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Liu F, Yang X, He Z, OuYang C, Yang X, Yang C. Using Targeted Next-Generation Sequencing to Diagnose Severe Pneumonia Due to Tropheryma Whipplei and Human Metapneumovirus: A Case Report and Literature Review. Infect Drug Resist 2024; 17:1863-1868. [PMID: 38745678 PMCID: PMC11092972 DOI: 10.2147/idr.s451477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 04/17/2024] [Indexed: 05/16/2024] Open
Abstract
Background In addition to the well-known Whipple's disease (WD), Tropheryma Whipplei (TW) can also lead to acute pneumonia. There is no unified consensus on the susceptible population, pathogenesis, clinical manifestations, diagnostic criteria, and treatment options for TW pneumonia. Clinical Presentation and Intervention This is an elderly patient with multiple injuries caused by falling from a building, and was transferred to intensive care unit (ICU) for mechanical ventilation and empirical anti-infection treatment due to severe pneumonia, and then the results of targeted next-generation sequencing (tNGS) in patient's bronchoalveolar lavage fluid (BALF) suggested TW and human metapneumovirus (HMPV) infection, and after switching to anti-infective therapy for TW, the patient was successfully extubated and transferred out of the ICU. Conclusion This is the first case of using tNGS to diagnose severe pneumonia caused by TW and HMPV. We hope that our study can serve as a reference for the diagnosis and treatment of related cases in the future.
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Affiliation(s)
- Fang Liu
- Department of Intensive Care Unit, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, People’s Republic of China
| | - XuYong Yang
- Department of Pediatrics, Gaoxin Hospital of The First Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
| | - Zhaohui He
- Department of Intensive Care Unit, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, People’s Republic of China
| | - Chenghong OuYang
- Department of Intensive Care Unit, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, People’s Republic of China
| | - Xiaogang Yang
- Department of Intensive Care Unit, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, People’s Republic of China
| | - Chunli Yang
- Department of Intensive Care Unit, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, People’s Republic of China
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2
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Jitvaropas R, Sawaswong V, Poovorawan Y, Auysawasdi N, Vuthitanachot V, Wongwairot S, Rodkvamtook W, Lindroth E, Payungporn S, Linsuwanon P. Identification of Bacteria and Viruses Associated with Patients with Acute Febrile Illness in Khon Kaen Province, Thailand. Viruses 2024; 16:630. [PMID: 38675971 PMCID: PMC11054472 DOI: 10.3390/v16040630] [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: 02/28/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
The majority of cases of undifferentiated acute febrile illness (AFI) in the tropics have an undefined etiology. In Thailand, AFI accounts for two-thirds of illnesses reported to the Ministry of Public Health. To characterize the bacterial and viral causes of these AFIs, we conducted molecular pathogen screening and serological analyses in patients who sought treatment in Chum Phae Hospital, Khon Kaen province, during the period from 2015 to 2016. Through integrated approaches, we successfully identified the etiology in 25.5% of cases, with dengue virus infection being the most common cause, noted in 17% of the study population, followed by scrub typhus in 3.8% and rickettsioses in 6.8%. Further investigations targeting viruses in patients revealed the presence of Guadeloupe mosquito virus (GMV) in four patients without other pathogen co-infections. The characterization of four complete genome sequences of GMV amplified from AFI patients showed a 93-97% nucleotide sequence identity with GMV previously reported in mosquitoes. Nucleotide substitutions resulted in amino acid differences between GMV amplified from AFI patients and mosquitoes, observed in 37 positions. However, these changes had undergone purifying selection pressure and potentially had a minimal impact on protein function. Our study suggests that the GMV strains identified in the AFI patients are relatively similar to those previously reported in mosquitoes, highlighting their potential role associated with febrile illness.
