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da Silva MK, Akash S, de Aquino JGF, Akter S, Fulco UL, Oliveira JIN. A newly discovered circovirus and its potential impact on human health and disease. Int J Surg 2024; 110:2523-2525. [PMID: 38363986 DOI: 10.1097/js9.0000000000001198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024]
Affiliation(s)
| | | | | | - Shahina Akter
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
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2
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Bezerra KC, Vieira CMAG, de Oliveira-Filho EF, Reis CRS, Oriá RB. Susceptibility of solid organ transplant recipients to viral pathogens with zoonotic potential: A mini-review. Braz J Infect Dis 2024; 28:103742. [PMID: 38670166 PMCID: PMC11078645 DOI: 10.1016/j.bjid.2024.103742] [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: 11/30/2023] [Revised: 02/28/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024] Open
Abstract
A substantial number of zoonotic diseases are caused by viral pathogens, representing a significant menace to public health, particularly to susceptible populations, such as pregnant women, the elderly, and immunocompromised individuals. Individuals who have undergone solid organ transplantation frequently experience immunosuppression, to prevent organ rejection, and, thus are more prone to opportunistic infections. Furthermore, the reactivation of dormant viruses can threaten transplant recipients and organ viability. This mini-review examines the up-to-date literature covering potential zoonotic and organ rejection-relevant viruses in solid organ transplant recipients. A comprehensive list of viruses with zoonotic potential is highlighted and the most important clinical outcomes in patients undergoing transplantation are described. Moreover, this mini-review calls attention to complex multifactorial events predisposing viral coinfections and the need for continuous health surveillance and research to understand better viral pathogens' transmission and pathophysiology dynamics in transplanted individuals.
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Affiliation(s)
- Karine C Bezerra
- Universidade Federal do Ceará, Faculdade de Medicina, Laboratório da Biologia da Cicatrização, Ontogenia e Nutrição de Tecidos, Fortaleza, CE, Brazil
| | - Carlos Meton A G Vieira
- Universidade Federal do Ceará, Faculdade de Medicina, Laboratório da Biologia da Cicatrização, Ontogenia e Nutrição de Tecidos, Fortaleza, CE, Brazil
| | | | - Christian Robson S Reis
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Microbiologia, Recife, PE, Brazil
| | - Reinaldo B Oriá
- Universidade Federal do Ceará, Faculdade de Medicina, Laboratório da Biologia da Cicatrização, Ontogenia e Nutrição de Tecidos, Fortaleza, CE, Brazil.
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3
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Opriessnig T, Xiao CT, Mueller NJ, Denner J. Emergence of novel circoviruses in humans and pigs and their possible importance for xenotransplantation and blood transfusions. Xenotransplantation 2024; 31:e12842. [PMID: 38501706 DOI: 10.1111/xen.12842] [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: 09/11/2023] [Revised: 11/17/2023] [Accepted: 12/19/2023] [Indexed: 03/20/2024]
Abstract
BACKGROUND As sequencing is becoming more broadly available, virus discovery continues. Small DNA viruses contribute to up to 60% of the overall virus load in pigs. Porcine circoviruses (PCVs) are small DNA viruses with a single-stranded circular genome. They are common in pig breeds and have not been properly addressed for their potential risk in xenotransplantation. Whereas PCV1 is non-pathogenic in pigs, PCV2 has been associated with various disease manifestations. Recently two new circoviruses have been described, PCV3 and PCV4. While PCV4 is currently present mainly in Asia, PCV3 is widely distributed, and has been identified in commercial pigs, wild boars, and pigs generated for xenotransplantation. In one case PCV3 was transmitted by pigs to baboons via heart transplantation. PCV3 pathogenicity in pigs was controversial initially, however, the virus was found to be associated with porcine dermatitis and nephropathy syndrome (PDNS), reproductive failure, and multisystemic inflammation. Inoculation studies with PCV3 infectious clones confirmed that PCV3 is pathogenic. Most importantly, recently discovered human circoviruses (CV) are closely related to PCV3. METHODS Literature was evaluated and summarized. A dendrogram of existing circoviruses in pigs, humans, and other animal species was created and assessed at the species level. RESULTS We found that human circoviruses can be divided into three species, human CV1, CV2, and CV3. Human CV2 and CV3 are closest to PCV3. CONCLUSIONS Circoviruses are ubiquitous. This communication should create awareness of PCV3 and the newly discovered human circoviruses, which may be a problem for blood transfusions and xenotransplantation in immune suppressed individuals.
