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Nurmukanova V, Matsvay A, Gordukova M, Shipulin G. Square the Circle: Diversity of Viral Pathogens Causing Neuro-Infectious Diseases. Viruses 2024; 16:787. [PMID: 38793668 PMCID: PMC11126052 DOI: 10.3390/v16050787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Neuroinfections rank among the top ten leading causes of child mortality globally, even in high-income countries. The crucial determinants for successful treatment lie in the timing and swiftness of diagnosis. Although viruses constitute the majority of infectious neuropathologies, diagnosing and treating viral neuroinfections remains challenging. Despite technological advancements, the etiology of the disease remains undetermined in over half of cases. The identification of the pathogen becomes more difficult when the infection is caused by atypical pathogens or multiple pathogens simultaneously. Furthermore, the modern surge in global passenger traffic has led to an increase in cases of infections caused by pathogens not endemic to local areas. This review aims to systematize and summarize information on neuroinvasive viral pathogens, encompassing their geographic distribution and transmission routes. Emphasis is placed on rare pathogens and cases involving atypical pathogens, aiming to offer a comprehensive and structured catalog of viral agents with neurovirulence potential.
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Affiliation(s)
- Varvara Nurmukanova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Alina Matsvay
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Maria Gordukova
- G. Speransky Children’s Hospital No. 9, 123317 Moscow, Russia
| | - German Shipulin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia
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2
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Camprubí-Ferrer D, Tomazatos A, Balerdi-Sarasola L, Cobuccio LG, Van Den Broucke S, Horváth B, Van Esbroeck M, Martinez MJ, Gandasegui J, Subirà C, Saloni M, Genton B, Bottieau E, Cadar D, Muñoz J. Assessing viral metagenomics for the diagnosis of acute undifferentiated fever in returned travellers: a multicenter cohort study. J Travel Med 2024; 31:taae029. [PMID: 38381609 DOI: 10.1093/jtm/taae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/09/2024] [Accepted: 02/17/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Up to 45% of febrile returning travellers remain undiagnosed after a thorough diagnostic work-up, even at referral centres. Although metagenomic next-generation sequencing (mNGS) has emerged as a promising tool, evidence of its usefulness in imported fever is very limited. METHODS Travellers returning with fever were prospectively recruited in three referral clinics from November 2017 to November 2019. Unbiased mNGS optimised for virus detection was performed on serum samples of participants with acute undifferentiated febrile illness (AUFI), and results were compared to those obtained by reference diagnostic methods (RDM). RESULTS Among 507 returned febrile travellers, 433(85.4%) presented with AUFI. Dengue virus (n = 86) and Plasmodium spp. (n = 83) were the most common causes of fever. 103/433(23.8%) AUFI remained undiagnosed at the end of the follow-up.Metagenomic next-generation sequencing unveiled potentially pathogenic microorganisms in 196/433(38.7%) AUFI. mNGS identifications were more common in patients with a shorter duration of fever (42.3% in ≤5 days vs 28.7% in >5 days, P = 0.005). Potential causes of fever were revealed in 25/103(24.2%) undiagnosed AUFI and 5/23(21.7%) travellers with severe undiagnosed AUFI. Missed severe aetiologies included eight bacterial identifications and one co-infection of B19 parvovirus and Aspergillus spp.Additional identifications indicating possible co-infections occurred in 29/316(9.2%) travellers with AUFI, and in 11/128(8.6%) travellers with severe AUFI, who had received a diagnosis through RDM. The most common co-infections detected in severe AUFI were caused by Gram-negative bacteria. Serum mNGS was unable to detect >50% of infectious diagnoses achieved by RDM and also yielded 607 non-pathogenic identifications. DISCUSSION mNGS of serum can be a valuable diagnostic tool for selected travellers with undiagnosed AUFI or severe disease in addition to reference diagnostic techniques, especially during the first days of symptoms. Nevertheless, mNGS results interpretation presents a great challenge. Further studies evaluating the performance of mNGS using different sample types and protocols tailored to non-viral agents are needed.
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Affiliation(s)
- Daniel Camprubí-Ferrer
- International Health Department ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Spain
| | - Alexandru Tomazatos
- Bernhard Nocht Institute for Tropical Medicine, National Reference Centre for Tropical Infectious Diseases, Hamburg, Germany
| | - Leire Balerdi-Sarasola
- International Health Department ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Spain
| | - Ludovico G Cobuccio
- Center for Primary Care and Public Health, University of Lausanne, Switzerland
| | | | - Balázs Horváth
- Bernhard Nocht Institute for Tropical Medicine, National Reference Centre for Tropical Infectious Diseases, Hamburg, Germany
| | - Marjan Van Esbroeck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Miguel J Martinez
- Microbiology Department, Hospital Clínic Barcelona, Barcelona, Spain
| | - Javier Gandasegui
- International Health Department ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Spain
| | - Carme Subirà
- International Health Department ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Spain
| | - Meritxell Saloni
- International Health Department ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Spain
| | - Blaise Genton
- Center for Primary Care and Public Health, University of Lausanne, Switzerland
| | - Emmanuel Bottieau
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Dániel Cadar
- Bernhard Nocht Institute for Tropical Medicine, National Reference Centre for Tropical Infectious Diseases, Hamburg, Germany
| | - Jose Muñoz
- International Health Department ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Spain
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3
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Yeboah R, Gorman R, Acheampong HK, Nyarko-Afriyie E, Aryeetey S, Tetteh HD, Owusu M, Yeboah ES, Adade T, Bonney J, Amoako YA, El-Duah P, Obiri-Danso K, Drosten C, Phillips RO, Sylverken AA. Clinical epidemiology, determinants, and outcomes of viral encephalitis in Ghana; a cross-sectional study. PLoS One 2024; 19:e0297277. [PMID: 38346087 PMCID: PMC10861038 DOI: 10.1371/journal.pone.0297277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 01/02/2024] [Indexed: 02/15/2024] Open
Abstract
Viral encephalitis is a rare, yet severe neurological disorder. It poses a significant public health threat due to its high morbidity and mortality. Despite the disproportionate burden of the disease in impoverished African countries, the true extent of the problem remains elusive due to the scarcity of accurate diagnostic methods. The absence of timely and effective diagnostic tools, particularly Real-time Polymerase Chain Reaction, has led to misguided treatment, and an underestimation of the disease burden in Ghana. We conducted a prospective cross-sectional study to determine the viral aetiologies of encephalitis among patients presenting to a major referral hospital in Ghana from May 2019 and August 2022. The study aimed at providing a comprehensive information on the clinical epidemiology, and outcomes of viral encephalitis in Ghana. Clinical samples were collected from patients presenting with signs and symptoms of encephalitis and tested for viral agents using real-time polymerase chain reaction. We assessed the clinical epidemiology, risk factors and outcome of individuals using descriptive and logistic regression analysis. Seventy-seven (77) patients were enrolled unto the study. The participants frequently presented with fever (85.7%), seizures (80.5%), lethargy (64.9%) and headache (50.6%). Viruses were detected in 40.3% of the study participants in either cerebrospinal fluid, rectal or oral swab samples. The most frequently detected viruses were cytomegalovirus (48.4%), enteroviruses (38.7%) and HSV (29.0%). Twenty-one (27.3%) of the patients died while on hospital admission. Gender (OR = 5.70 (1.536-1.172), p = 0.01), and negative polymerase chain reaction test results were identified as significant factors associated with death. Antiviral treatment increased the chance of survival of viral encephalitis patients by 21.8%. Our results validate the crucial role of molecular tools as essential for the rapid diagnosis of viral encephalitis, enabling effective treatment and improved patient outcomes. This study contributes valuable epidemiological and clinical insight into viral encephalitis in Ghana.