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Affiliation(s)
- Rungrat Jitvaropas
- Division of Biochemistry, Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathum Thani 12120, Thailand;
| | - Vorthon Sawaswong
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Nutthanun Auysawasdi
- Department of Entomology, US Medical Directorate-Armed Forces Research Institute of Medical Science, Bangkok 10400, Thailand; (N.A.); (S.W.); (E.L.)
| | | | - Sirima Wongwairot
- Department of Entomology, US Medical Directorate-Armed Forces Research Institute of Medical Science, Bangkok 10400, Thailand; (N.A.); (S.W.); (E.L.)
| | - Wuttikon Rodkvamtook
- Analytic Division, Royal Thai Army Component-Armed Forces Research Institute of Medical Science, Bangkok 10400, Thailand;
| | - Erica Lindroth
- Department of Entomology, US Medical Directorate-Armed Forces Research Institute of Medical Science, Bangkok 10400, Thailand; (N.A.); (S.W.); (E.L.)
| | - Sunchai Payungporn
- Center of Excellence in Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Piyada Linsuwanon
- Department of Entomology, US Medical Directorate-Armed Forces Research Institute of Medical Science, Bangkok 10400, Thailand; (N.A.); (S.W.); (E.L.)
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3
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Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
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Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
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4
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Kapoor V, Briese T, Ranjan A, Donovan WM, Mansukhani MM, Chowdhary R, Lipkin WI. Validation of the VirCapSeq-VERT system for differential diagnosis, detection, and surveillance of viral infections. J Clin Microbiol 2024; 62:e0061223. [PMID: 38095845 PMCID: PMC10793283 DOI: 10.1128/jcm.00612-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/06/2023] [Indexed: 01/18/2024] Open
Abstract
IMPORTANCE Broad range assay for accurate and sensitive diagnostics.
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Affiliation(s)
- Vishal Kapoor
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Rabindranath Tagore University, Bhopal, India
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Amit Ranjan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - William M. Donovan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Mahesh M. Mansukhani
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons,Columbia University, New York, New York, USA
| | | | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons,Columbia University, New York, New York, USA
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
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5
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Pérez-Rodríguez FJ, Laubscher F, Chudzinski V, Kaiser L, Cordey S. Direct Dengue Virus Genome Sequencing from Antigen NS1 Rapid Diagnostic Tests: A Proof-of-Concept with the Standard Q Dengue Duo Assay. Viruses 2023; 15:2167. [PMID: 38005845 PMCID: PMC10674465 DOI: 10.3390/v15112167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
With nearly half of the world's population being at risk of infection, dengue virus represents a major global health issue. The use of dengue antigen rapid diagnostic tests (Ag-RDTs) represents an alternative to PCR methods for the diagnosis of acute infections since they display excellent sensitivities and specificities and can be performed outside the laboratory. The high genetic diversity of the dengue virus genome represents a challenge for vaccine development, and the progressive expansion of this virus into previously nonendemic regions justifies the implementation of a genomic surveillance program. In this proof-of-concept study, we show the feasibility of sequencing dengue virus genomes directly from positive Ag-RDT (Standard Q Dengue Duo Test assay, n = 7) cassettes stored up to 31 days at room temperature after testing. For 5 of the 7 samples, a high number of reads were obtained allowing phylogenetic analyses to be carried out to determine not only the serotypes (dengue 1, 2, 3 and 4 were detected) but also the genotypes. Furthermore, in one sample, our unbiased metagenomic next-generation sequencing approach made it possible to detect epizootic hemorrhagic disease virus sequences, an arthropod-transmitted virus in ruminants. To conclude, as such an approach requires no cold storage or freezing of samples, dengue Ag-RDTs represent a very pragmatic and robust alternative for the genomic surveillance of dengue virus.
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Affiliation(s)
- Francisco-Javier Pérez-Rodríguez
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.-J.P.-R.); (F.L.); (V.C.); (L.K.)
- Swiss Reference Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Florian Laubscher
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.-J.P.-R.); (F.L.); (V.C.); (L.K.)
| | - Valentin Chudzinski
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.-J.P.-R.); (F.L.); (V.C.); (L.K.)
| | - Laurent Kaiser
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.-J.P.-R.); (F.L.); (V.C.); (L.K.)
- Swiss Reference Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.-J.P.-R.); (F.L.); (V.C.); (L.K.)
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6
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Gauthier NPG, Chorlton SD, Krajden M, Manges AR. Agnostic Sequencing for Detection of Viral Pathogens. Clin Microbiol Rev 2023; 36:e0011922. [PMID: 36847515 PMCID: PMC10035330 DOI: 10.1128/cmr.00119-22] [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] [Indexed: 03/01/2023] Open
Abstract
The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on a priori knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.