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Affiliation(s)
- Tanja Opriessnig
- Vaccines and Diagnostics Department, Moredun Research Institute, Penicuik, UK
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Chao-Ting Xiao
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Nicolas J Mueller
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University Zurich, Zurich, Switzerland
| | - Joachim Denner
- Institute of Virology, Free University Berlin, Berlin, Germany
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Pérot P, Da Rocha N, Farcet MR, Kreil TR, Eloit M. Human Circovirus is not detected in plasma pools for fractionation. Transfusion 2024; 64:16-18. [PMID: 37982366 DOI: 10.1111/trf.17604] [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: 07/04/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND Human Circovirus 1 and 2 were recently described in a French hepatitis case and in two Chinese drug users. Because of its small size and presumable high resistance to both inactivation and removal by nanofilters, such viruses-if determined to be even pathogenic-should be considered with respect to the safety of plasma derivatives. We, therefore, investigated the prevalence and titer of these viruses in plasma pools before fractionation. METHODS AND MATERIALS We tested for the presence of Human Circovirus 1 and 2 by qPCR in 48 plasma pools derived from healthy donors from Europe, USA, and Japan, corresponding to more than 200,000 plasma donations. RESULTS We did not detect the presence of Human Circovirus 1 and 2 in any of the plasma pools, with a limit of detection of 300-600 genome copies per mL of plasma. CONCLUSIONS These results indicate that high levels of circovirus are not widely prevalent in such donations.
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Affiliation(s)
- Philippe Pérot
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, The WOAH (OIE) Collaborating Center for the detection and identification in humans of emerging animal pathogens, Paris, France
| | - Nicolas Da Rocha
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, The WOAH (OIE) Collaborating Center for the detection and identification in humans of emerging animal pathogens, Paris, France
| | - Maria R Farcet
- Global Pathogen Safety, Takeda Manufacturing Austria AG, Vienna, Austria
| | - Thomas R Kreil
- Global Pathogen Safety, Takeda Manufacturing Austria AG, Vienna, Austria
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, The WOAH (OIE) Collaborating Center for the detection and identification in humans of emerging animal pathogens, Paris, France
- École Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
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5
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Fourgeaud J, Regnault B, Ok V, Da Rocha N, Sitterlé É, Mekouar M, Faury H, Milliancourt-Seels C, Jagorel F, Chrétien D, Bigot T, Troadec É, Marques I, Serris A, Seilhean D, Neven B, Frange P, Ferroni A, Lecuit M, Nassif X, Lortholary O, Leruez-Ville M, Pérot P, Eloit M, Jamet A. Performance of clinical metagenomics in France: a prospective observational study. THE LANCET. MICROBE 2024; 5:e52-e61. [PMID: 38048804 DOI: 10.1016/s2666-5247(23)00244-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) allows untargeted identification of a broad range of pathogens, including rare or novel microorganisms. Despite the recognition of mNGS as a valuable diagnostic tool for infections, the most relevant indications for this innovative strategy remain poorly defined. We aimed to assess the determinants of positivity and clinical utility of mNGS. METHODS In this observational study, we prospectively performed short-read shotgun metagenomics analysis as a second-line test (in cases of negative first-line test or when the symptoms were not fully explained by initial positive results) or as a first-line test in life-threatening situations requiring urgent non-targeted pathogen identification at the Necker-Enfants Malades Hospital (Paris, France). All sample types, clinical indications, and patient populations were included. Samples were accompanied by a mandatory form completed by the senior clinician or pathologist, on which the clinical level of suspected infection (defined as high or low) was indicated. We assessed the variables (gender, age, immune status, initial suspicion of infection, indication, and sample type) associated with mNGS pathogen detection using odds ratios (ORs) from multivariate logistic regression. Additional investigations were carried out using specific PCR or culture techniques, to confirm positive mNGS results, or when infectious suspicion was particularly high despite a negative mNGS result. FINDINGS Between Oct 29, 2019, and Nov 7, 2022, we analysed 742 samples collected from 523 patients. The