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De Koch MD, Krupovic M, Fielding R, Smith K, Schiavone K, Hall KR, Reid VS, Boyea D, Smith EL, Schmidlin K, Fontenele RS, Koonin EV, Martin DP, Kraberger S, Varsani A. Novel lineage of anelloviruses with large genomes identified in dolphins. J Virol 2024:e0137024. [PMID: 39665547 DOI: 10.1128/jvi.01370-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 11/27/2024] [Indexed: 12/13/2024] Open
Abstract
Anellovirus infections are ubiquitous in mammals but lack any clear disease association, suggesting a commensal virus-host relationship. Although anelloviruses have been identified in numerous mammalian hosts, their presence in members of the family Delphinidae has yet to be reported. Here, using a metagenomic approach, we characterize complete anellovirus genomes (n = 69) from four Delphinidae host species: short-finned pilot whale (Globicephala macrorhynchus, n = 19), killer whale (Orcinus orca, n = 9), false killer whale (Pseudorca crassidens, n = 6), and pantropical spotted dolphin (Steno attenuatus, n = 1). Sequence comparison of the open reading frame 1 (ORF1) encoding the capsid protein, the only conserved gene shared by all anelloviruses, shows that the Delphinidae anelloviruses form a novel genus-level clade that encompasses 22 unique species-level groupings. We provide evidence that different Delphinidae species can be co-infected by multiple anelloviruses belonging to distinct species groupings. Notably, the ORF1 protein of the Delphinidae anelloviruses is considerably larger than those encoded by all previously described anelloviruses from other hosts (spanning 14 vertebrate orders and including 27 families). Comprehensive analysis of the ORF1 sequences and predicted protein structures showed that the increased size of these proteins results from divergent elaborations within the capsid-distal P2 subdomain and elongation of the C-terminal domain of ORF1. Comparative structural and phylogenetic analyses suggest that acquisition of the P2 subdomain and its diversification occurred convergently in the anelloviruses associated with primate and Delphinidae hosts. Collectively, our results further the appreciation of diversity and evolution of the ubiquitous and enigmatic viruses in the family Anelloviridae. IMPORTANCE Anelloviruses are ubiquitous in mammals, but their infection has not yet been linked to any disease, suggesting a commensal virus-host relationship. Here, we describe the first anelloviruses associated with diverse species of dolphins. The dolphinid anelloviruses represent a new genus (tentatively named "Qoptorquevirus") and encode open reading frame 1 (ORF1) (capsid) proteins that are considerably larger than those encoded by previously described anelloviruses from other hosts. Comprehensive analysis of the ORF1 sequences and predicted protein structures revealed the underlying structural basis for such an extravagant ORF1 size and suggested that ORF1 size increased convergently in the anelloviruses associated with primate and Delphinidae hosts, respectively. Collectively, our results provide insights into the diversity and evolution of Anelloviridae. Further exploration of the anellovirus diversity, especially in the host species that have not yet been sampled, is expected to further clarify their evolutionary trajectory and explain the unusual virus-host commensal relationship.
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Affiliation(s)
- Matthew D De Koch
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Russell Fielding
- HTC Honors College, Coastal Carolina University, Conway, South Carolina, USA
| | - Kendal Smith
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Kelsie Schiavone
- Department of Earth and Environmental Systems, The University of the South, Sewanee, Tennessee, USA
| | - Katharine R Hall
- Department of Earth and Environmental Systems, The University of the South, Sewanee, Tennessee, USA
| | - Vincent S Reid
- Barrouallie Whaler's Project, Barrouallie, Saint Vincent and the Grenadines
| | - Diallo Boyea
- Independent Researcher, Barrouallie, Saint Vincent and the Grenadines
| | - Emma L Smith
- Department of Chemical and Biological Sciences, The University of the West Indies at Cave Hill, Bridgetown, Saint Michael, Barbados
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Western Cape, South Africa
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town, South Africa
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Li Y, Song TZ, Cao L, Zhang HD, Ma Y, Tian RR, Zheng YT, Zhang C. Large expansion of plasma commensal viruses is associated with SIV pathogenesis in Macaca leonina. SCIENCE ADVANCES 2024; 10:eadq1152. [PMID: 39356751 PMCID: PMC11446265 DOI: 10.1126/sciadv.adq1152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 08/26/2024] [Indexed: 10/04/2024]
Abstract
Human immunodeficiency virus-1 (HIV-1) infection disrupts the homeostatic equilibrium between the host and commensal microbes. However, the dynamic changes of plasma commensal viruses and their role in HIV/simian immunodeficiency virus (SIV) pathogenesis are rarely reported. Here, we investigated the longitudinal changes of plasma virome, inflammation levels, and disease markers using an SIV-infected Macaca leonina model. Large expansions of plasma Anelloviridae, Parvoviridae, Circoviridae and other commensal viruses, and elevated levels of inflammation and D-dimer were observed since the chronic phase of SIV infection. Anelloviridae abundance appears to correlate positively with the CD4+ T cell count but negatively with SIV load especially at the acute phase, whereas other commensal viruses' abundances show opposite correlations with the two disease markers. Antiretroviral therapy slightly reduces but does not substantially reverse the expansion of commensal viruses. Furthermore, 1387 primate anellovirus open reading frame 1 sequences of more than 1500 nucleotides were annotated. The data reveal different roles of commensal viruses in SIV pathogenesis.
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Affiliation(s)
- Yanpeng Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Tian-Zhang Song
- State Key Laboratory of Genetic Evolution and Animal Models, Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Le Cao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Han-Dan Zhang
- State Key Laboratory of Genetic Evolution and Animal Models, Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- College of Pharmacy and Chemistry, Dali University, Dali, Yunnan 671000, China
| | - Yingying Ma
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Ren-Rong Tian
- State Key Laboratory of Genetic Evolution and Animal Models, Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yong-Tang Zheng
- State Key Laboratory of Genetic Evolution and Animal Models, Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
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3
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Karamendin K, Goodman SJ, Kasymbekov Y, Kumar M, Nuralibekov S, Kydyrmanov A. Viral metagenomic survey of Caspian seals. Front Vet Sci 2024; 11:1461135. [PMID: 39359390 PMCID: PMC11445147 DOI: 10.3389/fvets.2024.1461135] [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: 07/07/2024] [Accepted: 08/26/2024] [Indexed: 10/04/2024] Open
Abstract
Introduction Viral diseases of pinnipeds cause substantial mortality and morbidity and can influence population demography. Viral metagenomic studies can therefore play an important role in pinniped health assessments and disease surveillance relevant to both individual species and in a "One Health" context. Methods This study used a metagenomic approach with high throughput sequencing to make the first assessment of viral diversity in Caspian seals (Pusa caspica), the only marine mammal species endemic to the Caspian Sea. Results Sequencing libraries from 35 seals sampled 2009-2020 were analysed, finding sequences from the viral families Circoviridae, Parvoviridae, Herpesviridae, Papillomaviridae, Picornaviridae, Caliciviridae, Cruciviridae, Anelloviridae, Smacoviridae, and Orthomyxoviridae, with additional detection of Adenoviridae via PCR. The similarity of viral contigs from Caspian seal to sequences recovered from other pinnipeds ranged from 63.74% (San Miguel sea lion calicivirus) to 78.79% (Seal anellovirus 4). Discussion Some findings represent novel viral species, but overall, the viral repertoire of Caspian seals is similar to available viromes from other pinnipeds. Among the sequences recovered were partial contigs for influenza B, representing only the second such molecular identification in marine mammals. This work provides a foundation for further studies of viral communities in Caspian seals, the diversity of viromes in pinnipeds more generally, and contributes data relevant for disease risk assessments in marine mammals.
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Affiliation(s)
- Kobey Karamendin
- Laboratory of Viral Ecology, Research and Production Center for Microbiology and Virology, Department of Virology, Almaty, Kazakhstan
| | - Simon J Goodman
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Yermukhammet Kasymbekov
- Laboratory of Viral Ecology, Research and Production Center for Microbiology and Virology, Department of Virology, Almaty, Kazakhstan
| | - Marat Kumar
- Laboratory of Viral Ecology, Research and Production Center for Microbiology and Virology, Department of Virology, Almaty, Kazakhstan
| | - Sardor Nuralibekov
- Laboratory of Viral Ecology, Research and Production Center for Microbiology and Virology, Department of Virology, Almaty, Kazakhstan
| | - Aidyn Kydyrmanov
- Laboratory of Viral Ecology, Research and Production Center for Microbiology and Virology, Department of Virology, Almaty, Kazakhstan
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4
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Vietzen H, Simonitsch C, Friedel B, Berger SM, Kühner LM, Furlano PL, Florian DM, Görzer I, Koblischke M, Aberle JH, Puchhammer-Stöckl E. Torque teno viruses exhaust and imprint the human immune system via the HLA-E/NKG2A axis. Front Immunol 2024; 15:1447980. [PMID: 39295866 PMCID: PMC11408220 DOI: 10.3389/fimmu.2024.1447980] [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: 06/12/2024] [Accepted: 08/09/2024] [Indexed: 09/21/2024] Open
Abstract
The ubiquitous Torque teno virus (TTV) establishes a chronically persistent infection in the human host. TTV has not been associated with any apparent disease, but, as part of the human virome, it may confer a regulatory imprint on the human immune system with as yet unclear consequences. However, so far, only few studies have characterized the TTV-specific immune responses or the overall immunological imprints by TTV. Here, we reveal that TTV infection leads to a highly exhausted TTV-specific CD8+ T-cell response, hallmarked by decreased IFN-γ production and the expression of the inhibitory NKG2A-receptor. On a functional level, we identified a panel of highly polymorphic TTV-encoded peptides that lead to an expansion of regulatory NKG2A+ natural killer, NKG2A+CD4+, and NKG2A+CD8+ T cells via the stabilization of the non-classical HLA-E molecule. Our results thus demonstrate that TTV leads to a distinct imprint on the human immune system that may further regulate overall human immune responses in infectious, autoimmune, and malignant diseases.
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Affiliation(s)
- Hannes Vietzen
- Center for Virology, Medical University Vienna, Vienna, Austria
| | - Cara Simonitsch
- Center for Virology, Medical University Vienna, Vienna, Austria
| | | | - Sarah M Berger
- Center for Virology, Medical University Vienna, Vienna, Austria
| | - Laura M Kühner
- Center for Virology, Medical University Vienna, Vienna, Austria
| | | | - David M Florian
- Center for Virology, Medical University Vienna, Vienna, Austria
| | - Irene Görzer
- Center for Virology, Medical University Vienna, Vienna, Austria
| | | | - Judith H Aberle
- Center for Virology, Medical University Vienna, Vienna, Austria
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5
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Giménez-Orenga K, Martín-Martínez E, Oltra E. Over-Representation of Torque Teno Mini Virus 9 in a Subgroup of Patients with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Pilot Study. Pathogens 2024; 13:751. [PMID: 39338942 PMCID: PMC11435283 DOI: 10.3390/pathogens13090751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/30/2024] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic disorder classified by the WHO as postviral fatigue syndrome (ICD-11 8E49 code). Diagnosing ME/CFS, often overlapping with fibromyalgia (FM), is challenging due to nonspecific symptoms and lack of biomarkers. The etiology of ME/CFS and FM is poorly understood, but evidence suggests viral infections play a critical role. This study employs microarray technology to quantitate viral RNA levels in immune cells from ME/CFS, FM, or co-diagnosed cases, and healthy controls. The results show significant overexpression of the Torque Teno Mini Virus 9 (TTMV9) in a subgroup of ME/CFS patients which correlate with abnormal HERV and immunological profiles. Increased levels of TTMV9 transcripts accurately discriminate this subgroup of ME/CFS patients from the other study groups, showcasing its potential as biomarker for patient stratification and the need for further research into its role in the disease. Validation of the findings seems granted in extended cohorts by continuation studies.
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Affiliation(s)
- Karen Giménez-Orenga
- Escuela de Doctorado, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain;
| | | | - Elisa Oltra
- Department of Pathology, School of Medicine and Health Sciences, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain
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6
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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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7
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Liou SH, Boggavarapu R, Cohen NR, Zhang Y, Sharma I, Zeheb L, Mukund Acharekar N, Rodgers HD, Islam S, Pitts J, Arze C, Swaminathan H, Yozwiak N, Ong T, Hajjar RJ, Chang Y, Swanson KA, Delagrave S. Structure of anellovirus-like particles reveal a mechanism for immune evasion. Nat Commun 2024; 15:7219. [PMID: 39174507 PMCID: PMC11341859 DOI: 10.1038/s41467-024-51064-8] [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: 12/18/2023] [Accepted: 07/26/2024] [Indexed: 08/24/2024] Open
Abstract
Anelloviruses are nonpathogenic viruses that comprise a major portion of the human virome. Despite being ubiquitous in the human population, anelloviruses (ANVs) remain poorly understood. Basic features of the virus, such as the identity of its capsid protein and the structure of the viral particle, have been unclear until now. Here, we use cryogenic electron microscopy to describe the first structure of an ANV-like particle. The particle, formed by 60 jelly roll domain-containing ANV capsid proteins, forms an icosahedral particle core from which spike domains extend to form a salient part of the particle surface. The spike domains come together around the 5-fold symmetry axis to form crown-like features. The base of the spike domain, the P1 subdomain, shares some sequence conservation between ANV strains while a hypervariable region, forming the P2 subdomain, is at the spike domain apex. We propose that this structure renders the particle less susceptible to antibody neutralization by hiding vulnerable conserved domains while exposing highly diverse epitopes as immunological decoys, thereby contributing to the immune evasion properties of anelloviruses. These results shed light on the structure of anelloviruses and provide a framework to understand their interactions with the immune system.