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Affiliation(s)
- Nick P. G. Gauthier
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Mel Krajden
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Amee R. Manges
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
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7
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Dong Y, Gao Y, Chai Y, Shou S. Use of Quantitative Metagenomics Next-Generation Sequencing to Confirm Fever of Unknown Origin and Infectious Disease. Front Microbiol 2022; 13:931058. [PMID: 35859749 PMCID: PMC9289621 DOI: 10.3389/fmicb.2022.931058] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
A body temperature >38.3°C that lasts ≥3 weeks and lacks a clear diagnosis after 1 week of standard hospital examination and treatment is called "fever of unknown origin" (FUO). The main causes of FUO are infections, hematological diseases, autoimmune diseases, and other non-infectious inflammatory diseases. In recent years, quantitative metagenomics next-generation sequencing (Q-mNGS) has been used widely to detect pathogenic microorganisms, especially in the contribution of rare or new (e.g., severe acute respiratory syndrome-coronavirus-2) pathogens. This review addresses the undetermined cause of fever and its evaluation by Q-mNGS.
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Affiliation(s)
- Yuxin Dong
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Yulei Gao
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Yanfen Chai
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Songtao Shou
- Department of Emergency Medicine, Tianjin Medical University General Hospital, Tianjin, China
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8
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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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9
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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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10
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Yinda CK, Seifert SN, Macmenamin P, van Doremalen N, Kim L, Bushmaker T, de Wit E, Quinones M, Munster VJ. A Novel Field-Deployable Method for Sequencing and Analyses of Henipavirus Genomes From Complex Samples on the MinION Platform. J Infect Dis 2021; 221:S383-S388. [PMID: 31784761 DOI: 10.1093/infdis/jiz576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Viruses in the genus Henipavirus encompass 2 highly pathogenic emerging zoonotic pathogens, Hendra virus (HeV) and Nipah virus (NiV). Despite the impact on human health, there is currently limited full-genome sequence information available for henipaviruses. This lack of full-length genomes hampers our ability to understand the molecular drivers of henipavirus emergence. Furthermore, rapidly deployable viral genome sequencing can be an integral part of outbreak response and epidemiological investigations to study transmission chains. In this study, we describe the development of a reverse-transcription, long-range polymerase chain reaction (LRPCR) assay for efficient genome amplification of NiV, HeV, and a related non-pathogenic henipavirus, Cedar virus (CedPV). We then demonstrated the utility of our method by amplifying partial viral genomes from 6 HeV-infected tissue samples from Syrian hamsters and 4 tissue samples from a NiV-infected African green monkey with viral loads as low as 52 genome copies/mg. We subsequently sequenced the amplified genomes on the portable Oxford Nanopore MinION platform and analyzed the data using a newly developed field-deployable bioinformatic pipeline. Our LRPCR assay allows amplification and sequencing of 2 or 4 amplicons in semi-nested reactions. Coupled with an easy-to-use bioinformatics pipeline, this method is particularly useful in the field during outbreaks in resource-poor environments.
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Affiliation(s)
- Claude Kwe Yinda
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Stephanie N Seifert
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Philip Macmenamin
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Neeltje van Doremalen
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Lewis Kim
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Trenton Bushmaker
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Emmie de Wit
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Mariam Quinones
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Vincent J Munster
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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11
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Fernandes JF, Laubscher F, Held J, Eckerle I, Docquier M, Grobusch MP, Mordmüller B, Kaiser L, Cordey S. Unbiased metagenomic next-generation sequencing of blood from hospitalized febrile children in Gabon. Emerg Microbes Infect 2021; 9:1242-1244. [PMID: 32524907 PMCID: PMC7448917 DOI: 10.1080/22221751.2020.1772015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- José Francisco Fernandes
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital Lambaréné, Gabon.,Institut für Tropenmedizin, Eberhard Karls Universität Tübingen Tübingen, Germany.,German Center for Infection Research (DZIF) Tübingen, Germany.,Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Division of Internal Medicine, Amsterdam University Medical Centers, location AMC, University of Amsterdam Amsterdam, The Netherlands