initial suspicion of infection was either high (n=470, 63%) or low (n=272, 37%). Causative or possibly causative pathogens were detected in 117 (25%) samples from patients with high initial suspicion of infection, versus nine (3%) samples analysed to rule out infection (OR 9·1, 95% CI 4·6-20·4; p<0·0001). We showed that mNGS had higher odds of detecting a causative or possibly causative pathogenic virus on CNS biopsies than CSF samples (4·1, 1·7-10·7; p=0·0025) and in samples from immunodeficient compared with immunocompetent individuals (2·4, 1·4-4·1; p=0·0013). Concordance with conventional confirmatory tests results was 103 (97%) of 106, when mNGS detected causative or possibly causative pathogens. Altogether, among 231 samples investigated by both mNGS and subsequent specific tests, discordant results were found in 69 (30%) samples, of which 58 (84%) were mNGS positive and specific tests negative, and 11 (16%) mNGS negative and specific tests positive. INTERPRETATION Major determinants of pathogen detection by mNGS are immune status and initial level of suspicion of infection. These findings will contribute, along with future studies, to refining the positioning of mNGS in diagnostic and treatment decision-making algorithms. FUNDING Necker-Enfants Malades Hospital and Institut Pasteur. TRANSLATION For the French translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Jacques Fourgeaud
- Université Paris Cité, FETUS, Paris, France; Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | - Béatrice Regnault
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France; Bioinformatics and Biostatistics Hub, Computational Biology Department, Institut Pasteur, Paris, France
| | - Vichita Ok
- Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | - Nicolas Da Rocha
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France
| | - Émilie Sitterlé
- Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | - Meryem Mekouar
- Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | - Hélène Faury
- Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | | | - Florence Jagorel
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France
| | - Delphine Chrétien
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France
| | - Thomas Bigot
- Bioinformatics and Biostatistics Hub, Computational Biology Department, Institut Pasteur, Paris, France
| | - Éric Troadec
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France
| | | | - Alexandra Serris
- Université Paris Cité, Centre d'Infectiologie Necker-Pasteur, IHU Imagine, Hôpital Necker, Paris, France
| | - Danielle Seilhean
- Département de Neuropathologie Raymond Escourolle, AP-HP-Sorbonne, Groupe Hospitalier Pitié-Salpêtrière, Paris, France; Institut du Cerveau-Paris Brain Institute-ICM, INSERM U1127, CNRS UMR7225, AP-HP, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Bénédicte Neven
- Pediatric Hematology Immunology and Rheumatology Unit, AP-HP, Hôpital Necker, Paris, France; Université Paris Cité, INSERM, Institut Imagine, Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Paris, France
| | - Pierre Frange
- Université Paris Cité, FETUS, Paris, France; Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | - Agnès Ferroni
- Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | - Marc Lecuit
- Université Paris Cité, Centre d'Infectiologie Necker-Pasteur, IHU Imagine, Hôpital Necker, Paris, France; Institut Pasteur, Université de Paris, INSERM U1117, Biology of Infection Unit, Paris, France; Institut Pasteur, National Reference Center and WHO Collaborating Center Listeria, Paris, France
| | - Xavier Nassif
- Université Paris Cité, CNRS, INSERM, Institut Necker-Enfants Malades, Team Pathogenesis of Systemic Infection, Paris, France
| | - Olivier Lortholary
- Université Paris Cité, Centre d'Infectiologie Necker-Pasteur, IHU Imagine, Hôpital Necker, Paris, France; Institut Pasteur, Centre National de Référence Mycoses Invasives et Antifongiques, Département de Mycologie, Labex IBEID, Paris, France
| | - Marianne Leruez-Ville
- Université Paris Cité, FETUS, Paris, France; Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | - Philippe Pérot
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France; Institut Pasteur, Centre National de Référence Mycoses Invasives et Antifongiques, Département de Mycologie, Labex IBEID, Paris, France
| | - Marc Eloit
- Institut Pasteur, Université Paris Cité, Pathogen Discovery Laboratory, Paris, France; Institut Pasteur, Université Paris Cité, The WOAH Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Paris, France; École Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - Anne Jamet
- Microbiology Department, AP-HP, Hôpital Necker, Paris, France; Université Paris Cité, CNRS, INSERM, Institut Necker-Enfants Malades, Team Pathogenesis of Systemic Infection, Paris, France.
