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Gong HY, Chen RX, Tan SM, Wang X, Chen JM, Zhang YL, Liao M. Viruses Identified in Shrews ( Soricidae) and Their Biomedical Significance. Viruses 2024; 16:1441. [PMID: 39339918 PMCID: PMC11437491 DOI: 10.3390/v16091441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Shrews (Soricidae) are common small wild mammals. Some species of shrews, such as Asian house shrews (Suncus murinus), have a significant overlap in their habitats with humans and domestic animals. Currently, over 190 species of viruses in 32 families, including Adenoviridae, Arenaviridae, Arteriviridae, Astroviridae, Anelloviridae, Bornaviridae, Caliciviridae, Chuviridae, Coronaviridae, Filoviridae, Flaviviridae, Hantaviridae, Hepadnaviridae, Hepeviridae, Nairoviridae, Nodaviridae, Orthoherpesviridae, Orthomyxoviridae, Paramyxoviridae, Parvoviridae, Phenuiviridae, Picobirnaviridae, Picornaviridae, Polyomaviridae, Poxviridae, Rhabdoviridae, Sedoreoviridae, Spinareoviridae, and three unclassified families, have been identified in shrews. Diverse shrew viruses, such as Borna disease virus 1, Langya virus, and severe fever with thrombocytopenia syndrome virus, cause diseases in humans and/or domestic animals, posing significant threats to public health and animal health. This review compiled fundamental information about shrews and provided a comprehensive summary of the viruses that have been detected in shrews, with the aim of facilitating a deep understanding of shrews and the diversity, epidemiology, and risks of their viruses.
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Affiliation(s)
- Huan-Yu Gong
- School of Animal Science and Technology, Foshan University, Foshan 528225, China
| | - Rui-Xu Chen
- School of Animal Science and Technology, Foshan University, Foshan 528225, China
| | - Su-Mei Tan
- School of Animal Science and Technology, Foshan University, Foshan 528225, China
| | - Xiu Wang
- School of Animal Science and Technology, Foshan University, Foshan 528225, China
| | - Ji-Ming Chen
- School of Animal Science and Technology, Foshan University, Foshan 528225, China
| | - Yuan-Long Zhang
- Guangdong Center for Animal Disease Prevention and Control, Guangzhou 510230, China
| | - Ming Liao
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510230, China
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Laubscher F, Kaiser L, Cordey S. SCANellome V2: Update of the Primate Anellovirus Reference Sequences Database. Viruses 2024; 16:1349. [PMID: 39339826 PMCID: PMC11435895 DOI: 10.3390/v16091349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 08/20/2024] [Accepted: 08/22/2024] [Indexed: 09/30/2024] Open
Abstract
Anelloviruses are ubiquitous in humans and represent a major component of the human virome. Its best-known representative is Torque teno virus (i.e., the Alphatorquevirus genus), which is considered a potential immunity biomarker. Recent metagenomic investigations revealed not only the extraordinary genomic diversity of anellovirus sequences, but also that co-detection of genera, genotypes, or species seems to be the rule in humans. SCANellome was developed to represent a user-friendly tool to analyze the primate (both human and non-human) anellovirus composition at the genus, species, and genotype level from metagenomics data based on an up-to-date database. This SCANellome update includes >900 additional reference sequences from GenBank. Using a clustering at 90% identity, the FASTA database was updated and generated 134 new representative sequences. Based on ORF1, the analysis of these new sequences indicates the presence of 206 potential new species, including four nonhuman primates, and adds four new non-human primate species which will be the subject of a proposal to the International Committee on Taxonomy of Viruses (ICTV). In addition, SCANellome V2 provides now the user with an interactive up-to-date phylogenetic analysis (of ORF1) to show the distribution among the 12 human and nonhuman primate genera of these new potential species. Finally, the Anelloviridae taxonomy was updated to rename species names in binomial format as required by the ICTV.
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Affiliation(s)
- Florian Laubscher
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.L.); (L.K.)
| | - Laurent Kaiser
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.L.); (L.K.)
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.L.); (L.K.)
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Yan T, Wang Z, Li R, Zhang D, Song Y, Cheng Z. Gyrovirus: current status and challenge. Front Microbiol 2024; 15:1449814. [PMID: 39220040 PMCID: PMC11362077 DOI: 10.3389/fmicb.2024.1449814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024] Open
Abstract
Gyrovirus (GyV) is small, single-stranded circular DNA viruses that has recently been assigned to the family Anelloviridae. In the last decade, many GyVs that have an apparent pan-tropism at the host level were identified by high-throughput sequencing (HTS) technology. As of now, they have achieved global distribution. Several species of GyVs have been demonstrated to be pathogenic to poultry, particularly chicken anemia virus (CAV), causing significant economic losses to the global poultry industry. Although GyVs are highly prevalent in various birds worldwide, their direct involvement in the etiology of specific diseases and the reasons for their ubiquity and host diversity are not fully understood. This review summarizes current knowledge about GyVs, with a major emphasis on their morphofunctional properties, epidemiological characteristics, genetic evolution, pathogenicity, and immunopathogenesis. Additionally, the association between GyVs and various diseases, as well as its potential impact on the poultry industry, have been discussed. Future prevention and control strategies have also been explored. These insights underscore the importance of conducting research to establish a virus culture system, optimize surveillance, and develop vaccines for GyVs.