| | - Florian Laubscher
- Division of Infectious Diseases and Laboratory of Virology, University of Geneva Hospitals Geneva, Switzerland.,University of Geneva Medical School Geneva, Switzerland
| | - Jana Held
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital Lambaréné, Gabon.,Institut für Tropenmedizin, Eberhard Karls Universität Tübingen Tübingen, Germany.,German Center for Infection Research (DZIF) Tübingen, Germany
| | - Isabella Eckerle
- Division of Infectious Diseases and Laboratory of Virology, University of Geneva Hospitals Geneva, Switzerland.,University of Geneva Medical School Geneva, Switzerland.,Geneva Centre for Emerging Viral Diseases Geneva, Switzerland
| | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva Geneva, Switzerland.,Department of Genetics and Evolution, University of Geneva Geneva, Switzerland
| | - Martin Peter Grobusch
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital Lambaréné, Gabon.,Institut für Tropenmedizin, Eberhard Karls Universität Tübingen Tübingen, Germany.,German Center for Infection Research (DZIF) Tübingen, Germany.,Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Division of Internal Medicine, Amsterdam University Medical Centers, location AMC, University of Amsterdam Amsterdam, The Netherlands
| | - Benjamin Mordmüller
- Centre de Recherches Médicales de Lambaréné (CERMEL), Albert Schweitzer Hospital Lambaréné, Gabon.,Institut für Tropenmedizin, Eberhard Karls Universität Tübingen Tübingen, Germany.,German Center for Infection Research (DZIF) Tübingen, Germany
| | - Laurent Kaiser
- Division of Infectious Diseases and Laboratory of Virology, University of Geneva Hospitals Geneva, Switzerland.,University of Geneva Medical School Geneva, Switzerland.,Geneva Centre for Emerging Viral Diseases Geneva, Switzerland
| | - Samuel Cordey
- Division of Infectious Diseases and Laboratory of Virology, University of Geneva Hospitals Geneva, Switzerland.,University of Geneva Medical School Geneva, Switzerland
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12
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Lipkin WI, Mishra N, Briese T. Screening for Viral Infections. ENCYCLOPEDIA OF VIROLOGY 2021. [PMCID: PMC7836304 DOI: 10.1016/b978-0-12-814515-9.00052-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This article reviews methods for diagnosis of viral infections including histopathology, culture, nucleic acid tests, and serology. We discuss the principles that underlie individual assays as well as their strengths and limitations. Our intent is to provide insights into selecting strategies for viral diagnosis and discovery that can be pursued by accessing more detailed and granular protocols.
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13
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Gleizes A, Laubscher F, Guex N, Iseli C, Junier T, Cordey S, Fellay J, Xenarios I, Kaiser L, Mercier PL. Virosaurus A Reference to Explore and Capture Virus Genetic Diversity. Viruses 2020; 12:v12111248. [PMID: 33139591 PMCID: PMC7693494 DOI: 10.3390/v12111248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 12/24/2022] Open
Abstract
The huge genetic diversity of circulating viruses is a challenge for diagnostic assays for emerging or rare viral diseases. High-throughput technology offers a new opportunity to explore the global virome of patients without preconception about the culpable pathogens. It requires a solid reference dataset to be accurate. Virosaurus has been designed to offer a non-biased, automatized and annotated database for clinical metagenomics studies and diagnosis. Raw viral sequences have been extracted from GenBank, and cleaned up to remove potentially erroneous sequences. Complete sequences have been identified for all genera infecting vertebrates, plants and other eukaryotes (insect, fungus, etc.). To facilitate the analysis of clinically relevant viruses, we have annotated all sequences with official and common virus names, acronym, genotypes, and genomic features (linear, circular, DNA, RNA, etc.). Sequences have been clustered to remove redundancy at 90% or 98% identity. The analysis of clustering results reveals the state of the virus genetic landscape knowledge. Because herpes and poxviruses were under-represented in complete genomes considering their potential diversity in nature, we used genes instead of complete genomes for those in Virosaurus.
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Affiliation(s)
- Anne Gleizes
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; (A.G.); (T.J.)
| | - Florian Laubscher
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (L.K.)
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; (N.G.); (C.I.)
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; (N.G.); (C.I.)
| | - Thomas Junier
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; (A.G.); (T.J.)
- Laboratory of Microbiology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Samuel Cordey
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (L.K.)
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Jacques Fellay
- Unité de Médecine de Précision, CHUV, 1015 Lausanne, Switzerland;
- School of Life Sciences, EPFL, 1015 Lausanne, Switzerland
- Host-Pathogen Genomics Laboratory, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ioannis Xenarios
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland;
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (L.K.)