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6
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Okoh GR, Ariel E, Whitmore D, Horwood PF. Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies. ECOHEALTH 2023; 20:427-440. [PMID: 38091182 DOI: 10.1007/s10393-023-01659-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 10/26/2023] [Indexed: 02/21/2024]
Abstract
The agile wallaby (Notamacropus agilis) is one of the most abundant marsupial species in northern Queensland and a competent host for the zoonotic Ross River virus. Despite their increased proximity and interactions with humans, little is known about the viruses carried by these animals, and whether any are of conservation or zoonotic importance. Metagenomics and molecular techniques were used in a complementary manner to identify and characterize novel viruses in the fecal samples of free-ranging agile wallabies. We detected a variety of novel marsupial-related viral species including agile wallaby atadenovirus 1, agile wallaby chaphamaparvovirus 1-2, agile wallaby polyomavirus 1-2, agile wallaby associated picobirnavirus 1-9, and a known macropod gammaherpesvirus 3. Phylogenetic analyses indicate that most of these novel viruses would have co-evolved with their hosts (agile wallabies). Additionally, non-marsupial viruses that infect bacteria (phages), plants, insects, and other eukaryotes were identified. This study highlighted the utility of non-invasive sampling as well as the integration of broad-based molecular assays (consensus PCR and next generation sequencing) for monitoring the emergence of potential pathogenic viruses in wildlife species. Furthermore, the novel marsupial viruses identified in this study will enrich the diversity of knowledge about marsupial viruses, and may be useful for developing diagnostics and vaccines.
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Affiliation(s)
- God'spower Richard Okoh
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia.
| | - Ellen Ariel
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - David Whitmore
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - Paul F Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia.
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7
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Hufsky F, Abecasis AB, Babaian A, Beck S, Brierley L, Dellicour S, Eggeling C, Elena SF, Gieraths U, Ha AD, Harvey W, Jones TC, Lamkiewicz K, Lovate GL, Lücking D, Machyna M, Nishimura L, Nocke MK, Renard BY, Sakaguchi S, Sakellaridi L, Spangenberg J, Tarradas-Alemany M, Triebel S, Vakulenko Y, Wijesekara RY, González-Candelas F, Krautwurst S, Pérez-Cataluña A, Randazzo W, Sánchez G, Marz M. The International Virus Bioinformatics Meeting 2023. Viruses 2023; 15:2031. [PMID: 37896809 PMCID: PMC10612056 DOI: 10.3390/v15102031] [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: 07/10/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 10/29/2023] Open
Abstract
The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24-26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting.