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Affiliation(s)
- Richmond Yeboah
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | | | | | - Sherihane Aryeetey
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | | | - Michael Owusu
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
- Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | | | - Titus Adade
- Department of Medicine, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Joseph Bonney
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
- Emergency Medicine Directorate, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Yaw Ampem Amoako
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
- Department of Medicine, Komfo Anokye Teaching Hospital, Kumasi, Ghana
- Department of Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Philip El-Duah
- Institute of Virology, Charite, Universitätsmedizin Berlin, Berlin, Germany
| | - Kwasi Obiri-Danso
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Christian Drosten
- Institute of Virology, Charite, Universitätsmedizin Berlin, Berlin, Germany
| | - Richard Odame Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
- Department of Medicine, Komfo Anokye Teaching Hospital, Kumasi, Ghana
- Department of Medicine, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
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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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Ye HL, Zhi MF, Chen BY, Lin WZ, Li YL, Huang SJ, Zhou LJ, Xu S, Zhang J, Zhang WC, Feng Q, Duan SZ. Alterations of oral and gut viromes in hypertension and/or periodontitis. mSystems 2024; 9:e0116923. [PMID: 38108668 PMCID: PMC10804974 DOI: 10.1128/msystems.01169-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 12/19/2023] Open
Abstract
The microbiota plays an important role in both hypertension (HTN) and periodontitis (PD), and PD exacerbates the development of HTN by oral and gut microbiota. Previous studies have focused on exploring the importance of the bacteriome in HTN and PD but overlooked the impact of the virome, which is also a member of the microbiota. We collected 180 samples of subgingival plaques, saliva, and feces from a cohort of healthy subjects (nHTNnPD), subjects with HTN (HTNnPD) or PD (PDnHTN), and subjects with both HTN and PD (HTNPD). We performed metagenomic sequencing to assess the roles of the oral and gut viromes in HTN and PD. The HTNnPD, PDnHTN, and HTNPD groups all showed significantly distinct beta diversity from the nHTNnPD group in saliva. We analyzed alterations in oral and gut viral composition in HTN and/or PD and identified significantly changed viruses in each group. Many viruses across three sites were significantly associated with blood pressure and other clinical parameters. Combined with these clinical associations, we found that Gillianvirus in subgingival plaques was negatively associated with HTN and that Torbevirus in saliva was positively associated with HTN. We found that Pepyhexavirus from subgingival plaques was indicated to be transferred to the gut. We finally evaluated viral-bacterial transkingdom interactions and found that viruses and bacteria may cooperate to affect HTN and PD. Correspondingly, HTN and PD may synergize to improve communications between viruses and bacteria.IMPORTANCEPeriodontitis (PD) and hypertension (HTN) are both highly prevalent worldwide and cause serious adverse outcomes. Increasing studies have shown that PD exacerbates HTN by oral and gut microbiota. Previous studies have focused on exploring the importance of the bacteriome in HTN and PD but overlooked the impact of the virome, even though viruses are common inhabitants in humans. Alterations in oral and gut viral diversity and composition contribute to diseases. The present study, for the first time, profiled the oral and gut viromes in HTN and/or PD. We identified key indicator viruses and their clinical implications in HTN and/or PD. We also investigated interactions between viruses and bacteria. This work improved the overall understanding of the viromes in HTN and PD, providing vital insights into the role of the virome in the development of HTN and PD.
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Affiliation(s)
- Hui-Lin Ye
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Center for Stomatology, Shanghai Key Laboratory of Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Meng-Fan Zhi
- Department of Human Microbiome, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, China
| | - Bo-Yan Chen
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Center for Stomatology, Shanghai Key Laboratory of Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Wen-Zhen Lin
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Center for Stomatology, Shanghai Key Laboratory of Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Yu-Lin Li
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Center for Stomatology, Shanghai Key Laboratory of Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Shi-Jia Huang
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Center for Stomatology, Shanghai Key Laboratory of Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Lu-Jun Zhou
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Center for Stomatology, Shanghai Key Laboratory of Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Shuo Xu
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Center for Stomatology, Shanghai Key Laboratory of Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jun Zhang
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Center for Stomatology, Shanghai Key Laboratory of Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Wu-Chang Zhang
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Center for Stomatology, Shanghai Key Laboratory of Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Qiang Feng
- Department of Human Microbiome, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, China
| | - Sheng-Zhong Duan
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Center for Stomatology, Shanghai Key Laboratory of Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, China
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Lu Y, Zhang Y, Lou Z, He X, Zhang Q, Zhang Q, Zhao S, Chen H, Zhu H, Song Z, Zhang R, Ma C, Liu D. Metagenomic next-generation sequencing of cell-free DNA for the identification of viruses causing central nervous system infections. Microbiol Spectr 2024; 12:e0226423. [PMID: 38095471 PMCID: PMC10783088 DOI: 10.1128/spectrum.02264-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/22/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE This study provides significant new data on the application of metagenomic next-generation sequencing (mNGS) to clinical diagnostics of central nervous system (CNS) viral infections, which can have high mortality rates and severe sequelae. Conventional diagnostic procedures for identifying viruses can be inefficient and rely on preconceived assumptions about the pathogen, making mNGS an appealing alternative. However, the effectiveness of mNGS is affected by the presence of human DNA contamination, which can be minimized by using cell-free DNA (cfDNA) instead of whole-cell DNA (wcDNA). This multi-center retrospective study of patients with suspected viral CNS infection found that mNGS using cfDNA had a significantly lower proportion of human DNA and higher sensitivity for detecting viruses than mNGS using wcDNA. Herpesviruses, particularly VZV, were found to be the most common DNA viruses in these patients. Overall, mNGS using cfDNA is a promising complementary diagnostic method for detecting CNS viral infections.