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Philippe Le Mercier
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, 1011 Geneva, Switzerland
- Correspondence:
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14
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Mitchell SL, Simner PJ. Next-Generation Sequencing in Clinical Microbiology: Are We There Yet? Clin Lab Med 2020; 39:405-418. [PMID: 31383265 DOI: 10.1016/j.cll.2019.05.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Next-generation sequencing (NGS) applications have been transitioning from research tools to diagnostic methods and are becoming more commonplace in clinical microbiology laboratories. These applications include (1) whole-genome sequencing, (2) targeted next-generation sequencing methods, and (3) metagenomic next-generation sequencing. The introduction of these methods into the clinical microbiology laboratory has led to the theoretic question of "Will NGS-based methods supplant traditional methods for strain typing, identification, and antimicrobial susceptibility prediction?" The authors address this question and discuss where we are at now with clinical NGS applications for infectious diseases, what does the future hold, and at what cost?
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Affiliation(s)
- Stephanie L Mitchell
- Department of Pathology, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, 4401 Penn Avenue, Main Hospital, Floor B, #269, Pittsburgh, PA 15224, USA
| | - Patricia J Simner
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B1-193, 600 North Wolfe Street, Baltimore, MD 21287-7093, USA.
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15
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Fahsbender E, Charlys da-Costa A, Elise Gill D, Augusto de Padua Milagres F, Brustulin R, Julio Costa Monteiro F, Octavio da Silva Rego M, Soares D’Athaide Ribeiro E, Cerdeira Sabino E, Delwart E. Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus. PLoS One 2020; 15:e0229993. [PMID: 32134963 PMCID: PMC7058308 DOI: 10.1371/journal.pone.0229993] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
Plasma from patients with dengue-like symptoms was collected in 2013 to 2016 from the Brazilian states of Tocantins and Amapa. 781 samples testing negative for IgM against Dengue, Zika, and Chikungunya viruses and for flaviviruses, alphaviruses and enteroviruses RNA using RT-PCRs were analyzed using viral metagenomics. Viral particles-associated nucleic acids were enriched, randomly amplified, and deep sequenced in 102 mini-pools generating over 2 billion reads. Sequence data was analyzed for the presence of known and novel eukaryotic viral reads. Anelloviruses were detected in 80%, human pegivirus 1 in 19%, and parvovirus B19 in 17% of plasma pools. HIV and enteroviruses were detected in two pools each. Previously uncharacterized viral genomes were also identified, and their presence in single plasma samples confirmed by PCR. Chapparvovirus and ambidensovirus genomes, both in the Parvoviridae family, were partially characterized showing 33% and 34% identity in their NS1 sequences to their closest relative. Molecular surveillance using pre-existing plasma from febrile patients provides a readily scalable approach for the detection of novel, potentially emerging, viruses.
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Affiliation(s)
- Elizabeth Fahsbender
- Vitalant Research Institute, San Francisco, CA, United States of America
- UCSF Dept. of Laboratory Medicine, University of California–San Francisco, San Francisco, CA, United States of America
| | - Antonio Charlys da-Costa
- School of Medicine & Institute of Tropical Medicine, University of Sao Paulo, Infectious Disease, Sao Paulo, Brazil
| | - Danielle Elise Gill
- School of Medicine & Institute of Tropical Medicine, University of Sao Paulo, Infectious Disease, Sao Paulo, Brazil
| | - Flavio Augusto de Padua Milagres
- Public Health Laboratory State (LACEN/TO), Secretary of Health of Tocantins, Palmas, TO, Brazil
- Federal University of Tocantins, Palmas, Tocantins, Brazil
| | - Rafael Brustulin
- Public Health Laboratory State (LACEN/TO), Secretary of Health of Tocantins, Palmas, TO, Brazil
- Federal University of Tocantins, Palmas, Tocantins, Brazil
| | | | | | | | - Ester Cerdeira Sabino
- School of Medicine & Institute of Tropical Medicine, University of Sao Paulo, Infectious Disease, Sao Paulo, Brazil
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, United States of America
- UCSF Dept. of Laboratory Medicine, University of California–San Francisco, San Francisco, CA, United States of America
- * E-mail:
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16