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Affiliation(s)
- Shu-Hao Liou
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
- Carbon Biosciences, Waltham, MA, 02451, USA
| | | | - Noah R Cohen
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
- AbbVie Bioresearch Center, Worcester, MA, 01605, USA
| | - Yue Zhang
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | - Ishwari Sharma
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | - Lynn Zeheb
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | | | - Hillary D Rodgers
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | - Saadman Islam
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
- GSK, Cambridge, MA, 02139, USA
| | - Jared Pitts
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | - Cesar Arze
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | - Harish Swaminathan
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
- DaCapo Brainscience, Cambridge, MA, 02139, USA
| | - Nathan Yozwiak
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
- Gene and Cell Therapy Institute, Mass General Brigham, Cambridge, MA, 02139, USA
| | - Tuyen Ong
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | - Roger J Hajjar
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
- Gene and Cell Therapy Institute, Mass General Brigham, Cambridge, MA, 02139, USA
| | - Yong Chang
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
| | - Kurt A Swanson
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA.
| | - Simon Delagrave
- Ring Therapeutics, 140 First Street Suite 300, Cambridge, MA, 02139, USA
- Delagrave Life Sciences, LLC, Sudbury, MA, 01776, USA
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8
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Weary TE, Mehta KPM, Goldberg TL. Novel Gammapapillomavirus type in the nasal cavity of a wild red colobus (Piliocolobus tephrosceles). Access Microbiol 2024; 6:000866.v3. [PMID: 39165252 PMCID: PMC11334581 DOI: 10.1099/acmi.0.000866.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 08/01/2024] [Indexed: 08/22/2024] Open
Abstract
Papillomaviruses (PVs) are double-stranded, circular, epitheliotropic DNA viruses causing benign warts (papillomas) or inducing dysplasia that can progress to cancer. Although they have been identified in all vertebrate taxa, most classified types are human PVs (HPVs); relatively little is known about PVs in other species. Here we characterize a novel Gammapapillomavirus type, PtepPV1, from a nasal swab of a wild red colobus (Piliocolobus tephrosceles) in Kibale National Park, Uganda. The virus has a genome of 6576 bases, encoding the seven canonical early (E) ORFs (E6, E7, E1, E2, E4, E1^E4 and E8^E2) and two late (L) ORFs (L1 and L2) of the gammapapillomaviruses, and is 81.0% similar to HPV-mSK_118, detected in a cutaneous wart from an immunocompromised human patient, in the L1 gene at the amino acid level. Alphapapillomaviruses (genus Alphapapillomavirus) cause anogenital carcinomas such as cervical cancer and have been described previously in several nonhuman primates. However, the first gammapapillomavirus (genus Gammapapillomavirus), which cause transient cutaneous infections, was not described until 2019 in a healthy rhesus macaque (Macaca mulatta) genital swab. The new virus from red colobus, PtepPV1, has many genomic features encoded by high-risk oncogenic PVs, such as the E7 gene LXSXE and CXXC motifs, suggesting potential for pRb and zinc-finger binding, respectively. To our knowledge, PtepPV1 is also the first reported nonhuman primate PV found in the nasal cavity. PtepPV1 expands the known host range, geographical distribution, tissue tropism and biological characteristics of nonhuman primate PVs.
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Affiliation(s)
- Taylor E. Weary
- Department of Pathobiological Sciences, University of Wisconsin-Madison School of Veterinary Medicine, Madison, WI, USA
| | - Kavi P. M. Mehta
- Department of Comparative Biosciences, University of Wisconsin-Madison School of Veterinary Medicine, Madison, WI, USA
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison School of Veterinary Medicine, Madison, WI, USA
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9
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Niccolai E, Pedone M, Martinelli I, Nannini G, Baldi S, Simonini C, Di Gloria L, Zucchi E, Ramazzotti M, Spezia PG, Maggi F, Quaranta G, Masucci L, Bartolucci G, Stingo FC, Mandrioli J, Amedei A. Amyotrophic lateral sclerosis stratification: unveiling patterns with virome, inflammation, and metabolism molecules. J Neurol 2024; 271:4310-4325. [PMID: 38644373 PMCID: PMC11233352 DOI: 10.1007/s00415-024-12348-7] [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: 01/30/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/23/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is an untreatable and clinically heterogeneous condition primarily affecting motor neurons. The ongoing quest for reliable biomarkers that mirror the disease status and progression has led to investigations that extend beyond motor neurons' pathology, encompassing broader systemic factors such as metabolism, immunity, and the microbiome. Our study contributes to this effort by examining the potential role of microbiome-related components, including viral elements, such as torque tenovirus (TTV), and various inflammatory factors, in ALS. In our analysis of serum samples from 100 ALS patients and 34 healthy controls (HC), we evaluated 14 cytokines, TTV DNA load, and 18 free fatty acids (FFA). We found that the evaluated variables are effective in differentiating ALS patients from healthy controls. In addition, our research identifies four unique patient clusters, each characterized by distinct biological profiles. Intriguingly, no correlations were found with site of onset, sex, progression rate, phenotype, or C9ORF72 expansion. A remarkable aspect of our findings is the discovery of a gender-specific relationship between levels of 2-ethylhexanoic acid and patient survival. In addition to contributing to the growing body of evidence suggesting altered peripheral immune responses in ALS, our exploratory research underscores metabolic diversity challenging conventional clinical classifications. If our exploratory findings are validated by further research, they could significantly impact disease understanding and patient care customization. Identifying groups based on biological profiles might aid in clustering patients with varying responses to treatments.
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Affiliation(s)
- Elena Niccolai
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Matteo Pedone
- Department of Statistics, Computer Science, Applications "G. Parenti", University of Florence, Florence, Italy
| | - Ilaria Martinelli
- Neurology Unit, Department of Neuroscience, Azienda Ospedaliero Universitaria Di Modena, Modena, Italy
| | - Giulia Nannini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Simone Baldi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Cecilia Simonini
- Neurology Unit, Department of Neuroscience, Azienda Ospedaliero Universitaria Di Modena, Modena, Italy
| | - Leandro Di Gloria
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Elisabetta Zucchi
- Neurology Unit, Department of Neuroscience, Azienda Ospedaliero Universitaria Di Modena, Modena, Italy
| | - Matteo Ramazzotti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Pietro Giorgio Spezia
- Department of Translational Research, Retrovirus Center - University of Pisa, Pisa, Italy
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani - IRCCS, Rome, Italy
| | - Gianluca Quaranta
- Department of Laboratory and Infectious Sciences, A. Gemelli University Hospital IRCCS, Rome, Italy
| | - Luca Masucci
- Department of Laboratory and Infectious Sciences, A. Gemelli University Hospital IRCCS, Rome, Italy
| | - Gianluca Bartolucci
- Department of Neurosciences, Psychology, Drug Research and Child Health Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Florence, Italy
| | - Francesco Claudio Stingo
- Department of Statistics, Computer Science, Applications "G. Parenti", University of Florence, Florence, Italy
| | - Jessica Mandrioli
- Neurology Unit, Department of Neuroscience, Azienda Ospedaliero Universitaria Di Modena, Modena, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
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10
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Tsai HK, Sabbagh MF, Montesion M, Williams EA, Arbini A, Boué DR, Harris EM, Wachter F, Grimmett L, Place AE, Lucas F, Nardi V, Kim AS, Brugnara C, Degar B, Pollard J, Harris MH, Bledsoe JR. Acute Promyelocytic Leukemia With Torque Teno Mini Virus::RARA Fusion: An Approach to Screening and Diagnosis. Mod Pathol 2024; 37:100509. [PMID: 38704030 DOI: 10.1016/j.modpat.2024.100509] [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: 03/22/2024] [Accepted: 04/20/2024] [Indexed: 05/06/2024]
Abstract
Acute promyelocytic leukemia (APL) with variant RARA translocation is linked to over 15 partner genes. Recent publications encompassing 6 cases have expanded the spectrum of RARA partners to torque teno mini virus (TTMV). This entity is likely underrecognized due to the lack of clinician and pathologist familiarity, inability to detect the fusion using routine testing modalities, and informatic challenges in its recognition within next-generation sequencing (NGS) data. We describe a clinicopathologic approach and provide the necessary tools to screen and diagnose APL with TTMV::RARA using existing clinical DNA- or RNA-based NGS assays, which led to the identification of 4 cases, all without other known cytogenetic/molecular drivers. One was identified prospectively and 3 retrospectively, including 2 from custom automated screening of multiple data sets (50,257 cases of hematopoietic malignancy, including 4809 acute myeloid leukemia/myeloid sarcoma/APL cases). Two cases presented as myeloid sarcoma, including 1 with multiple relapses after acute myeloid leukemia-type chemotherapy and hematopoietic stem cell transplant. Two cases presented as leukemia, had a poor response to induction chemotherapy, but achieved remission upon reinduction (including all-trans retinoic acid in 1 case) and subsequent hematopoietic stem cell transplant. Neoplastic cells demonstrated features of APL including frequent azurophilic granules and dim/absent CD34 and HLA-DR expression. RARA rearrangement was not detected by karyotype or fluorescent in situ hybridization. Custom analysis of NGS fusion panel data identified TTMV::RARA rearrangements and, in the prospectively identified case, facilitated monitoring in sequential bone marrow samples. APL with TTMV::RARA is a rare leukemia with a high rate of treatment failure in described cases. The diagnosis should be considered in leukemias with features of APL that lack detectable RARA fusions and other drivers, and may be confirmed by appropriate NGS tests with custom informatics. Incorporation of all-trans retinoic acid may have a role in treatment but requires accurate recognition of the fusion for appropriate classification as APL.
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Affiliation(s)
- Harrison K Tsai
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mark F Sabbagh
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Erik A Williams
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center, and Jackson Memorial Hospitals, Miami, Florida; Foundation Medicine Inc, Boston, Massachusetts
| | - Arnaldo Arbini
- Department of Pathology, NYU Grossman School of Medicine, New York City, New York
| | - Daniel R Boué
- Department of Pathology & Laboratory Medicine, Nationwide Children's Hospital and The Ohio State University, Columbus, Ohio
| | - Emily M Harris
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Franziska Wachter
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Leslie Grimmett
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Andrew E Place
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Fabienne Lucas
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Annette S Kim
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Barbara Degar
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Jessica Pollard
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jacob R Bledsoe
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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11
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Tayebwa DS, Hyeroba D, Dunn CD, Dunay E, Richard JC, Biryomumaisho S, Acai JO, Goldberg TL. Viruses of free-roaming and hunting dogs in Uganda show elevated prevalence, richness and abundance across a gradient of contact with wildlife. J Gen Virol 2024; 105:002011. [PMID: 39045787 PMCID: PMC11316573 DOI: 10.1099/jgv.0.002011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/03/2024] [Indexed: 07/25/2024] Open
Abstract
Domestic dogs (Canis lupus familiaris) live with humans, frequently contact other animals and may serve as intermediary hosts for the transmission of viruses. Free-roaming dogs, which account for over 70% of the world's domestic dog population, may pose a particularly high risk in this regard. We conducted an epidemiological study of dog viromes in three locations in Uganda, representing low, medium and high rates of contact with wildlife, ranging from dogs owned specifically for traditional hunting in a biodiversity and disease 'hotspot' to pets in an affluent suburb. We quantified rates of contact between dogs and wildlife through owner interviews and conducted canine veterinary health assessments. We then applied broad-spectrum viral metagenomics to blood plasma samples, from which we identified 46 viruses, 44 of which were previously undescribed, in three viral families, Sedoreoviridae, Parvoviridae and Anelloviridae. All 46 viruses (100 %) occurred in the high-contact population of dogs compared to 63 % and 39 % in the medium- and low-contact populations, respectively. Viral prevalence ranged from 2.1 % to 92.0 % among viruses and was highest, on average, in the high-contact population (22.3 %), followed by the medium-contact (12.3 %) and low-contact (4.8 %) populations. Viral richness (number of viruses per dog) ranged from 0 to 27 and was markedly higher, on average, in the high-contact population (10.2) than in the medium-contact (5.7) or low-contact (2.3) populations. Viral richness was strongly positively correlated with the number of times per year that a dog was fed wildlife and negatively correlated with the body condition score, body temperature and packed cell volume. Viral abundance (cumulative normalized metagenomic read density) varied 124-fold among dogs and was, on average, 4.1-fold higher and 2.4-fold higher in the high-contact population of dogs than in the low-contact or medium-contact populations, respectively. Viral abundance was also strongly positively correlated with the number of times per year that a dog was fed wildlife, negatively correlated with packed cell volume and positively correlated with white blood cell count. These trends were driven by nine viruses in the family Anelloviridae, genus Thetatorquevirus, and by one novel virus in the family Sedoreoviridae, genus Orbivirus. The genus Orbivirus contains zoonotic viruses and viruses that dogs can acquire through ingestion of infected meat. Overall, our findings show that viral prevalence, richness and abundance increased across a gradient of contact between dogs and wildlife and that the health status of the dog modified viral infection. Other ecological, geographic and social factors may also have contributed to these trends. Our finding of a novel orbivirus in dogs with high wildlife contact supports the idea that free-roaming dogs may serve as intermediary hosts for viruses of medical importance to humans and other animals.