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Affiliation(s)
- Yuying Lu
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
- Key laboratory of Microbial Molecular Biology of Hunan Province, Hunan Provincial Center for Disease Control and Prevention, Changsha, China
| | - Ye Zhang
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Zheng Lou
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Xiaomin He
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Qinghua Zhang
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Qingxia Zhang
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Shu Zhao
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Han Chen
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Haixia Zhu
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Zhi Song
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Ruxu Zhang
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Caiyu Ma
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
- Department of Neurology, The Affiliated Changsha Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Ding Liu
- Department of Neurology, The Third Xiangya Hospital of Central South University, Changsha, China
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7
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Cebriá-Mendoza M, Beamud B, Andreu-Moreno I, Arbona C, Larrea L, Díaz W, Sanjuán R, Cuevas JM. Human Anelloviruses: Influence of Demographic Factors, Recombination, and Worldwide Diversity. Microbiol Spectr 2023; 11:e0492822. [PMID: 37199659 PMCID: PMC10269794 DOI: 10.1128/spectrum.04928-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023] Open
Abstract
Anelloviruses represent the major and most diverse component of the healthy human virome, referred to as the anellome. In this study, we determined the anellome of 50 blood donors, forming two sex- and age-matched groups. Anelloviruses were detected in 86% of the donors. The number of detected anelloviruses increased with age and was approximately twice as high in men as in women. A total of 349 complete or nearly complete genomes were classified as belonging to torque teno virus (TTV), torque teno mini virus (TTMV), and torque teno midi virus (TTMDV) anellovirus genera (197, 88, and 64 sequences, respectively). Most donors had intergenus (69.8%) or intragenus (72.1%) coinfections. Despite the limited number of sequences, intradonor recombination analysis showed 6 intragenus recombination events in ORF1. As thousands of anellovirus sequences have been described recently, we finally analyzed the global diversity of human anelloviruses. Species richness and diversity were close to saturation in each anellovirus genus. Recombination was found to be the main factor promoting diversity, although its effect was significantly lower in TTV than in TTMV and TTMDV. Overall, our results suggest that differences in diversity between genera may be caused by variations in the relative contribution of recombination. IMPORTANCE Anelloviruses are the most common human infectious viruses and are considered essentially harmless. Compared to other human viruses, they are characterized by enormous diversity, and recombination is suggested to play an important role in their diversification and evolution. Here, by analyzing the composition of the plasma anellome of 50 blood donors, we find that recombination is also a determinant of viral evolution at the intradonor level. On a larger scale, analysis of anellovirus sequences currently available in databases shows that their diversity is close to saturation and differs among the three human anellovirus genera and that recombination is the main factor explaining this intergenus variability. Global characterization of anellovirus diversity could provide clues about possible associations between certain virus variants and pathologies, as well as facilitate the implementation of unbiased PCR-based detection protocols, which may be relevant for using anelloviruses as endogenous markers of immune status.
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Affiliation(s)
- María Cebriá-Mendoza
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
| | - Beatriz Beamud
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
- FISABIO-Salud Pública, Generalitat Valenciana, Valencia, Spain
| | - Iván Andreu-Moreno
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
| | - Cristina Arbona
- Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain
| | - Luís Larrea
- Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain
| | - Wladimiro Díaz
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
- Genomic and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region (FISABIO), Valencia, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
- Department of Genetics, Universitat de València, Valencia, Spain
| | - José M. Cuevas
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
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8
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Discovery and comparative genomic analysis of a novel equine anellovirus, representing the first complete Mutorquevirus genome. Sci Rep 2023; 13:3703. [PMID: 36878942 PMCID: PMC9988894 DOI: 10.1038/s41598-023-30875-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
The complete genome of a novel torque teno virus species (Torque teno equus virus 2 (TTEqV2) isolate Alberta/2018) was obtained by high-throughput sequencing (HTS) of nucleic acid extracted from the lung and liver tissue of a Quarter Horse gelding that died of nonsuppurative encephalitis in Alberta, Canada. The 2805 nucleotide circular genome is the first complete genome from the Mutorquevirus genus and has been approved as a new species by the International Committee on Taxonomy of Viruses. The genome contains several characteristic features of torque teno virus (TTV) genomes, including an ORF1 encoding a putative 631 aa capsid protein with an arginine-rich N-terminus, several rolling circle replication associated amino acid motifs, and a downstream polyadenylation signal. A smaller overlapping ORF2 encodes a protein with an amino acid motif (WX7HX3CXCX5H) which, in general, is highly conserved in TTVs and anelloviruses. The UTR contains two GC-rich tracts, two highly conserved 15 nucleotide sequences, and what appears to be an atypical TATA-box sequence also observed in two other TTV genera. Codon usage analysis of TTEqV2 and 11 other selected anelloviruses from five host species revealed a bias toward adenine ending (A3) codons in the anelloviruses, while in contrast, A3 codons were observed at a low frequency in horse and the four other associated host species examined. Phylogenetic analysis of TTV ORF1 sequences available to date shows TTEqV2 clusters with the only other currently reported member of the Mutorquevirus genus, Torque teno equus virus 1 (TTEqV1, KR902501). Genome-wide pairwise alignment of TTEqV2 and TTEqV1 shows the absence of several highly conserved TTV features within the UTR of TTEqV1, suggesting it is incomplete and TTEqV2 is the first complete genome within the genus Mutorquevirus.
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Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122048. [PMID: 36556413 PMCID: PMC9784588 DOI: 10.3390/life12122048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.
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Affiliation(s)
- Cristian Bassi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Paola Guerriero
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Marina Pierantoni
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Elisa Callegari
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Silvia Sabbioni
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-053-245-5319
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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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Jiao J, Zhang X. Post-infantile Giant Cell Hepatitis: A Literature Review and Meta-analysis. JOURNAL OF CLINICAL AND TRANSLATIONAL PATHOLOGY 2022; 2:100-107. [PMID: 37092012 PMCID: PMC10117396 DOI: 10.14218/jctp.2022.00016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Post-infantile giant cell hepatitis (PIGCH) is a rare disease entity in adults with a multifactorial etiology and widely variable clinical courses and outcomes. The factors associated with the worse outcomes of this disease entity are still unclear. We identified 68 PIGCH patients by searching PubMed and performed meta-analysis. Among the 68 patients, 32% of the cases were associated with autoimmune disorders, followed by 21% associated with viral infections, 10% with medication, and 7% with malignancy. Twenty-four percent of the patients had more than one etiological factor, and 6% had other uncommon etiologies or an etiology that could not be identified. At the time of this report, 17 patients had died of the disease (poor outcome), and 51 patients remained alive with the disease (good outcome). Compared to the patients with a good outcome, the patients with a poor outcome were characterized by older age, lower levels of platelets and albumin, higher level of total bilirubin, and a diffuse distribution pattern of giant cells in the liver. There were no differences in gender distribution, aminotransferase, alkaline phosphatase, gamma-glutamyl transferase, etiological distribution, or other histological features, including interface hepatitis, necrosis, lobular inflammation, portal inflammation, cholestasis, or fibrosis. Further studies would be needed to better understand the disease mechanisms and unmask any additional etiological factors and targeted therapies.