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Balaman N, Gazi U, Imir T, Sanlidag T, Ruh E, Tosun O, Ozkul A, Taylan-Ozkan A. Serological screening of West Nile virus among blood donors in northern Cyprus. J Med Virol 2020; 92:1035-1039. [PMID: 31925797 DOI: 10.1002/jmv.25669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/07/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND West Nile virus (WNV) is a neurotropic arbovirus that can also be transmitted through blood transfusion. Even though its geographic distribution has been expanding, there has not yet been any epidemiological data on WNV in northern Cyprus. The aim of our study is to fill this gap by using donated blood samples. METHODS Samples collected from the main government hospital blood bank in Nicosia were analyzed by anti-WNV enzyme-linked immunosorbent assay (ELISA) (immunoglobulin M [IgM] and immunoglobulin G [IgG]). Seropositive samples were subjected to plaque reduction neutralization test (PRNT) for confirmation and analyzed by ELISA IgG avidity test and reverse transcription real-time polymerase chain reaction (rRT-PCR). RESULTS Of the 760 sera samples, 2 (0.3%) were IgM+ and 31 (4.1%) were IgG+. Neutralization activity was detected in none (0.0%) of the IgM+ and 26 (83.9%) of IgG+ donor specimens. ELISA IgG avidity test reported high avidity in 21 (67.7%) and low avidity in one (3.2%) IgG+ sample. PRNT-confirmed anti-WNV IgG+ samples exhibited only borderline (19.2%) or high avidity (80.8%) values. rRT-PCR results were negative for both IgM+ and IgG+ samples. CONCLUSION Anti-WNV antibodies were detected in northern Cyprus among blood donors. The establishment of preventive measures and evaluation of the geographic extent of the WNV in northern Cyprus are highly recommended.
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Affiliation(s)
- Nagat Balaman
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia, Cyprus
| | - Umut Gazi
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia, Cyprus
| | - Turgut Imir
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia, Cyprus
| | - Tamer Sanlidag
- Research Centre of Experimental Health Sciences, Near East University, Nicosia, Cyprus.,Department of Medical Microbiology, Faculty of Medicine, Celal Bayar University, Manisa, Turkey
| | - Emrah Ruh
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia, Cyprus
| | - Ozgur Tosun
- Department of Biostatistics, Faculty of Medicine, Near East University, Nicosia, Cyprus
| | - Aykut Ozkul
- Department of Virology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
| | - Aysegul Taylan-Ozkan
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia, Cyprus.,Department of Medical Microbiology, Faculty of Medicine, Hitit University, Corum, Turkey
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17
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Schibler M, Brito F, Zanella MC, Zdobnov EM, Laubscher F, L'Huillier AG, Ambrosioni J, Wagner N, Posfay-Barbe KM, Docquier M, Schiffer E, Savoldelli GL, Fournier R, Lenggenhager L, Cordey S, Kaiser L. Viral Sequences Detection by High-Throughput Sequencing in Cerebrospinal Fluid of Individuals with and without Central Nervous System Disease. Genes (Basel) 2019; 10:genes10080625. [PMID: 31431002 PMCID: PMC6723360 DOI: 10.3390/genes10080625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/12/2019] [Accepted: 08/14/2019] [Indexed: 12/16/2022] Open
Abstract
Meningitis, encephalitis, and myelitis are various forms of acute central nervous system (CNS) inflammation, which can coexist and lead to serious sequelae. Known aetiologies include infections and immune-mediated processes. Despite advances in clinical microbiology over the past decades, the cause of acute CNS inflammation remains unknown in approximately 50% of cases. High-throughput sequencing was performed to search for viral sequences in cerebrospinal fluid (CSF) samples collected from 26 patients considered to have acute CNS inflammation of unknown origin, and 10 patients with defined causes of CNS diseases. In order to better grasp the clinical significance of viral sequence data obtained in CSF, 30 patients without CNS disease who had a lumbar puncture performed during elective spinal anaesthesia were also analysed. One case of human astrovirus (HAstV)-MLB2-related meningitis and disseminated infection was identified. No other viral sequences that can easily be linked to CNS inflammation were detected. Viral sequences obtained in all patient groups are discussed. While some of them reflect harmless viral infections, others result from reagent or sample contamination, as well as index hopping. Altogether, this study highlights the potential of high-throughput sequencing in identifying previously unknown viral neuropathogens, as well as the interpretation issues related to its application in clinical microbiology.
