence of TTV infection in eastern Taiwan indigenes and indentified new phylogenetic groups from the infected individual. Both intra- and inter-phylogenetic group mix-infections can be found from one healthy person. Our study has further broadened the field of human TTVs and proposed a robust criterion for classification of the major TTV phylogenetic groups.
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Affiliation(s)
- Kuang-Liang Hsiao
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Li-Yu Wang
- Department of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Chiung-Ling Lin
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Hsin-Fu Liu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
- Department of Nursing, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan
- * E-mail:
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42
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Zhou C, Zhang S, Gong Q, Hao A. A novel gemycircularvirus in an unexplained case of child encephalitis. Virol J 2015; 12:197. [PMID: 26596706 PMCID: PMC4657213 DOI: 10.1186/s12985-015-0431-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 11/17/2015] [Indexed: 12/21/2022] Open
Abstract
Background Recently, a diverse group of viruses with circular, replication initiator protein(Rep) encoding, single stranded DNA (CRESS-DNA) genomes, were discovered from wide range of eukaryotic organisms ranging from mammals to fungi. Gemycircularvirus belongs to a distinct group of CRESS-DNA genomes and is classified under the genus name of Gemycircularvirus. Findings Here, a novel gemycircularvirus named GeTz1 from cerebrospinal fluid sample of a child with unexplainable encephalitis was characterized. The novel gemycircularvirus encodes two major proteins, including a capsid protein (Cap) and a replication-associated protein (Rep). Phylogenetic analysis based on the amino acid sequence of Rep indicated that GeTz1 clusters with one gemycircularvirus discovered from bird (KF371633), sharing 46.6 % amino acid sequence identity with each other. Conclusion A novel gemycircularvirus was discovered from cerebrospinal fluid sample of a child with unexplainable encephalitis. Further studies, such as testing human sera for specific antibodies, should be performed to investigate whether gemycircularvirus infects human and is associated with encephalitis.
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Affiliation(s)
- Chenglin Zhou
- Department of Laboratory Medicine, Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu, 225300, China.
| | - Shibing Zhang
- Department of Laboratory Medicine, the First People's Hospital of Suqian, Suqian, Jiangsu, 223800, China.
| | - Qin Gong
- Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu, 225300, China.
| | - Aimin Hao
- Department of Laboratory Medicine, the Second People's Hospital of Wuxi, Wuxi, Jiangsu, 214002, China.
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43
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Gut DNA viromes of Malawian twins discordant for severe acute malnutrition. Proc Natl Acad Sci U S A 2015; 112:11941-6. [PMID: 26351661 DOI: 10.1073/pnas.1514285112] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The bacterial component of the human gut microbiota undergoes a definable program of postnatal development. Evidence is accumulating that this program is disrupted in children with severe acute malnutrition (SAM) and that their persistent gut microbiota immaturity, which is not durably repaired with current ready-to-use therapeutic food (RUTF) interventions, is causally related to disease pathogenesis. To further characterize gut microbial community development in healthy versus malnourished infants/children, we performed a time-series metagenomic study of DNA isolated from virus-like particles (VLPs) recovered from fecal samples collected during the first 30 mo of postnatal life from eight pairs of mono- and dizygotic Malawian twins concordant for healthy growth and 12 twin pairs discordant for SAM. Both members of discordant pairs were sampled just before, during, and after treatment with a peanut-based RUTF. Using Random Forests and a dataset of 17,676 viral contigs assembled from shotgun sequencing reads of VLP DNAs, we identified viruses that distinguish different stages in the assembly of the gut microbiota in the concordant healthy twin pairs. This developmental program is impaired in both members of SAM discordant pairs and not repaired with RUTF. Phage plus members of the Anelloviridae and Circoviridae families of eukaryotic viruses discriminate discordant from concordant healthy pairs. These results disclose that apparently healthy cotwins in discordant pairs have viromes associated with, although not necessarily mediators, of SAM; as such, they provide a human model for delineating normal versus perturbed postnatal acquisition and retention of the gut microbiota's viral component in populations at risk for malnutrition.