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Affiliation(s)
| | - Xuchen Zhang
- Correspondence to: Xuchen Zhang, Department of Pathology, Yale University School of Medicine, 310 Cedar Street, PO Box 208023, New Haven, CT 06510, United States. Tel: +1 203-785-6010, Fax: +1 203-737-2922,
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Morsli M, Lavigne JP, Drancourt M. Direct Metagenomic Diagnosis of Community-Acquired Meningitis: State of the Art. Front Microbiol 2022; 13:926240. [PMID: 35865915 PMCID: PMC9294516 DOI: 10.3389/fmicb.2022.926240] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Current routine diagnosis of community-acquired meningitis (CAM) by multiplex real-time polymerase chain reaction (RT-PCR) is limited in the number of tested pathogens and their full characterisation, requiring additional in vitro investigations to disclose genotype and antimicrobial susceptibility. We reviewed 51 studies published through December 2021 reporting metagenomic next generation sequencing (mNGS) directly applied to the cerebrospinal fluid (CSF). This approach, potentially circumventing the above-mentioned limitations, indicated 1,248 investigated patients, and 617 patients dually investigated by routine diagnosis and mNGS, in whom 116 microbes were detected, including 50 by mNGS only, nine by routine methods only, and 57 by both routine methods and mNGS. Of 217 discordant CSF findings, 103 CSF samples were documented by mNGS only, 87 CSF samples by routine methods only, and 27 CSF samples in which the pathogen identified by mNGS was different than that found using routine methods. Overall, mNGS allowed for diagnosis and genomic surveillance of CAM causative pathogens in real-time, with a cost which is competitive with current routine multiplex RT-PCR. mNGS could be implemented at point-of-care (POC) laboratories as a part of routine investigations to improve the diagnosis and molecular epidemiology of CAM, particularly in the event of failure of routine assays.
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Affiliation(s)
- Madjid Morsli
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jean Philippe Lavigne
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, Nîmes, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Laboratoire de Microbiologie, Assistance Publique-Hôpitaux de Marseille, IHU Méditerranée Infection, Marseille, France
- *Correspondence: Michel Drancourt,
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Bal A, Destras G, Sabatier M, Pichon M, Regue H, Oriol G, Gillet Y, Lina B, Brengel-Pesce K, Josset L, Morfin F. Metagenomic Analysis Reveals High Abundance of Torque Teno Mini Virus in the Respiratory Tract of Children with Acute Respiratory Illness. Viruses 2022; 14:v14050955. [PMID: 35632697 PMCID: PMC9143613 DOI: 10.3390/v14050955] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/30/2023] Open
Abstract
Human Anelloviridae is a highly prevalent viral family, including three main genera—Alphatorquevirus (Torque teno virus, TTV), Betatorquevirus (Torque teno mini virus, TTMV), and Gammatorquevirus (Torque teno midi virus, TTMDV). To date, the characterization of Anelloviridae in the respiratory tract of children with acute respiratory infection (ARI) has been poorly reported and mainly focused on TTV. We performed a metagenomic analysis of eight respiratory samples collected from children with an ARI of unknown etiology (eight samples tested negative with a multiplex PCR assay, out of the 39 samples initially selected based on negative routine diagnostic testing). A total of 19 pediatric respiratory samples that tested positive for respiratory syncytial virus (RSV, n = 13) or influenza virus (n = 6) were also sequenced. Anelloviridae reads were detected in 16/27 samples, including 6/8 negative samples, 7/13 RSV samples and 3/6 influenza samples. For samples with a detection of at least one Anelloviridae genus, TTMV represented 87.1 (66.1−99.2)% of Anelloviridae reads, while TTV and TTMDV represented 0.8 (0.0−9.6)% and 0.7 (0.0−7.1)%, respectively (p < 0.001). Our findings highlight a high prevalence of TTMV in respiratory samples of children with an ARI of unknown etiology, as well as in samples with an RSV or influenza infection. Larger studies are needed to explore the role of TTMV in childhood respiratory diseases.
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Affiliation(s)
- Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, 69004 Lyon, France; (A.B.); (G.D.); (M.S.); (B.L.)
- Univ Lyon, Université Lyon 1, CIRI, Inserm U1111 CNRS UMR5308, Virpath, 69007 Lyon, France
- GenEPII Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France;
| | - Gregory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, 69004 Lyon, France; (A.B.); (G.D.); (M.S.); (B.L.)
- Univ Lyon, Université Lyon 1, CIRI, Inserm U1111 CNRS UMR5308, Virpath, 69007 Lyon, France
- GenEPII Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France;
| | - Marina Sabatier
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, 69004 Lyon, France; (A.B.); (G.D.); (M.S.); (B.L.)
- Univ Lyon, Université Lyon 1, CIRI, Inserm U1111 CNRS UMR5308, Virpath, 69007 Lyon, France
| | - Maxime Pichon
- Bacteriology Laboratory, Infectious Agents Department, Centre Hospitalier Universitaire de Poitiers, 86021 Poitiers, France;
- Inserm U1070 Pharmacology of Antimicrobial Agents and Resistance, University of Poitiers, 86073 Poitiers, France
| | - Hadrien Regue
- GenEPII Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France;
| | - Guy Oriol
- Laboratoire Commun de Recherche HCL-bioMerieux, Centre Hospitalier Lyon Sud, 69495 Pierre-Bénite, France; (G.O.); (K.B.-P.)
| | - Yves Gillet
- Hospices Civils de Lyon, Urgences Pédiatriques, Hôpital Femme Mère Enfant, 69500 Bron, France;
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, 69004 Lyon, France; (A.B.); (G.D.); (M.S.); (B.L.)
- Univ Lyon, Université Lyon 1, CIRI, Inserm U1111 CNRS UMR5308, Virpath, 69007 Lyon, France
- GenEPII Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France;
| | - Karen Brengel-Pesce
- Laboratoire Commun de Recherche HCL-bioMerieux, Centre Hospitalier Lyon Sud, 69495 Pierre-Bénite, France; (G.O.); (K.B.-P.)
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, 69004 Lyon, France; (A.B.); (G.D.); (M.S.); (B.L.)
- Univ Lyon, Université Lyon 1, CIRI, Inserm U1111 CNRS UMR5308, Virpath, 69007 Lyon, France
- GenEPII Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France;
- Correspondence: (L.J.); (F.M.)
| | - Florence Morfin
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Hospices Civils de Lyon, 69004 Lyon, France; (A.B.); (G.D.); (M.S.); (B.L.)
- Univ Lyon, Université Lyon 1, CIRI, Inserm U1111 CNRS UMR5308, Virpath, 69007 Lyon, France
- GenEPII Platform, Institut des Agents Infectieux, Hospices Civils de Lyon, 69004 Lyon, France;
- Correspondence: (L.J.); (F.M.)
