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Dal Lago S, Brani P, Ietto G, Dalla Gasperina D, Gianfagna F, Giaroni C, Bosi A, Drago Ferrante F, Genoni A, Manzoor HZ, Ambrosini A, De Cicco M, Quartarone CD, Khemara S, Carcano G, Maggi F, Baj A. Torque Teno Virus: A Promising Biomarker in Kidney Transplant Recipients. Int J Mol Sci 2024; 25:7744. [PMID: 39062987 PMCID: PMC11277443 DOI: 10.3390/ijms25147744] [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: 05/08/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Torque Teno Virus (TTV) is a ubiquitous component of the human virome, not associated with any disease. As its load increases when the immune system is compromised, such as in kidney transplant (KT) recipients, TTV load monitoring has been proposed as a method to assess immunosuppression. In this prospective study, TTV load was measured in plasma and urine samples from 42 KT recipients, immediately before KT and in the first 150 days after it. Data obtained suggest that TTV could be a relevant marker for evaluating immune status and could be used as a guide to predict the onset of infectious complications in the follow-up of KT recipients. Since we observed no differences considering distance from transplantation, while we found a changing trend in days before viral infections, we suggest to consider changes over time in the same subjects, irrespective of time distance from transplantation.
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Affiliation(s)
- Sara Dal Lago
- Nephrology Department, ASST Sette Laghi, University of Insubria, 21100 Varese, Italy
| | - Paola Brani
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Giuseppe Ietto
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Daniela Dalla Gasperina
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Francesco Gianfagna
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
- Mediterranea Cardiocentro, 80122 Napoli, Italy
| | - Cristina Giaroni
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Annalisa Bosi
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| | | | - Angelo Genoni
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Hafza Zahira Manzoor
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Andrea Ambrosini
- Nephrology Department, ASST Sette Laghi, University of Insubria, 21100 Varese, Italy
| | - Marco De Cicco
- Nephrology Department, ASST Sette Laghi, University of Insubria, 21100 Varese, Italy
| | | | - Sara Khemara
- Nephrology Department, ASST Sette Laghi, University of Insubria, 21100 Varese, Italy
| | - Giulio Carcano
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases L. Spallanzani—IRCCS, 00149 Rome, Italy
| | - Andreina Baj
- Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy
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Yu XW, Wang Q, Liu L, Zhou ZJ, Cai T, Yuan HM, Tang MA, Peng J, Ye SB, Yang XH, Deng XB, Ge XY. Detection and Genomic Characterization of Torque Teno Virus in Pneumoconiosis Patients in China. Viruses 2024; 16:1059. [PMID: 39066222 PMCID: PMC11281462 DOI: 10.3390/v16071059] [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: 05/17/2024] [Revised: 06/17/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024] Open
Abstract
Pneumoconiosis is a common occupational disease that can worsen with accompanying infection. Torque teno virus (TTV) is a prevalent human virus with multiple genotypes that can chronically and persistently infect individuals. However, the prevalence of TTV in pneumoconiosis patients is still unclear. This research aims to detect the presence and prevalence of TTV in the alveolar lavage fluid of pneumoconiosis patients in the Hunan Province of China using PCR. As a result, a 65.5% positive rate (19 out of 29) of TTV was detected. The TTV detection rate varies among different stages of silicosis and different pneumoconiosis patient ages. Nine novel TTV genomes ranging in size from 3719 to 3908 nt, named TTV HNPP1, HNPP2, HNPP3, HNPP4, HNPP5, HNPP6-1, HNPP6-2, HNPP7-1 and HNPP7-2, were identified. A genomic comparison and phylogenetic analysis indicated that these nine TTVs represent five different species with high genetic diversity which belong to the genus Alphatorquevirus. HNPP6-1 and HNPP6-2 belong to TTV3, HNPP5 belongs to TTV13, HNPP1 belongs to TTV24, HNPP4 belongs to TTV20, and the others belong to TTV19. The genomes of TTV HNPP1, HNPP6-1, and HNPP6-2 contain three putative open reading frames (ORFs) coding for proteins, ORF1, ORF2, and ORF3, while the other six TTV genomes contain two ORFs coding for proteins, ORF1 and ORF2. These results provide the first description of TTV epidemiology in pneumoconiosis patients in China. The newly identified TTV genome sequences reveal the high genetic diversity of TTV in pneumoconiosis patients and could contribute to a deeper understanding of TTV retention and infection in humans.
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Affiliation(s)
- Xiao-Wei Yu
- Hunan Prevention and Treatment Institute for Occupational Diseases, Changsha 410003, China; (X.-W.Y.); (L.L.); (T.C.); (H.-M.Y.); (M.-A.T.); (J.P.); (X.-H.Y.)
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China; (Z.-J.Z.); (S.-B.Y.)
| | - Qiong Wang
- Department of Basic Biology, Changsha Medical University, Changsha 410219, China;
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha 410219, China
| | - Lang Liu
- Hunan Prevention and Treatment Institute for Occupational Diseases, Changsha 410003, China; (X.-W.Y.); (L.L.); (T.C.); (H.-M.Y.); (M.-A.T.); (J.P.); (X.-H.Y.)
| | - Zhi-Jian Zhou
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China; (Z.-J.Z.); (S.-B.Y.)
| | - Tuo Cai
- Hunan Prevention and Treatment Institute for Occupational Diseases, Changsha 410003, China; (X.-W.Y.); (L.L.); (T.C.); (H.-M.Y.); (M.-A.T.); (J.P.); (X.-H.Y.)
| | - Hua-Ming Yuan
- Hunan Prevention and Treatment Institute for Occupational Diseases, Changsha 410003, China; (X.-W.Y.); (L.L.); (T.C.); (H.-M.Y.); (M.-A.T.); (J.P.); (X.-H.Y.)
| | - Mei-An Tang
- Hunan Prevention and Treatment Institute for Occupational Diseases, Changsha 410003, China; (X.-W.Y.); (L.L.); (T.C.); (H.-M.Y.); (M.-A.T.); (J.P.); (X.-H.Y.)
| | - Jian Peng
- Hunan Prevention and Treatment Institute for Occupational Diseases, Changsha 410003, China; (X.-W.Y.); (L.L.); (T.C.); (H.-M.Y.); (M.-A.T.); (J.P.); (X.-H.Y.)
| | - Sheng-Bao Ye
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China; (Z.-J.Z.); (S.-B.Y.)
| | - Xiu-Hong Yang
- Hunan Prevention and Treatment Institute for Occupational Diseases, Changsha 410003, China; (X.-W.Y.); (L.L.); (T.C.); (H.-M.Y.); (M.-A.T.); (J.P.); (X.-H.Y.)
| | - Xiao-Bin Deng
- Hunan Prevention and Treatment Institute for Occupational Diseases, Changsha 410003, China; (X.-W.Y.); (L.L.); (T.C.); (H.-M.Y.); (M.-A.T.); (J.P.); (X.-H.Y.)
| | - Xing-Yi Ge
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China; (Z.-J.Z.); (S.-B.Y.)
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Viral agents (2nd section). Transfusion 2024; 64 Suppl 1:S19-S207. [PMID: 38394038 DOI: 10.1111/trf.17630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 02/25/2024]
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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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Pradère P, Zajacova A, Bos S, Le Pavec J, Fisher A. Molecular monitoring of lung allograft health: is it ready for routine clinical use? Eur Respir Rev 2023; 32:230125. [PMID: 37993125 PMCID: PMC10663940 DOI: 10.1183/16000617.0125-2023] [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: 06/21/2023] [Accepted: 10/16/2023] [Indexed: 11/24/2023] Open
Abstract
Maintenance of long-term lung allograft health in lung transplant recipients (LTRs) requires a fine balancing act between providing sufficient immunosuppression to reduce the risk of rejection whilst at the same time not over-immunosuppressing individuals and exposing them to the myriad of immunosuppressant drug side-effects that can cause morbidity and mortality. At present, lung transplant physicians only have limited and rather blunt tools available to assist them with this task. Although therapeutic drug monitoring provides clinically useful information about single time point and longitudinal exposure of LTRs to immunosuppressants, it lacks precision in determining the functional level of immunosuppression that an individual is experiencing. There is a significant gap in our ability to monitor lung allograft health and therefore tailor optimal personalised immunosuppression regimens. Molecular diagnostics performed on blood, bronchoalveolar lavage or lung tissue that can detect early signs of subclinical allograft injury, differentiate rejection from infection or distinguish cellular from humoral rejection could offer clinicians powerful tools in protecting lung allograft health. In this review, we look at the current evidence behind molecular monitoring in lung transplantation and ask if it is ready for routine clinical use. Although donor-derived cell-free DNA and tissue transcriptomics appear to be the techniques with the most immediate clinical potential, more robust data are required on their performance and additional clinical value beyond standard of care.
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Affiliation(s)
- Pauline Pradère
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
- Department of Respiratory Diseases, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph and Paris Saclay University, Paris, France
| | - Andrea Zajacova
- Prague Lung Transplant Program, Department of Pneumology, Motol University Hospital and 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Saskia Bos
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
- Institute of Transplantation, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Jérôme Le Pavec
- Department of Respiratory Diseases, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph and Paris Saclay University, Paris, France
| | - Andrew Fisher
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
- Institute of Transplantation, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
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Kuczaj A, Przybyłowski P, Hrapkowicz T. Torque Teno Virus (TTV)-A Potential Marker of Immunocompetence in Solid Organ Recipients. Viruses 2023; 16:17. [PMID: 38275952 PMCID: PMC10818937 DOI: 10.3390/v16010017] [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: 11/19/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Torque Teno Virus (TTV), first discovered in 1997, is a non-pathogenic, highly prevalent virus with a notable presence in the human virome. TTV has garnered attention as a potential indicator of immunocompetence in recipients of solid organ transplants. In this review, we discuss the role of TTV as a potential marker for immunosuppression optimization, prediction of graft rejection, and as an indicator of opportunistic infections. We discuss TTV's behavior over the course of time after transplantation, TTV's implications in different immunosuppressive regimens, and potential utility in vaccinations. The review synthetizes findings from various studies depicting its potential clinical utility for future personalized patient care.
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Affiliation(s)
- Agnieszka Kuczaj
- Department of Cardiac, Vascular and Endovascular Surgery and Transplantology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland; (P.P.); (T.H.)
- Silesian Center for Heart Diseases, 41-800 Zabrze, Poland
| | - Piotr Przybyłowski
- Department of Cardiac, Vascular and Endovascular Surgery and Transplantology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland; (P.P.); (T.H.)
- Silesian Center for Heart Diseases, 41-800 Zabrze, Poland
| | - Tomasz Hrapkowicz
- Department of Cardiac, Vascular and Endovascular Surgery and Transplantology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland; (P.P.); (T.H.)