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Affiliation(s)
| | | | | | | | | | - Ziqiang Cheng
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai’an, China
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4
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Esser PL, Quintanares GHR, Langhans B, Heger E, Böhm M, Jensen BEOLE, Esser S, Lübke N, Fätkenheuer G, Lengauer T, Klein F, Oette M, Rockstroh JK, Boesecke C, Di Cristanziano V, Kaiser R, Pirkl M. Torque Teno Virus Load Is Associated With Centers for Disease Control and Prevention Stage and CD4+ Cell Count in People Living With Human Immunodeficiency Virus but Seems Unrelated to AIDS-Defining Events and Human Pegivirus Load. J Infect Dis 2024; 230:e437-e446. [PMID: 38230877 PMCID: PMC11326818 DOI: 10.1093/infdis/jiae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/02/2024] [Accepted: 01/11/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Torque teno virus (TTV) is part of the human virome. TTV load was related to the immune status in patients after organ transplantation. We hypothesize that TTV load could be an additional marker for immune function in people living with HIV (PLWH). METHODS In this analysis, serum samples of PLWH from the RESINA multicenter cohort were reanalyzed for TTV. Investigated clinical and epidemiological parameters included human pegivirus load, patient age and sex, HIV load, CD4+ T-cell count (Centers for Disease Control and Prevention [CDC] stage 1, 2, or 3), and CDC clinical stage (1993 CDC classification system; stage A, B, or C) before initiation of antiretroviral therapy. Regression analysis was used to detect possible associations among parameters. RESULTS Our analysis confirmed TTV as a strong predictor of CD4+ T-cell count and CDC class 3. This relationship was used to propose a first classification of TTV load with regard to clinical stage. We found no association with clinical CDC stages A-C. The human pegivirus load was inversely correlated with HIV load but not TTV load. CONCLUSIONS TTV load was associated with immunodeficiency in PLWH. Neither TTV nor HIV load were predictive for the clinical categories of HIV infection.
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Affiliation(s)
- Pia L Esser
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Bonn, Germany
| | - Gibran H Rubio Quintanares
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Cologne, Germany
- Paul Ehrlich Institute, Langen, Germany
- Infectious Disease Department, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico
| | - Bettina Langhans
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Bonn, Germany
| | - Eva Heger
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Cologne, Germany
| | - Michael Böhm
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Cologne, Germany
| | - Björn-Erik O L E Jensen
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stefan Esser
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Nadine Lübke
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Gerd Fätkenheuer
- Department of Internal Medicine I, University Hospital Cologne, Cologne, Germany
| | - Thomas Lengauer
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Cologne, Germany
| | - Florian Klein
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Mark Oette
- Clinic for General Medicine, Gastroenterology, and Infectious Diseases, Augustinerinnen Hospital, Cologne, Germany
| | - Juergen K Rockstroh
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Bonn, Germany
| | - Christoph Boesecke
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Bonn, Germany
| | - Veronica Di Cristanziano
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Cologne, Germany
| | - Rolf Kaiser
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Cologne, Germany
- EuResist Network, Rome, Italy
| | - Martin Pirkl
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Cologne, Germany
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Paietta EN, Kraberger S, Lund MC, Vargas KL, Custer JM, Ehmke E, Yoder AD, Varsani A. Diverse Circular DNA Viral Communities in Blood, Oral, and Fecal Samples of Captive Lemurs. Viruses 2024; 16:1099. [PMID: 39066262 PMCID: PMC11281440 DOI: 10.3390/v16071099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Few studies have addressed viral diversity in lemurs despite their unique evolutionary history on the island of Madagascar and high risk of extinction. Further, while a large number of studies on animal viromes focus on fecal samples, understanding viral diversity across multiple sample types and seasons can reveal complex viral community structures within and across species. Groups of captive lemurs at the Duke Lemur Center (Durham, NC, USA), a conservation and research center, provide an opportunity to build foundational knowledge on lemur-associated viromes. We sampled individuals from seven lemur species, i.e., collared lemur (Eulemur collaris), crowned lemur (Eulemur coronatus), blue-eyed black lemur (Eulemur flavifrons), ring-tailed lemur (Lemur catta), Coquerel's sifaka (Propithecus coquereli), black-and-white ruffed lemur (Varecia variegata variegata), and red ruffed lemur (Varecia rubra), across two lemur families (Lemuridae, Indriidae). Fecal, blood, and saliva samples were collected from Coquerel's sifaka and black-and-white ruffed lemur individuals across two sampling seasons to diversify virome biogeography and temporal sampling. Using viral metagenomic workflows, the complete genomes of anelloviruses (n = 4), cressdnaviruses (n = 47), caudoviruses (n = 15), inoviruses (n = 34), and microviruses (n = 537) were determined from lemur blood, feces, and saliva. Many virus genomes, especially bacteriophages, identified in this study were present across multiple lemur species. Overall, the work presented here uses a viral metagenomics approach to investigate viral communities inhabiting the blood, oral cavity, and feces of healthy captive lemurs.