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Negrey JD, Mitani JC, Wrangham RW, Otali E, Reddy RB, Pappas TE, Grindle KA, Gern JE, Machanda ZP, Muller MN, Langergraber KE, Thompson ME, Goldberg TL. Viruses associated with ill health in wild chimpanzees. Am J Primatol 2022; 84:e23358. [PMID: 35015311 PMCID: PMC8853648 DOI: 10.1002/ajp.23358] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 02/03/2023]
Abstract
Viral infection is a major cause of ill health in wild chimpanzees (Pan troglodytes), but most evidence to date has come from conspicuous disease outbreaks with high morbidity and mortality. To examine the relationship between viral infection and ill health during periods not associated with disease outbreaks, we conducted a longitudinal study of wild eastern chimpanzees (P. t. schweinfurthii) in the Kanyawara and Ngogo communities of Kibale National Park, Uganda. We collected standardized, observational health data for 4 years and then used metagenomics to characterize gastrointestinal viromes (i.e., all viruses recovered from fecal samples) in individual chimpanzees before and during episodes of clinical disease. We restricted our analyses to viruses thought to infect mammals or primarily associated with mammals, discarding viruses associated with nonmammalian hosts. We found 18 viruses (nine of which were previously identified in this population) from at least five viral families. Viral richness (number of viruses per sample) did not vary by health status. By contrast, total viral load (normalized proportion of sequences mapping to viruses) was significantly higher in ill individuals compared with healthy individuals. Furthermore, when ill, Kanyawara chimpanzees exhibited higher viral loads than Ngogo chimpanzees, and males, but not females, exhibited higher infection rates with certain viruses and higher total viral loads as they aged. Post-hoc analyses, including the use of a machine-learning classification method, indicated that one virus, salivirus (Picornaviridae), was the main contributor to health-related and community-level variation in viral loads. Another virus, chimpanzee stool-associated virus (chisavirus; unclassified Picornavirales), was associated with ill health at Ngogo but not at Kanyawara. Chisavirus, chimpanzee adenovirus (Adenoviridae), and bufavirus (Parvoviridae) were also associated with increased age in males. Associations with sex and age are consistent with the hypothesis that nonlethal viral infections cumulatively reflect or contribute to senescence in long-lived species such as chimpanzees.
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Affiliation(s)
- Jacob D. Negrey
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Section on Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27101, USA
| | - John C. Mitani
- Department of Anthropology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Richard W. Wrangham
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | | | - Rachna B. Reddy
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Tressa E. Pappas
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Kristine A. Grindle
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Zarin P. Machanda
- Department of Anthropology, Tufts University, Medford, MA, 02155, USA
| | - Martin N. Muller
- Department of Anthropology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Kevin E. Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85287, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ, 85287, USA
| | | | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
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Ning SY, Zhou MM, Yang J, Zeng J, Wang JP. Viral metagenomics reveals two novel anelloviruses in feces of experimental rats. Virol J 2021; 18:252. [PMID: 34930331 PMCID: PMC8686219 DOI: 10.1186/s12985-021-01723-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/08/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Rodents are widely distributed and are the natural reservoirs of a diverse group of zoonotic viruses. Thus, analyzing the viral diversity harbored by rodents could assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases. Rodents are commonly used in animal testing, particularly mice and rats. Experimental rats are important animal models, and a history of pathogenic infections in these animals will directly affect the animal trial results. The pathogenicity of Anellovirus (AV) remains poorly understood due to the lack of a suitable model cell line or animal to support the viral cycle. This study aimed to discover possible anelloviruses from the virome in feces of experimental rats by viral metagenomic technique. METHODS Fecal samples were collected from 10 commercial SD rats and pooled into a sample pool and then subjected to libraries construction which was then sequenced on Illumina MiSeq platform. The sequenced reads were analyzed using viral metagenomic analysis pipeline and two novel anelloviruses (AVs) were identified from fecal sample of experimental rats. The prevalence of these two viruses was investigated by conventional PCR. RESULTS The complete genomic sequence of these two AVs were determined and fully characterized, with strain name ratane153-zj1 and ratane153-zj2. The circular genomes of ratane153-zj1 and ratane153-zj2 are 2785 nt and 1930 nt in length, respectively, and both include three ORFs. Ratane153-zj1 closely clustered with members within the genus Wawtorquevirus and formed a separate branch based on the phylogenetic tree constructed over the amino acid sequence of ORF1 of the two AVs identified in this study and other related AVs. While the complete amino acid sequences of ORF1 of ratane153-zj2 (nt 335 to 1390) had the highest sequence identity with an unclassified AV (GenBank No. ATY37438) from Chinchilla lanigera, and they clustered with one AV (GenBank No. QYD02305) belonging to the genus Etatorquevirus from Lynx rufus. Conventional PCR with two sets of specific primers designed based on the two genomes, respectively, showed that they were detectable at a low frequency in cohorts of experimental rats. CONCLUSION Our study expanded the genome diversity of AVs and provided genetic background information of viruses existed in experimental rats.
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Affiliation(s)
- Song-Yi Ning
- Joint Institute of Molecular Etiology Diagnosis, Donghai County People's Hospital, Jiangsu University, Donghai, 222300, Jiangsu, China
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Ming-Ming Zhou
- School of Nursing, Taihu University of Wuxi, Wuxi, 214063, Jiangsu, China
| | - Jie Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Jian Zeng
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Jia-Ping Wang
- Department of Clinical Laboratory, Donghai County People's Hospital, Donghai, 222300, Jiangsu, China.
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Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. MICROBIOME 2021; 9:241. [PMID: 34911583 PMCID: PMC8672519 DOI: 10.1186/s40168-021-01195-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/14/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. METHODOLOGY We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. RESULTS We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). CONCLUSIONS There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.
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Affiliation(s)
- Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Centre of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Regina E Abotsi
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Lemese Ah Tow
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lehana Thabane
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, Ontario, Canada
- Centre for Evaluation of Medicine, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicola M Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- School of Biomedical Sciences, University of Western Australia, M504, Perth, WA, 6009, Australia.
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17
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Abstract
Anelloviruses are small negative-sense single-stranded DNA viruses with genomes ranging in size from 1.6 to 3.9 kb. The family Anelloviridae comprised 14 genera before the present changes. However, in the last five years, a large number of diverse anelloviruses have been identified in various organisms. Here, we undertake a global analysis of mammalian anelloviruses whose full genome sequences have been determined and have an intact open reading frame 1 (ORF1). We established new criteria for the classification of anelloviruses, and, based on our analyses, we establish new genera and species to accommodate the unclassified anelloviruses. We also note that based on the updated species demarcation criteria, some previously assigned species (n = 10) merge with other species. Given the rate at which virus sequence data are accumulating, and with the identification of diverse anelloviruses, we acknowledge that the taxonomy will have to be dynamic and continuously evolve to accommodate new members.
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18
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Yang J, Wang H, Zhang X, Yang S, Xu H, Zhang W. Viral metagenomic identification of a novel anellovirus in blood sample of a child with atopic dermatitis. J Med Virol 2021; 93:4038-4041. [PMID: 33058155 DOI: 10.1002/jmv.26603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 12/15/2022]
Abstract
Here, using viral metagenomics, a novel anellovirus with strain name HuAV-zj-ad1 was detected in blood sample from a child with atopic dermatitis. The complete genome sequence of HuAV-zj-ad1 was determined and fully characterized. The circular genome of HuAV-zj-ad1 is 2841 nt in length and includes four polyprotein ORFs. Phylogenetic analysis and pairwise sequence comparisons based on the amino acid sequences of ORF1, ORF2, ORF3, ORF4 indicated that HuAV-zj-ad1 belonged to a novel species within the genus Betatorquevirus. Polymerase chain reaction screening results showed this anellovirus was not present 50 blood samples from normal children. Whether this novel species of anellovirus has association with a certain disease needs further study.