- Silesian Center for Heart Diseases, 41-800 Zabrze, Poland
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Sajiki AF, Koyanagi Y, Ushida H, Kawano K, Fujita K, Okuda D, Kawabe M, Yamada K, Suzumura A, Kachi S, Kaneko H, Komatsu H, Usui Y, Goto H, Nishiguchi KM. Association Between Torque Teno Virus and Systemic Immunodeficiency in Patients With Uveitis With a Suspected Infectious Etiology. Am J Ophthalmol 2023; 254:80-86. [PMID: 37356647 DOI: 10.1016/j.ajo.2023.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/27/2023] [Accepted: 06/03/2023] [Indexed: 06/27/2023]
Abstract
PURPOSE To determine the correlation between the presence of torque teno virus (TTV) in the aqueous humor of patients with uveitis and clinical information, including immunodeficiency history. DESIGN Multicenter, retrospective, cross-sectional study. METHODS Fifty-eight patients with uveitis with a suspected infectious etiology and 24 controls with cataract or age-related macular degeneration were included. We used quantitative polymerase chain reaction to test all subjects for TTV and multiplex polymerase chain reaction to test uveitis subjects for common ocular pathogens. When possible, both serum and aqueous humor samples were tested. Ocular TTV positivity was compared with age, sex, and a history of systemic immunodeficiency with logistic analysis. RESULTS Ocular TTV positivity was found in 23%, 11%, and 0% of patients with herpetic uveitis, nonherpetic uveitis, and controls, respectively. Among patients with herpes infection, positivity for ocular TTV was found in 43%, 8%, 14%, and 50% of patients with cytomegalovirus retinitis, iridocyclitis, acute retinal necrosis, and Epstein-Barr virus-positive uveitis, respectively. Patients with cytomegalovirus retinitis showed a significantly higher rate of ocular TTV infection than controls (P = .008). Serum analysis revealed TTV positivity in 90% of patients with uveitis and in 100% of controls. Age- and gender-adjusted logistic analysis revealed a correlation between ocular TTV positivity and systemic immunodeficiency (P = .01), but no correlations between ocular TTV and age, gender, or viral pathogenic type. CONCLUSIONS These findings suggest that positivity for ocular TTV was correlated with a clinical history of systemic immunodeficiency.
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Affiliation(s)
- Ai Fujita Sajiki
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.).
| | - Yoshito Koyanagi
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Hiroaki Ushida
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.).
| | - Kenichi Kawano
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.); Department of Ophthalmology, Yokkaichi Municipal Hospital, Yokkaichi, Japan (K.K.)
| | - Kosuke Fujita
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Daishi Okuda
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Mitsuki Kawabe
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Kazuhisa Yamada
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Ayana Suzumura
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Shu Kachi
- Shohzankai Medical Foundation, Miyake Eye Hospital, Nagoya, Japan (S.K.)
| | - Hiroki Kaneko
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
| | - Hiroyuki Komatsu
- Department of Ophthalmology, Tokyo Medical University, Tokyo, Japan (H.K., Y.U., H.G.)
| | - Yoshihiko Usui
- Department of Ophthalmology, Tokyo Medical University, Tokyo, Japan (H.K., Y.U., H.G.)
| | - Hiroshi Goto
- Department of Ophthalmology, Tokyo Medical University, Tokyo, Japan (H.K., Y.U., H.G.)
| | - Koji M Nishiguchi
- From the Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan (A.F.S., Y.K., H.U., K.K., K.F., D.O., M.K., K.Y., A.S., H.K., K.M.N.)
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Vigil K, Aw TG. Comparison of de novo assembly using long-read shotgun metagenomic sequencing of viruses in fecal and serum samples from marine mammals. Front Microbiol 2023; 14:1248323. [PMID: 37808316 PMCID: PMC10556685 DOI: 10.3389/fmicb.2023.1248323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Viral diseases of marine mammals are difficult to study, and this has led to a limited knowledge on emerging known and unknown viruses which are ongoing threats to animal health. Viruses are the leading cause of infectious disease-induced mass mortality events among marine mammals. Methods In this study, we performed viral metagenomics in stool and serum samples from California sea lions (Zalophus californianus) and bottlenose dolphins (Tursiops truncates) using long-read nanopore sequencing. Two widely used long-read de novo assemblers, Canu and Metaflye, were evaluated to assemble viral metagenomic sequencing reads from marine mammals. Results Both Metaflye and Canu assembled similar viral contigs of vertebrates, such as Parvoviridae, and Poxviridae. Metaflye assembled viral contigs that aligned with one viral family that was not reproduced by Canu, while Canu assembled viral contigs that aligned with seven viral families that was not reproduced by Metaflye. Only Canu assembled viral contigs from dolphin and sea lion fecal samples that matched both protein and nucleotide RefSeq viral databases using BLASTx and BLASTn for Anelloviridae, Parvoviridae and Circoviridae families. Viral contigs assembled with Canu aligned with torque teno viruses and anelloviruses from vertebrate hosts. Viruses associated with invertebrate hosts including densoviruses, Ambidensovirus, and various Circoviridae isolates were also aligned. Some of the invertebrate and vertebrate viruses reported here are known to potentially cause mortality events and/or disease in different seals, sea stars, fish, and bivalve species. Discussion Canu performed better by producing the most viral contigs as compared to Metaflye with assemblies aligning to both protein and nucleotide databases. This study suggests that marine mammals can be used as important sentinels to surveil marine viruses that can potentially cause diseases in vertebrate and invertebrate hosts.
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Affiliation(s)
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, United States
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Ding Y, Wan M, Li Z, Ma X, Zhang W, Xu M. Comparison of the gut virus communities between patients with Crohn's disease and healthy individuals. Front Microbiol 2023; 14:1190172. [PMID: 37396350 PMCID: PMC10311494 DOI: 10.3389/fmicb.2023.1190172] [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: 03/20/2023] [Accepted: 05/18/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction The escalating incidence of Crohn's disease (CD), a debilitating ailment that ravages individuals and their families, has become a formidable issue over recent decades. Method In this study, fecal samples from patients with CD and healthy individuals were investigated by means of viral metagenomics. Results The fecal virome was analyzed and some suspected disease-causing viruses were described. A polyomavirus named HuPyV with 5,120 base pairs (bp) was found in the disease group. In a preliminary analysis employing large T region-specific primers, it was found that HuPyV was present in 3.2% (1/31) of healthy samples and 43.2% (16/37) of disease samples. Additionally, two other viruses from the anellovirus and CRESS-DNA virus families were found in fecal samples from CD patients. The complete genome sequences of these two viruses were described respectively, and the phylogenetic trees have been built using the anticipated amino acid sequences of the viral proteins. Discussion Further research is required to elucidate the relationship between these viruses and the onset and development of Crohn's disease.
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Affiliation(s)
- Yuzhu Ding
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Mengtian Wan
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zheng Li
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiao Ma
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
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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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11
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Patterson CM, Jolly EC, Burrows F, Ronan NJ, Lyster H. Conventional and Novel Approaches to Immunosuppression in Lung Transplantation. Clin Chest Med 2023; 44:121-136. [PMID: 36774159 DOI: 10.1016/j.ccm.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Most therapeutic advances in immunosuppression have occurred over the past few decades. Although modern strategies have been effective in reducing acute cellular rejection, excess immunosuppression comes at the price of toxicity, opportunistic infection, and malignancy. As our understanding of the immune system and allograft rejection becomes more nuanced, there is an opportunity to evolve immunosuppression protocols to optimize longer term outcomes while mitigating the deleterious effects of traditional protocols.
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Affiliation(s)
- Caroline M Patterson
- Transplant Continuing Care Unit, Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Elaine C Jolly
- Division of Renal Medicine, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Fay Burrows
- Department of Pharmacy, St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Nicola J Ronan
- Transplant Continuing Care Unit, Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Haifa Lyster
- Cardiothoracic Transplant Unit, Royal Brompton and Harefield Hospitals, Part of Guy's & St Thomas' NHS Foundation Trust, London, United Kingdom; Kings College, London, United Kingdom; Pharmacy Department, Royal Brompton and Harefield Hospitals, Part of Guy's & St Thomas' NHS Foundation Trust, London, United Kingdom.
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12
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Genetic Analysis of Torque Teno Canis Virus Identified in Republic of Korea. Vet Sci 2022; 9:vetsci9120693. [PMID: 36548854 PMCID: PMC9782174 DOI: 10.3390/vetsci9120693] [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: 11/02/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Torque teno canis virus (TTCaV) is an approximately 2.8 kb circular single-stranded DNA virus known to cause infections in dogs. However, its incidence in Republic of Korea remains unknown. In this study, 135 dog fecal samples were collected to determine TTCaV infection status in Republic of Korea. Based on polymerase chain reaction (PCR) analysis, 13 of 135 (9.6%) dogs tested positive for TTCaV. Three full-length genome sequences (GenBank IDs: MZ503910, MZ503911, and MZ503912) were obtained from the positive specimens. Phylogenetic tree construction and sequence identity, similarity plot, and recombination analyses were performed using these three full-length genomic sequences. Among the three full-length genomes, MZ503912 was determined to be a recombinant virus based on analysis with the reference TTCaV strains. This novel virus strain might have been generated by recombination between TTCaV strain KX827768 discovered in China and MZ503910 discovered in Republic of Korea. This is the first report to determine the incidence, genetic variation, and recombination of TTCaV in dogs in Republic of Korea. Further studies are needed to elucidate TTCaV pathogenesis in dogs.
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13
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Zhu Y, Zhao W, Yang X, Zhang Y, Lin X, Weng X, Wang Y, Cheng C, Chi Y, Wei H, Peng Z, Hu Z. Metagenomic next-generation sequencing for identification of central nervous system pathogens in HIV-infected patients. Front Microbiol 2022; 13:1055996. [PMID: 36458193 PMCID: PMC9705764 DOI: 10.3389/fmicb.2022.1055996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2023] Open
Abstract
Although considerable interest in metagenomic next-generation sequencing (mNGS) has been attracted in recent years, limited data are available regarding the performance of mNGS in HIV-associated central nervous system (CNS) infection. Here, we conducted a retrospectively analyzing of the cerebrospinal fluid (CSF) mNGS reports and other clinical data from 80 HIV-infected patients admitted to the Second Hospital of Nanjing, China from March, 2018 to March, 2022. In our study, CSF mNGS reported negative result, mono-infection, and mixed infection in 8.8, 36.2, and 55% of the patients, respectively. Epstein-Barr virus (EBV), positive in 52.5% of samples, was the most commonly reported pathogen, followed by cytomegalovirus (CMV), John Cunningham virus (JCV), torque teno virus (TTV), cryptococcus neoformans (CN), toxoplasma Gondii (TE), and mycobacterium tuberculosis (MTB). 76.2% of the EBV identification and 54.2% of the CMV identification were not considered clinically important, and relative less sequence reads were reported in the clinical unimportant identifications. The clinical importance of the presence of TTV in CSF was not clear. Detection of JCV, CN, or TE was 100% suggestive of specific CNS infection, however, 60% of the MTB reports were considered contamination. Moreover, of the 44 (55%) mixed infections reported by mNGS, only 4 (5%) were considered clinical important, and mNGS failed to identify one mixed infection. Additionally, except for MTB, CSF mNGS tended to have high sensitivity to identify the above-mentioned pathogens (almost with 100% sensitivity). Even all the diagnostic strategies were evaluated, the cause of neurological symptoms remained undetermined in 6 (7.5%) patients. Overall, our results suggest that mNGS is a very sensitive tool for detecting common opportunistic CNS pathogen in HIV-infected patients, although its performance in CNS tuberculosis is unsatisfactory. EBV and CMV are commonly detected by CSF mNGS, however, the threshold of a clinical important detection remains to be defined.