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Affiliation(s)
- Franziska Hufsky
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Ana B. Abecasis
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisboa, Portugal
| | - Artem Babaian
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
- Donnelly Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Sebastian Beck
- Leibniz Institute of Virology, Department Viral Zoonoses—One Health, 20251 Hamburg, Germany;
| | - Liam Brierley
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Health Data Science, University of Liverpool, Liverpool L69 3GF, UK
| | - Simon Dellicour
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 av. FD Roosevelt, 1050 Bruxelles, Belgium
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, University of Leuven, 3000 Leuven, Belgium
| | - Christian Eggeling
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Max-Wien-Platz 1, 07743 Jena, Germany
| | - Santiago F. Elena
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de Valencia, Catedratico Agustin Escardino 9, 46980 Valencia, Spain
| | - Udo Gieraths
- Institute of Virology, Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Anh D. Ha
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Will Harvey
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Terry C. Jones
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute of Virology, Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Kevin Lamkiewicz
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Gabriel L. Lovate
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Dominik Lücking
- Max-Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Martin Machyna
- Paul-Ehrlich-Institut, Host-Pathogen-Interactions, 63225 Langen, Germany
| | - Luca Nishimura
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Maximilian K. Nocke
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department for Molecular & Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Bernard Y. Renard
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, 14482 Potsdam, Germany
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka 569-8686, Japan;
| | - Lygeri Sakellaridi
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Jannes Spangenberg
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Maria Tarradas-Alemany
- Computational Genomics Lab., Department of Genetics, Microbiology and Statistics, Institut de Biomedicina UB (IBUB), Universitat de Barcelona (UB), 08028 Barcelona, Spain
| | - Sandra Triebel
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Yulia Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Rajitha Yasas Wijesekara
- Institute for Bioinformatics, University of Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Fernando González-Candelas
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de Valencia, Catedratico Agustin Escardino 9, 46980 Valencia, Spain
- Joint Research Unit “Infection and Public Health” FISABIO, University of Valencia, 46010 Valencia, Spain
| | - Sarah Krautwurst
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Alba Pérez-Cataluña
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Walter Randazzo
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Gloria Sánchez
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Manja Marz
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Michael Stifel Center Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07745 Jena, Germany
- Leibniz Institute for Age Research—Fritz Lippman Institute, 07745 Jena, Germany
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8
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Vasinioti VI, Pellegrini F, Buonavoglia A, Capozza P, Cardone R, Diakoudi G, Desario C, Catella C, Vicenza T, Lucente MS, Di Martino B, Camero M, Elia G, Decaro N, Martella V, Lanave G. Investigating the genetic diversity of CRESS DNA viruses in cats identifies a novel feline circovirus and unveils exposure of cats to canine circovirus. Res Vet Sci 2023; 161:86-95. [PMID: 37327693 DOI: 10.1016/j.rvsc.2023.06.011] [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: 04/12/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/18/2023]
Abstract
Circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA viruses include Circoviruses which have been found in several animal species and in human specimens. Circoviruses are associated with severe disease in pigs and birds and with respiratory and gastrointestinal disorders and systemic disease in dogs. In cats there are only a few anecdotical studies reporting CRESS DNA viruses. In this study, a total of 530 samples (361 sera, 131 stools, and 38 respiratory swabs) from cats, were screened for the presence of CRESS DNA viruses. Overall, 48 (9.0%) of 530 samples tested positive using a pan-Rep PCR. A total of 30 Rep sequences were obtained. Ten sequences of fecal origin were tightly related to each other (82.4-100% nt identity) and more distantly related to mongoose circoviruses (68.3 to 77.2% nt identity). At genome level these circoviruses displayed the highest nt identity (74.3-78.7%) to mongoose circoviruses thus representing a novel circovirus species. Circoviruses from different animal hosts (n = 12) and from humans (n = 8) were also identified. However, six Rep sequences were obtained from serum samples, including canine circoviruses, a human cyclovirus and human and fish-associated CRESS DNA viruses. The presence of these viruses in the sera would imply, to various extent, virus replication in the animal host, able to sustain viremia. Overall, these findings indicate a wide genetic diversity of CRESS DNA viruses in cats and warrant further investigations.
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Affiliation(s)
- Violetta Iris Vasinioti
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Francesco Pellegrini
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Alessio Buonavoglia
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Paolo Capozza
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Roberta Cardone
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Georgia Diakoudi
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Costantina Desario
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Cristiana Catella
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Teresa Vicenza
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Maria Stella Lucente
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Barbara Di Martino
- Department of Veterinary Medicine, Università degli Studi di Teramo, SP18, 64100 Teramo, Italy
| | - Michele Camero
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Gabriella Elia
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Gianvito Lanave
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy.