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Affiliation(s)
- Dickson S. Tayebwa
- Department of Veterinary Pharmacy Clinical and Comparative Medicine, School of Veterinary Medicine and Animal Resources, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - David Hyeroba
- Department of Veterinary Pharmacy Clinical and Comparative Medicine, School of Veterinary Medicine and Animal Resources, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Christopher D. Dunn
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, 1656 Linden Drive, Madison, Wisconsin, 53706, USA
| | - Emily Dunay
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, 1656 Linden Drive, Madison, Wisconsin, 53706, USA
| | - Jordan C. Richard
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, 1656 Linden Drive, Madison, Wisconsin, 53706, USA
| | - Savino Biryomumaisho
- Department of Veterinary Pharmacy Clinical and Comparative Medicine, School of Veterinary Medicine and Animal Resources, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - James O. Acai
- Department of Veterinary Pharmacy Clinical and Comparative Medicine, School of Veterinary Medicine and Animal Resources, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, 1656 Linden Drive, Madison, Wisconsin, 53706, USA
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12
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Zou S, Chen Z, Tan Y, Tan M, Guo W, Wu S, Liu J, Song S, Peng Y, Wang M, Liang K. Microbiomes detected by cerebrospinal fluid metagenomic next-generation sequencing among patients with and without HIV with suspected central nervous system infection. HIV Med 2024; 25:794-804. [PMID: 38515324 DOI: 10.1111/hiv.13634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 03/02/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND Opportunistic infections in the central nervous system (CNS) can be a serious threat to people living with HIV. Early aetiological diagnosis and targeted treatment are crucial but difficult. Metagenomic next-generation sequencing (mNGS) has significant advantages over traditional detection methods. However, differences in the cerebrospinal fluid (CSF) microbiome profiles of patients living with and without HIV with suspected CNS infections using mNGS and conventional testing methods have not yet been adequately evaluated. METHODS We conducted a retrospective cohort study in the first hospital of Changsha between January 2019 and June 2022 to investigate the microbiomes detected using mNGS of the CSF of patients living with and without HIV with suspected CNS infections. The pathogens causing CNS infections were concurrently identified using both mNGS and traditional detection methods. The spectrum of pathogens identified was compared between the two groups. RESULTS Overall, 173 patients (140 with and 33 without HIV) with suspected CNS infection were enrolled in our study. In total, 106 (75.7%) patients with and 16 (48.5%) patients without HIV tested positive with mNGS (p = 0.002). Among the enrolled patients, 71 (50.7%) with HIV and five (15.2%) without HIV tested positive for two or more pathogens (p < 0.001). Patients with HIV had significantly higher proportions of fungus (20.7% vs. 3.0%, p = 0.016) and DNA virus (59.3% vs. 21.2%, p < 0.001) than those without HIV. Epstein-Barr virus (33.6%) was the most commonly identified potential pathogen in the CSF of patients living with HIV using mNGS, followed by cytomegalovirus (20.7%) and torque teno virus (13.8%). The top three causative pathogens identified in patients without HIV were Streptococcus (18.2%), Epstein-Barr virus (12.1%), and Mycobacterium tuberculosis (9.1%). In total, 113 patients living with HIV were diagnosed as having CNS infections. The rate of pathogen detection in people living with HIV with a CNS infection was significantly higher with mNGS than with conventional methods (93.8% vs. 15.0%, p < 0.001). CONCLUSION CSF microbiome profiles differ between patients living with and without HIV with suspected CNS infection. mNGS is a powerful tool for the diagnosis of CNS infection among people living with HIV, especially in those with mixed infections.
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Affiliation(s)
- Shi Zou
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Zhong Chen
- The Institute of HIV/AIDS, The First Hospital of Changsha, Changsha, China
| | - Yuting Tan
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Miao Tan
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wei Guo
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Pathology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Songjie Wu
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
- Department of Nosocomial Infection Management, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jie Liu
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
| | - Shihui Song
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yongquan Peng
- Graduate Collaborative Training Base of the First Hospital of Changsha, Hengyang Medical School, Uni-versity of South China, Hengyang, China
| | - Min Wang
- The Institute of HIV/AIDS, The First Hospital of Changsha, Changsha, China
| | - Ke Liang
- Department of Infectious Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China
- Department of Nosocomial Infection Management, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment, Wuhan, China
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13
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Spezia PG, Carletti F, Novazzi F, Specchiarello E, Genoni A, Drago Ferrante F, Minosse C, Matusali G, Mancini N, Focosi D, Antonelli G, Girardi E, Maggi F. Torquetenovirus Viremia Quantification Using Real-Time PCR Developed on a Fully Automated, Random-Access Platform. Viruses 2024; 16:963. [PMID: 38932255 PMCID: PMC11209079 DOI: 10.3390/v16060963] [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: 05/21/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Quantification of Torquetenovirus (TTV) viremia is becoming important for evaluating the status of the immune system in solid organ transplant recipients, monitoring the appearance of post-transplant complications, and controlling the efficacy of maintenance immunosuppressive therapy. Thus, diagnostic approaches able to scale up TTV quantification are needed. Here, we report on the development and validation of a real-time PCR assay for TTV quantification on the Hologic Panther Fusion® System by utilizing its open-access channel. The manual real-time PCR previously developed in our laboratories was optimized to detect TTV DNA on the Hologic Panther Fusion® System. The assay was validated using clinical samples. The automated TTV assay has a limit of detection of 1.6 log copies per ml of serum. Using 112 samples previously tested via manual real-time PCR, the concordance in TTV detection was 93% between the assays. When the TTV levels were compared, the overall agreement between the methods, as assessed using Passing-Bablok linear regression and Bland-Altman analyses, was excellent. In summary, we validated a highly sensitive and accurate method for the diagnostic use of TTV quantification on a fully automated Hologic Panther Fusion® System. This will greatly improve the turnaround time for TTV testing and better support the laboratory diagnosis of this new viral biomarker.
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Affiliation(s)
- Pietro Giorgio Spezia
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy; (P.G.S.); (E.S.); (C.M.); (G.M.); (F.M.)
| | - Fabrizio Carletti
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy; (P.G.S.); (E.S.); (C.M.); (G.M.); (F.M.)
| | - Federica Novazzi
- Laboratory of Medical Microbiology and Virology, Department of Medicine and Technological Innovation, Italy; Ospedale di Circolo e Fondazione Macchi, University of Insubria, 21100 Varese, Italy; (F.N.); (A.G.); (F.D.F.); (N.M.)
| | - Eliana Specchiarello
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy; (P.G.S.); (E.S.); (C.M.); (G.M.); (F.M.)
| | - Angelo Genoni
- Laboratory of Medical Microbiology and Virology, Department of Medicine and Technological Innovation, Italy; Ospedale di Circolo e Fondazione Macchi, University of Insubria, 21100 Varese, Italy; (F.N.); (A.G.); (F.D.F.); (N.M.)
| | - Francesca Drago Ferrante
- Laboratory of Medical Microbiology and Virology, Department of Medicine and Technological Innovation, Italy; Ospedale di Circolo e Fondazione Macchi, University of Insubria, 21100 Varese, Italy; (F.N.); (A.G.); (F.D.F.); (N.M.)
| | - Claudia Minosse
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy; (P.G.S.); (E.S.); (C.M.); (G.M.); (F.M.)
| | - Giulia Matusali
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy; (P.G.S.); (E.S.); (C.M.); (G.M.); (F.M.)
| | - Nicasio Mancini
- Laboratory of Medical Microbiology and Virology, Department of Medicine and Technological Innovation, Italy; Ospedale di Circolo e Fondazione Macchi, University of Insubria, 21100 Varese, Italy; (F.N.); (A.G.); (F.D.F.); (N.M.)
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy;
| | - Guido Antonelli
- Laboratory of Microbiology and Virology, Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy;
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy;
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy; (P.G.S.); (E.S.); (C.M.); (G.M.); (F.M.)
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14
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Bogza A, King IL, Maurice CF. Worming into infancy: Exploring helminth-microbiome interactions in early life. Cell Host Microbe 2024; 32:639-650. [PMID: 38723604 DOI: 10.1016/j.chom.2024.04.009] [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: 02/23/2024] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 06/06/2024]
Abstract
There is rapidly growing awareness of microbiome assembly and function in early-life gut health. Although many factors, such as antibiotic use and highly processed diets, impinge on this process, most research has focused on people residing in high-income countries. However, much of the world's population lives in low- and middle-income countries (LMICs), where, in addition to erratic antibiotic use and suboptimal diets, these groups experience unique challenges. Indeed, many children in LMICs are infected with intestinal helminths. Although helminth infections are strongly associated with diverse developmental co-morbidities and induce profound microbiome changes, few studies have directly examined whether intersecting pathways between these components of the holobiont shape health outcomes in early life. Here, we summarize microbial colonization within the first years of human life, how helminth-mediated changes to the gut microbiome may affect postnatal growth, and why more research on this relationship may improve health across the lifespan.
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Affiliation(s)
- Andrei Bogza
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada; McGill Centre for Microbiome Research, McGill University, Montreal, QC, Canada; Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Irah L King
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada; McGill Centre for Microbiome Research, McGill University, Montreal, QC, Canada; Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
| | - Corinne F Maurice
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada; McGill Centre for Microbiome Research, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada.
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15
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Wu H, Zhou HY, Zheng H, Wu A. Towards Understanding and Identification of Human Viral Co-Infections. Viruses 2024; 16:673. [PMID: 38793555 PMCID: PMC11126107 DOI: 10.3390/v16050673] [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: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Viral co-infections, in which a host is infected with multiple viruses simultaneously, are common in the human population. Human viral co-infections can lead to complex interactions between the viruses and the host immune system, affecting the clinical outcome and posing challenges for treatment. Understanding the types, mechanisms, impacts, and identification methods of human viral co-infections is crucial for the prevention and control of viral diseases. In this review, we first introduce the significance of studying human viral co-infections and summarize the current research progress and gaps in this field. We then classify human viral co-infections into four types based on the pathogenic properties and species of the viruses involved. Next, we discuss the molecular mechanisms of viral co-infections, focusing on virus-virus interactions, host immune responses, and clinical manifestations. We also summarize the experimental and computational methods for the identification of viral co-infections, emphasizing the latest advances in high-throughput sequencing and bioinformatics approaches. Finally, we highlight the challenges and future directions in human viral co-infection research, aiming to provide new insights and strategies for the prevention, control, diagnosis, and treatment of viral diseases. This review provides a comprehensive overview of the current knowledge and future perspectives on human viral co-infections and underscores the need for interdisciplinary collaboration to address this complex and important topic.
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Affiliation(s)
- Hui Wu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211100, China;
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Hang-Yu Zhou
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211100, China;
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
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16
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Gu Y, Wang Z, Xia X, Zhao G. Nocardia farcinica brain abscess with torque teno virus co-infection: A case report. Heliyon 2024; 10:e28632. [PMID: 38590894 PMCID: PMC11000006 DOI: 10.1016/j.heliyon.2024.e28632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
Background Brain abscesses caused by Nocardia are rare and difficult to diagnose. Nocardia farcinica is among the most common species; however, the conventional diagnosis of N. farcinica infection consists of cerebrospinal fluid (CSF) and blood culture and Gram staining. These procedures prolong the time to diagnosis and initiating treatment. Case presentation A 69-year-old woman with diabetes mellitus presented with headaches and dizziness persisting for 2 weeks, which was initially diagnosed as a brain abscess. Due to the unusual presentation and rapid progression of symptoms, she underwent surgical resection of the brain abscess. No pathogens were detected in blood or CSF cultures. However, metagenomic next-generation sequencing (mNGS) identified N. farcinica and Torque teno virus in pus extracted from the abscesses. The patient received appropriate antibiotic therapy and recovered fully without any residual neurological deficits. Conclusion mNGS useful for prompt diagnosis and selection of antibiotic therapy for brain abscesses caused by Nocardia. Surgical intervention is necessary in some cases.
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Affiliation(s)
- Yuting Gu
- Department of Emergency Medicine, The First People's Hospital of Kunshan, Kunshan, 215300, Jiangsu, China
- The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Zide Wang
- The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Xiaohua Xia
- Department of Emergency Medicine, The First People's Hospital of Kunshan, Kunshan, 215300, Jiangsu, China
| | - Guang Zhao
- Department of Emergency Medicine, The First People's Hospital of Kunshan, Kunshan, 215300, Jiangsu, China
- The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province, China
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17
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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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18
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Brüssow H. Pandemic preparedness: On the efficacy of non-pharmaceutical interventions in COVID-19 and about approaches to predict future pandemic viruses. Microb Biotechnol 2024; 17:e14431. [PMID: 38465466 PMCID: PMC10926049 DOI: 10.1111/1751-7915.14431] [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: 02/03/2024] [Accepted: 02/15/2024] [Indexed: 03/12/2024] Open
Abstract
With three major viral pandemics over the last 100 years, namely the Spanish flu, AIDS and COVID-19 each claiming many millions of lives, pandemic preparedness has become an important issue for public health. The economic, social and political consequences of the upheaval caused by such pandemics also represent a major challenge for governments with respect to sustainable development goals. The field of pandemic preparedness is vast and the current article can only address selected aspects. The article looks first backwards and addresses the question of the efficacy of non-pharmaceutical interventions (NPI) on the trajectory of the COVID-19 pandemic. The article looks then forward by asking to what extent viral candidates for future pandemics can be predicted by virome analyses from metagenome and transcriptome sequencing, by focusing on the virome from specific animal species and using ecological and epidemiological data about spillover viral infections in veterinary and human medicine. As a comprehensive overview on pandemic preparedness is beyond the capacity of a single reviewer, only selected topics will be discussed using recent key scientific publications. Since COVID-19 has not run its course, a computational program able to predict the future evolution of SARS-CoV-2 is mentioned that could assist proactive mRNA vaccine developments against possible future variants of concern. Ending the COVID-19 epidemic necessitates mucosal vaccines that can suppress the transmission of SARS-CoV-2 and therefore this article closes by discussing a promising and versatile protein nanoparticle experimental vaccine approach for inhalation that does not depend on needles nor a cold chain for distribution.