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Affiliation(s)
- Jie Yang
- Department of Dermatology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hao Wang
- Department of Clinical Laboratory, Huai'an Hospital, Xuzhou Medical University, Huai'an, Jiangsu, China
| | - Xiaodan Zhang
- Zhenjiang Center for Disease Prevention and Control, Zhenjiang, Jiangsu, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hui Xu
- Department of Dermatology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
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19
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Cordey S, Laubscher F, Hartley MA, Junier T, Keitel K, Docquier M, Guex N, Iseli C, Vieille G, Le Mercier P, Gleizes A, Samaka J, Mlaganile T, Kagoro F, Masimba J, Said Z, Temba H, Elbanna GH, Tapparel C, Zanella MC, Xenarios I, Fellay J, D'Acremont V, Kaiser L. Blood virosphere in febrile Tanzanian children. Emerg Microbes Infect 2021; 10:982-993. [PMID: 33929935 PMCID: PMC8171259 DOI: 10.1080/22221751.2021.1925161] [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] [Indexed: 12/16/2022]
Abstract
Viral infections are the leading cause of childhood acute febrile illnesses motivating consultation in sub-Saharan Africa. The majority of causal viruses are never identified in low-resource clinical settings as such testing is either not part of routine screening or available diagnostic tools have limited ability to detect new/unexpected viral variants. An in-depth exploration of the blood virome is therefore necessary to clarify the potential viral origin of fever in children. Metagenomic next-generation sequencing is a powerful tool for such broad investigations, allowing the detection of RNA and DNA viral genomes. Here, we describe the blood virome of 816 febrile children (<5 years) presenting at outpatient departments in Dar es Salaam over one-year. We show that half of the patients (394/816) had at least one detected virus recognized as causes of human infection/disease (13.8% enteroviruses (enterovirus A, B, C, and rhinovirus A and C), 12% rotaviruses, 11% human herpesvirus type 6). Additionally, we report the detection of a large number of viruses (related to arthropod, vertebrate or mammalian viral species) not yet known to cause human infection/disease, highlighting those who should be on the radar, deserve specific attention in the febrile paediatric population and, more broadly, for surveillance of emerging pathogens.Trial registration: ClinicalTrials.gov identifier: NCT02225769.
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Affiliation(s)
- Samuel Cordey
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.,Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Florian Laubscher
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.,Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Mary-Anne Hartley
- Centre for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland.,Intelligent Global Health, Machine Learning and Optimization Laboratory, EPFL, Lausanne, Switzerland
| | - Thomas Junier
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kristina Keitel
- Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland.,Department of Paediatric Emergency Medicine, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva, Geneva, Switzerland.,Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne and EPFL, Lausanne, Switzerland
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne and EPFL, Lausanne, Switzerland
| | - Gael Vieille
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.,Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Anne Gleizes
- SwissProt group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | | | - Frank Kagoro
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - John Masimba
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - Zamzam Said
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | | | - Gasser H Elbanna
- Intelligent Global Health, Machine Learning and Optimization Laboratory, EPFL, Lausanne, Switzerland
| | - Caroline Tapparel
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Marie-Celine Zanella
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.,Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ioannis Xenarios
- Health2030 Genome Center, Geneva, Switzerland.,Agora Center, University of Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Valérie D'Acremont
- Centre for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland.,Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.,Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
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20
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Deep viral blood metagenomics reveals extensive anellovirus diversity in healthy humans. Sci Rep 2021; 11:6921. [PMID: 33767340 PMCID: PMC7994813 DOI: 10.1038/s41598-021-86427-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023] Open
Abstract
Human blood metagenomics has revealed the presence of different types of viruses in apparently healthy subjects. By far, anelloviruses constitute the viral family that is more frequently found in human blood, although amplification biases and contaminations pose a major challenge in this field. To investigate this further, we subjected pooled plasma samples from 120 healthy donors in Spain to high-speed centrifugation, RNA and DNA extraction, random amplification, and massive parallel sequencing. Our results confirm the extensive presence of anelloviruses in such samples, which represented nearly 97% of the total viral sequence reads obtained. We assembled 114 different viral genomes belonging to this family, revealing remarkable diversity. Phylogenetic analysis of ORF1 suggested 28 potentially novel anellovirus species, 24 of which were validated by Sanger sequencing to discard artifacts. These findings underscore the importance of implementing more efficient purification procedures that enrich the viral fraction as an essential step in virome studies and question the suggested pathological role of anelloviruses.
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21
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Grinde B. Viruses belonging to Anelloviridae or Circoviridae as a possible cause of chronic fatigue. J Transl Med 2020; 18:485. [PMID: 33317538 PMCID: PMC7734913 DOI: 10.1186/s12967-020-02666-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/04/2020] [Indexed: 11/10/2022] Open
Abstract
Chronic fatigue often starts with an acute viral infection-as witnessed in the case of SARS-CoV-2-but indirect consequences of these infections are presumably the actual cause of the condition. As recently reviewed in this journal, the culprit could be a virus already present in the patient. The review covers several types of viruses, but concludes that the question is still open. The focus is on well known, pathogenic viruses for which there are ample diagnostic tools. I argue that there is one lesser-known group of viruses, the related anello- and circoviruses, which ought to be investigated. More or less everyone harbours at least one strain of these viruses in the blood, while not in the spinal fluid. They normally replicate at a low level, but their activity increases in an immune suppressed host; and there are cases where they do reach the brain. The initial infection could facilitate their access to the brain.
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Affiliation(s)
- Bjørn Grinde
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Skøyen, PO Box 222, 0213, Oslo, Norway.