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9
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Kane Y, Chen J, Li L, Descorps-Declère S, Wong G, Berthet N. Diverse single-stranded DNA viruses from viral metagenomics on a cynopterus bat in China. Heliyon 2023; 9:e18270. [PMID: 37520955 PMCID: PMC10374907 DOI: 10.1016/j.heliyon.2023.e18270] [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: 05/29/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023] Open
Abstract
Bats serve as reservoirs for many emerging viruses. Cressdnaviruses can infect a wide range of animals, including agricultural species, such as pigs, in which porcine circoviruses cause severe gastroenteritis. New cressdnaviruses have also attracted considerable attention recently, due to their involvement with infectious diseases. However, little is known about their host range and many cressdnaviruses remain poorly characterized. We identified and characterized 11 contigs consisting of previously unknown cressdnaviruses from a rectal swab sample of a Cynopterus bat collected in Yunnan Province, China, in 2011. Full genomes of two cressdnaviruses (OQ267680, 2069 nt; OQ351951, 2382 nt), and a nearly complete genome for a third (OQ267683, 2361 nt) were obtained. Phylogenetic analyses and the characteristics of these viral genomes suggest a high degree of ssDNA virus diversity. These results shed light on cressdnavirus diversity and the probable role of Cynopterus bats as their hosts.
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Affiliation(s)
- Yakhouba Kane
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Stéphane Descorps-Declère
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Gary Wong
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Nicolas Berthet
- Centre for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens Unit, Shanghai 200031, China
- Institut Pasteur, Unité Environnement et Risque Infectieux, Cellule D’Intervention Biologique D’Urgence, 75015 Paris, France
- Institut Pasteur, Université Paris-Cité, Unité Epidémiologie et Physiopathologie des Virus Oncogènes, 75724 Paris, France
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10
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Kende J, Bonomi M, Temmam S, Regnault B, Pérot P, Eloit M, Bigot T. Virus Pop-Expanding Viral Databases by Protein Sequence Simulation. Viruses 2023; 15:1227. [PMID: 37376527 DOI: 10.3390/v15061227] [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: 05/02/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 06/29/2023] Open
Abstract
The improvement of our knowledge of the virosphere, which includes unknown viruses, is a key area in virology. Metagenomics tools, which perform taxonomic assignation from high throughput sequencing datasets, are generally evaluated with datasets derived from biological samples or in silico spiked samples containing known viral sequences present in public databases, resulting in the inability to evaluate the capacity of these tools to detect novel or distant viruses. Simulating realistic evolutionary directions is therefore key to benchmark and improve these tools. Additionally, expanding current databases with realistic simulated sequences can improve the capacity of alignment-based searching strategies for finding distant viruses, which could lead to a better characterization of the "dark matter" of metagenomics data. Here, we present Virus Pop, a novel pipeline for simulating realistic protein sequences and adding new branches to a protein phylogenetic tree. The tool generates simulated sequences with substitution rate variations that are dependent on protein domains and inferred from the input dataset, allowing for a realistic representation of protein evolution. The pipeline also infers ancestral sequences corresponding to multiple internal nodes of the input data phylogenetic tree, enabling new sequences to be inserted at various points of interest in the group studied. We demonstrated that Virus Pop produces simulated sequences that closely match the structural and functional characteristics of real protein sequences, taking as an example the spike protein of sarbecoviruses. Virus Pop also succeeded at creating sequences that resemble real sequences not included in the databases, which facilitated the identification of a novel pathogenic human circovirus not included in the input database. In conclusion, Virus Pop is helpful for challenging taxonomic assignation tools and could help improve databases to better detect distant viruses.
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Affiliation(s)
- Julia Kende
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, F-75015 Paris, France
| | - Massimiliano Bonomi
- Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, F-75015 Paris, France
| | - Sarah Temmam
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, F-75015 Paris, France
| | - Béatrice Regnault
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, F-75015 Paris, France
| | - Philippe Pérot
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, F-75015 Paris, France
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, F-75015 Paris, France
- Ecole Nationale Vétérinaire d'Alfort, F-94700 Maisons-Alfort, France
| | - Thomas Bigot
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, F-75015 Paris, France
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, F-75015 Paris, France
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