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Affiliation(s)
- Harald Brüssow
- Laboratory of Gene Technology, Department of BiosystemsKU LeuvenLeuvenBelgium
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19
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Cao Z, Fan D, Sun Y, Huang Z, Li Y, Su R, Zhang F, Li Q, Yang H, Zhang F, Miao Y, Lan P, Wu X, Zuo T. The gut ileal mucosal virome is disturbed in patients with Crohn's disease and exacerbates intestinal inflammation in mice. Nat Commun 2024; 15:1638. [PMID: 38388538 PMCID: PMC10884039 DOI: 10.1038/s41467-024-45794-y] [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: 07/20/2023] [Accepted: 02/01/2024] [Indexed: 02/24/2024] Open
Abstract
Gut bacteriome dysbiosis is known to be implicated in the pathogenesis of inflammatory bowel disease (IBD). Crohn's disease (CD) is an IBD subtype with extensive mucosal inflammation, yet the mucosal virome, an empirical modulator of the bacteriome and mucosal immunity, remains largely unclear regarding its composition and role. Here, we exploited trans-cohort CD patients and healthy individuals to compositionally and functionally investigate the small bowel (terminal ileum) virome and bacteriome. The CD ileal virome was characterised by an under-representation of both lytic and temperate bacteriophages (especially those targeting bacterial pathogens), particularly in patients with flare-up. Meanwhile, the virome-bacteriome ecology in CD ileal mucosa was featured by a lack of Bifidobacterium- and Lachnospiraceae-led mutualistic interactions between bacteria and bacteriophages; surprisingly it was more pronounced in CD remission than flare-up, underlining the refractory and recurrent nature of mucosal inflammation in CD. Lastly, we substantiated that ileal virions from CD patients causally exacerbated intestinal inflammation in IBD mouse models, by reshaping a gut virome-bacteriome ecology preceding intestinal inflammation (microbial trigger) and augmenting microbial sensing/defence pathways in the intestine cells (host response). Altogether, our results highlight the significance of mucosal virome in CD pathogenesis and importance of mucosal virome restoration in CD therapeutics.
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Affiliation(s)
- Zhirui Cao
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Centre, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Dejun Fan
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Gastrointestinal Endoscopy, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yang Sun
- Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China.
- Yunnan Province Clinical Research Centre for Digestive Diseases, Kunming, Yunnan, China.
- Yunnan Geriatric Medical Centre, Kunming, Yunnan, China.
| | - Ziyu Huang
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Centre, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yue Li
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Centre, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Runping Su
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Centre, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Feng Zhang
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Centre, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qing Li
- Department of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hongju Yang
- Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Geriatric Medical Centre, Kunming, Yunnan, China
| | - Fen Zhang
- Department of Food Science and Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Yinglei Miao
- Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Centre for Digestive Diseases, Kunming, Yunnan, China
| | - Ping Lan
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
- Biomedical Innovation Centre, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaojian Wu
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China.
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Biomedical Innovation Centre, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Tao Zuo
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China.
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Centre for Faecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Biomedical Innovation Centre, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
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20
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Baker JL, Mark Welch JL, Kauffman KM, McLean JS, He X. The oral microbiome: diversity, biogeography and human health. Nat Rev Microbiol 2024; 22:89-104. [PMID: 37700024 PMCID: PMC11084736 DOI: 10.1038/s41579-023-00963-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2023] [Indexed: 09/14/2023]
Abstract
The human oral microbiota is highly diverse and has a complex ecology, comprising bacteria, microeukaryotes, archaea and viruses. These communities have elaborate and highly structured biogeography that shapes metabolic exchange on a local scale and results from the diverse microenvironments present in the oral cavity. The oral microbiota also interfaces with the immune system of the human host and has an important role in not only the health of the oral cavity but also systemic health. In this Review, we highlight recent advances including novel insights into the biogeography of several oral niches at the species level, as well as the ecological role of candidate phyla radiation bacteria and non-bacterial members of the oral microbiome. In addition, we summarize the relationship between the oral microbiota and the pathology of oral diseases and systemic diseases. Together, these advances move the field towards a more holistic understanding of the oral microbiota and its role in health, which in turn opens the door to the study of novel preventive and therapeutic strategies.
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Affiliation(s)
- Jonathon L Baker
- Oregon Health & Science University, Portland, OR, USA
- J. Craig Venter Institute, La Jolla, CA, USA
- UC San Diego School of Medicine, La Jolla, CA, USA
| | - Jessica L Mark Welch
- The Forsyth Institute, Cambridge, MA, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
| | | | | | - Xuesong He
- The Forsyth Institute, Cambridge, MA, USA.
- Harvard School of Dental Medicine, Boston, MA, USA.
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21
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Sabbaghian M, Gheitasi H, Shekarchi AA, Tavakoli A, Poortahmasebi V. The mysterious anelloviruses: investigating its role in human diseases. BMC Microbiol 2024; 24:40. [PMID: 38281930 PMCID: PMC10823751 DOI: 10.1186/s12866-024-03187-7] [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: 11/14/2023] [Accepted: 01/08/2024] [Indexed: 01/30/2024] Open
Abstract
Anelloviruses (AVs) that infect the human population are members of the Anelloviridae family. They are widely distributed in human populations worldwide. Torque teno virus (TTV) was the first virus of this family to be identified and is estimated to be found in the serum of 80-90% of the human population. Sometime after the identification of TTV, Torque teno mini virus (TTMV) and Torque teno midi virus (TTMDV) were also identified and classified in this family. Since identifying these viruses, have been detected in various types of biological fluids of the human body, including blood and urine, as well as vital organs such as the liver and kidney. They can be transmitted from person to person through blood transfusions, fecal-oral contact, and possibly sexual intercourse. Recent studies on these newly introduced viruses show that although they are not directly related to human disease, they may be indirectly involved in initiating or exacerbating some human population-related diseases and viral infections. Among these diseases, we can mention various types of cancers, immune system diseases, viral infections, hepatitis, and AIDS. Also, they likely use the microRNAs (miRNAs) they encode to fulfill this cooperative role. Also, in recent years, the role of proliferation and their viral load, especially TTV, has been highlighted to indicate the immune system status of immunocompromised people or people who undergo organ transplants. Here, we review the possible role of these viruses in diseases that target humans and highlight them as important viruses that require further study. This review can provide new insights to researchers.
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Affiliation(s)
- Mohammad Sabbaghian
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamidreza Gheitasi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Akbar Shekarchi
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahmad Tavakoli
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Vahdat Poortahmasebi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
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22
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Timmerman AL, Schönert ALM, van der Hoek L. Anelloviruses versus human immunity: how do we control these viruses? FEMS Microbiol Rev 2024; 48:fuae005. [PMID: 38337179 PMCID: PMC10883694 DOI: 10.1093/femsre/fuae005] [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: 11/09/2023] [Revised: 12/22/2023] [Accepted: 02/08/2024] [Indexed: 02/12/2024] Open
Abstract
One continuous companion and one of the major players in the human blood virome are members of the Anelloviridae family. Anelloviruses are probably found in all humans, infection occurs early in life and the composition (anellome) is thought to remain stable and personal during adulthood. The stable anellome implies a great balance between the host immune system and the virus. However, the lack of a robust culturing system hampers direct investigation of interactions between virus and host cells. Other techniques, however, including next generation sequencing, AnelloScan-antibody tests, evolution selection pressure analysis, and virus protein structures, do provide new insights into the interactions between anelloviruses and the host immune system. This review aims at providing an overview of the current knowledge on the immune mechanisms acting on anelloviruses and the countering viral mechanisms allowing immune evasion.
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Affiliation(s)
- Anne L Timmerman
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, the Netherlands
| | - Antonia L M Schönert
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, the Netherlands
| | - Lia van der Hoek
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Postbus 22660, 1100 DD, Amsterdam, the Netherlands
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23
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Timmerman AL, Commandeur L, Deijs M, Burggraaff MGJM, Lavell AHA, van der Straten K, Tejjani K, van Rijswijk J, van Gils MJ, Sikkens JJ, Bomers MK, van der Hoek L. The Impact of First-Time SARS-CoV-2 Infection on Human Anelloviruses. Viruses 2024; 16:99. [PMID: 38257799 PMCID: PMC10818381 DOI: 10.3390/v16010099] [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: 12/14/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Members of the Anelloviridae family dominate the blood virome, emerging early in life. The anellome, representing the variety of anelloviruses within an individual, stabilizes by adulthood. Despite their supposedly commensal nature, elevated anellovirus concentrations under immunosuppressive treatment indicate an equilibrium controlled by immunity. Here, we investigated whether anelloviruses are sensitive to the immune activation that accompanies a secondary infection. As a model, we investigated 19 health care workers (HCWs) with initial SARS-CoV-2 infection, with blood sampling performed pre and post infection every 4 weeks in a 3-month-follow-up during the early 2020 COVID-19 pandemic. A concurrently followed control group (n = 27) remained SARS-CoV-2-negative. Serum anellovirus loads were measured using qPCR. A significant decrease in anellovirus load was found in the first weeks after SARS-CoV-2 infection, whereas anellovirus concentrations remained stable in the uninfected control group. A restored anellovirus load was seen approximately 10 weeks after SARS-CoV-2 infection. For five subjects, an in-time anellome analysis via Illumina sequencing could be performed. In three of the five HCWs, the anellome visibly changed during SARS-CoV-2 infection and returned to baseline in two of these cases. In conclusion, anellovirus loads in blood can temporarily decrease upon an acute secondary infection.
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Affiliation(s)
- Anne L. Timmerman
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Lisanne Commandeur
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Maarten G. J. M. Burggraaff
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - A. H. Ayesha Lavell
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
- Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Karlijn van der Straten
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Khadija Tejjani
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Jacqueline van Rijswijk
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Marit J. van Gils
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
| | - Jonne J. Sikkens
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
- Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Marije K. Bomers
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
- Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (A.L.T.); (L.C.); (M.D.); (M.G.J.M.B.); (K.T.); (J.v.R.); (M.J.v.G.)
- Amsterdam Institute for Infection and Immunity, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands (J.J.S.); (M.K.B.)
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24
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Cavalcante LTF, Cosentino MAC, D’arc M, Moreira FRR, Mouta R, Augusto AM, Troccoli F, Soares MA, Santos AF. Characterization of a new anellovirus species infecting an ocelot (Leopardus pardalis) in Brazil. Genet Mol Biol 2023; 46:e20230015. [PMID: 38051353 PMCID: PMC10697133 DOI: 10.1590/1678-4685-gmb-2023-0015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 10/06/2023] [Indexed: 12/07/2023] Open
Abstract
A complete genome of the first anellovirus infecting the wild felid Leopardus pardalis (ocelot) and a partial genome were assembled and annotated through high-throughput sequencing protocols followed by Sanger sequencing validation. The full-length virus obtained comprises 2,003 bp, while the partial genome comprises 1,224 bp. Phylogenetic analysis grouped these two sequences in two distinct clusters related to previously described Felidae anelloviruses. The ORF1 of the partial genome was identified as a new species provisionally called Torque teno ocelot virus, with 53.6% identity with its sister lineage. The complete genome was inferred as a new representative of the Torque teno felid virus 3 species, with 73.28% identity to the closest reference. This study expands known virus diversity and the host span of anelloviruses.