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Affiliation(s)
- Yunqi Zhu
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wenxuan Zhao
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xihong Yang
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuanyuan Zhang
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaoling Lin
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xing Weng
- BGI Infection Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Yali Wang
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
- Clinical Infectious Disease Center of Nanjing, Nanjing, China
| | - Cong Cheng
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
- Clinical Infectious Disease Center of Nanjing, Nanjing, China
| | - Yun Chi
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
- Clinical Infectious Disease Center of Nanjing, Nanjing, China
| | - Hongxia Wei
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
- Clinical Infectious Disease Center of Nanjing, Nanjing, China
| | - Zhihang Peng
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhiliang Hu
- Department of Infectious Disease, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Clinical Infectious Disease Center of Nanjing, Nanjing, China
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14
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Cosentino MAC, D’arc M, Moreira FRR, Cavalcante LTDF, Mouta R, Coimbra A, Schiffler FB, Miranda TDS, Medeiros G, Dias CA, Souza AR, Tavares MCH, Tanuri A, Soares MA, dos Santos AFA. Discovery of two novel Torque Teno viruses in Callithrix penicillata provides insights on Anelloviridae diversification dynamics. Front Microbiol 2022; 13:1002963. [PMID: 36160188 PMCID: PMC9493276 DOI: 10.3389/fmicb.2022.1002963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
The development of high-throughput sequencing (HTS) technologies and metagenomics protocols deeply impacted the discovery of viral diversity. Moreover, the characterization of novel viruses in the Neotropical primates (NP) is central for the comprehension of viral evolution dynamics in those hosts, due to their evolutionary proximity to Old World primates, including humans. In the present work, novel anelloviruses were detected and characterized through HTS protocols in the NP Callithrix penicillata, the common black-tufted marmoset. De novo assembly of generated sequences was carried out, and a total of 15 contigs were identified with complete Anelloviridae ORF1 gene, two of them including a flanking GC-rich region, confirming the presence of two whole novel genomes of ~3 kb. The identified viruses were monophyletic within the Epsilontorquevirus genus, a lineage harboring previously reported anelloviruses infecting hosts from the Cebidae family. The genetic divergence found in the new viruses characterized two novel species, named Epsilontorquevirus callithrichensis I and II. The phylogenetic pattern inferred for the Epsilontorquevirus genus was consistent with the topology of their host species tree, echoing a virus-host diversification model observed in other viral groups. This study expands the host span of Anelloviridae and provides insights into their diversification dynamics, highlighting the importance of sampling animal viral genomes to obtain a clearer depiction of their long-term evolutionary processes.
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Affiliation(s)
- Matheus Augusto Calvano Cosentino
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mirela D’arc
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Filipe Romero Rebello Moreira
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Infectious Diseases Epidemiology, Imperial College London, London, United Kingdom
| | | | - Ricardo Mouta
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amanda Coimbra
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Francine Bittencourt Schiffler
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thamiris dos Santos Miranda
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriel Medeiros
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cecilia A. Dias
- Centro de Primatologia, Universidade de Brasília, Brasília, Brazil
| | | | | | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo Alves Soares
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - André Felipe Andrade dos Santos
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- *Correspondence: André Felipe Andrade dos Santos,
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15
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First Report of TTSuV1 in Domestic Swiss Pigs. Viruses 2022; 14:v14050870. [PMID: 35632612 PMCID: PMC9146045 DOI: 10.3390/v14050870] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/08/2022] [Accepted: 04/21/2022] [Indexed: 12/14/2022] Open
Abstract
Serum prevalence of Torque teno sus viruses (TTSuV1 and k2; family Anelloviridae) is known to be high in the porcine population worldwide but pathogenesis and associated pathomorphological lesions remain to be elucidated. In this study, quantitative real-time PCR for detection of TTSuV1 was performed in 101 porcine samples of brain tissue, with animals showing inflammatory lesions or no histological changes. Additionally, a pathomorphological and immunohistochemical characterization of possible lesions was carried out. Selected cases were screened by TTSuV1 in situ hybridization. Furthermore, TTSuV1 quantitative real-time PCR in splenic and pulmonary tissue and in situ hybridization (ISH) in spleen, lungs, mesenteric lymph node, heart, kidney, and liver were performed in 22 animals. TTSuV1 was detected by PCR not only in spleen and lung but also in brain tissue (71.3%); however, in general, spleen and lung tissue displayed lower Ct values than the brain. Positive TTSuV1 results were frequently associated with the morphological diagnosis of non-suppurative encephalitis. Single TTSuV1-positive lymphocytes were detected by ISH in the brain but also in lungs, spleen, mesenteric lymph node and in two cases of non-suppurative myocarditis. A pathogenetic role of a TTSuV1 infection as a co-factor for non-suppurative encephalitides cannot be ruled out.
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16
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Liu H, Zhang Y, Chen G, Sun S, Wang J, Chen F, Liu C, Zhuang Q. Diagnostic Significance of Metagenomic Next-Generation Sequencing for Community-Acquired Pneumonia in Southern China. Front Med (Lausanne) 2022; 9:807174. [PMID: 35242783 PMCID: PMC8885724 DOI: 10.3389/fmed.2022.807174] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Background The morbidity and mortality of community-acquired pneumonia are relatively high, but many pneumonia pathogens cannot be identified accurately. As a new pathogen detection technology, metagenomic next-generation sequencing (mNGS) has been applied more and more clinically. We aimed to evaluate the diagnostic significance of mNGS for community-acquired pneumonia (CAP) in the south of China. Methods Our study selected CAP patients who visited the 3rd Xiangya Hospital from May 2019 to April 2021. Pathogens in bronchoalveolar lavage fluid (BALF) specimens were detected using mNGS and traditional microbiological culture. mNGS group: detected by both mNGS and BALF culture; control group: detected only by BALF or sputum culture. The diagnostic performance of pathogens and the antibiotic adjustments were compared within mNGS group. Results The incidence of acute respiratory distress syndrome (ARDS) was 28.3% in the mNGS group and 17.3% in the control group. Within the mNGS group, the positive rate of pathogens detected by mNGS was 64%, thus by BALF culture was only 28%. Pathogens detected by mNGS were consisted of bacteria (55%), fungi (18%), special pathogens (18%), and viruses (9%). The most detected pathogen by mNGS was Chlamydia psittaci. Among the pathogen-positive cases, 26% was not pathogen-covered by empirical antibiotics, so most of which were made an antibiotic adjustment. Conclusions mNGS can detect pathogens in a more timely and accurate manner and assist clinicians to adjust antibiotics in time. Therefore, we recommend mNGS as the complementary diagnosis of severe pneumonia or complicated infections.
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Affiliation(s)
- Hanying Liu
- Department of Respiratory Diseases, The 3rd Xiangya Hospital, Central South University, Changsha, China
| | - Ying Zhang
- Transplantation Center, The 3rd Xiangya Hospital, Central South University, Changsha, China
| | - Guiyang Chen
- Department of Cardiology, Hunan Aerospace Hospital, Changsha, China
| | - Shenghua Sun
- Department of Respiratory Diseases, The 3rd Xiangya Hospital, Central South University, Changsha, China
| | - Jiangang Wang
- Department of Health Management, The 3rd Xiangya Hospital, Central South University, Changsha, China
| | | | - Chun Liu
- Department of Respiratory Diseases, The 3rd Xiangya Hospital, Central South University, Changsha, China
| | - Quan Zhuang
- Transplantation Center, The 3rd Xiangya Hospital, Central South University, Changsha, China.,Research Center of National Health Ministry on Transplantation Medicine, Changsha, China
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17
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Shah D, Brown JR, Lee JC, Carpenter ML, Wall G, Breuer J. Use of a sample-to-result shotgun metagenomics platform for the detection and quantification of viral pathogens in paediatric immunocompromised patients. JOURNAL OF CLINICAL VIROLOGY PLUS 2022; 2:None. [PMID: 35755957 PMCID: PMC9200058 DOI: 10.1016/j.jcvp.2022.100073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/11/2022] [Accepted: 03/17/2022] [Indexed: 11/19/2022] Open
Abstract
The Galileo Viral Panel metagenomic sequencing platform was compared to singleplex qPCR for the detection and quantification of DNA viruses in immunocompromised paediatric patients. Galileo had high qualitative and quantitative agreement with qPCR. Galileo was able to detect additional viruses not targeted in routine testing.
Background Infections by several DNA viruses can severely impact outcomes in paediatric immunocompromised patients. Current testing, which is generally limited to singleplex qPCR assays, can miss both common and rarer viruses if they are not targeted. Objectives To evaluate the performance of the Galileo Viral Panel (Galileo), a sample-to-result shotgun metagenomics platform for the detection and quantification of 12 DNA viruses, compared to standard of care qPCR assays. Study design A clinical performance evaluation was carried out using 43 prospectively collected EDTA plasma samples positive for one or more DNA viruses. Agreement between assays was assessed by overall, positive, and negative percent agreement, as well as quantitative agreement by linear regression and Bland-Altman analysis. Results Overall positive percent agreement was 84% (95% CI: 76%-90%), and negative percent agreement was 95% (95% CI: 92%-97%). There was a high correlation between Galileo and qPCR for ADV, CMV, EBV, and VZV (R2 = 0.91) and a mean difference by Bland Altman of -0.43 log10 IU or cp/ml (95% limits of agreement, -1.37 to 0.51). In addition, there was a high correlation between Galileo Signal Score and qPCR for TTV (R2 = 0.85). Conclusion We observed high qualitative and quantitative agreement between qPCR and Galileo. Galileo identified additional viruses that were not tested with routine qPCR and could impact clinical outcomes.
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Affiliation(s)
- Divya Shah
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, UK
| | - Julianne R. Brown
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, UK
| | - Jack C.D. Lee
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, UK
| | | | | | - Judith Breuer
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, UK
- Division of Infection and Immunity, University College London, UK
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18
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Redondo N, Navarro D, Aguado JM, Fernández-Ruiz M. Viruses, friends and foes: The case of Torque Teno virus and the net state of immunosuppression. Transpl Infect Dis 2021; 24:e13778. [PMID: 34933413 DOI: 10.1111/tid.13778] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/16/2021] [Accepted: 12/05/2021] [Indexed: 11/30/2022]
Abstract
New reliable biomarkers are needed to improve individual risk assessment for post-transplant infection, acute graft rejection and other immune-related complications after solid organ transplantation (SOT) and allogeneic hematopoietic stem cell transplantation (allo-HSCT). One promising strategy relies on the monitoring of replication kinetics of virome components as functional surrogate for the net state of immunosuppression. Torque Teno Virus (TTV) is a small, non-enveloped, circular, single-stranded DNA anellovirus with no attributable pathological effects. A major component of the human blood virome, TTV exhibits various features that facilitate its application as immune biomarker: high prevalence rates, nearly ubiquitous distribution, stable viral loads with little intra-individual variability, insensitivity to antiviral drugs, and availability of commercial PCR assays for DNA quantification. The present review summarizes the available studies supporting the use of post-transplant TTV viremia to predict patient and graft outcomes after SOT and allo-HSCT. Taken together, this evidence suggests that high or increasing TTV DNA levels precede the occurrence of infectious complications in the SOT setting, whereas low or decreasing viral loads are associated with the development of acute rejection. The interpretation in allo-HSCT recipients is further complicated by complex interplay with the underlying disease, conditioning regimen and timing of recovery of lymphocyte counts, although TTV kinetics may act as a marker of immunological reconstitution at the early post-transplant period. The standardization of PCR methods and reporting units for TTV DNAemia and the results from ongoing interventional trials evaluating a TTV load-guided strategy to adjust immunosuppressive therapy are achievements expected in the coming years. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Natalia Redondo
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Spain
| | - David Navarro
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Spain.,Department of Microbiology, Hospital Clínico Universitario, Instituto de Investigación Sanitaria INCLIVA, Valencia, Spain.,Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - José María Aguado
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Spain.,Department of Medicine, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Mario Fernández-Ruiz
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Spain.,Department of Medicine, School of Medicine, Universidad Complutense, Madrid, Spain
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19
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Marongiu L, Landry JJM, Rausch T, Abba ML, Delecluse S, Delecluse H, Allgayer H. Metagenomic analysis of primary colorectal carcinomas and their metastases identifies potential microbial risk factors. Mol Oncol 2021; 15:3363-3384. [PMID: 34328665 PMCID: PMC8637581 DOI: 10.1002/1878-0261.13070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/09/2021] [Accepted: 07/29/2021] [Indexed: 12/18/2022] Open
Abstract
The paucity of microbiome studies at intestinal tissues has contributed to a yet limited understanding of potential viral and bacterial cofactors of colorectal cancer (CRC) carcinogenesis or progression. We analysed whole-genome sequences of CRC primary tumours, their corresponding metastases and matched normal tissue for sequences of viral, phage and bacterial species. Bacteriome analysis showed Fusobacterium nucleatum, Streptococcus sanguinis, F. Hwasookii, Anaerococcus mediterraneensis and further species enriched in primary CRCs. The primary CRC of one patient was enriched for F. alocis, S. anginosus, Parvimonas micra and Gemella sp. 948. Enrichment of Escherichia coli strains IAI1, SE11, K-12 and M8 was observed in metastases together with coliphages enterobacteria phage φ80 and Escherichia phage VT2φ_272. Virome analysis showed that phages were the most preponderant viral species (46%), the main families being Myoviridae, Siphoviridae and Podoviridae. Primary CRCs were enriched for bacteriophages, showing five phages (Enterobacteria, Bacillus, Proteus, Streptococcus phages) together with their pathogenic hosts in contrast to normal tissues. The most frequently detected, and Blast-confirmed, viruses included human endogenous retrovirus K113, human herpesviruses 7 and 6B, Megavirus chilensis, cytomegalovirus (CMV) and Epstein-Barr virus (EBV), with one patient showing EBV enrichment in primary tumour and metastases. EBV was PCR-validated in 80 pairs of CRC primary tumour and their corresponding normal tissues; in 21 of these pairs (26.3%), it was detectable in primary tumours only. The number of viral species was increased and bacterial species decreased in CRCs compared with normal tissues, and we could discriminate primary CRCs from metastases and normal tissues by applying the Hutcheson t-test on the Shannon indices based on viral and bacterial species. Taken together, our results descriptively support hypotheses on microorganisms as potential (co)risk factors of CRC and extend putative suggestions on critical microbiome species in CRC metastasis.