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22
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Perlejewski K, Pawełczyk A, Bukowska-Ośko I, Rydzanicz M, Dzieciątkowski T, Paciorek M, Makowiecki M, Caraballo Cortés K, Grochowska M, Radkowski M, Laskus T. Search for Viral Infections in Cerebrospinal Fluid From Patients With Autoimmune Encephalitis. Open Forum Infect Dis 2020; 7:ofaa468. [PMID: 33209955 PMCID: PMC7643957 DOI: 10.1093/ofid/ofaa468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/30/2020] [Indexed: 12/19/2022] Open
Abstract
Background It has been reported that virus-mediated brain tissue damage can lead to autoimmune encephalitis (AE) characterized by the presence of antibodies against neuronal surface antigens. In the study, we investigate the presence of viruses in cerebrospinal fluid (CSF) from patients with AE using reverse transcription polymerase chain reaction (RT-PCR)/PCR and shotgun metagenomics. Methods CSF samples collected from 200 patients with encephalitis were tested for the presence of antibodies against antiglutamate receptor (NMDAR), contactin-associated protein 2 (CASPR2), glutamate receptors (type AMPA1/2), leucine-rich glioma-inactivated protein 1 (LGI1), dipeptidyl aminopeptidase-like protein 6 (DPPX), and GABA B receptor, and those found positive were further analyzed with real-time RT-PCR/PCR for common viral neuroinfections and shotgun DNA- and RNA-based metagenomics. Results Autoantibodies against neuronal cells were detected in CSF from 8 individuals (4% of all encephalitis patients): 7 (3.5%) had anti-NMDAR and 1 (0.5%) had anti-GABA B. RT-PCR/PCR identified human herpes virus type 1 (HSV-1; 300 copies/mL) and the representative of Enterovirus genus (550 copies/mL) in 1 patient each. Torque teno virus (TTV) was found in another patient using metagenomic analysis, and its presence was confirmed by specific PCR. Conclusions We detected the presence of HSV, TTV, and Enterovirus genus in CSF samples from 3 out of 8 AE patients. These findings support the concept of viral involvement in the pathogenesis of this disease.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | | | | | - Marcin Paciorek
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Michał Makowiecki
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marta Grochowska
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
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23
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Sabatier M, Bal A, Destras G, Regue H, Quéromès G, Cheynet V, Lina B, Bardel C, Brengel-Pesce K, Navratil V, Josset L. Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms 2020; 8:E1539. [PMID: 33036303 PMCID: PMC7601816 DOI: 10.3390/microorganisms8101539] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/25/2022] Open
Abstract
Viral metagenomics next-generation sequencing (mNGS) is increasingly being used to characterize the human virome. The impact of viral nucleic extraction on virome profiling has been poorly studied. Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods used for viral mNGS: two automated platforms (eMAG; MagNA Pure 24, MP24) and the manual QIAamp Viral RNA Mini Kit (QIAamp). Clinical respiratory samples (positive for Respiratory Syncytial Virus or Herpes Simplex Virus), one mock sample (including five viruses isolated from respiratory samples), and a no-template control (NTC) were extracted and processed through an mNGS workflow. QIAamp yielded a lower proportion of viral reads for both clinical and mock samples. The sample cross-contamination was higher when using MP24, with up to 36.09% of the viral reads mapping to mock viruses in the NTC (vs. 1.53% and 1.45% for eMAG and QIAamp, respectively). The highest number of viral reads mapping to bacteriophages in the NTC was found with QIAamp, suggesting reagent contamination. Our results highlight the importance of the extraction method choice for accurate virome characterization.
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Affiliation(s)
- Marina Sabatier
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Antonin Bal
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Grégory Destras
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Hadrien Regue
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
| | - Grégory Quéromès
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
| | - Valérie Cheynet
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Claire Bardel
- Université Lyon 1, Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, F-69100 Villeurbanne, France;
| | - Karen Brengel-Pesce
- Laboratoire Commun de Recherche Hospices Civils de Lyon—bioMérieux, Centre Hospitalier Lyon Sud, F-69310 Pierre-Bénite, France; (V.C.); (K.B.-P.)
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Université Claude Bernard Lyon 1, F-69000 Lyon, France;
- European Virus Bioinformatics Center, Leutragraben 1, D-07743 Jena, Germany
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France; (M.S.); (A.B.); (G.D.); (H.R.); (B.L.)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France;
- Centre National de Référence France-Sud des Virus des Infections Respiratoires, Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
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24
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Perlejewski K, Bukowska-Ośko I, Rydzanicz M, Pawełczyk A, Caraballo Cortѐs K, Osuch S, Paciorek M, Dzieciątkowski T, Radkowski M, Laskus T. Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations. Sci Rep 2020; 10:16173. [PMID: 32999423 PMCID: PMC7528011 DOI: 10.1038/s41598-020-73156-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/07/2020] [Indexed: 12/12/2022] Open
Abstract
Identification of pathogens causing viral encephalitis remains challenging, and in over 50% of cases the etiologic factor remains undetermined. Next-generation sequencing (NGS) based metagenomics has been successfully used to detect novel and rare infections, but its value for routine diagnosis of encephalitis remains unclear. The aim of the present study was to determine the sensitivity of shotgun metagenomic sequencing protocols, which include preamplification, and testing it against cerebrospinal fluid (CSF) samples from encephalitis patients. For sensitivity testing HIV and HBV positive sera were serially diluted in CSF from an uninfected patient. NGS repeatedly detected HIV and HBV sequences present at concentrations from 105 to 102 and from 105 to 10 viral copies/reaction, respectively. However, when the same protocols were applied to RT-PCR/PCR positive CSF samples from 6 patients with enteroviral encephalitis (median viral load 47 copies/ml) and 15 patients with HSV, CMV or VZV encephalitis (median viral load 148 copies/ml), only 7 (28.6%) were identified as positive. In conclusions, while NGS has the advantage of being able to identify a wide range of potential pathogens it seems to be less sensitive compared to the standard amplification-based assays in the diagnosis of encephalitis, where low viral loads are common.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland.
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of the Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortѐs
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Sylwia Osuch
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marcin Paciorek
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | | | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
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25
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Carbo EC, Buddingh EP, Karelioti E, Sidorov IA, Feltkamp MC, Borne PAVD, Verschuuren JJ, Kroes AC, Claas EC, de Vries JJ. Improved diagnosis of viral encephalitis in adult and pediatric hematological patients using viral metagenomics. J Clin Virol 2020; 130:104566. [DOI: 10.1016/j.jcv.2020.104566] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/23/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023]
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26
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Manso CF, Bibby DF, Mohamed H, Brown DWG, Zuckerman M, Mbisa JL. Enhanced Detection of DNA Viruses in the Cerebrospinal Fluid of Encephalitis Patients Using Metagenomic Next-Generation Sequencing. Front Microbiol 2020; 11:1879. [PMID: 32903437 PMCID: PMC7435129 DOI: 10.3389/fmicb.2020.01879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/16/2020] [Indexed: 12/16/2022] Open
Abstract
The long and expanding list of viral pathogens associated with causing encephalitis confounds current diagnostic procedures, and in up to 50% of cases, the etiology remains undetermined. Sequence-agnostic metagenomic next-generation sequencing (mNGS) obviates the need to specify targets in advance and thus has great potential in encephalitis diagnostics. However, the low relative abundance of viral nucleic acids in clinical specimens poses a significant challenge. Our protocol employs two novel techniques to selectively remove human material at two stages, significantly increasing the representation of viral material. Our bioinformatic workflow using open source protein- and nucleotide sequence-matching software balances sensitivity and specificity in diagnosing and characterizing any DNA viruses present. A panel of 12 cerebrospinal fluid (CSFs) from encephalitis cases was retrospectively interrogated by mNGS, with concordant results in seven of nine samples with a definitive DNA virus diagnosis, and a different herpesvirus was identified in the other two. In two samples with an inconclusive diagnosis, DNA viruses were detected and in a virus-negative sample, no viruses were detected. This assay has the potential to detect DNA virus infections in cases of encephalitis of unknown etiology and to improve the current screening tests by identifying new and emerging agents.