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Affiliation(s)
- Manuel Schibler
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland.
| | - Francisco Brito
- Swiss Institute of Bioinformatics, 1206 Geneva, Switzerland
- Department of Genetic Medicine and Development, Faculty of Medicine of Geneva, 1206 Geneva, Switzerland
| | - Marie-Céline Zanella
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Evgeny M Zdobnov
- Swiss Institute of Bioinformatics, 1206 Geneva, Switzerland
- Department of Genetic Medicine and Development, Faculty of Medicine of Geneva, 1206 Geneva, Switzerland
| | - Florian Laubscher
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Arnaud G L'Huillier
- Paediatric Infectious Diseases Unit, Department of Women-Children-Teenagers, Geneva University Hospitals and Medical School, 1205 Geneva, Switzerland
| | - Juan Ambrosioni
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Noémie Wagner
- Paediatric Infectious Diseases Unit, Department of Women-Children-Teenagers, Geneva University Hospitals and Medical School, 1205 Geneva, Switzerland
| | - Klara M Posfay-Barbe
- Paediatric Infectious Diseases Unit, Department of Women-Children-Teenagers, Geneva University Hospitals and Medical School, 1205 Geneva, Switzerland
| | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva, 1206 Geneva, Switzerland
| | - Eduardo Schiffer
- Anaesthesiology Division, Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland
- Faculty of Medicine of Geneva, University of Geneva, 1205 Geneva, Switzerland
| | - Georges L Savoldelli
- Anaesthesiology Division, Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland
- Faculty of Medicine of Geneva, University of Geneva, 1205 Geneva, Switzerland
| | - Roxane Fournier
- Anaesthesiology Division, Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Lauriane Lenggenhager
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland
- Faculty of Medicine of Geneva, University of Geneva, 1205 Geneva, Switzerland
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18
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Chen F, Knutson TP, Braun E, Jiang Y, Rossow S, Marthaler DG. Semi-quantitative duplex RT-PCR reveals the low occurrence of Porcine Pegivirus and Atypical Porcine Pestivirus in diagnostic samples from the United States. Transbound Emerg Dis 2019; 66:1420-1425. [PMID: 30806022 PMCID: PMC6849716 DOI: 10.1111/tbed.13154] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/24/2019] [Accepted: 02/16/2019] [Indexed: 02/06/2023]
Abstract
Porcine Pegivirus (PPgV) and Atypical Porcine Pestivirus (APPV) are two recently identified porcine viruses. In this study, the identification of two viruses by metagenomic sequencing, and a duplex semi‐quantitative RT‐PCR was developed to detect these pathogens simultaneously. The PPgV strain Minnesota‐1/2016 had a 95.5%–96.3% nucleotide identity and clustered with the recently identified US PPgV strains, which is a distant clade from the German PPgV strains. The APPV strain Minnesota‐1/2016 shared an 87.3%–92.0% nucleotide identity with the other global APPV strains identity but only shared an 82.8%–83.0% nucleotide identity with clade II consisting of strain identified in China. Detection of both PPgV and APPV was 9.0% of the diagnostic cases. Co‐infection of PPgV and APPV was identified in 7.5% of the diagnostic cases. The occurrence and genetic characterization of PPgV and APPV further enhance our knowledge regarding these new pathogens in the United States.
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Affiliation(s)
- Fangzhou Chen
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Todd P Knutson
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Eli Braun
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Yin Jiang
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Stephanie Rossow
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Douglas G Marthaler
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
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19
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Waldvogel-Abramowski S, Taleb S, Alessandrini M, Preynat-Seauve O. Viral Metagenomics of Blood Donors and Blood-Derived Products Using Next-Generation Sequencing. Transfus Med Hemother 2019; 46:87-93. [PMID: 31191194 DOI: 10.1159/000499088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
Transfusion-transmitted infections remain a permanent threat in medicine. It keeps the burden of the past, marked by serious infections transmitted by transfusion, and is constantly threatened by emerging viruses. The global rise of immunosuppression among patients undergoing frequent transfusions exacerbates this problem. Over the past decade, criteria for donor selection have become increasingly more stringent. Although routine nucleic acid testing (NAT) for virus-specific detection has become more sensitive, these safety measures are only valuable for a limited number of select viruses. The scientific approach to this is however changing, with the goal of trying to identify infectious agents in donor units as early as possible to mitigate the risk of a clinically relevant infection. To this end, and in addition to an epidemiological surveillance of the general population, researchers are adopting new methods to discover emerging infectious agents, while simultaneously screening for an extended number of viruses in donors. Next-generation sequencing (NGS) offers the opportunity to explore the entire viral landscape in blood donors, the so-called metagenomics, to investigate severe transfusion reactions of unknown etiology. In the not too distant future, one could imagine this platform being used for routine testing of donated blood products.