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Affiliation(s)
- Luigi Marongiu
- Department of Experimental Surgery – Cancer MetastasisMedical Faculty MannheimRuprecht‐Karls University of HeidelbergMannheimGermany
| | | | - Tobias Rausch
- Genomics Core FacilityEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Mohammed L. Abba
- Department of Experimental Surgery – Cancer MetastasisMedical Faculty MannheimRuprecht‐Karls University of HeidelbergMannheimGermany
| | | | | | - Heike Allgayer
- Department of Experimental Surgery – Cancer MetastasisMedical Faculty MannheimRuprecht‐Karls University of HeidelbergMannheimGermany
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20
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Mujahid Al-Shuwaikh A, Abbas khudair E, Basil Hanna D. Phylogenetic and molecular evolutionary analysis of SENV DNA isolated from Iraqi Hepatitis Patients. BIONATURA 2021. [DOI: 10.21931/rb/2021.06.04.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
SEN Virus (SENV) is a newly discovered group of transmissible, hepatotropic, single-stranded, circular, non-enveloped DNA viruses that are distantly linked to the widely distributed Torque Teno Virus (TTV) family. This research aimed to use nucleotide sequencing to identify the genetic alterations of SEN-V and to investigate the similarities between isolates. Seven DNA samples of SENV, which were previously extracted from blood of post transfusion hepatitis, were used to identify the genetic variation of SEN-V by nucleotide sequencing. According to the current analysis results, specific primer pairs were used to detect SENV DNA sequences isolated from Iraqi patients with hepatitis; however, those specific primers can also detect two new variants of SENV that are closely related to the Torque Teno Virus. In addition, four SENV isolates showed several substitution mutations, and one of them revealed the replacement of Proline (P) at position 11 with Serine (S). Only one local isolate of SENV was 100% identical to the Iranian isolate (GenBank acc. no. GQ452051.1) from thalassemia.
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Affiliation(s)
| | - Ealaf Abbas khudair
- Microbiology Department, College of Medicine, Al-Nahrain University, Baghdad – Iraq
| | - Dalya Basil Hanna
- Department of Clinical Laboratory Sciences, College of Pharmacy, Mustansiriyah University, Baghdad, Iraq
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21
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Marongiu L, Allgayer H. Viruses in colorectal cancer. Mol Oncol 2021; 16:1423-1450. [PMID: 34514694 PMCID: PMC8978519 DOI: 10.1002/1878-0261.13100] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/15/2021] [Accepted: 09/10/2021] [Indexed: 12/23/2022] Open
Abstract
Increasing evidence suggests that microorganisms might represent at least highly interesting cofactors in colorectal cancer (CRC) oncogenesis and progression. Still, associated mechanisms, specifically in colonocytes and their microenvironmental interactions, are still poorly understood. Although, currently, at least seven viruses are being recognized as human carcinogens, only three of these – Epstein–Barr virus (EBV), human papillomavirus (HPV) and John Cunningham virus (JCV) – have been described, with varying levels of evidence, in CRC. In addition, cytomegalovirus (CMV) has been associated with CRC in some publications, albeit not being a fully acknowledged oncovirus. Moreover, recent microbiome studies set increasing grounds for new hypotheses on bacteriophages as interesting additional modulators in CRC carcinogenesis and progression. The present Review summarizes how particular groups of viruses, including bacteriophages, affect cells and the cellular and microbial microenvironment, thereby putatively contributing to foster CRC. This could be achieved, for example, by promoting several processes – such as DNA damage, chromosomal instability, or molecular aspects of cell proliferation, CRC progression and metastasis – not necessarily by direct infection of epithelial cells only, but also by interaction with the microenvironment of infected cells. In this context, there are striking common features of EBV, CMV, HPV and JCV that are able to promote oncogenesis, in terms of establishing latent infections and affecting p53‐/pRb‐driven, epithelial–mesenchymal transition (EMT)‐/EGFR‐associated and especially Wnt/β‐catenin‐driven pathways. We speculate that, at least in part, such viral impacts on particular pathways might be reflected in lasting (e.g. mutational or further genomic) fingerprints of viruses in cells. Also, the complex interplay between several species within the intestinal microbiome, involving a direct or indirect impact on colorectal and microenvironmental cells but also between, for example, phages and bacterial and viral pathogens, and further novel species certainly might, in part, explain ongoing difficulties to establish unequivocal monocausal links between specific viral infections and CRC.
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Affiliation(s)
- Luigi Marongiu
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Ruprecht-Karls-University of Heidelberg, Mannheim, Germany
| | - Heike Allgayer
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Ruprecht-Karls-University of Heidelberg, Mannheim, Germany
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22
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Abade Dos Santos FA, Portela SJ, Nogueira T, Carvalho CL, de Sousa R, Duarte MD. Harmless or Threatening? Interpreting the Results of Molecular Diagnosis in the Context of Virus-Host Relationships. Front Microbiol 2021; 12:647730. [PMID: 34093464 PMCID: PMC8175621 DOI: 10.3389/fmicb.2021.647730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/27/2021] [Indexed: 01/15/2023] Open
Abstract
Molecular methods, established in the 1980s, expanded and delivered tools for the detection of vestigial quantities of nucleic acids in biological samples. Nucleotide sequencing of these molecules reveals the identity of the organism it belongs to. However, the implications of such detection are often misinterpreted as pathogenic, even in the absence of corroborating clinical evidence. This is particularly significant in the field of virology where the concepts of commensalism, and other benign or neutral relationships, are still very new. In this manuscript, we review some fundamental microbiological concepts including commensalism, mutualism, pathogenicity, and infection, giving special emphasis to their application in virology, in order to clarify the difference between detection and infection. We also propose a system for the correct attribution of terminology in this context.
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Affiliation(s)
- Fábio A Abade Dos Santos
- National Institute for Agrarian and Veterinary Research, Oeiras, Portugal.,Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Sara J Portela
- Harrogate District Hospital NHS Foundation Trust, Harrogate, United Kingdom
| | - Teresa Nogueira
- National Institute for Agrarian and Veterinary Research, Oeiras, Portugal.,Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Carina L Carvalho
- National Institute for Agrarian and Veterinary Research, Oeiras, Portugal
| | - Rita de Sousa
- National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Margarida D Duarte
- National Institute for Agrarian and Veterinary Research, Oeiras, Portugal.,Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
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23
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Li Y, Handley SA, Baldridge MT. The dark side of the gut: Virome-host interactions in intestinal homeostasis and disease. J Exp Med 2021; 218:e20201044. [PMID: 33760921 PMCID: PMC8006857 DOI: 10.1084/jem.20201044] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022] Open
Abstract
The diverse enteric viral communities that infect microbes and the animal host collectively constitute the gut virome. Although recent advances in sequencing and analysis of metaviromes have revealed the complexity of the virome and facilitated discovery of new viruses, our understanding of the enteric virome is still incomplete. Recent studies have uncovered how virome-host interactions can contribute to beneficial or detrimental outcomes for the host. Understanding the complex interactions between enteric viruses and the intestinal immune system is a prerequisite for elucidating their role in intestinal diseases. In this review, we provide an overview of the enteric virome composition and summarize recent findings about how enteric viruses are sensed by and, in turn, modulate host immune responses during homeostasis and disease.
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Affiliation(s)
- Yuhao Li
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Scott A. Handley
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - Megan T. Baldridge
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO
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24
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Ramzi M, Iravani Saadi M, Zarei T, Yaghobi R, Arandi N. Association Between Cytotoxic T-Lymphocyte Antigen 4 Gene Polymorphisms and Torque Teno Virus Infection After Hematopoietic Stem Cell Transplantation. EXP CLIN TRANSPLANT 2021; 19:259-263. [DOI: 10.6002/ect.2017.0105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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25
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Ahmad I, Valverde A, Siddiqui H, Schaller S, Naqvi AR. Viral MicroRNAs: Interfering the Interferon Signaling. Curr Pharm Des 2020; 26:446-454. [PMID: 31924149 DOI: 10.2174/1381612826666200109181238] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/22/2019] [Indexed: 12/23/2022]
Abstract
Interferons are secreted cytokines with potent antiviral, antitumor and immunomodulatory functions. As the first line of defense against viruses, this pathway restricts virus infection and spread. On the contrary, viruses have evolved ingenious strategies to evade host immune responses including the interferon pathway. Multiple families of viruses, in particular, DNA viruses, encode microRNA (miR) that are small, non-protein coding, regulatory RNAs. Virus-derived miRNAs (v-miR) function by targeting host and virus-encoded transcripts and are critical in shaping host-pathogen interaction. The role of v-miRs in viral pathogenesis is emerging as demonstrated by their function in subverting host defense mechanisms and regulating fundamental biological processes such as cell survival, proliferation, modulation of viral life-cycle phase. In this review, we will discuss the role of v-miRs in the suppression of host genes involved in the viral nucleic acid detection, JAK-STAT pathway, and cytokine-mediated antiviral gene activation to favor viral replication and persistence. This information has yielded new insights into our understanding of how v-miRs promote viral evasion of host immunity and likely provide novel antiviral therapeutic targets.