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Affiliation(s)
| | - Matheus A. C. Cosentino
- Universidade Federal do Rio de Janeiro, Departamento de Genética, Ilha do Fundão, RJ, Brazil
| | - Mirela D’arc
- Universidade Federal do Rio de Janeiro, Departamento de Genética, Ilha do Fundão, RJ, Brazil
| | - Filipe R. R. Moreira
- Universidade Federal do Rio de Janeiro, Departamento de Genética, Ilha do Fundão, RJ, Brazil
| | - Ricardo Mouta
- Universidade Federal do Rio de Janeiro, Departamento de Genética, Ilha do Fundão, RJ, Brazil
| | | | | | - Marcelo A. Soares
- Universidade Federal do Rio de Janeiro, Departamento de Genética, Ilha do Fundão, RJ, Brazil
- Instituto Nacional de Câncer, Programa de Oncovirologia, Rio de Janeiro, RJ, Brazil
| | - André F. Santos
- Universidade Federal do Rio de Janeiro, Departamento de Genética, Ilha do Fundão, RJ, Brazil
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25
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Wang X, Cheng J, Jiang Y, Ou J, Cai S, Xu L, Zhong L, Xiao Y, Hu X, Lu G, Yuan L. Natural recombination of the torque teno canis virus within the ORF1, -2, and -3 genes and the untranslated region. Virus Res 2023; 338:199227. [PMID: 37793437 PMCID: PMC10582477 DOI: 10.1016/j.virusres.2023.199227] [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: 08/23/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
Abstract
The torque teno canis virus (TTCaV) was first reported in 2001 and it shares similarities with the known Torque teno virus (TTV) in terms of genomic organization and putative transcriptional features. It is a single-stranded DNA virus characterized by high rates of recombination and nucleotide substitution, like RNA viruses. Studies reported recombination events in torque teno virus; however, there is limited reporting of TTCaV reorganization events. This study screened fecal samples from domestic dogs in Henan Province. There was a positivity rate of 16.5% (19/115) for TTCaV. Four nearly complete TTCaV genomes, namely Canine/HeNan/4, 5, 6, and 13/2019, were obtained from the 19 positive fecal samples, whose genome sequence was obtained using gap-filling PCR. Sequence analysis revealed two unique amino acid mutation sites in the TTCaV strains, K278Q (compared with the first isolate Cf-TTV10 in Japan) and V/L268I (compared with the TTCaV strain from southern China). Subsequently, 17 near full-length TTCaV genome sequences were subjected to phylogenetic and recombination detection program analyzes. We obtained evidence supporting recombination events in the Chinese TTCaV strains. These findings suggest that mutation and recombination occurred in the three individual gene segments (ORF1, ORF2, ORF3) and the untranslated region, an area of major recombination in the Chinese TTCaV strain GX265 genome. Interestingly, the TTCaV strain (Canine/HeNan/6/2019) was a major parent involved in the genetic recombination of the GX265 strain. This study provides insights into the genetic variability and evolution of TTCaV.
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Affiliation(s)
- Xuyang Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Jiaojiao Cheng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Yujie Jiang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Jiajun Ou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Siqi Cai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Liang Xu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Lintao Zhong
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Yuqing Xiao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Xuerui Hu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Gang Lu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China.
| | - Liguo Yuan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China.
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26
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Abbate I, Rozera G, Cimini E, Carletti F, Tartaglia E, Rubino M, Pittalis S, Esvan R, Gagliardini R, Mondi A, Mazzotta V, Camici M, Girardi E, Vaia F, Puro V, Antinori A, Maggi F. Kinetics of TTV Loads in Peripheral Blood Mononuclear Cells of Early Treated Acute HIV Infections. Viruses 2023; 15:1931. [PMID: 37766337 PMCID: PMC10537844 DOI: 10.3390/v15091931] [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: 08/26/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Torquetenovirus (TTV) is the most abundant component of the human blood virome and its replication is controlled by a functioning immune system. In this study, TTV replication was evaluated in 21 people with acute HIV infection (AHI) and immune reconstitution following antiretroviral therapy (ART). PBMC-associated TTV and HIV-1 DNA, as well as plasma HIV-1 RNA, were measured by real-time PCR. CD4 and CD8 differentiation, activation, exhaustion, and senescence phenotypes were analyzed by flow cytometry. Thirteen healthy donors (HD) and twenty-eight chronically infected HIV individuals (CHI), late presenters at diagnosis, were included as control groups. TTV replication in AHI seems to be controlled by the immune system being higher than in HD and lower than in CHI. During ART, a transient increase in TTV DNA levels was associated with a significant perturbation of activation and senescence markers on CD8 T cells. TTV loads were positively correlated with the expansion of CD8 effector memory and CD57+ cells. Our results shed light on the kinetics of TTV replication in the context of HIV acute infection and confirm that the virus replication is strongly regulated by the modulation of the immune system.
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Affiliation(s)
- Isabella Abbate
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (I.A.); (G.R.); (F.C.); (F.M.)
| | - Gabriella Rozera
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (I.A.); (G.R.); (F.C.); (F.M.)
| | - Eleonora Cimini
- Laboratory of Cellular Immunology and Pharmacology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (E.T.); (M.R.)
| | - Fabrizio Carletti
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (I.A.); (G.R.); (F.C.); (F.M.)
| | - Eleonora Tartaglia
- Laboratory of Cellular Immunology and Pharmacology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (E.T.); (M.R.)
| | - Marika Rubino
- Laboratory of Cellular Immunology and Pharmacology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (E.T.); (M.R.)
| | - Silvia Pittalis
- AIDS Referral Center, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (S.P.); (R.E.); (V.P.)
| | - Rozenn Esvan
- AIDS Referral Center, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (S.P.); (R.E.); (V.P.)
| | - Roberta Gagliardini
- Clinical Infectious Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (R.G.); (A.M.); (V.M.); (M.C.); (A.A.)
| | - Annalisa Mondi
- Clinical Infectious Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (R.G.); (A.M.); (V.M.); (M.C.); (A.A.)
| | - Valentina Mazzotta
- Clinical Infectious Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (R.G.); (A.M.); (V.M.); (M.C.); (A.A.)
| | - Marta Camici
- Clinical Infectious Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (R.G.); (A.M.); (V.M.); (M.C.); (A.A.)
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy;
| | - Francesco Vaia
- General Direction, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy;
| | - Vincenzo Puro
- AIDS Referral Center, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (S.P.); (R.E.); (V.P.)
| | - Andrea Antinori
- Clinical Infectious Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (R.G.); (A.M.); (V.M.); (M.C.); (A.A.)
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy; (I.A.); (G.R.); (F.C.); (F.M.)
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27
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Wang X, Chen X, Song X, Cao L, Yang S, Shen Q, Ji L, Lu X, Zhang W. Identification of novel anelloviruses in the blood of giant panda (Ailuropoda melanoleuca). Comp Immunol Microbiol Infect Dis 2023; 100:102038. [PMID: 37572592 DOI: 10.1016/j.cimid.2023.102038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/15/2023] [Accepted: 08/02/2023] [Indexed: 08/14/2023]
Abstract
In recent years, the continuous development of metagenomics has revealed that in addition to the digestive tract, some viruses are also common in mammalian blood. To explore and monitor potential novel viruses, in April 2015, a blood sample was collected from a healthy captive giant panda at the Chengdu Research Base of Giant Panda Breeding in Sichuan Province, China. The genomes of 25 different anelloviruses containing the complete ORF1 region have been identified. The BLASTp results showed that the amino acid sequence identity of these viruses with the best match in GenBank ranged from 27.15% to 41.29%. Based on phylogenetic analysis and SDT (Species Demarcation Tool) analysis of the complete ORF1 regions of these 25 viruses, these sequences were deduced to represent one or several novel virus genera or species. This virological study has increased our understanding of the diversity of anelloviruses in the blood of giant pandas, but further laboratory analysis is needed to verify its possible pathogenicity.
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Affiliation(s)
- Xiaochun Wang
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xurong Chen
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xulai Song
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ling Cao
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shixing Yang
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Quan Shen
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Likai Ji
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiang Lu
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
| | - Wen Zhang
- Department of laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.
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28
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Briese T, Tokarz R, Bateman L, Che X, Guo C, Jain K, Kapoor V, Levine S, Hornig M, Oleynik A, Quan PL, Wong WH, Williams BL, Vernon SD, Klimas NG, Peterson DL, Montoya JG, Ian Lipkin W. A multicenter virome analysis of blood, feces, and saliva in myalgic encephalomyelitis/chronic fatigue syndrome. J Med Virol 2023; 95:e28993. [PMID: 37526404 DOI: 10.1002/jmv.28993] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/08/2023] [Accepted: 07/16/2023] [Indexed: 08/02/2023]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is estimated to affect 0.4%-2.5% of the global population. Most cases are unexplained; however, some patients describe an antecedent viral infection or response to antiviral medications. We report here a multicenter study for the presence of viral nucleic acid in blood, feces, and saliva of patients with ME/CFS using polymerase chain reaction and high-throughput sequencing. We found no consistent group-specific differences other than a lower prevalence of anelloviruses in cases compared to healthy controls. Our findings suggest that future investigations into viral infections in ME/CFS should focus on adaptive immune responses rather than surveillance for viral gene products.
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Affiliation(s)
- Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | | | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Vishal Kapoor
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | | | - Mady Hornig
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Alexandra Oleynik
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Phenix-Lan Quan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Wai H Wong
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Brent L Williams
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | | | - Nancy G Klimas
- Institute for Neuro-Immune Medicine, College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, Florida, USA
- Bruce W. Carter Miami Veterans Affairs Medical Center, Geriatric Research Education and Research Center, Miami, Florida, USA
| | | | - Jose G Montoya
- Jack S. Remington Laboratory for Specialty Diagnostics of Toxoplasmosis, Palo Alto Medical Foundation, Palo Alto, USA
| | - Walter Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
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29
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Zhang X, Park WD, Thijssen M, Xu Y, Tse LPV, Pourkarim MR, Aurora R, Fan X. Expansion of Betatorquevirus and/or Gammatorquevirus in Patients with Severe Clinical Outcomes of the Liver Diseases. Viruses 2023; 15:1635. [PMID: 37631978 PMCID: PMC10457780 DOI: 10.3390/v15081635] [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: 05/30/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Anellovirus (AV) is a ubiquitous virus in the human population. Individuals can be infected with multiple AV genera and species to form a heterogeneous repertoire, termed the anellome. Using advanced methods, we examined the anellomes from 12 paired serum and liver samples, as well as 2701 subjects with different clinical diagnoses. Overall, anellomes are remarkably individualized, with significant among-group differences (Kruskal-Wallis test p = 6.6 × 10-162 for richness and p = 7.48 × 10-162 for Shannon entropy). High dissimilarity scores (beta diversity) were observed between patient groups, except for paired serum and liver samples. At the population level, the relative abundance of combinational AV genus Betatorquevirus (torque teno mini viruses, TTMV), and Gammatorquevirus (torque teno midi viruses, TTMDV) exhibited an exponential distribution with a low bound point at 32%. Defined by this value, the AV TTMV/TTMDV-expanded anellome was significantly enriched among patients with acute liver failure (31.7%) and liver transplantation (40.7%), compared with other patient groups (χ2 test: p = 4.1 × 10-8-3.2 × 10-3). Therefore, anellome heterogeneity may be predictive of clinical outcomes in certain diseases, such as liver disease. The consistency of anellome between paired serum and liver samples indicates that a liquid biopsy approach would be suitable for longitudinal studies to clarify the causality of the AV TTMV/TTMDV-expanded anellome in the outcomes of liver disease.
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Affiliation(s)
- Xiaoan Zhang
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
- School of Clinical Medicine, Henan University of Science and Technology, Luoyang 471000, China
| | - William D. Park
- Department of Molecular Microbiology & Immunology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Marijn Thijssen
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Yanjuan Xu
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Long Ping Victor Tse
- Department of Molecular Microbiology & Immunology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Mahmoud Reza Pourkarim
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Rajeev Aurora
- Department of Molecular Microbiology & Immunology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Xiaofeng Fan
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
- Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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30
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Fry TL, Owens LA, Ketz AC, Atwood TC, Dunay E, Goldberg TL. Serum Virome of Southern Beaufort Sea polar bears ( Ursus maritimus) during a period of rapid climate change. CONSERVATION PHYSIOLOGY 2023; 11:coad054. [PMID: 39070777 PMCID: PMC10375943 DOI: 10.1093/conphys/coad054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/02/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2024]
Abstract
Climate change affects the behavior, physiology and life history of many Arctic wildlife species. It can also influence the distribution and ecology of infectious agents. The southern Beaufort Sea (SB) subpopulation of polar bears (Ursus maritimus) has experienced dramatic behavioral changes due to retreating sea ice and other climate-related factors, but the effects of these changes on physiology and infection remain poorly understood. Using serum from polar bears sampled between 2004 and 2015 and metagenomic DNA sequencing, we identified 48 viruses, all of the family Anelloviridae. Anelloviruses are small, ubiquitous infectious agents with circular single-stranded DNA genomes that are not known to cause disease but, in humans, covary in diversity and load with immunological compromise. We therefore examined the usefulness of anelloviruses as biomarkers of polar bear physiological stress related to climate and habitat use. Polar bear anelloviruses sorted into two distinct clades on a phylogenetic tree, both of which also contained anelloviruses of giant pandas (Ailuropoda melanoleuca), another ursid. Neither anellovirus diversity nor load were associated with any demographic variables, behavioral factors or direct physiological measures. However, pairwise genetic distances between anelloviruses were positively correlated with pairwise differences in sampling date, suggesting that the polar bear "anellome" is evolving over time. These findings suggest that anelloviruses are not a sensitive indicator of polar physiological stress, but they do provide a baseline for evaluating future changes to polar bear viromes.
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Affiliation(s)
- Tricia L Fry
- School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53706
| | - Leah A Owens
- School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53706
| | - Alison C Ketz
- Wisconsin Cooperative Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, WI, 53706
| | - Todd C Atwood
- Alaska Science Center, U. S. Geological Survey, Anchorage, AK 99508
| | - Emily Dunay
- School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53706
| | - Tony L Goldberg
- School of Veterinary Medicine, University of Wisconsin, Madison, WI, 53706
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31
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Laubscher F, Kaiser L, Cordey S. SCANellome: Analysis of the Genomic Diversity of Human and Non-Human Primate Anelloviruses from Metagenomics Data. Viruses 2023; 15:1575. [PMID: 37515261 PMCID: PMC10384568 DOI: 10.3390/v15071575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Anelloviruses are extremely prevalent in the human population and are considered to be commensal parts of the human virome. The best-known member in humans is the Torque teno virus. Recent metagenomic next-generation sequencing investigations have helped reveal the considerable number of species and genotypes from the same genus that can be co-detected within a single individual and that this diversity increases as a function of age during the first months/years of life. As a result, to date, the bioinformatics analysis of this genetic diversity remains complex and constraining for researchers. Here, we present SCANellome, a user-friendly tool to investigate the anellome composition at the genus, species, and genotype levels of samples from metagenomics data generated by the Illumina and Nanopore platforms. SCANellome is based on an in-house up-to-date database that includes all human and non-human primate anellovirus reference sequences available on GenBank and meets the latest classification criteria established by the International Committee on Taxonomy of Viruses.