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44
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Brajão de Oliveira K. Torque teno virus: a ubiquitous virus. Rev Bras Hematol Hemoter 2015; 37:357-8. [PMID: 26670392 PMCID: PMC4678778 DOI: 10.1016/j.bjhh.2015.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 07/23/2015] [Indexed: 11/03/2022] Open
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45
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Kapusinszky B, Mulvaney U, Jasinska AJ, Deng X, Freimer N, Delwart E. Local Virus Extinctions following a Host Population Bottleneck. J Virol 2015; 89:8152-61. [PMID: 26018153 PMCID: PMC4524239 DOI: 10.1128/jvi.00671-15] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 03/13/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A small number of African green monkeys (AGMs) were introduced into the Caribbean from West Africa in the 1600s. To determine the impact of this population bottleneck on the AGM virome, we used metagenomics to compare the viral nucleic acids in the plasma of 43 wild AGMs from West Africa (Gambia) to those in 44 AGMs from the Caribbean (St. Kitts and Nevis). Three viruses were detected in the blood of Gambian primates: simian immunodeficiency virus (SIVagm; in 42% of animals), a novel simian pegivirus (SPgVagm; in 7% of animals), and numerous novel simian anelloviruses (in 100% of animals). Only anelloviruses were detected in the Caribbean AGMs with a prevalence and levels of viral genetic diversity similar to those in the Gambian animals. A host population bottleneck therefore resulted in the exclusion of adult-acquired SIV and pegivirus from the Caribbean AGMs. The successful importation of AGM anelloviruses into the Caribbean may be the result of their early transmission to infants, very high prevalence in African AGMs, and frequent coinfections with as many as 11 distinct variants. IMPORTANCE The extent to which viruses can persist in small isolated populations depends on multiple host, viral, and environmental factors. The absence of prior infections may put an immunologically naive population at risk for disease outbreaks. Isolated populations originating from a small number of founder individuals are therefore considered at increased risk following contact with populations with a greater variety of viruses. Here, we compared the plasma virome of West African green monkeys to that in their descendants after importation of a small number of animals to the Caribbean. A lentivirus and a pegivirus were found in the West African population but not in the Caribbean population. Highly diverse anelloviruses were found in both populations. A small founder population, limited to infants and young juvenile monkeys, may have eliminated the sexually transmitted viruses from the Caribbean AGMs, while anelloviruses, acquired at an earlier age, persisted through the host population bottleneck.
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Affiliation(s)
- Beatrix Kapusinszky
- Blood Systems Research Institute, San Francisco, California, USA Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Usha Mulvaney
- Blood Systems Research Institute, San Francisco, California, USA University of San Francisco, Department of Biology, San Francisco, California, USA
| | - Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, California, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California, USA Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Nelson Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, California, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, USA Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California, USA
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46
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Li L, Giannitti F, Low J, Keyes C, Ullmann LS, Deng X, Aleman M, Pesavento PA, Pusterla N, Delwart E. Exploring the virome of diseased horses. J Gen Virol 2015; 96:2721-2733. [PMID: 26044792 DOI: 10.1099/vir.0.000199] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Metagenomics was used to characterize viral genomes in clinical specimens of horses with various organ-specific diseases of unknown aetiology. A novel parvovirus as well as a previously described hepacivirus closely related to human hepatitis C virus and equid herpesvirus 2 were identified in the cerebrospinal fluid of horses with neurological signs. Four co-infecting picobirnaviruses, including an unusual genome with fused RNA segments, and a divergent anellovirus were found in the plasma of two febrile horses. A novel cyclovirus genome was characterized from the nasal secretion of another febrile animal. Lastly, a small circular DNA genome with a Rep gene, from a virus we called kirkovirus, was identified in the liver and spleen of a horse with fatal idiopathic hepatopathy. This study expands the number of viruses found in horses, and characterizes their genomes to assist future epidemiological studies of their transmission and potential association with various equine diseases.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Federico Giannitti
- California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA.,Instituto Nacional de Investigación Agropecuaria, La Estanzuela, Colonia, Uruguay
| | - Jason Low
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Casey Keyes
- Department of Biology, University of San Francisco, San Francisco, CA, USA
| | - Leila S Ullmann
- Department of Microbiology and Immunology, UNESP Sao Paulo State University, Sao Paulo, Brazil
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Monica Aleman