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Affiliation(s)
- Sophie Waldvogel-Abramowski
- Laboratory of Immunohematology, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland.,Blood Transfusion Center, Department of Medical Specialties, Geneva University Hospitals, Geneva, Switzerland
| | - Sofiane Taleb
- Laboratory of Clinical Biology, Foch University Hospitals, Suresnes, France
| | - Marco Alessandrini
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Olivier Preynat-Seauve
- Laboratory of Therapy and Stem Cells, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland.,Department of Medical Specialties of internal Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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20
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Abstract
BacCapSeq is a method for differential diagnosis of bacterial infections and defining antimicrobial sensitivity profiles that has the potential to reduce morbidity and mortality, health care costs, and the inappropriate use of antibiotics that contributes to the development of antimicrobial resistance. We report a platform that increases the sensitivity of high-throughput sequencing for detection and characterization of bacteria, virulence determinants, and antimicrobial resistance (AMR) genes. The system uses a probe set comprised of 4.2 million oligonucleotides based on the Pathosystems Resource Integration Center (PATRIC) database, the Comprehensive Antibiotic Resistance Database (CARD), and the Virulence Factor Database (VFDB), representing 307 bacterial species that include all known human-pathogenic species, known antimicrobial resistance genes, and known virulence factors, respectively. The use of bacterial capture sequencing (BacCapSeq) resulted in an up to 1,000-fold increase in bacterial reads from blood samples and lowered the limit of detection by 1 to 2 orders of magnitude compared to conventional unbiased high-throughput sequencing, down to a level comparable to that of agent-specific real-time PCR with as few as 5 million total reads generated per sample. It detected not only the presence of AMR genes but also biomarkers for AMR that included both constitutive and differentially expressed transcripts.
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21
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Lustig Y, Sofer D, Bucris ED, Mendelson E. Surveillance and Diagnosis of West Nile Virus in the Face of Flavivirus Cross-Reactivity. Front Microbiol 2018; 9:2421. [PMID: 30369916 PMCID: PMC6194321 DOI: 10.3389/fmicb.2018.02421] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 09/21/2018] [Indexed: 01/20/2023] Open
Abstract
West Nile Virus (WNV) is an arthropod-borne flavivirus whose zoonotic cycle includes both mosquitoes and birds as amplifiers and humans and horses as dead-end hosts. In recent years WNV has been spreading globally and is currently endemic in Africa, The Middle East, India, Australia, central and southern Europe, and the Americas. Integrated surveillance schemes and environmental data aim to detect viral circulation and reduce the risk of infection for the human population emphasizing the critical role for One Health principles in public health. Approximately 20% of WNV infected patients develop West Nile Fever while in less than 1%, infection results in West Nile Neurological Disease. Currently, the diagnosis of WNV infection is primarily based on serology, since molecular identification of WNV RNA is unreliable due to the short viremia. The recent emergence of Zika virus epidemic in America and Asia has added another layer of complexity to WNV diagnosis due to significant cross-reactivity between several members of the Flaviviridae family such as Zika, dengue, Usutu, and West Nile viruses. Diagnosis is especially challenging in persons living in regions with flavivirus co-circulation as well as in travelers from WNV endemic countries traveling to Zika or dengue infected areas or vise-versa. Here, we review the recent studies implementing WNV surveillance of mosquitoes and birds within the One Health initiative. Furthermore, we discuss the utility of novel molecular methods, alongside traditional molecular and serological methods, in WNV diagnosis and epidemiological research.
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Affiliation(s)
- Yaniv Lustig
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Danit Sofer
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Efrat Dahan Bucris
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat Gan, Israel.,School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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