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Affiliation(s)
- Imran Ahmad
- Mucosal Immunology Lab, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, IL 60612, United States
| | - Araceli Valverde
- Mucosal Immunology Lab, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, IL 60612, United States
| | - Hasan Siddiqui
- Mucosal Immunology Lab, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, IL 60612, United States
| | - Samantha Schaller
- Mucosal Immunology Lab, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, IL 60612, United States
| | - Afsar R Naqvi
- Mucosal Immunology Lab, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, IL 60612, United States
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26
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Toppinen M, Pratas D, Väisänen E, Söderlund-Venermo M, Hedman K, Perdomo MF, Sajantila A. The landscape of persistent human DNA viruses in femoral bone. Forensic Sci Int Genet 2020; 48:102353. [PMID: 32668397 DOI: 10.1016/j.fsigen.2020.102353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/24/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
The imprints left by persistent DNA viruses in the tissues can testify to the changes driving virus evolution as well as provide clues on the provenance of modern and ancient humans. However, the history hidden in skeletal remains is practically unknown, as only parvovirus B19 and hepatitis B virus DNA have been detected in hard tissues so far. Here, we investigated the DNA prevalences of 38 viruses in femoral bone of recently deceased individuals. To this end, we used quantitative PCRs and a custom viral targeted enrichment followed by next-generation sequencing. The data was analyzed with a tailor-made bioinformatics pipeline. Our findings revealed bone to be a much richer source of persistent DNA viruses than earlier perceived, discovering ten additional ones, including several members of the herpes- and polyomavirus families, as well as human papillomavirus 31 and torque teno virus. Remarkably, many of the viruses found have oncogenic potential and/or may reactivate in the elderly and immunosuppressed individuals. Thus, their persistence warrants careful evaluation of their clinical significance and impact on bone biology. Our findings open new frontiers for the study of virus evolution from ancient relics as well as provide new tools for the investigation of human skeletal remains in forensic and archaeological contexts.
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Affiliation(s)
- Mari Toppinen
- Department of Virology, University of Helsinki, Finland
| | - Diogo Pratas
- Department of Virology, University of Helsinki, Finland; Department of Electronics, Telecommunications and Informatics, University of Aveiro, Portugal; Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Portugal
| | | | | | - Klaus Hedman
- Department of Virology, University of Helsinki, Finland; HUSLAB, Helsinki University Hospital, Finland
| | | | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Finland; Forensic Medicine Unit, Finnish Institute of Health and Welfare, Finland.
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27
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Cornejo Castro EM, Marshall V, Lack J, Lurain K, Immonen T, Labo N, Fisher NC, Ramaswami R, Polizzotto MN, Keele BF, Yarchoan R, Uldrick TS, Whitby D. Dual infection and recombination of Kaposi sarcoma herpesvirus revealed by whole-genome sequence analysis of effusion samples. Virus Evol 2020; 6:veaa047. [PMID: 34211736 PMCID: PMC7474928 DOI: 10.1093/ve/veaa047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Kaposi sarcoma herpesvirus (KSHV) is the etiological agent of three malignancies, Kaposi sarcoma (KS), primary effusion lymphoma (PEL) and KSHV-associated multicentric Castelman disease. KSHV infected patients may also have an interleukin six-related KSHV-associated inflammatory cytokine syndrome. KSHV-associated diseases occur in only a minority of chronically KSHV-infected individuals and often in the setting of immunosuppression. Mechanisms by which KSHV genomic variations and systemic co-infections may affect the pathogenic pathways potentially leading to these diseases have not been well characterized in vivo. To date, the majority of comparative genetic analyses of KSHV have been focused on a few regions scattered across the viral genome. We used next-generation sequencing techniques to investigate the taxonomic groupings of viruses from malignant effusion samples from fourteen participants with advanced KSHV-related malignancies, including twelve with PEL and two with KS and elevated KSHV viral load in effusions. The genomic diversity and evolutionary characteristics of nine isolated, near full-length KSHV genomes revealed extensive evidence of mosaic patterns across all these genomes. Further, our comprehensive NGS analysis allowed the identification of two distinct KSHV genome sequences in one individual, consistent with a dual infection. Overall, our results provide significant evidence for the contribution of KSHV phylogenomics to the origin of KSHV subtypes. This report points to a wider scope of studies to establish genome-wide patterns of sequence diversity and define the possible pathogenic role of sequence variations in KSHV-infected individuals.
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Affiliation(s)
- Elena M Cornejo Castro
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, MD 21702, USA
| | - Vickie Marshall
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, MD 21702, USA
| | - Justin Lack
- Advanced Biomedical Computing Center, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Kathryn Lurain
- HIV and AIDS Malignancy Branch, National Cancer Institute, 10 Center Dr, Bethesda, MD 20814, USA
| | - Taina Immonen
- Retroviral Evolution Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, MD 21702, USA
| | - Nazzarena Labo
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, MD 21702, USA
| | - Nicholas C Fisher
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, MD 21702, USA
| | - Ramya Ramaswami
- HIV and AIDS Malignancy Branch, National Cancer Institute, 10 Center Dr, Bethesda, MD 20814, USA
| | - Mark N Polizzotto
- HIV and AIDS Malignancy Branch, National Cancer Institute, 10 Center Dr, Bethesda, MD 20814, USA
| | - Brandon F Keele
- Retroviral Evolution Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, MD 21702, USA
| | - Robert Yarchoan
- HIV and AIDS Malignancy Branch, National Cancer Institute, 10 Center Dr, Bethesda, MD 20814, USA
| | - Thomas S Uldrick
- HIV and AIDS Malignancy Branch, National Cancer Institute, 10 Center Dr, Bethesda, MD 20814, USA
| | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, MD 21702, USA
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28
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Møller HD, Ramos-Madrigal J, Prada-Luengo I, Gilbert MTP, Regenberg B. Near-Random Distribution of Chromosome-Derived Circular DNA in the Condensed Genome of Pigeons and the Larger, More Repeat-Rich Human Genome. Genome Biol Evol 2020; 12:3762-3777. [PMID: 31882998 PMCID: PMC6993614 DOI: 10.1093/gbe/evz281] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2019] [Indexed: 12/15/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) elements of chromosomal origin are known to be common in a number of eukaryotic species. However, it remains to be addressed whether genomic features such as genome size, the load of repetitive elements within a genome, and/or animal physiology affect the number of eccDNAs. Here, we investigate the distribution and numbers of eccDNAs in a condensed and less repeat-rich genome compared with the human genome, using Columba livia domestica (domestic rock pigeon) as a model organism. By sequencing eccDNA in blood and breast muscle from three pigeon breeds at various ages and with different flight behavior, we characterize 30,000 unique eccDNAs. We identify genomic regions that are likely hotspots for DNA circularization in breast muscle, including genes involved in muscle development. We find that although eccDNA counts do not correlate with the biological age in pigeons, the number of unique eccDNAs in a nonflying breed (king pigeons) is significantly higher (9-fold) than homing pigeons. Furthermore, a comparison between eccDNA from skeletal muscle in pigeons and humans reveals ∼9-10 times more unique eccDNAs per human nucleus. The fraction of eccDNA sequences, derived from repetitive elements, exist in proportions to genome content, that is, human 72.4% (expected 52.5%) and pigeon 8.7% (expected 5.5%). Overall, our results support that eccDNAs are common in pigeons, that the amount of unique eccDNA types per nucleus can differ between species as well as subspecies, and suggest that eccDNAs from repeats are found in proportions relative to the content of repetitive elements in a genome.
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Affiliation(s)
- Henrik Devitt Møller
- Department of Biology, University of Copenhagen, Denmark.,Department of Biology, Institute of Biochemistry, ETH Zürich, Switzerland
| | | | | | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Denmark.,NTNU University Museum, Trondheim, Norway
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29
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Kumata R, Ito J, Takahashi K, Suzuki T, Sato K. A tissue level atlas of the healthy human virome. BMC Biol 2020; 18:55. [PMID: 32493363 PMCID: PMC7269688 DOI: 10.1186/s12915-020-00785-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Human-resident microbes can influence both health and disease. Investigating the microbiome using next-generation sequencing technology has revealed examples of mutualism and conflict between microbes and humans. Comparing to bacteria, the viral component of the microbiome (i.e., the "virome") is understudied. Somatic tissues of healthy individuals are usually inaccessible for the virome sampling; therefore, there is limited understanding of the presence and distribution of viruses in tissues in healthy individuals and how virus infection associates with human gene expression and perturbs immunological homeostasis. RESULTS To characterize the human virome in a tissue-specific manner, here we performed meta-transcriptomic analysis using the RNA-sequencing dataset from the Genotype-Tissue Expression (GTEx) Project. We analyzed the 8991 RNA-sequencing data obtained from 51 somatic tissues from 547 individuals and successfully detected 39 viral species in at least one tissue. We then investigated associations between virus infection and human gene expression and human disease onset. We detected some expected relationships; for instance, hepatitis C virus infection in the liver was strongly associated with interferon-stimulated gene upregulation and pathological findings of chronic hepatitis. The presence of herpes simplex virus type 1 in one subject's brain strongly associated with immune gene expression. While torque teno virus was detected in a broad range of human tissues, it was not associated with interferon responses. Being notable in light of its association with lymphoproliferative disorders, Epstein-Barr virus infection in the spleen and blood was associated with an increase in plasma cells in healthy subjects. Human herpesvirus 7 was often detected in the stomach; intriguingly, it associated with the proportion of human leukocytes in the stomach as well as digestive gene expression. Moreover, virus infections in the local tissues associated with systemic immune responses in circulating blood. CONCLUSIONS To our knowledge, this study is the first comprehensive investigation of the human virome in a variety of tissues in healthy individuals through meta-transcriptomic analysis. Further investigation of the associations described here, and application of this analytical pipeline to additional datasets, will be useful to reveal the impact of viral infections on human health.
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Affiliation(s)
- Ryuichi Kumata
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan
| | - Kenta Takahashi
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 1628640, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 1628640, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan. .,CREST, Japan Science and Technology Agency, Saitama, 3220012, Japan.
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30
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Chong Y, Lee JY, Kang CS, Lee EJ. Identification of Torque Teno Virus/Torque Teno-Like Minivirus in the Cervical Lymph Nodes of Kikuchi-Fujimoto Lymphadenitis Patients (Histiocytic Necrotizing Lymphadenitis): A Possible Key to Idiopathic Disease. Biomed Hub 2020; 5:1-5. [PMID: 32775328 DOI: 10.1159/000506501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 02/11/2020] [Indexed: 11/19/2022] Open
Abstract
Kikuchi-Fujimoto disease (KFD) is rare, and many infectious agents have been suspected for its etiology. This report presents an interesting case of KFD found with torque teno virus/torque teno minivirus (TTV/TTMV), which closely resembles the circovirus that causes necrotizing lymphadenitis in pigs. Three Korean patients showed several enlarged lymph nodes in their neck. Quantitative polymerase chain reaction (qPCR) and subsequent DNA sequencing for TTV/TTMV using formalin-fixed paraffin-embedded tissue were performed. Histologic examination demonstrated typical features of KFD. qPCR showed successful amplification of TTV/TTMV, and DNA sequencing confirmed the results. It is the first report of TTV/TTMV presence in three patients with KFD.