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Patricia A Pesavento
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA, USA
| | - Nicola Pusterla
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, CA, USA
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Görzer I, Jaksch P, Kundi M, Seitz T, Klepetko W, Puchhammer-Stöckl E. Pre-transplant plasma Torque Teno virus load and increase dynamics after lung transplantation. PLoS One 2015; 10:e0122975. [PMID: 25894323 PMCID: PMC4404260 DOI: 10.1371/journal.pone.0122975] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 02/02/2015] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The human Torque Teno virus (TTV) causes persistent viremia in most immunocompetent individuals. Elevated TTV levels are observed after solid organ transplantation and are related to the extent of immunosuppression especially during the phase of maintenance immunosuppression. However, the extent to which the TTV increase in the early phase post-transplantation is associated with the patient's immunosuppressive state is unclear. OBJECTIVES In this study, we assessed the TTV increase dynamics in detail during the first three months after lung transplantation under a defined immunosuppressive regimen and in relation to the pre-transplant TTV level. STUDY DESIGN Forty-six lung transplant recipients (LTRs) were included in this prospective longitudinal study. All received alemtuzumab induction combined with tacrolimus and corticosteroids immunosuppressive therapy. Plasma TTV DNA was monitored before transplantation and regularly within the first three months post-transplantation (n = 320 samples; mean sampling interval: 12.2 days). RESULTS In 43/46 LTRs (93%), TTV DNA was detectable before transplantation (median 4.4 log10 copies/mL; range: 2.0-6.4). All 46 LTRs showed a TTV increase post-transplantation, which followed a sigmoidal-shaped curve before the median peak level of 9.4 log10 copies/mL (range: 7.6-10.7) was reached at a median of day 67 (range: 41-92). The individual TTV DNA doubling times (range: 1.4-20.1 days) significantly correlated with the pre-transplant TTV levels calculated over 30 or 60 days post-transplantation (r = 0.61, 0.54, respectively; both P < 0.001), but did not correlate with the mean tacrolimus blood levels. Pre-transplant TTV levels were not associated with time and level of the patients' post-transplant TTV peak load. CONCLUSION The TTV level may be used to mirror the state of immunosuppression only after the patients' initial peak TTV level is reached.
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Affiliation(s)
- Irene Görzer
- Department of Virology, Medical University of Vienna, Vienna, Austria
| | - Peter Jaksch
- Division of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Michael Kundi
- Institute of Environmental Health, Medical University of Vienna, Vienna, Austria
| | - Tamara Seitz
- Department of Virology, Medical University of Vienna, Vienna, Austria
| | - Walter Klepetko
- Division of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
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Shaheli M, Yaghobi R, Rezaeian A, Iravani Saadi M, Ramzi M. Study of the Associations Between TT Virus Single and Mixed Infections With Leukemia. Jundishapur J Microbiol 2015; 8:e18212. [PMID: 26034552 PMCID: PMC4449851 DOI: 10.5812/jjm.8(4)2015.18212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 10/23/2014] [Accepted: 11/02/2014] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The pathogenic association of Transfusion Transmitted Virus or Torque teno Virus (TT Virus) single and mixed infections with leukemia was under evaluation in these years but confront with controversies. This hypothesis is based on the higher prevalence of TT Virus infection in patients with leukemia compared with controls. OBJECTIVES The aim of this study was to determine the frequency of TT Virus, Cytomegalovirus (CMV), Hepatitis B Virus (HBV), and Hepatitis C Virus (HCV) infections in patients with leukemia and healthy controls. PATIENTS AND METHODS In this cross sectional study, 95 patients with leukemia and 100 healthy controls who were admitted to the Namazi Hospital affiliated to the Shiraz University of Medical Sciences, Shiraz, Iran, were enrolled between years 2012 and 2013. Blood samples treated with EDTA were collected from each patient with leukemia and controls. The existence of TT Virus infection was analyzed using the semi-nested PCR method. The immunological prevalence of HBV and HCV infections were evaluated using HBs-Ag and HCV-Ab ELISA based protocols, respectively. Active CMV infection was also evaluated using an immunofluorescence method. Also risk factors of leukemia and viral infections were statistically analyzed in patients with leukemia. RESULTS The TT Virus infection was significantly found in 40 of 95 (42.1%) and 12 of 100 (12%) patients with leukemia and controls, respectively. The HBs-Ag and HCV-Ab were detected in 27 of 95 (28.4%) and 18 of 69 (26.1%) patients with leukemia but were not found in the controls. Active CMV infection was also found in 11 of 69 (16%) patients and none of the controls. Significant co-infection of TT Virus was found with HBV (15 of 40; 37.5%), HCV (14 of 40; 35%) and CMV (7 of 40; 17.5%) in patients with leukemia. CONCLUSIONS Confirmation of the significantly higher frequency of TT Virus, HBV, HCV and CMV single infection and their co-infection in patients with leukemia compared with healthy controls, emphasizes the determinative role of TT Virus pathogenesis in clinical outcomes observed in patients with leukemia, which requires extensive evaluation by further studies.