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Affiliation(s)
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Michael C. Lund
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Karla L. Vargas
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joy M. Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Erin Ehmke
- Duke Lemur Center, Duke University, Durham, NC 27708, USA
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
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6
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Sahnan S, Olivo D, Custer JM, Bandoo RA, Jackson D, Lund MC, McGraw H, Regney M, Aguiar de Souza Penha V, Neil J, Drake D, McGraw K, Varsani A, Kraberger S. Genome analysis of gyroviruses identified in waterfowl in Arizona (USA). Arch Virol 2024; 169:120. [PMID: 38753261 DOI: 10.1007/s00705-024-06049-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/29/2024] [Indexed: 06/13/2024]
Abstract
Gyroviruses are small single-stranded DNA (ssDNA) viruses that are largely associated with birds. Chicken anemia virus is the most extensively studied gyrovirus due to its disease impact on the poultry industry. However, we know much less about gyroviruses infecting other avian species. To investigate gyroviruses infecting waterfowl, we determined six complete genome sequences that fall into three gyrovirus groups, referred to as waterfowl gyrovirus 1 (n = 3), 2 (n = 2), and 3 (n = 1), in organs from hunter-harvested waterfowl from Arizona (USA). The waterfowl gyrovirus 1 variants were identified in multiple organs of a single American wigeon and represent a tentative new species. The waterfowl gyrovirus 2 variants were identified in the livers of two American wigeons and share >70% VP1 nucleotide sequence identity with gyrovirus 9, previously identified in the spleen of a Brazilian Pekin duck (MT318123) and a human fecal sample (KP742975). Waterfowl gyrovirus 3 was identified in a northern pintail spleen sample, and it shares >73% VP1 nucleotide sequence identity with two gyrovirus 13 sequences previously identified in Brazilian Pekin duck spleens (MT318125 and MT318127). These gyroviruses are the first to be identified in waterfowl in North America, as well as in American wigeons and northern pintails.
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Affiliation(s)
- Shawnpreet Sahnan
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Diego Olivo
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Rohan A Bandoo
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Danny Jackson
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85719, USA
| | - Michael C Lund
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Hannah McGraw
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Melanie Regney
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Victor Aguiar de Souza Penha
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Organismal and Evolutionary Research Programme, University of Helsinki, Helsinki, Finland
| | - Julia Neil
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Dean Drake
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Kevin McGraw
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA.
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA.
- Structural Biology Research Unit, Department of Integrative, Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa.
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA.
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Anantharam R, Duchen D, Cox AL, Timp W, Thomas DL, Clipman SJ, Kandathil AJ. Long-Read Nanopore-Based Sequencing of Anelloviruses. Viruses 2024; 16:723. [PMID: 38793605 PMCID: PMC11125752 DOI: 10.3390/v16050723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Routinely used metagenomic next-generation sequencing (mNGS) techniques often fail to detect low-level viremia (<104 copies/mL) and appear biased towards viruses with linear genomes. These limitations hinder the capacity to comprehensively characterize viral infections, such as those attributed to the Anelloviridae family. These near ubiquitous non-pathogenic components of the human virome have circular single-stranded DNA genomes that vary in size from 2.0 to 3.9 kb and exhibit high genetic diversity. Hence, species identification using short reads can be challenging. Here, we introduce a rolling circle amplification (RCA)-based metagenomic sequencing protocol tailored for circular single-stranded DNA genomes, utilizing the long-read Oxford Nanopore platform. The approach was assessed by sequencing anelloviruses in plasma drawn from people who inject drugs (PWID) in two geographically distinct cohorts. We detail the methodological adjustments implemented to overcome difficulties inherent in sequencing circular genomes and describe a computational pipeline focused on anellovirus detection. We assessed our protocol across various sample dilutions and successfully differentiated anellovirus sequences in conditions simulating mixed infections. This method provides a robust framework for the comprehensive characterization of circular viruses within the human virome using the Oxford Nanopore.