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Affiliation(s)
- Yosep Chong
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ji Young Lee
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Chang Suk Kang
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Pathology, Samkwang Medical Laboratories, Seoul, Republic of Korea
| | - Eun Jung Lee
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Pathology, Shinwon Medical Foundation, Gwangmyeong-si, Republic of Korea
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31
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Sarairah H, Bdour S, Gharaibeh W. The Molecular Epidemiology and Phylogeny of Torque Teno Virus (TTV) in Jordan. Viruses 2020; 12:v12020165. [PMID: 32023916 PMCID: PMC7077251 DOI: 10.3390/v12020165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/18/2022] Open
Abstract
Torque teno virus (TTV) is the most common component of the human blood virobiota. Little is known, however, about the prevalence of TTV in humans and the most common farm domesticates in Jordan, or the history and modality of TTV transmission across species lines. We therefore tested sera from 396 Jordanians and 171 farm animals for the presence of TTV DNA using nested 5'-UTR-PCR. We then performed phylogenetic, ordination and evolutionary diversity analyses on detected DNA sequences. We detected a very high prevalence of TTV in Jordanians (~96%); much higher than in farm animal domesticates (~29% pooled over species). TTV prevalence in the human participants is not associated with geography, demography or physical attributes. Phylogenetic, ordination and evolutionary diversity analyses indicated that TTV is transmitted readily between humans across the geography of the country and between various species of animal domesticates. However, the majority of animal TTV isolates seem to derive from a single human-to-animal transmission event in the past, and current human-animal transmission in either direction is relatively rare. In conclusion, animal TTV in Jordan is historically derived from human variants; however, ongoing human-animal TTV exchange is minimal and zoonotic infection seems to be of limited importance.
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Affiliation(s)
- Haneen Sarairah
- Department of Biological Sciences, Faculty of Science, The University of Jordan, Amman 11942, Jordan
| | - Salwa Bdour
- Department of the Clinical Laboratory Sciences, Faculty of Science, The University of Jordan, Amman 11942, Jordan
- Correspondence: (S.B.); (W.G.); Tel.: +962-6-5355000 (ext. 22233) (S.B.); +962-6-5355000 (ext. 22205) (W.G.)
| | - Waleed Gharaibeh
- Department of Biological Sciences, Faculty of Science, The University of Jordan, Amman 11942, Jordan
- Correspondence: (S.B.); (W.G.); Tel.: +962-6-5355000 (ext. 22233) (S.B.); +962-6-5355000 (ext. 22205) (W.G.)
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32
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Shah AA, Wang D, Hirsch E. Nucleic Acid-Based Screening of Maternal Serum to Detect Viruses in Women with Labor or PROM. Reprod Sci 2020; 27:537-544. [PMID: 31925769 DOI: 10.1007/s43032-019-00051-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/12/2019] [Indexed: 01/12/2023]
Abstract
The purpose of this study was to determine whether timing of the initiating event of spontaneous labor (either uterine contractions with intact fetal membranes or rupture of membranes prior to labor (PROM)) is associated with maternal viral infection. It was a prospective case control study of women with either spontaneous labor or PROM occurring < 37 weeks' gestation ("cases") or at term ("controls"). An initial unbiased screen for viruses was performed with next-generation sequencing (NGS) in serum pooled from eight cases delivered by C/S and represents a range of gestational ages, membrane rupture status, and presence or absence of chorioamnionitis. Custom PCR was used to query individual patient samples from the original cohort. The NGS screen generated 15 million reads. Seven unique viral sequences were detected in two cases, all identified as torque teno virus (TTV), an ubiquitous DNA anellovirus of no known pathogenicity. Using nested and semi-nested PCR, sera from 72 patients (47 cases and 25 matched controls, stratified by ROM status) were screened for the 3 subtypes of anelloviruses (TTV, TTMDV, or TTMV). These were found in 43/47 cases (91%) and 16/25 controls (64%) (p = 0.012, OR = 5.9 (95% CI = 1.4-29.9)). In logistic regression, pregnant women with at least one type of anellovirus were more likely to experience preterm labor than those with no anellovirus (p = 0.03, aOR = 4.6, CI = 1.2-18.7). Among women experiencing a spontaneous initiating event of labor, TTV virus was more likely to be present in the serum of preterm than term patients. TTV may have a role in determining the timing of parturition.
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Affiliation(s)
- Ankit A Shah
- Department of Obstetrics and Gynecology, NorthShore University Health System, 2650 Ridge Ave, Evanston, IL, USA.,Department of Obstetrics and Gynecology, Pritzker School of Medicine, University of Chicago, 5801 S Ellis Ave, Chicago, IL, 60637, USA
| | - David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO, 63110, USA
| | - Emmet Hirsch
- Department of Obstetrics and Gynecology, NorthShore University Health System, 2650 Ridge Ave, Evanston, IL, USA. .,Department of Obstetrics and Gynecology, Pritzker School of Medicine, University of Chicago, 5801 S Ellis Ave, Chicago, IL, 60637, USA.
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33
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Cancer Treatment Goes Viral: Using Viral Proteins to Induce Tumour-Specific Cell Death. Cancers (Basel) 2019; 11:cancers11121975. [PMID: 31817939 PMCID: PMC6966515 DOI: 10.3390/cancers11121975] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/24/2022] Open
Abstract
Cell death is a tightly regulated process which can be exploited in cancer treatment to drive the killing of the tumour. Several conventional cancer therapies including chemotherapeutic agents target pathways involved in cell death, yet they often fail due to the lack of selectivity they have for tumour cells over healthy cells. Over the past decade, research has demonstrated the existence of numerous proteins which have an intrinsic tumour-specific toxicity, several of which originate from viruses. These tumour-selective viral proteins, although from distinct backgrounds, have several similar and interesting properties. Though the mechanism(s) of action of these proteins are not fully understood, it is possible that they can manipulate several cell death modes in cancer exemplifying the intricate interplay between these pathways. This review will discuss our current knowledge on the topic and outstanding questions, as well as deliberate the potential for viral proteins to progress into the clinic as successful cancer therapeutics.
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Chong Y, Lee JY, Thakur N, Kang CS, Lee EJ. Strong association of Torque teno virus/Torque teno-like minivirus to Kikuchi-Fujimoto lymphadenitis (histiocytic necrotizing lymphadenitis) on quantitative analysis. Clin Rheumatol 2019; 39:925-931. [PMID: 31782015 DOI: 10.1007/s10067-019-04851-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/06/2019] [Accepted: 11/08/2019] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Kikuchi-Fujimoto disease (KFD) is a rare benign lymphadenitis that mainly involves cervical lymph nodes of young Asian women with unknown etiology. Recently, we experienced a case of KFD found with Torque teno virus/Torque teno-like mini virus (TTV/TTMV) from a 26-year-old woman. TTV/TTMV is a genus of Circoviridae that causes necrotizing lymphadenitis in pigs, which shares the key histologic finding of KFD. The purpose of this study is to investigate the pathogenic role of TTV/TTMV in KFD by quantitative polymerase chain reaction (qPCR) analysis. METHOD We performed two-step qPCR specific to TTV/TTMV with formalin-fixed paraffin-embedded tissue of sequentially selected 100 KFD patients and 50 randomly selected, matched normal controls. Consequent direct sequencing was done for confirmation with PCR products. RESULTS PCR amplification of TTV and TTMV was found in a significantly higher proportion in KFDs than normal controls (TTV, 85% vs. 18%, p < 0.000; TTMV, 91% vs. 24%, p < 0.000). After the sequencing, KFD samples showed more sequence matching than control samples for TTMV (94% vs. 30%, p < 0.000). CONCLUSION This finding strongly suggests the possible implication of TTV/TTMV in the pathogenesis of KFD. Animal or in vivo experimental design should be followed in the future.Key Points• Kikuchi-Fujimoto disease (KFD) is rare and its etiology is still unclear.• Torque teno/Torque teno-like minivirus (TTV/TTMV) is a recently introduced virus in the Circoviridae family that causes necrotizing lymphadenitis in pigs, histologically similar to KFD.• We discovered the significantly increased TTV/TTMV viral loads in the KFD patients than normal controls, which implicates TTV/TTMV in the pathogenesis of KFD.
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Affiliation(s)
- Yosep Chong
- Department of Hospital Pathology, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 10, 63-ro, Yeongdeungpo-gu, Seoul, 07345, Republic of Korea.
| | - Ji Young Lee
- Department of Hospital Pathology, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 10, 63-ro, Yeongdeungpo-gu, Seoul, 07345, Republic of Korea
| | - Nishant Thakur
- Department of Hospital Pathology, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 10, 63-ro, Yeongdeungpo-gu, Seoul, 07345, Republic of Korea
| | - Chang Suk Kang
- Department of Hospital Pathology, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 10, 63-ro, Yeongdeungpo-gu, Seoul, 07345, Republic of Korea.,Department of Pathology, Samkwang Medical Laboratories, 57, Baumoe-ro 41-gil, Seocho-gu, Seoul, 06742, Republic of Korea
| | - Eun Jung Lee
- Department of Hospital Pathology, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 10, 63-ro, Yeongdeungpo-gu, Seoul, 07345, Republic of Korea
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Jaksch P, Kundi M, Görzer I, Muraközy G, Lambers C, Benazzo A, Hoetzenecker K, Klepetko W, Puchhammer-Stöckl E. Torque Teno Virus as a Novel Biomarker Targeting the Efficacy of Immunosuppression After Lung Transplantation. J Infect Dis 2019; 218:1922-1928. [PMID: 30053048 DOI: 10.1093/infdis/jiy452] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/17/2018] [Indexed: 12/17/2022] Open
Abstract
Torque teno viruses (TTV) are small DNA-viruses, of the genus Alphatorquevirus, whose replication is linked to immune status. TTV load may be an indicator for efficacy of IS in lung transplant recipients (LTRs). In a prospective single-center-study 143 LTRs were followed up and tested by quantitative TTV-DNA PCR. Using multivariate Cox-regression contribution of TTV-load to the occurrence of severe infections, chronic lung allograft dysfunction (CLAD), acute cellular rejection (ACR), and death was assessed. During follow-up 28 (20%) patients developed infections with a rate of 7.7 per 100 patient-years (PY). The hazard-ratio (HR) associated with a one-log10 increase of TTV-load before the event was 5.05. CLAD occurred with a rate of 6.0%-PY. HR for a 1 log10 increase of the lowest TTV level before the event was 0.71 (CI: 0.54-0.93). TTV-load predicts clinical events and may be useful to optimize IS during the first years of follow-up of LTRs.
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Affiliation(s)
- Peter Jaksch
- Division of Thoracic Surgery, Department of Surgery
| | | | - Irene Görzer
- Department of Virology, Medical University of Vienna, Austria
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O'Brien E, Xagoraraki I. A water-focused one-health approach for early detection and prevention of viral outbreaks. One Health 2019; 7:100094. [PMID: 31080867 PMCID: PMC6501061 DOI: 10.1016/j.onehlt.2019.100094] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 12/21/2022] Open
Abstract
Despite consistent efforts to protect public health there is still a heavy burden of viral disease, both in the United States and abroad. In addition to conventional medical treatment, there is a need for a holistic approach for early detection and prevention of viral outbreaks at a population level. One-Health is a relatively new integrative approach to the solving of global health challenges. A key component to the One-Health approach is the notion that human health, animal health, and environmental health are all innately interrelated. One-Health interventions, initiated by veterinary doctors, have proven to be effective in controlling outbreaks, but thus far the applications focus on zoonotic viruses transmitted from animals to humans. Environmental engineers and environmental scientists hold a critical role in the further development of One-Health approaches that include water-related transport and transmission of human, animal, and zoonotic viruses. In addition to waterborne viruses, the proposed approach is applicable to a wide range of viruses that are found in human excrement since contaminated water-based surveillance systems may be used for early detection of viral disease. This paper proposes a greater One-Health based framework that involves water-related pathways. The first step in the proposed framework is the identification of critical exposure pathways of viruses in the water environment. Identification of critical pathways informs the second and third steps, which include water-based surveillance systems for early detection at a population level and implementation of intervention approaches to block the critical pathways of exposure.