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Affiliation(s)
- Marjan Shaheli
- Department of Biology, Arsanjan Branch, Islamic Azad University, Arsanjan, IR Iran
| | - Ramin Yaghobi
- Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran
- Corresponding author: Ramin Yaghobi, Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran. Tel: +98-7116476331, Fax: +98-7116476331, E-mail:
| | - Abbasali Rezaeian
- Department of Microbiology, Jahrom Branch, Islamic Azad University, Jahrom, IR Iran
| | | | - Mani Ramzi
- Hematology Research Center and Bone Marrow Transplant Unit, Shiraz University of Medical Sciences, Shiraz, IR Iran
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49
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Smits SL, Schapendonk CME, van Beek J, Vennema H, Schürch AC, Schipper D, Bodewes R, Haagmans BL, Osterhaus ADME, Koopmans MP. New viruses in idiopathic human diarrhea cases, the Netherlands. Emerg Infect Dis 2015; 20:1218-22. [PMID: 24964003 PMCID: PMC4073879 DOI: 10.3201/eid2007.140190] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Emerging viral infections can be identified by using a viral metagenomics approach for clinical human material. Diarrhea samples of patients with unexplained gastroenteritis from the Netherlands were analyzed by using viral metagenomics. Novel circular DNA viruses, bufaviruses, and genogroup III picobirnaviruses were identified. These data expand our knowledge of the human virome.
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50
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Kluba J, Linnenweber-Held S, Heim A, Ang AM, Raggub L, Broecker V, Becker JU, Schulz TF, Schwarz A, Ganzenmueller T. A rolling circle amplification screen for polyomaviruses other than BKPyV in renal transplant recipients confirms high prevalence of urinary JCPyV shedding. Intervirology 2015; 58:88-94. [PMID: 25677461 DOI: 10.1159/000369210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 10/20/2014] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Multiple novel human polyomaviruses (HPyVs) have been discovered in the last few years. These or other, unknown, nephrotropic HPyVs may potentially be shed in urine. METHODS To search for known and unknown HPyVs we investigated BKPyV-negative urine samples from 105 renal transplant recipients (RTR) by rolling circle amplification (RCA) analysis and quantitative JCPyV PCR. Clinical data was analysed to identify risk factors for urinary polyomavirus shedding. RESULTS In 10% (11/105) of the urine samples RCA with subsequent sequencing revealed JCPyV, but no other HPyV sequences. Using quantitative JCPyV PCR, 24% (25/105) of the samples tested positive. Overall sensitivities of RCA of 44% (11/25) in detecting JCPyV in JCPyV DNA-positive urine and 67% (10/15) for samples with JCPyV loads >10,000 copies/ml can be assumed. Despite frequent detectable urinary shedding of JCPyV in our cohort, this could not be correlated with clinical risk factors. CONCLUSION Routine urinary JCPyV monitoring in BKPyV-negative RTR without suspected polyomavirus-associated nephropathy might be of limited diagnostic value. As RCA works in a sequence-independent manner, detection of novel and known polyomaviruses shed in sufficient quantities is feasible. High-level shedding of HPyVs other than BKPyV or JCPyV in the urine of RTR is unlikely to occur.
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Affiliation(s)
- Jeanette Kluba
- Institute of Virology, Hannover Medical School, Hannover, Germany
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