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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
| | - Laurent Kaiser
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
- 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
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32
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Gryaznova M, Smirnova Y, Burakova I, Morozova P, Nesterova E, Gladkikh M, Mikhaylov E, Syromyatnikov M. Characteristics of the Fecal Microbiome of Piglets with Diarrhea Identified Using Shotgun Metagenomics Sequencing. Animals (Basel) 2023; 13:2303. [PMID: 37508080 PMCID: PMC10376196 DOI: 10.3390/ani13142303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Diarrhea in piglets is one of the most common diseases leading to high mortality and, as a result, to economic losses. Shotgun metagenomic sequencing was performed on the DNBSEQ-G50, MGI system to study the role of the fecal microbiome in the development of diarrhea in newborn piglets. Analysis of the study data showed that the composition of the fecal microbiome at the level of bacteria and fungi did not differ in piglets with diarrhea from the healthy group. Bacteria belonging to the phyla Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria were the most abundant. However, a higher level of bacterial alpha diversity was observed in the group of piglets with diarrhea, which may be due to dysbacteriosis and inflammation. The study of the virome showed the difference between the two types of phages: Bacteroides B40-8 prevailed in diseased piglets, while Escherichia virus BP4 was found in greater numbers in healthy piglets. The results of our study suggest that the association between the fecal microbiome and susceptibility to diarrhea in suckling piglets may have been previously overestimated.
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Affiliation(s)
- Mariya Gryaznova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Yuliya Smirnova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Inna Burakova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - Polina Morozova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Ekaterina Nesterova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Mariya Gladkikh
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - Evgeny Mikhaylov
- FSBSI All-Russian Veterinary Research Institute of Pathology, Pharmacology and Therapy, 394061 Voronezh, Russia
| | - Mikhail Syromyatnikov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
- FSBSI All-Russian Veterinary Research Institute of Pathology, Pharmacology and Therapy, 394061 Voronezh, Russia
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33
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Cao L, Ma Y, Wan Z, Li B, Tian W, Zhang C, Li Y. Longitudinal anellome dynamics in the upper respiratory tract of children with acute respiratory tract infections. Virus Evol 2023; 9:vead045. [PMID: 37674817 PMCID: PMC10478798 DOI: 10.1093/ve/vead045] [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: 04/27/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 09/08/2023] Open
Abstract
Anelloviruses (AVs) are ubiquitous in humans and are the most abundant components of the commensal virome. Previous studies on the diversity, transmission, and persistence of AVs mainly focused on the blood or transplanted tissues from adults; however, the profile of the anellome in the respiratory tract in children are barely known. We investigated the anellome profile and their dynamics in the upper respiratory tract from a cohort of children with acute respiratory tract infections (ARTIs). Different to that in adult, betatorquevirus is the most abundant genus, followed by alphatorquevirus. We found that the relative abundance of betatorquevirus was higher in earlier time points, and in contrast, the abundance of alphatorquevirus was higher in later time points; these results might suggest that betatorquevirus decreased with age and alphatorquevirus increased with age in childhood. No difference regarding the diversity and abundance of anellome was found between single and multiple ARTIs, consistent with the idea that AV is not associated with certain disease. Most AVs are transient, and a small proportion (8 per cent) of them were found to be possibly persistent, with persistence time ranging from 1 month to as long as 56 months. Furthermore, the individual respiratory anellome appeared to be unique and dynamic, and the replacement of existing AVs with new ones are common over different time points. These findings demonstrate that betatorquevirus may be the early colonizer in children, and the individual respiratory anellome is unique, which are featured by both chronic infections and AV community replacement.
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Affiliation(s)
- Le Cao
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Yingying Ma
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People’s Hospital, 99 North Gulou Road, Taizhou 225300, China
| | - Bing Li
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Weimin Tian
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
| | - Yanpeng Li
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China
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34
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Gao J, Liu C, Yi J, Shi Y, Li H, Liu H. Genomic Characteristics of Feline Anelloviruses Isolated from Domestic Cats in Shanghai, China. Vet Sci 2023; 10:444. [PMID: 37505849 PMCID: PMC10385657 DOI: 10.3390/vetsci10070444] [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: 06/15/2023] [Revised: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023] Open
Abstract
Viral metagenomics techniques allow the high-throughput discovery of possible pathogens carried by companion animals from their feces and other excreta. In this study, the viral metagenomics of 22 groups of fecal samples from domestic cats revealed a high prevalence of feline anelloviruses (FcTTV) infection in domestic cats in Shanghai, China. Serum samples from 30 cat individuals were further detected by polymerase chain reaction, and an average positive rate of 36.67% (11/30) of FcTTV infection was found. Next, the full-length sequences of five Shanghai FcTTV variants were obtained and submitted to GenBank with access numbers OP186140 to OP186144. Phylogenetic analysis indicates that the Shanghai FcTTV variants have relatively consistent genomic characteristics, with two variants from Zhejiang 2019 and one variant from the Czech Republic 2010. The recombination event analysis of the variants showed that one variant (OP186141_SH-02) had a primary parental sequence derived from a variant (KM229764) from the Czech Republic in 2010, while the secondary parental sequence was derived from OP186140_SH-01. The results revealed that FcTTV infection is prevalent in domestic cats and that the use of viral metagenomics to rapidly identify some infecting viruses whose hosts lack clinical features would be an effective approach.
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Affiliation(s)
- Jun Gao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Chengqian Liu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Jianzhong Yi
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Ying Shi
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Hong Li
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Huili Liu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
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Brüssow H. Viral infections at the animal-human interface-Learning lessons from the SARS-CoV-2 pandemic. Microb Biotechnol 2023; 16:1397-1411. [PMID: 37338856 DOI: 10.1111/1751-7915.14269] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 06/21/2023] Open
Abstract
This Lilliput explores the current epidemiological and virological arguments for a zoonotic origin of the COVID-19 pandemic. While the role of bats, pangolins and racoon dogs as viral reservoirs has not yet been proven, a spill-over of a coronavirus infection from animals into humans at the Huanan food market in Wuhan has a much greater plausibility than alternative hypotheses such as a laboratory virus escape, deliberate genetic engineering or introduction by cold chain food products. This Lilliput highlights the dynamic nature of the animal-human interface for viral cross-infections from humans into feral white tail deer or farmed minks (reverse zoonosis). Surveillance of viral infections at the animal-human interface is an urgent task since live animal markets are not the only risks for future viral spill-overs. Climate change will induce animal migration which leads to viral exchanges between animal species that have not met in the past. Environmental change and deforestation will also increase contact between animals and humans. Developing an early warning system for emerging viral infections becomes thus a societal necessity not only for human but also for animal and environmental health (One Health concept). Microbiologists have developed tools ranging from virome analysis in key suspects such as viral reservoirs (bats, wild game animals, bushmeat) and in humans exposed to wild animals, to wastewater analysis to detect known and unknown viruses circulating in the human population and sentinel studies in animal-exposed patients with fever. Criteria need to be developed to assess the virulence and transmissibility of zoonotic viruses. An early virus warning system is costly and will need political lobbying. The accelerating number of viral infections with pandemic potential over the last decades should provide the public pressure to extend pandemic preparedness for the inclusion of early viral alert systems.
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Affiliation(s)
- Harald Brüssow
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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Cebriá-Mendoza M, Beamud B, Andreu-Moreno I, Arbona C, Larrea L, Díaz W, Sanjuán R, Cuevas JM. Human Anelloviruses: Influence of Demographic Factors, Recombination, and Worldwide Diversity. Microbiol Spectr 2023; 11:e0492822. [PMID: 37199659 PMCID: PMC10269794 DOI: 10.1128/spectrum.04928-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023] Open
Abstract
Anelloviruses represent the major and most diverse component of the healthy human virome, referred to as the anellome. In this study, we determined the anellome of 50 blood donors, forming two sex- and age-matched groups. Anelloviruses were detected in 86% of the donors. The number of detected anelloviruses increased with age and was approximately twice as high in men as in women. A total of 349 complete or nearly complete genomes were classified as belonging to torque teno virus (TTV), torque teno mini virus (TTMV), and torque teno midi virus (TTMDV) anellovirus genera (197, 88, and 64 sequences, respectively). Most donors had intergenus (69.8%) or intragenus (72.1%) coinfections. Despite the limited number of sequences, intradonor recombination analysis showed 6 intragenus recombination events in ORF1. As thousands of anellovirus sequences have been described recently, we finally analyzed the global diversity of human anelloviruses. Species richness and diversity were close to saturation in each anellovirus genus. Recombination was found to be the main factor promoting diversity, although its effect was significantly lower in TTV than in TTMV and TTMDV. Overall, our results suggest that differences in diversity between genera may be caused by variations in the relative contribution of recombination. IMPORTANCE Anelloviruses are the most common human infectious viruses and are considered essentially harmless. Compared to other human viruses, they are characterized by enormous diversity, and recombination is suggested to play an important role in their diversification and evolution. Here, by analyzing the composition of the plasma anellome of 50 blood donors, we find that recombination is also a determinant of viral evolution at the intradonor level. On a larger scale, analysis of anellovirus sequences currently available in databases shows that their diversity is close to saturation and differs among the three human anellovirus genera and that recombination is the main factor explaining this intergenus variability. Global characterization of anellovirus diversity could provide clues about possible associations between certain virus variants and pathologies, as well as facilitate the implementation of unbiased PCR-based detection protocols, which may be relevant for using anelloviruses as endogenous markers of immune status.
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Affiliation(s)
- María Cebriá-Mendoza
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
| | - Beatriz Beamud
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
- FISABIO-Salud Pública, Generalitat Valenciana, Valencia, Spain
| | - Iván Andreu-Moreno
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
| | - Cristina Arbona
- Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain
| | - Luís Larrea
- Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain
| | - Wladimiro Díaz
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
- Genomic and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region (FISABIO), Valencia, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
- Department of Genetics, Universitat de València, Valencia, Spain
| | - José M. Cuevas
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
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Butkovic A, Kraberger S, Smeele Z, Martin DP, Schmidlin K, Fontenele RS, Shero MR, Beltran RS, Kirkham AL, Aleamotu’a M, Burns JM, Koonin EV, Varsani A, Krupovic M. Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein. Virus Evol 2023; 9:vead035. [PMID: 37325085 PMCID: PMC10266747 DOI: 10.1093/ve/vead035] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/15/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Anelloviruses are highly prevalent in diverse mammals, including humans, but so far have not been linked to any disease and are considered to be part of the 'healthy virome'. These viruses have small circular single-stranded DNA (ssDNA) genomes and encode several proteins with no detectable sequence similarity to proteins of other known viruses. Thus, anelloviruses are the only family of eukaryotic ssDNA viruses currently not included in the realm Monodnaviria. To gain insights into the provenance of these enigmatic viruses, we sequenced more than 250 complete genomes of anelloviruses from nasal and vaginal swab samples of Weddell seal (Leptonychotes weddellii) from Antarctica and a fecal sample of grizzly bear (Ursus arctos horribilis) from the USA and performed a comprehensive family-wide analysis of the signature anellovirus protein ORF1. Using state-of-the-art remote sequence similarity detection approaches and structural modeling with AlphaFold2, we show that ORF1 orthologs from all Anelloviridae genera adopt a jelly-roll fold typical of viral capsid proteins (CPs), establishing an evolutionary link to other eukaryotic ssDNA viruses, specifically, circoviruses. However, unlike CPs of other ssDNA viruses, ORF1 encoded by anelloviruses from different genera display remarkable variation in size, due to insertions into the jelly-roll domain. In particular, the insertion between β-strands H and I forms a projection domain predicted to face away from the capsid surface and function at the interface of virus-host interactions. Consistent with this prediction and supported by recent experimental evidence, the outermost region of the projection domain is a mutational hotspot, where rapid evolution was likely precipitated by the host immune system. Collectively, our findings further expand the known diversity of anelloviruses and explain how anellovirus ORF1 proteins likely diverged from canonical jelly-roll CPs through gradual augmentation of the projection domain. We suggest assigning Anelloviridae to a new phylum, 'Commensaviricota', and including it into the kingdom Shotokuvirae (realm Monodnaviria), alongside Cressdnaviricota and Cossaviricota.