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Affiliation(s)
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
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Abstract
The immense global burden of infectious disease outbreaks and the need to establish prediction and prevention systems have been recognized by the World Health Organization (WHO), the National Institutes of Health (NIH), the United States Agency of International Development (USAID), the Bill and Melinda Gates Foundation, and the international scientific community. Despite multiple efforts, this infectious burden is still increasing. For example, it has been reported that between 1.5 and 12 million people die each year from waterborne diseases and diarrheal diseases are listed within the top 15 leading causes of death worldwide. Rapid population growth, climate change, natural disasters, immigration, globalization, and the corresponding sanitation and waste management challenges are expected to intensify the problem in the years to come.
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Complete Genome Sequence of a Rodent Torque Teno Virus in Hainan Island, China. Microbiol Resour Announc 2018; 7:MRA01074-18. [PMID: 30533797 PMCID: PMC6256484 DOI: 10.1128/mra.01074-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/17/2018] [Indexed: 11/20/2022] Open
Abstract
Torque teno virus (TTV) has been reported in a wide range of mammals. In this study, we sequenced and analyzed the complete genome of a genetic variant of a rodent TTV, RoTTV3-HMU1 (Hainan Medical University 1). The virus was found in a rat (Rattus norvegicus) in a residential area of Hainan Island, China.
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Vargas-Ruiz A, García-Camacho LA, Ramírez-Alvarez H, Rangel-Rodriguez IC, Alonso-Morales RA, Sánchez-Betancourt JI. Molecular characterization of the ORF2 of Torque teno sus virus 1a and Torque teno sus virus 1b detected in cases of postweaning multisystemic wasting syndrome in Mexico. Transbound Emerg Dis 2018; 65:1806-1815. [PMID: 30035377 DOI: 10.1111/tbed.12956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 05/28/2018] [Accepted: 06/18/2018] [Indexed: 02/05/2023]
Abstract
Worldwide Torque teno sus virus (TTSuV, genus Iotatorquevirus) species have been regarded as possible agents associated with porcine circovirus-associated disease. Iotatorquevirus species possess high genomic variability, suggesting that diverse genotypes are widely geographically distributed. In this study, we validated the genomic variability of Iotaroquevirus species in pigs with postweaned multisystemic wasting syndrome. Genomic DNA from nine TTSuV1a-positive tissues and 15 TTSuV1b-positive tissues was used to amplify the complete ORF2 of each species by nested PCR to perform a molecular characterization. It was found that Mexican TTSuV1a sequences belong to genotype B, sharing phylogenetic origin, high nucleic acid and amino acid sequence similarity and dominant epitope conformation with commercially linked countries, such as the United States, Canada and China, whereas the Mexican TTSuV1b sequences belong to genotype A, being more divergent among each other and displaying low nucleotide identity with worldwide genotype A sequences. In both Iotatorquevirus species, a PTPase-like signature motif was identified in the predicted amino acid sequence, being more conserved for Mexican TTSuV1b sequences than for Mexican TTSuV1a sequences, in which several substitutions were observed. These changes may influence the conformation of dominant epitopes as different arrays were determined among TTSuV1a genotypes. ORF2 variability may account for pathogenic differences by modifying viral replication and immune response, as depicted for human TTV.
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Affiliation(s)
- Alejandro Vargas-Ruiz
- College of Superior Studies (FESC), National University of Mexico (UNAM), Estado de México, México
| | | | - Hugo Ramírez-Alvarez
- College of Superior Studies (FESC), National University of Mexico (UNAM), Estado de México, México
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Crane A, Goebel ME, Kraberger S, Stone AC, Varsani A. Novel anelloviruses identified in buccal swabs of Antarctic fur seals. Virus Genes 2018; 54:719-723. [DOI: 10.1007/s11262-018-1585-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/29/2018] [Indexed: 11/27/2022]
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Kulifaj D, Durgueil-Lariviere B, Meynier F, Munteanu E, Pichon N, Dubé M, Joannes M, Essig M, Hantz S, Barranger C, Alain S. Development of a standardized real time PCR for Torque teno viruses (TTV) viral load detection and quantification: A new tool for immune monitoring. J Clin Virol 2018; 105:118-127. [PMID: 29957546 DOI: 10.1016/j.jcv.2018.06.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/17/2018] [Accepted: 06/08/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Torque teno viruses (TTV) are small DNA viruses whose replication is closely linked to immune status. A growing number of publications underlined the potential of TTV viral load as an indicator of immunosuppression. OBJECTIVES To demonstrate the analytical performance of the first standardized RUO (Research Use Only) assay to detect and quantify human TTV DNA in whole blood and plasma. STUDY DESIGN We established analytical performances for TTV load measurement in various populations. The TTV kinetics were followed in kidney recipients. TTV viral load was analyzed on whole blood samples from 42 kidney recipients follow-up, 53 kidney deceased donors and 31 healthy volunteers. RESULTS The qPCR TTV assay detects the most prevalent human TTV genotypes and does not cross react with other viruses. Limit of detection was 2.2 log10 copies/mL in whole blood and plasma, linearity and precision were demonstrated over the range 1.61 to 10.61 log10 copies/mL in whole blood. Prevalence of TTV DNA in blood differed significantly among groups: 45% in healthy volunteers, 74% in donors and 83% in kidney recipients. In kidney recipients, early TTV kinetics were comparable to those previously observed with in-house assays in other transplant settings: viral load increased from an average of 4.3 log10 to 7.9 log10 copies/mL within the first 75 days post transplantation. CONCLUSION This TTV assay showed high analytical sensitivity, specificity, linearity and precision. It is a useful standardized tool to further evaluate TTV load as a biomarker of immune status that could improve individual treatment strategy.
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Affiliation(s)
- Dorian Kulifaj
- UMR INSERM 1092, Université de Limoges, National Reference Center For Herpesviruses, Bacteriology-Virology-Hygiene Department, CHU Limoges, 2 ave ML King, 87000, Limoges, France; bioMérieux, 138 rue Louis Pasteur, Parc technologique Delta Sud, 09340, Verniolle, France
| | | | - Faustine Meynier
- bioMérieux, Centre Christophe Mérieux, 5 rue des Berges, 38024, Grenoble cedex 01, Grenoble, France
| | - Eliza Munteanu
- UMR INSERM 1092, Université de Limoges, National Reference Center For Herpesviruses, Bacteriology-Virology-Hygiene Department, CHU Limoges, 2 ave ML King, 87000, Limoges, France
| | - Nicolas Pichon
- Intensive Care Unit Department, CHU Limoges, 2 ave ML King, 87000, Limoges, France
| | - Manon Dubé
- bioMérieux, 138 rue Louis Pasteur, Parc technologique Delta Sud, 09340, Verniolle, France
| | - Martine Joannes
- bioMérieux, 138 rue Louis Pasteur, Parc technologique Delta Sud, 09340, Verniolle, France
| | - Marie Essig
- Nephrology and Transplantation Department, CHU Limoges, 2 ave ML King, 87000, Limoges, France
| | - Sébastien Hantz
- UMR INSERM 1092, Université de Limoges, National Reference Center For Herpesviruses, Bacteriology-Virology-Hygiene Department, CHU Limoges, 2 ave ML King, 87000, Limoges, France
| | - Côme Barranger
- bioMérieux, 138 rue Louis Pasteur, Parc technologique Delta Sud, 09340, Verniolle, France.
| | - Sophie Alain
- UMR INSERM 1092, Université de Limoges, National Reference Center For Herpesviruses, Bacteriology-Virology-Hygiene Department, CHU Limoges, 2 ave ML King, 87000, Limoges, France.
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Xiong YQ, Mo Y, Chen MJ, Cai W, He WQ, Chen Q. Detection and phylogenetic analysis of torque teno virus (TTV) carried by murine rodents and house shrews in China. Virology 2018; 516:189-195. [PMID: 29407376 DOI: 10.1016/j.virol.2018.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/16/2018] [Accepted: 01/22/2018] [Indexed: 12/25/2022]
Abstract
Between May 2015 and May 2017, 496 animals (473 murine rodents and 23 house shrews) were captured in six regions of China. A total of 22.8% (113/496) of throat swabs, 29.1% (142/488) of fecal samples and 23.8% (54/227) of serum samples tested positive for rodent torque teno virus 3 (RoTTV3). The positive rate in Rattus norvegicus was higher than the rate in Rattus tanezumi and Rattus losea. Of 23 house shrews, one throat swab and one serum sample were positive for RoTTV3. Ten murine rodents were simultaneously positive for RoTTV3 in throat swab, fecal and serum samples. Phylogenetic analysis showed that the 12 near-full length genomes of RoTTVs sequences obtained in this study represented a novel RoTTV genotype (RoTTV3). In conclusion, high prevalence rates of RoTTV3 were found in three common murine rodents in China, and the RoTTV3 obtained in this study were classified as a novel genotype of RoTTV.
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Affiliation(s)
- Yi-Quan Xiong
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, 1838 Guangzhou North Road, Guangzhou 510515, China
| | - Yun Mo
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, 1838 Guangzhou North Road, Guangzhou 510515, China
| | - Ming-Ji Chen
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, 1838 Guangzhou North Road, Guangzhou 510515, China
| | - Wei Cai
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, 1838 Guangzhou North Road, Guangzhou 510515, China
| | - Wen-Qiao He
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, 1838 Guangzhou North Road, Guangzhou 510515, China
| | - Qing Chen
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, 1838 Guangzhou North Road, Guangzhou 510515, China.
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Li W, Yang S, Wang Y, Zhu W, Ni P, Zhu S, Xu J, Lu R, Zhou C. A novel torque teno mini virus in the blood of the patient with lymphoma. Future Virol 2018. [DOI: 10.2217/fvl-2017-0113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To characterize a novel anellovirus and analyze the relationship of the novel anellovirus with other anelloviruses. Materials & methods: Twenty-one serum samples of lymphoma patients were collected and viral metagenomics method was used to identify the novel anellovirus; CLUSTALW1.8 and MEGA6.0 was used to perform phylogenetic analysis; prevalence investigation was performed by nest PCR. Results: A novel anellovirus was discovered from two patients with lymphoma. The complete genome of torque teno mini virus (TTMV)-SHA is 2880 nt in length. Phylogenetic analysis based on ORF1 indicated that TTMV-SHA clusters with EF538882 sharing 62.5% sequence similarity, and the sequences divergence is 54%. Conclusion: TTMV (SHA) belonged to a novel anellovirus species, whether this novel anellovirus is associated with lymphoma needs further studies.