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Affiliation(s)
- Carmen F Manso
- Virus Reference Department, Public Health England, London, United Kingdom
| | - David F Bibby
- Virus Reference Department, Public Health England, London, United Kingdom
| | - Hodan Mohamed
- Virus Reference Department, Public Health England, London, United Kingdom
| | - David W G Brown
- Virus Reference Department, Public Health England, London, United Kingdom.,Laboratorio de Virus Respiratorios e do Sarampo, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
| | - Mark Zuckerman
- South London Specialist Virology Centre, King's College Hospital NHS Foundation Trust, London, United Kingdom
| | - Jean L Mbisa
- Virus Reference Department, Public Health England, London, United Kingdom
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Bal A, Oriol G, Josset L, Generenaz L, Sarkozy C, Sesques P, Salles G, Morfin F, Lina B, Becker J, Reynier F, Mallet F, Pachot A, Cheynet V, Brengel-Pesce K, Trouillet-Assant S. Metagenomic Investigation of Torque Teno Mini Virus-SH in Hematological Patients. Front Microbiol 2019; 10:1898. [PMID: 31620095 PMCID: PMC6759482 DOI: 10.3389/fmicb.2019.01898] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 07/31/2019] [Indexed: 11/28/2022] Open
Abstract
A new member of Anelloviridae, named torque teno mini virus (TTMV)-SH, was recently identified in the serum of three Hodgkin’s lymphoma patients suggesting that TTMV-SH may be associated with this type of hematological malignancy. We investigated by metagenomic analysis the presence of TTMV-SH-related viruses in plasma samples (n = 323) collected from patients with various hematological malignancies (multiple myeloma (MM, n = 256), non-Hodgkin’s lymphoma (NHL, n = 20), acute myeloid leukemia (n = 10)) and from healthy donors (n = 37). TTMV-SH-related strains were identified in 24 samples corresponding to four MM and one NHL patients. Phylogenic analysis revealed that the 24 isolates were close to the TTMV-SH strains previously identified, sharing 79.6–86.7% ORF1 nucleotide sequence identity. These results suggest that TTMV-SH-related viruses might be found in hematological diseases other than Hodgkin’s lymphoma. Due to the high genetic variability within Anelloviridae species, the association between a particular medical condition and a new genotype should be interpreted with caution.
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Affiliation(s)
- Antonin Bal
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France.,Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France.,CIRI, Inserm U1111 CNRS UMR5308, Virpath, Univ Lyon, Université Lyon 1, Lyon, France
| | - Guy Oriol
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Laurence Josset
- Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France.,CIRI, Inserm U1111 CNRS UMR5308, Virpath, Univ Lyon, Université Lyon 1, Lyon, France
| | - Laurence Generenaz
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Clémentine Sarkozy
- Service d'hématologie clinique, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Pierre Sesques
- Service d'hématologie clinique, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Gilles Salles
- Service d'hématologie clinique, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Florence Morfin
- Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France.,CIRI, Inserm U1111 CNRS UMR5308, Virpath, Univ Lyon, Université Lyon 1, Lyon, France
| | - Bruno Lina
- Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France.,CIRI, Inserm U1111 CNRS UMR5308, Virpath, Univ Lyon, Université Lyon 1, Lyon, France
| | - Jérémie Becker
- BIOASTER, Genomics and Transcriptomics Technological Unit, Lyon, France
| | - Frédéric Reynier
- BIOASTER, Genomics and Transcriptomics Technological Unit, Lyon, France
| | - François Mallet
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Alexandre Pachot
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Valérie Cheynet
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Karen Brengel-Pesce
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Sophie Trouillet-Assant
- Laboratoire Commun de Recherche Hospices Civils de Lyon - bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France.,CIRI, Inserm U1111 CNRS UMR5308, Virpath, Univ Lyon, Université Lyon 1, Lyon, France
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28
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Kufner V, Plate A, Schmutz S, Braun DL, Günthard HF, Capaul R, Zbinden A, Mueller NJ, Trkola A, Huber M. Two Years of Viral Metagenomics in a Tertiary Diagnostics Unit: Evaluation of the First 105 Cases. Genes (Basel) 2019; 10:genes10090661. [PMID: 31470675 PMCID: PMC6770117 DOI: 10.3390/genes10090661] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 01/28/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) can capture the full spectrum of viral pathogens in a specimen and has the potential to become an all-in-one solution for virus diagnostics. To date, clinical application is still in an early phase and limitations remain. Here, we evaluated the impact of viral mNGS for cases analyzed over two years in a tertiary diagnostics unit. High throughput mNGS was performed upon request by the treating clinician in cases where the etiology of infection remained unknown or the initial differential diagnosis was very broad. The results were compared to conventional routine testing regarding outcome and workload. In total, 163 specimens from 105 patients were sequenced. The main sample types were cerebrospinal fluid (34%), blood (33%) and throat swabs (10%). In the majority of the cases, viral encephalitis/meningitis or respiratory infection was suspected. In parallel, conventional virus diagnostic tests were performed (mean 18.5 individually probed targets/patients). mNGS detected viruses in 34 cases (32%). While often confirmatory, in multiple cases, the identified viruses were not included in the selected routine diagnostic tests. Two years of mNGS in a tertiary diagnostics unit demonstrated the advantages of a single, untargeted approach for comprehensive, rapid and efficient virus diagnostics, confirming the utility of mNGS in complementing current routine tests.
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Affiliation(s)
- Verena Kufner
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Andreas Plate
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Dominique L Braun
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Huldrych F Günthard
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Riccarda Capaul
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Andrea Zbinden
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Nicolas J Mueller
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland.
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland.
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland.
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29
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Chapman R, Rybicki EP. Use of a Novel Enhanced DNA Vaccine Vector for Preclinical Virus Vaccine Investigation. Vaccines (Basel) 2019; 7:vaccines7020050. [PMID: 31200559 PMCID: PMC6632145 DOI: 10.3390/vaccines7020050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 12/14/2022] Open
Abstract
DNA vaccines are stable, safe, and cost effective to produce and relatively quick and easy to manufacture. However, to date, DNA vaccines have shown relatively poor immunogenicity in humans despite promising preclinical results. Consequently, a number of different approaches have been investigated to improve the immunogenicity of DNA vaccines. These include the use of improved delivery methods, adjuvants, stronger promoters and enhancer elements to increase antigen expression, and codon optimization of the gene of interest. This review describes the creation and use of a DNA vaccine vector containing a porcine circovirus (PCV-1) enhancer element that significantly increases recombinant antigen expression and immunogenicity and allows for dose sparing. A 172 bp region containing the PCV-1 capsid protein promoter (Pcap) and a smaller element (PC; 70 bp) within this were found to be equally effective. DNA vaccines containing the Pcap region expressing various HIV-1 antigens were found to be highly immunogenic in mice, rabbits, and macaques at 4-10-fold lower doses than normally used and to be highly effective in heterologous prime-boost regimens. By lowering the amount of DNA used for immunization, safety concerns over injecting large amounts of DNA into humans can be overcome.
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Affiliation(s)
- Rosamund Chapman
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa.
| | - Edward P Rybicki
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa.
- Biopharming Research Unit, Department of Molecular & Cell Biology, University of Cape Town, PB X3 Rondebosch, Cape Town 7701, South Africa.
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