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Affiliation(s)
- Anamarija Butkovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, Paris 75015, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Zoe Smeele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Darren P Martin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Michelle R Shero
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Rd, Woods Hole, MA 02543, USA
| | - Roxanne S Beltran
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Amy L Kirkham
- U.S. Fish and Wildlife Service, Marine Mammals Management, 1011 E, Tudor Road, Anchorage, AK 99503, USA
| | - Maketalena Aleamotu’a
- School of Environmental and Life Sciences, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Jennifer M Burns
- Department of Biological Sciences, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, 1 Anzio Road, Cape Town 7925, South Africa
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, Paris 75015, France
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Thijssen M, Tacke F, Van Espen L, Cassiman D, Naser Aldine M, Nevens F, Van Ranst M, Matthijnssens J, Pourkarim MR. Plasma virome dynamics in chronic hepatitis B virus infected patients. Front Microbiol 2023; 14:1172574. [PMID: 37228370 PMCID: PMC10203228 DOI: 10.3389/fmicb.2023.1172574] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023] Open
Abstract
The virome remains an understudied domain of the human microbiome. The role of commensal viruses on the outcome of infections with known pathogens is not well characterized. In this study we aimed to characterize the longitudinal plasma virome dynamics in chronic hepatitis B virus (HBV) infected patients. Eighty-five longitudinal plasma samples were collected from 12 chronic HBV infected individuals that were classified in the four stages of HBV infection. The virome was characterized with an optimized viral extraction protocol and deep-sequenced on a NextSeq 2500 platform. The plasma virome was primarily composed of members of the Anello- Flavi-, and Hepadnaviridae (HBV) families. The virome structure and dynamics did not correlate with the different stages of chronic HBV infection nor with the administration of antiviral therapy. We observed a higher intrapersonal similarity of viral contigs. Genomic analysis of viruses observed in multiple timepoint demonstrated the presence of a dynamic community. This study comprehensively assessed the blood virome structure in chronic HBV infected individuals and provided insights in the longitudinal development of this viral community.
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Affiliation(s)
- Marijn Thijssen
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Campus Virchow-Klinikum and Campus Charité Mitte, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lore Van Espen
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - David Cassiman
- Department of Gastroenterology and Hepatology, University Hospital Leuven, Leuven, Belgium
| | - Mahmoud Naser Aldine
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Frederik Nevens
- Department of Gastroenterology and Hepatology, University Hospital Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Mahmoud Reza Pourkarim
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Health Policy Research Centre, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
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Ryabchenko B, Šroller V, Horníková L, Lovtsov A, Forstová J, Huérfano S. The interactions between PML nuclear bodies and small and medium size DNA viruses. Virol J 2023; 20:82. [PMID: 37127643 PMCID: PMC10152602 DOI: 10.1186/s12985-023-02049-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/23/2023] [Indexed: 05/03/2023] Open
Abstract
Promyelocytic leukemia nuclear bodies (PM NBs), often referred to as membraneless organelles, are dynamic macromolecular protein complexes composed of a PML protein core and other transient or permanent components. PML NBs have been shown to play a role in a wide variety of cellular processes. This review describes in detail the diverse and complex interactions between small and medium size DNA viruses and PML NBs that have been described to date. The PML NB components that interact with small and medium size DNA viruses include PML protein isoforms, ATRX/Daxx, Sp100, Sp110, HP1, and p53, among others. Interaction between viruses and components of these NBs can result in different outcomes, such as influencing viral genome expression and/or replication or impacting IFN-mediated or apoptotic cell responses to viral infection. We discuss how PML NB components abrogate the ability of adenoviruses or Hepatitis B virus to transcribe and/or replicate their genomes and how papillomaviruses use PML NBs and their components to promote their propagation. Interactions between polyomaviruses and PML NBs that are poorly understood but nevertheless suggest that the NBs can serve as scaffolds for viral replication or assembly are also presented. Furthermore, complex interactions between the HBx protein of hepadnaviruses and several PML NBs-associated proteins are also described. Finally, current but scarce information regarding the interactions of VP3/apoptin of the avian anellovirus with PML NBs is provided. Despite the considerable number of studies that have investigated the functions of the PML NBs in the context of viral infection, gaps in our understanding of the fine interactions between viruses and the very dynamic PML NBs remain. The complexity of the bodies is undoubtedly a great challenge that needs to be further addressed.
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Affiliation(s)
- Boris Ryabchenko
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Vojtěch Šroller
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Lenka Horníková
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Alexey Lovtsov
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Jitka Forstová
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Sandra Huérfano
- Department of Genetics and Microbiology, Faculty of Science, BIOCEV, Charles University, Vestec, 25250, Czech Republic.
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Zanella MC, Vu DL, Hosszu-Fellous K, Neofytos D, Van Delden C, Turin L, Poncet A, Simonetta F, Masouridi-Levrat S, Chalandon Y, Cordey S, Kaiser L. Longitudinal Detection of Twenty DNA and RNA Viruses in Allogeneic Hematopoietic Stem Cell Transplant Recipients Plasma. Viruses 2023; 15:v15040928. [PMID: 37112908 PMCID: PMC10142697 DOI: 10.3390/v15040928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Metagenomics revealed novel and routinely overlooked viruses, representing sources of unrecognized infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT). We aim to describe DNA and RNA virus prevalence and kinetics in allo-HSCT recipients' plasma for one year post HSCT. We included 109 adult patients with first allo-HSCT from 1 March 2017 to 31 January 2019 in this observational cohort study. Seventeen DNA and three RNA viral species were screened with qualitative and/or quantitative r(RT)-PCR assays using plasma samples collected at 0, 1, 3, 6, and 12 months post HSCT. TTV infected 97% of patients, followed by HPgV-1 (prevalence: 26-36%). TTV (median 3.29 × 105 copies/mL) and HPgV-1 (median 1.18 × 106 copies/mL) viral loads peaked at month 3. At least one Polyomaviridae virus (BKPyV, JCPyV, MCPyV, HPyV6/7) was detected in >10% of patients. HPyV6 and HPyV7 prevalence reached 27% and 12% at month 3; CMV prevalence reached 27%. HSV, VZV, EBV, HHV-7, HAdV and B19V prevalence remained <5%. HPyV9, TSPyV, HBoV, EV and HPg-V2 were never detected. At month 3, 72% of patients had co-infections. TTV and HPgV-1 infections were highly prevalent. BKPyV, MCPyV and HPyV6/7 were frequently detected relative to classical culprits. Further investigation is needed into associations between these viral infections and immune reconstitution or clinical outcomes.
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Affiliation(s)
- Marie-Céline Zanella
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Diem-Lan Vu
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Krisztina Hosszu-Fellous
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, 1211 Geneva, Switzerland
| | - Dionysios Neofytos
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Chistian Van Delden
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Lara Turin
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Antoine Poncet
- Center for Clinical Research, Department of Health and Community Medicine, University of Geneva, 1206 Geneva, Switzerland
- Division of Clinical Epidemiology, Department of Health and Community Medicine, University Hospital of Geneva, 1211 Geneva, Switzerland
| | - Federico Simonetta
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Stavroula Masouridi-Levrat
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Yves Chalandon
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Samuel Cordey
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, 1211 Geneva, Switzerland
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Brüssow H. The human microbiome project at ten years - some critical comments and reflections on "our third genome", the human virome. MICROBIOME RESEARCH REPORTS 2023; 2:7. [PMID: 38045612 PMCID: PMC10688805 DOI: 10.20517/mrr.2022.20] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/02/2023] [Accepted: 03/21/2023] [Indexed: 12/05/2023]
Abstract
The Human Microbiome Project (HMP) has raised great expectations claiming the far-reaching influence of the microbiome on human health and disease ranging from obesity and malnutrition to effects going well beyond the gut. So far, with the notable exception of fecal microbiota transplantation in Clostridioides difficile infection, practical application of microbiome intervention has only achieved modest clinical effects. It is argued here that we need criteria for the link between microbiome and disease modelled on the links between pathogens and infectious disease in Koch's postulates. The most important question is whether the microbiome change is a cause of the given disease or a consequence of a pathology leading to disease where the microbiome change is only a parallel event without a causal connection to the disease - in philosophical parlance, an epiphenomenon. Also discussed here is whether human virome research is a necessary complement to the microbiome project with a high potential for practical applications.
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Affiliation(s)
- Harald Brüssow
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Leuven B-3001, Belgium
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42
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Lasagna A, Piralla A, Borgetto S, Quaccini M, Baldanti F, Pedrazzoli P. Torque teno virus and cancers: current knowledge. Future Virol 2023. [DOI: 10.2217/fvl-2022-0111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Aim: The aim of this systematic review is to assess the current knowledge about the relationship between Torque teno virus (TTV) and cancer in different settings. Methods: A systematic search was conducted in Medline via PubMed, Embase and Cochrane Library from the inception to the end of January 2023. Results: 34 articles were included in the qualitative synthesis of this review and 2145 patients with solid tumors have been analyzed. The most prevalent cancer types were hepatocellular carcinoma (HCC) and lung cancer. Conclusion: TTV has proven its role as a marker of functional immune competence in the setting of hematopoietic stem cell transplantation (HSCT), but in the oncological field is yet to be defined.
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Affiliation(s)
- Angioletta Lasagna
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100, Pavia, Italy
| | - Antonio Piralla
- Microbiology & Virology Department, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100, Pavia, Italy
| | - Sabrina Borgetto
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100, Pavia, Italy
| | - Mattia Quaccini
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100, Pavia, Italy
| | - Fausto Baldanti
- Microbiology & Virology Department, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100, Pavia, Italy
- Dept. of Clinical Surgical Diagnostic & Pediatric Sciences, University of Pavia, Viale Camillo Golgi 19, 27100, Pavia, Italy
| | - Paolo Pedrazzoli
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, Viale Camillo Golgi 19, 27100, Pavia, Italy
- Dept. of Internal Medicine & Medical Therapy, University of Pavia, Viale Camillo Golgi 19, 27100, Pavia, Italy
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Stout MJ, Brar AK, Herter BN, Rankin A, Wylie KM. The plasma virome in longitudinal samples from pregnant patients. Front Cell Infect Microbiol 2023; 13:1061230. [PMID: 36844406 PMCID: PMC9949529 DOI: 10.3389/fcimb.2023.1061230] [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: 10/04/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction Nucleic acid from viruses is common in peripheral blood, even in asymptomatic individuals. How physiologic changes of pregnancy impact host-virus dynamics for acute, chronic, and latent viral infections is not well described. Previously we found higher viral diversity in the vagina during pregnancy associated with preterm birth (PTB) and Black race. We hypothesized that higher diversity and viral copy numbers in the plasma would show similar trends. Methods To test this hypothesis, we evaluated longitudinally collected plasma samples from 23 pregnant patients (11 term and 12 preterm) using metagenomic sequencing with ViroCap enrichment to enhance virus detection. Sequence data were analyzed with the ViroMatch pipeline. Results We detected nucleic acid from at least 1 virus in at least 1 sample from 87% (20/23) of the maternal subjects. The viruses represented 5 families: Herpesviridae, Poxviridae, Papillomaviridae, Anelloviridae, and Flaviviridae. We analyzed cord plasma from 18 of the babies from those patients and found nucleic acid from viruses in 33% of the samples (6/18) from 3 families: Herpesviridae, Papillomaviridae, and Anelloviridae. Some viral genomes were found in both maternal plasma and cord plasma from maternal-fetal pairs (e.g. cytomegalovirus, anellovirus). We found that Black race associated with higher viral richness (number of different viruses detected) in the maternal blood samples (P=0.003), consistent with our previous observations in vaginal samples. We did not detect associations between viral richness and PTB or the trimester of sampling. We then examined anelloviruses, a group of viruses that is ubiquitous and whose viral copy numbers fluctuate with immunological state. We tested anellovirus copy numbers in plasma from 63 pregnant patients sampled longitudinally using qPCR. Black race associated with higher anellovirus positivity (P<0.001) but not copy numbers (P=0.1). Anellovirus positivity and copy numbers were higher in the PTB group compared to the term group (P<0.01, P=0.003, respectively). Interestingly, these features did not occur at the time of delivery but appeared earlier in pregnancy, suggesting that although anelloviruses were biomarkers for PTB they were not triggering parturition. Discussion These results emphasize the importance of longitudinal sampling and diverse cohorts in studies of virome dynamics during pregnancy.
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Affiliation(s)
- Molly J. Stout
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Anoop K. Brar
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Brandi N. Herter
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Ananda Rankin
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
| | - Kristine M. Wylie
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States
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Dynamics of Human Anelloviruses in Plasma and Clinical Outcomes Following Kidney Transplantation. Transplantation 2023; 107:511-520. [PMID: 36042550 DOI: 10.1097/tp.0000000000004292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Torque teno virus, the major member of the genus Alphatorquevirus , is an emerging biomarker of the net state of immunosuppression after kidney transplantation. Genetic diversity constitutes a main feature of the Anelloviridae family, although its posttransplant dynamics and clinical correlates are largely unknown. METHODS The relative abundance of Alphatorquevirus , Betatorquevirus , and Gammatorquevirus genera was investigated by high-throughput sequencing in plasma specimens obtained at various points during the first posttransplant year (n = 91 recipients). Total loads of all members of the Anelloviridae family were also quantified by an "in-house" polymerase chain reaction assay targeting conserved DNA sequences (n = 195 recipients). In addition to viral kinetics, clinical study outcomes included serious infection, immunosuppression-related adverse event (opportunistic infection and cancer)' and acute rejection. RESULTS Alphatorquevirus DNA was detected in all patients at every point, with an increase from pretransplantation to month 1. A variable proportion of recipients had detectable Betatorquevirus and Gammatorquevirus at lower frequencies. At least 1 change in the predominant genus (mainly as early transition to Alphatorquevirus predominance) was shown in 35.6% of evaluable patients. Total anelloviruses DNA levels increased from baseline to month 1, to peak by month 3 and decrease thereafter, and were higher in patients treated with T-cell depleting agents. There was a significant albeit weak-to-moderate correlation between total anelloviruses and TTV DNA levels. No associations were found between the predominant Anelloviridae genus or total anelloviruses DNA levels and clinical outcomes. CONCLUSIONS Our study provides novel insight into the evolution of the anellome after kidney transplantation.