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Affiliation(s)
- Wang Li
- Clinical Laboratory Center, Taizhou People's Hospital, Hailing District, Taizhou, Jiangsu 225300, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Yanchun Wang
- Department of Clinical Laboratory, Shanghai Cancer Center, Fudan University, Shanghai 200032, China
| | - Wenjun Zhu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Ping Ni
- Clinical Laboratory Center, Taizhou People's Hospital, Hailing District, Taizhou, Jiangsu 225300, China
| | - Shuai Zhu
- Clinical Laboratory Center, Taizhou People's Hospital, Hailing District, Taizhou, Jiangsu 225300, China
| | - Juan Xu
- Clinical Laboratory Center, Taizhou People's Hospital, Hailing District, Taizhou, Jiangsu 225300, China
| | - Renquan Lu
- Department of Clinical Laboratory, Shanghai Cancer Center, Fudan University, Shanghai 200032, China
| | - Chenglin Zhou
- Clinical Laboratory Center, Taizhou People's Hospital, Hailing District, Taizhou, Jiangsu 225300, China
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Madi N, Al-Nakib W, Mustafa AS, Habibi N. Metagenomic analysis of viral diversity in respiratory samples from patients with respiratory tract infections in Kuwait. J Med Virol 2017; 90:412-420. [PMID: 29083040 PMCID: PMC7167075 DOI: 10.1002/jmv.24984] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 09/19/2017] [Accepted: 10/12/2017] [Indexed: 12/22/2022]
Abstract
A metagenomic approach based on target independent next‐generation sequencing has become a known method for the detection of both known and novel viruses in clinical samples. This study aimed to use the metagenomic sequencing approach to characterize the viral diversity in respiratory samples from patients with respiratory tract infections. We have investigated 86 respiratory samples received from various hospitals in Kuwait between 2015 and 2016 for the diagnosis of respiratory tract infections. A metagenomic approach using the next‐generation sequencer to characterize viruses was used. According to the metagenomic analysis, an average of 145, 019 reads were identified, and 2% of these reads were of viral origin. Also, metagenomic analysis of the viral sequences revealed many known respiratory viruses, which were detected in 30.2% of the clinical samples. Also, sequences of non‐respiratory viruses were detected in 14% of the clinical samples, while sequences of non‐human viruses were detected in 55.8% of the clinical samples. The average genome coverage of the viruses was 12% with the highest genome coverage of 99.2% for respiratory syncytial virus, and the lowest was 1% for torque teno midi virus 2. Our results showed 47.7% agreement between multiplex Real‐Time PCR and metagenomics sequencing in the detection of respiratory viruses in the clinical samples. Though there are some difficulties in using this method to clinical samples such as specimen quality, these observations are indicative of the promising utility of the metagenomic sequencing approach for the identification of respiratory viruses in patients with respiratory tract infections.
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Affiliation(s)
- Nada Madi
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Widad Al-Nakib
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Abu Salim Mustafa
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Nazima Habibi
- Research Core Facility and OMICS Research Unit, Faculty of Medicine, Kuwait University, Safat, Kuwait
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Ng TFF, Dill JA, Camus AC, Delwart E, Van Meir EG. Two new species of betatorqueviruses identified in a human melanoma that metastasized to the brain. Oncotarget 2017; 8:105800-105808. [PMID: 29285293 PMCID: PMC5739680 DOI: 10.18632/oncotarget.22400] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 10/25/2017] [Indexed: 12/21/2022] Open
Abstract
The role of viral infections in the etiology of brain cancer remains uncertain. Prior studies mostly focused on transcriptome or viral DNA integrated in tumor cells. To investigate for the presence of viral particles, we performed metagenomics sequencing on viral capsid-protected nucleic acids from 12 primary and 8 metastatic human brain tumors. One brain tumor metastasized from a skin melanoma harbored two new human anellovirus species, Torque teno mini virus Emory1 (TTMV Emory1) and Emory2 (TTMV Emory2), while the remaining 19 samples did not reveal any exogenous viral sequences. Their genomes share 63-67% identity with other TTMVs, and phylogenetic clustering supports their classification within the Betatorquevirus genus. This is the first identification of betatorqueviruses in brain tumors. The viral DNA was in its expected non-integrated circular form, and it is unclear if the viruses contributed to tumor formation. Whether the viruses originated from blood, or the primary skin tumor could not be ascertained. Overall, our results demonstrate the usefulness of viral metagenomics to detect previously unknown exogenous virus in human brain tumors. They further suggest that active viral infections are rare events in brain tumors, but support a follow-up larger scale study to quantify their frequency in different brain tumor subtypes.
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Affiliation(s)
- Terry Fei Fan Ng
- Blood Systems Research Institute, San Francisco, California, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California, USA.,Department of Pathology, University of Georgia, Athens, Georgia, USA.,Current/Present address: DVD, NCIRD, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jennifer A Dill
- Department of Pathology, University of Georgia, Athens, Georgia, USA
| | - Alvin C Camus
- Department of Pathology, University of Georgia, Athens, Georgia, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Erwin G Van Meir
- Departments of Neurosurgery and Hematology & Medical Oncology, Winship Cancer Institute and School of Medicine, Emory University, Atlanta, Georgia, USA
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Detection of a new species of torque teno mini virus from the gingival epithelium of patients with periodontitis. Virus Genes 2017; 53:823-830. [PMID: 28866831 DOI: 10.1007/s11262-017-1505-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 08/16/2017] [Indexed: 12/12/2022]
Abstract
We describe a novel species of torque teno mini virus called TTMV-204, which was isolated from the gingival epithelium of patients with periodontitis and characterized using viral metagenomics. The sequence of the full genome is 2824 nt in length. Phylogenetic analysis and genetic analyses show classic Betatorquevirus species organization with less than 40% amino acid similarity in ORF1. The prevalence of TTMV-204 in the periodontitis patient population was 18.75% (15/80), which was higher than in periodontally healthy individuals (10.00%, 10/80). However, the difference of the TTMV-204 prevalence between two groups was not statistically significant (p = 0.115). Further investigation is required to determine whether this new virus is associated with inflammation.
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Abbas AA, Diamond J, Chehoud C, Chang B, Kotzin J, Young J, Imai I, Haas A, Cantu E, Lederer D, Meyer K, Milewski R, Olthoff K, Shaked A, Christie J, Bushman F, Collman R. The Perioperative Lung Transplant Virome: Torque Teno Viruses Are Elevated in Donor Lungs and Show Divergent Dynamics in Primary Graft Dysfunction. Am J Transplant 2017; 17:1313-1324. [PMID: 27731934 PMCID: PMC5389935 DOI: 10.1111/ajt.14076] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/12/2016] [Accepted: 09/26/2016] [Indexed: 01/25/2023]
Abstract
Primary graft dysfunction (PGD) is a principal cause of early morbidity and mortality after lung transplantation, but its pathogenic mechanisms are not fully clarified. To date, studies using standard clinical assays have not linked microbial factors to PGD. We previously used comprehensive metagenomic methods to characterize viruses in lung allografts >1 mo after transplant and found that levels of Anellovirus, mainly torque teno viruses (TTVs), were significantly higher than in nontransplanted healthy controls. We used quantitative polymerase chain reaction to analyze TTV and shotgun metagenomics to characterize full viral communities in acellular bronchoalveolar lavage from donor organs and postreperfusion allografts in PGD and non-PGD lung transplant recipient pairs. Unexpectedly, TTV DNA levels were elevated 100-fold in donor lungs compared with healthy adults (p = 0.0026). Although absolute TTV levels did not differ by PGD status, PGD cases showed a smaller increase in TTV levels from before to after transplant than did control recipients (p = 0.041). Metagenomic sequencing revealed mainly TTV and bacteriophages of respiratory tract bacteria, but no viral taxa distinguished PGD cases from controls. These findings suggest that conditions associated with brain death promote TTV replication and that greater immune activation or tissue injury associated with PGD may restrict TTV abundance in the lung.
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Affiliation(s)
- A. A. Abbas
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J.M. Diamond
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - C. Chehoud
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - B. Chang
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J.J. Kotzin
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J.C. Young
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - I. Imai
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - A.R. Haas
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - E. Cantu
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - D.J. Lederer
- Departments of Medicine and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY
| | - K. Meyer
- School of Medicine and Public Health, University of Wisconsin, Madison, WI
| | - R.K. Milewski
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - K.M. Olthoff
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - A. Shaked
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - J.D. Christie
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - F.D. Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Corresponding authors: Frederic Bushman: , Ronald Collman:
| | - R.G. Collman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA,Corresponding authors: Frederic Bushman: , Ronald Collman:
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49
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Lempp C, Jungwirth N, Grilo ML, Reckendorf A, Ulrich A, van Neer A, Bodewes R, Pfankuche VM, Bauer C, Osterhaus ADME, Baumgärtner W, Siebert U. Pathological findings in the red fox (Vulpes vulpes), stone marten (Martes foina) and raccoon dog (Nyctereutes procyonoides), with special emphasis on infectious and zoonotic agents in Northern Germany. PLoS One 2017; 12:e0175469. [PMID: 28399176 PMCID: PMC5388480 DOI: 10.1371/journal.pone.0175469] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/27/2017] [Indexed: 11/18/2022] Open
Abstract
Anthropogenic landscape changes contributed to the reduction of availability of habitats to wild animals. Hence, the presence of wild terrestrial carnivores in urban and peri-urban sites has increased considerably over the years implying an increased risk of interspecies spillover of infectious diseases and the transmission of zoonoses. The present study provides a detailed characterisation of the health status of the red fox (Vulpes vulpes), stone marten (Martes foina) and raccoon dog (Nyctereutes procyonoides) in their natural rural and peri-urban habitats in Schleswig-Holstein, Germany between November 2013 and January 2016 with focus on zoonoses and infectious diseases that are potentially threatening to other wildlife or domestic animal species. 79 red foxes, 17 stone martens and 10 raccoon dogs were collected from traps or hunts. In order to detect morphological changes and potential infectious diseases, necropsy and pathohistological work-up was performed. Additionally, in selected animals immunohistochemistry (influenza A virus, parvovirus, feline leukemia virus, Borna disease virus, tick-borne encephalitis, canine adenovirus, Neospora caninum, Toxoplasma gondii and Listeria monocytogenes), next-generation sequencing, polymerase chain reaction (fox circovirus) and serum-neutralisation analysis (canine distemper virus) were performed. Furthermore, all animals were screened for fox rabies virus (immunofluorescence), canine distemper virus (immunohistochemistry) and Aujeszky's disease (virus cultivation). The most important findings included encephalitis (n = 16) and pneumonia (n = 20). None of the investigations revealed a specific cause for the observed morphological alterations except for one animal with an elevated serum titer of 1:160 for canine distemper. Animals displayed macroscopically and/or histopathologically detectable infections with parasites, including Taenia sp., Toxocara sp. and Alaria alata. In summary, wildlife predators carry zoonotic parasitic disease and suffer from inflammatory diseases of yet unknown etiology, possibly bearing infectious potential for other animal species and humans. This study highlights the value of monitoring terrestrial wildlife following the "One Health" notion, to estimate the incidence and the possible spread of zoonotic pathogens and to avoid animal to animal spillover as well as transmission to humans.
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Affiliation(s)
- Charlotte Lempp
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
| | - Nicole Jungwirth
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
- Center for Systems Neuroscience, Hannover, Germany
| | - Miguel L. Grilo
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Schleswig-Holstein, Germany
| | - Anja Reckendorf
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Schleswig-Holstein, Germany
| | - Arlena Ulrich
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Schleswig-Holstein, Germany
| | - Abbo van Neer
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Schleswig-Holstein, Germany
| | - Rogier Bodewes
- Department of Viroscience, The Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Vanessa M. Pfankuche
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
- Center for Systems Neuroscience, Hannover, Germany
| | - Christian Bauer
- Institute of Parasitology, Justus Liebig University Giessen, Giessen, Germany
| | - Albert D. M. E. Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
- Center for Systems Neuroscience, Hannover, Germany
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Schleswig-Holstein, Germany
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50
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Abstract
Micro-organisms and higher organisms have evolved together and interact in complex ways. Only a small percentage of microbes are inherently pathogenic. Pathogenicity, the ability of infectious agents to cause disease, must be interpreted in the context of the properties of both transmissible agent and host. Understanding this interplay is important to developing methods to prevent infection and reduce the severity of disease. The initial step in infection is usually adherence, mediated by the interaction of surface structures on the pathogen with host cell membrane proteins or carbohydrates. This often presents excellent targets for immunity. Intracellular pathogens have evolved methods to neutralize the cellular defenses that can destroy invaders.
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