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Affiliation(s)
- Raghavendran Anantharam
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (R.A.)
| | - Dylan Duchen
- Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT 06511, USA;
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Andrea L. Cox
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (R.A.)
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - David L. Thomas
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (R.A.)
| | - Steven J. Clipman
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (R.A.)
| | - Abraham J. Kandathil
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (R.A.)
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8
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Albert E, Giménez E, Hernani R, Piñana JL, Solano C, Navarro D. Torque Teno Virus DNA Load in Blood as an Immune Status Biomarker in Adult Hematological Patients: The State of the Art and Future Prospects. Viruses 2024; 16:459. [PMID: 38543824 PMCID: PMC10974055 DOI: 10.3390/v16030459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/11/2024] [Accepted: 03/15/2024] [Indexed: 05/23/2024] Open
Abstract
A solid body of scientific evidence supports the assumption that Torque teno virus (TTV) DNA load in the blood compartment may behave as a biomarker of immunosuppression in solid organ transplant recipients; in this clinical setting, high or increasing TTV DNA levels precede the occurrence of infectious complications, whereas the opposite anticipates the development of acute rejection. The potential clinical value of the TTV DNA load in blood to infer the risk of opportunistic viral infection or immune-related (i.e., graft vs. host disease) clinical events in the hematological patient, if any, remains to be determined. In fact, contradictory data have been published on this matter in the allo-SCT setting. Studies addressing this topic, which we review and discuss herein, are highly heterogeneous as regards design, patient characteristics, time points selected for TTV DNA load monitoring, and PCR assays used for TTV DNA quantification. Moreover, clinical outcomes are often poorly defined. Prospective, ideally multicenter, and sufficiently powered studies with well-defined clinical outcomes are warranted to elucidate whether TTV DNA load monitoring in blood may be of any clinical value in the management of hematological patients.
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Affiliation(s)
- Eliseo Albert
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, 46010 Valencia, Spain; (E.A.); (E.G.)
| | - Estela Giménez
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, 46010 Valencia, Spain; (E.A.); (E.G.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, 28029 Madrid, Spain
| | - Rafael Hernani
- Hematology Service, Hospital Clínico Universitario, INCLIVA Health Research Institute, 46010 Valencia, Spain; (R.H.); (J.L.P.); (C.S.)
| | - José Luis Piñana
- Hematology Service, Hospital Clínico Universitario, INCLIVA Health Research Institute, 46010 Valencia, Spain; (R.H.); (J.L.P.); (C.S.)
| | - Carlos Solano
- Hematology Service, Hospital Clínico Universitario, INCLIVA Health Research Institute, 46010 Valencia, Spain; (R.H.); (J.L.P.); (C.S.)
- Department of Medicine, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, 46010 Valencia, Spain; (E.A.); (E.G.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, 28029 Madrid, Spain
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain
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9
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Kaszab E, Bali K, Marton S, Ursu K, Farkas SL, Fehér E, Domán M, Martella V, Bányai K. Metagenomic Identification of Novel Eukaryotic Viruses with Small DNA Genomes in Pheasants. Animals (Basel) 2024; 14:237. [PMID: 38254406 PMCID: PMC10812470 DOI: 10.3390/ani14020237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
A panel of intestinal samples collected from common pheasants (Phasianus colchicus) between 2008 and 2017 was used for metagenomic investigation using an unbiased enrichment protocol and different bioinformatic pipelines. The number of sequence reads in the metagenomic analysis ranged from 1,419,265 to 17,507,704 with a viral sequence read rate ranging from 0.01% to 59%. When considering the sequence reads of eukaryotic viruses, RNA and DNA viruses were identified in the samples, including but not limited to coronaviruses, reoviruses, parvoviruses, and CRESS DNA viruses (i.e., circular Rep-encoding single-stranded DNA viruses). Partial or nearly complete genome sequences were reconstructed of at least three different parvoviruses (dependoparvovirus, aveparvovirus and chaphamaparvovirus), as well as gyroviruses and diverse CRESS DNA viruses. Generating information of virus diversity will serve as a basis for developing specific diagnostic tools and for structured epidemiological investigations, useful to assess the impact of these novel viruses on animal health.
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Affiliation(s)
- Eszter Kaszab
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
- One Health Institute, Faculty of Health Sciences, University of Debrecen, 4032 Debrecen, Hungary
| | - Krisztina Bali
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
| | - Szilvia Marton
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
| | - Krisztina Ursu
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, 1143 Budapest, Hungary;
| | - Szilvia L. Farkas
- Department of Obstetrics and Food Animal Medicine Clinic, University of Veterinary Medicine, 1078 Budapest, Hungary;
| | - Enikő Fehér
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
| | - Marianna Domán
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy;
| | - Krisztián Bányai
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, 1078 Budapest, Hungary
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