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Kaczorowska J, Timmerman AL, Deijs M, Kinsella CM, Bakker M, van der Hoek L. Anellovirus evolution during long-term chronic infection. Virus Evol 2023; 9:vead001. [PMID: 36726484 PMCID: PMC9885978 DOI: 10.1093/ve/vead001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/19/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Human anelloviruses (AVs) are extremely genetically diverse, are widespread in the human population, and cause chronic infections. However, the evolutionary dynamics of AVs within single hosts is currently unknown, and it is unclear whether these changes have an implication on the long-term persistence of AVs in the host. Here, we assessed the evolutionary dynamics of six AV lineages during 30 years of chronic infection at single host resolution. The total number of substitutions and the number of variable sites increased over time. However, not all substitutions reached population fixation, showing that AV lineages form heterogeneous swarms within the host. Most substitutions occurred within a hypervariable region (HVR) located between nucleotide positions 800 and 1,300 of ORF1, which is known to be located within the spike domain. Different regions of the ORF1 gene undergo either positive or negative selection pressure. Sites under strong diversifying selection pressure were detected in the HVR, while the majority of the sites under purifying selection were detected outside this region. The HVR may play the role of an immunological decoy that prevents antibodies from binding to more vulnerable parts of ORF1. Moreover, the frequent substitutions in this region may increase the chances of AV particles escaping immune recognition.
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Affiliation(s)
| | | | - Martin Deijs
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands,Amsterdam Institute for Infection and Immunity, Postbus 22660, Amsterdam 1100 DD, The Netherlands
| | | | - Margreet Bakker
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands,Amsterdam Institute for Infection and Immunity, Postbus 22660, Amsterdam 1100 DD, The Netherlands
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Dunay E, Owens LA, Dunn CD, Rukundo J, Atencia R, Cole MF, Cantwell A, Emery Thompson M, Rosati AG, Goldberg TL. Viruses in sanctuary chimpanzees across Africa. Am J Primatol 2023; 85:e23452. [PMID: 36329642 PMCID: PMC9812903 DOI: 10.1002/ajp.23452] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Infectious disease is a major concern for both wild and captive primate populations. Primate sanctuaries in Africa provide critical protection to thousands of wild-born, orphan primates confiscated from the bushmeat and pet trades. However, uncertainty about the infectious agents these individuals potentially harbor has important implications for their individual care and long-term conservation strategies. We used metagenomic next-generation sequencing to identify viruses in blood samples from chimpanzees (Pan troglodytes) in three sanctuaries in West, Central, and East Africa. Our goal was to evaluate whether viruses of human origin or other "atypical" or unknown viruses might infect these chimpanzees. We identified viruses from eight families: Anelloviridae, Flaviviridae, Genomoviridae, Hepadnaviridae, Parvoviridae, Picobirnaviridae, Picornaviridae, and Rhabdoviridae. The majority (15/26) of viruses identified were members of the family Anelloviridae and represent the genera Alphatorquevirus (torque teno viruses) and Betatorquevirus (torque teno mini viruses), which are common in chimpanzees and apathogenic. Of the remaining 11 viruses, 9 were typical constituents of the chimpanzee virome that have been identified in previous studies and are also thought to be apathogenic. One virus, a novel tibrovirus (Rhabdoviridae: Tibrovirus) is related to Bas-Congo virus, which was originally thought to be a human pathogen but is currently thought to be apathogenic, incidental, and vector-borne. The only virus associated with disease was rhinovirus C (Picornaviridae: Enterovirus) infecting one chimpanzee subsequent to an outbreak of respiratory illness at that sanctuary. Our results suggest that the blood-borne virome of African sanctuary chimpanzees does not differ appreciably from that of their wild counterparts, and that persistent infection with exogenous viruses may be less common than often assumed.
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Affiliation(s)
- Emily Dunay
- Department of Pathobiological Sciences, School of Veterinary MedicineUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Leah A. Owens
- Department of Pathobiological Sciences, School of Veterinary MedicineUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Christopher D. Dunn
- Department of Pathobiological Sciences, School of Veterinary MedicineUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Joshua Rukundo
- Ngamba Island Chimpanzee Sanctuary/Chimpanzee TrustEntebbeUganda
| | - Rebeca Atencia
- Jane Goodall Institute CongoPointe‐NoireRepublic of Congo
| | - Megan F. Cole
- Department of AnthropologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Averill Cantwell
- Department of PsychologyUniversity of MichiganAnn ArborMichiganUSA
| | | | - Alexandra G. Rosati
- Department of PsychologyUniversity of MichiganAnn ArborMichiganUSA
- Department of AnthropologyUniversity of MichiganAnn ArborMichiganUSA
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, School of Veterinary MedicineUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
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Spezia PG, Focosi D, Baj A, Novazzi F, Ferrante FD, Carletti F, Minosse C, Matusali G, Maggi F. TTV and other anelloviruses: The astonishingly wide spread of a viral infection. ASPECTS OF MOLECULAR MEDICINE 2023; 1:None. [PMID: 37398508 PMCID: PMC10308510 DOI: 10.1016/j.amolm.2023.100006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 07/04/2023]
Abstract
The broad family of viruses known as anelloviruses (AV) infects both humans and numerous animal species. They have a tiny, covalently closed single-stranded DNA genome and the astonishing capacity to infect a very high percentage of healthy and ill people with chronic infections that could last a lifetime. AV, and particularly the prototype Torquetenovirus, have established a successful interaction with the host's immune system and the rate at which they replicate is a gauge to measure overall immune function, even though many aspects of their life cycle and pathogenesis are still poorly understood.
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Affiliation(s)
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Andreina Baj
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Federica Novazzi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | | | - Fabrizio Carletti
- Laboratory of Virology and Biosafety Laboratories, National Institute of Infectious Diseases “L. Spallanzani” IRCCS, Rome, Italy
| | - Claudia Minosse
- Laboratory of Virology and Biosafety Laboratories, National Institute of Infectious Diseases “L. Spallanzani” IRCCS, Rome, Italy
| | - Giulia Matusali
- Laboratory of Virology and Biosafety Laboratories, National Institute of Infectious Diseases “L. Spallanzani” IRCCS, Rome, Italy
| | - Fabrizio Maggi
- Laboratory of Virology and Biosafety Laboratories, National Institute of Infectious Diseases “L. Spallanzani” IRCCS, Rome, Italy
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Mochochoko BM, Pohl CH, O’Neill HG. Candida albicans-enteric viral interactions-The prostaglandin E 2 connection and host immune responses. iScience 2022; 26:105870. [PMID: 36647379 PMCID: PMC9839968 DOI: 10.1016/j.isci.2022.105870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The human microbiome comprises trillions of microorganisms residing within different mucosal cavities and across the body surface. The gut microbiota modulates host susceptibility to viral infections in several ways, and microbial interkingdom interactions increase viral infectivity within the gut. Candida albicans, a frequently encountered fungal species in the gut, produces highly structured biofilms and eicosanoids such as prostaglandin E2 (PGE2), which aid in viral protection and replication. These biofilms encompass viruses and provide a shield from antiviral drugs or the immune system. PGE2 is a key modulator of active inflammation with the potential to regulate interferon signaling upon microbial invasion or viral infections. In this review, we raise the perspective of gut interkingdom interactions involving C. albicans and enteric viruses, with a special focus on biofilms, PGE2, and viral replication. Ultimately, we discuss the possible implications of C. albicans-enteric virus associations on host immune responses, particularly the interferon signaling pathway.
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Affiliation(s)
- Bonang M. Mochochoko
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, 9301, South Africa
| | - Carolina H. Pohl
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, 9301, South Africa,Corresponding author
| | - Hester G. O’Neill
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, 9301, South Africa,Corresponding author
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Kinsella CM, Edridge AWD, van Zeggeren IE, Deijs M, van de Beek D, Brouwer MC, van der Hoek L. Bacterial ribosomal RNA detection in cerebrospinal fluid using a viromics approach. Fluids Barriers CNS 2022; 19:102. [PMID: 36550487 PMCID: PMC9773461 DOI: 10.1186/s12987-022-00400-5] [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: 09/22/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In patients with central nervous system (CNS) infections identification of the causative pathogen is important for treatment. Metagenomic next-generation sequencing techniques are increasingly being applied to identify causes of CNS infections, as they can detect any pathogen nucleic acid sequences present. Viromic techniques that enrich samples for virus particles prior to sequencing may simultaneously enrich ribosomes from bacterial pathogens, which are similar in size to small viruses. METHODS We studied the performance of a viromic library preparation technique (VIDISCA) combined with low-depth IonTorrent sequencing (median ~ 25,000 reads per sample) for detection of ribosomal RNA from common pathogens, analyzing 89 cerebrospinal fluid samples from patients with culture proven bacterial meningitis. RESULTS Sensitivity and specificity to Streptococcus pneumoniae (n = 24) before and after optimizing threshold parameters were 79% and 52%, then 88% and 90%. Corresponding values for Neisseria meningitidis (n = 22) were 73% and 93%, then 67% and 100%, Listeria monocytogenes (n = 24) 21% and 100%, then 27% and 100%, and Haemophilus influenzae (n = 18) 56% and 100%, then 71% and 100%. A higher total sequencing depth, no antibiotic treatment prior to lumbar puncture, increased disease severity, and higher c-reactive protein levels were associated with pathogen detection. CONCLUSION We provide proof of principle that a viromic approach can be used to correctly identify bacterial ribosomal RNA in patients with bacterial meningitis. Further work should focus on increasing assay sensitivity, especially for problematic species (e.g. L. monocytogenes), as well as profiling additional pathogens. The technique is most suited to research settings and examination of idiopathic cases, rather than an acute clinical setting.
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Affiliation(s)
- Cormac M. Kinsella
- grid.7177.60000000084992262Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,Amsterdam Institute for Infection and Immunity, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Arthur W. D. Edridge
- grid.7177.60000000084992262Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,Amsterdam Institute for Infection and Immunity, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Ingeborg E. van Zeggeren
- grid.7177.60000000084992262Amsterdam UMC, Department of Neurology, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neuroinfection and Inflammation, Amsterdam, The Netherlands
| | - Martin Deijs
- grid.7177.60000000084992262Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,Amsterdam Institute for Infection and Immunity, Postbus 22660, 1100 DD Amsterdam, The Netherlands
| | - Diederik van de Beek
- grid.7177.60000000084992262Amsterdam UMC, Department of Neurology, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neuroinfection and Inflammation, Amsterdam, The Netherlands
| | - Matthijs C. Brouwer
- grid.7177.60000000084992262Amsterdam UMC, Department of Neurology, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,grid.484519.5Amsterdam Neuroscience, Neuroinfection and Inflammation, Amsterdam, The Netherlands
| | - Lia van der Hoek
- grid.7177.60000000084992262Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands ,Amsterdam Institute for Infection and Immunity, Postbus 22660, 1100 DD Amsterdam, The Netherlands
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50
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Timmerman AL, Kaczorowska J, Deijs M, Bakker M, van der Hoek L. Control of Human Anelloviruses by Cytosine to Uracil Genome Editing. mSphere 2022; 7:e0050622. [PMID: 36374042 PMCID: PMC9769745 DOI: 10.1128/msphere.00506-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Anelloviruses are the most common viruses infecting humans. Every human carries a nonpathogenic personal anellovirus virome (anellome), yet it is unknown which mechanisms contribute to its stability. Here, we assessed the dynamics and impact of a host antiviral defense mechanism-cytidine deaminase activity leading to C to U editing in anelloviruses-on the stability of the anellome. We investigated anellome sequence data obtained from serum samples collected every 6 months from two healthy subjects followed for more than 30 years. The subjects were infected by a total of 64 anellovirus lineages. Minus-stranded C to U editing was observed in lineages belonging to the Alpha-, Beta-, and Gammatorquevirus genera. The edited genomes were present within virus particles, therefore editing must have occurred at the late stages of the virus life cycle. Editing was favored by 5'-TC contexts in the virus genome, indicating that apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like, catalytic subunit 3 or A3 (APOBEC3) proteins are involved. Within a lineage, mutational dynamics varied over time and few fixations of mutations were detected, indicating that C to U editing is a dead end for a virus genome. We detected an editing coldspot in the GC-rich regions, suggesting that the GC-rich region is crucial for genome packaging, since only packaged virus particles were included in the analysis. Finally, we noticed a lineage-specific reduced concentration after an editing event, yet no clearance. In conclusion, cytidine deaminase activity does not clear anelloviruses, nor does it play a major role in virus evolution, but it does contribute to the stability of the anellome. IMPORTANCE Despite significant attention on anellovirus research, the interaction between the anellovirus virome and the human host remains unknown. We show the dynamics of APOBEC3-mediated cytidine deaminase activity on anelloviruses during a 30-year period of chronic infection and postulate that this antiviral mechanism controls anelloviruses. These results expand our knowledge of anellovirus-host interactions, which may be important for the design of gene therapies.
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Affiliation(s)
- Anne L. Timmerman
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Joanna Kaczorowska
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Martin Deijs
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Margreet Bakker
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Lia van der Hoek
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
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