1
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Farr RJ, Godde N, Cowled C, Sundaramoorthy V, Green D, Stewart C, Bingham J, O'Brien CM, Dearnley M. Machine Learning Identifies Cellular and Exosomal MicroRNA Signatures of Lyssavirus Infection in Human Stem Cell-Derived Neurons. Front Cell Infect Microbiol 2022; 11:783140. [PMID: 35004351 PMCID: PMC8739477 DOI: 10.3389/fcimb.2021.783140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/07/2021] [Indexed: 12/17/2022] Open
Abstract
Despite being vaccine preventable, rabies (lyssavirus) still has a significant impact on global mortality, disproportionally affecting children under 15 years of age. This neurotropic virus is deft at avoiding the immune system while travelling through neurons to the brain. Until recently, research efforts into the role of non-coding RNAs in rabies pathogenicity and detection have been hampered by a lack of human in vitro neuronal models. Here, we utilized our previously described human stem cell-derived neural model to investigate the effect of lyssavirus infection on microRNA (miRNA) expression in human neural cells and their secreted exosomes. Conventional differential expression analysis identified 25 cellular and 16 exosomal miRNAs that were significantly altered (FDR adjusted P-value <0.05) in response to different lyssavirus strains. Supervised machine learning algorithms determined 6 cellular miRNAs (miR-99b-5p, miR-346, miR-5701, miR-138-2-3p, miR-651-5p, and miR-7977) were indicative of lyssavirus infection (100% accuracy), with the first four miRNAs having previously established roles in neuronal function, or panic and impulsivity-related behaviors. Another 4-miRNA signatures in exosomes (miR-25-3p, miR-26b-5p, miR-218-5p, miR-598-3p) can independently predict lyssavirus infected cells with >99% accuracy. Identification of these robust lyssavirus miRNA signatures offers further insight into neural lineage responses to infection and provides a foundation for utilizing exosome miRNAs in the development of next-generation molecular diagnostics for rabies.
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Affiliation(s)
- Ryan J Farr
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory at the Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Nathan Godde
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory at the Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Christopher Cowled
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity at the Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Vinod Sundaramoorthy
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory at the Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Diane Green
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory at the Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Cameron Stewart
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health and Biosecurity at the Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - John Bingham
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory at the Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Carmel M O'Brien
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing, Clayton, VIC, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | - Megan Dearnley
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australian Animal Health Laboratory at the Australian Centre for Disease Preparedness, Geelong, VIC, Australia
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2
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Barrett J, Höger A, Agnihotri K, Oakey J, Skerratt LF, Field HE, Meers J, Smith C. An unprecedented cluster of Australian bat lyssavirus in Pteropus conspicillatus indicates pre-flight flying fox pups are at risk of mass infection. Zoonoses Public Health 2020; 67:435-442. [PMID: 32311218 DOI: 10.1111/zph.12703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/21/2019] [Accepted: 03/06/2020] [Indexed: 11/29/2022]
Abstract
In November 2017, two groups of P. conspicillatus pups from separate locations in Far North Queensland presented with neurological signs consistent with Australian bat lyssavirus (ABLV) infection. These pups (n = 11) died over an 11-day period and were submitted to a government laboratory for testing where ABLV infection was confirmed. Over the next several weeks, additional ABLV cases in flying foxes in Queensland were also detected. Brain tissue from ABLV-infected flying foxes during this period, as well as archived brain tissue, was selected for next-generation sequencing. Phylogenetic analysis suggests that the two groups of pups were each infected from single sources. They were likely exposed while in crèche at night as their dams foraged. This study identifies crèche-age pups at a potentially heightened risk for mass ABLV infection.
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Affiliation(s)
- Janine Barrett
- Department of Agriculture and Fisheries, Biosecurity Queensland, Brisbane, QLD, Australia
| | - Alison Höger
- University of Queensland, Gatton, QLD, Australia
| | - Kalpana Agnihotri
- Department of Agriculture and Fisheries, Biosecurity Queensland, Brisbane, QLD, Australia
| | - Jane Oakey
- Department of Agriculture and Fisheries, Biosecurity Queensland, Brisbane, QLD, Australia
| | | | - Hume E Field
- University of Queensland, Gatton, QLD, Australia.,EcoHealth Alliance, New York, NY, USA
| | - Joanne Meers
- University of Queensland, Gatton, QLD, Australia
| | - Craig Smith
- Department of Agriculture and Fisheries, Biosecurity Queensland, Brisbane, QLD, Australia
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3
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Sundaramoorthy V, Godde N, J. Farr R, Green D, M. Haynes J, Bingham J, O’Brien CM, Dearnley M. Modelling Lyssavirus Infections in Human Stem Cell-Derived Neural Cultures. Viruses 2020; 12:E359. [PMID: 32218146 PMCID: PMC7232326 DOI: 10.3390/v12040359] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/02/2020] [Accepted: 03/20/2020] [Indexed: 12/20/2022] Open
Abstract
Rabies is a zoonotic neurological infection caused by lyssavirus that continues to result in devastating loss of human life. Many aspects of rabies pathogenesis in human neurons are not well understood. Lack of appropriate ex-vivo models for studying rabies infection in human neurons has contributed to this knowledge gap. In this study, we utilize advances in stem cell technology to characterize rabies infection in human stem cell-derived neurons. We show key cellular features of rabies infection in our human neural cultures, including upregulation of inflammatory chemokines, lack of neuronal apoptosis, and axonal transmission of viruses in neuronal networks. In addition, we highlight specific differences in cellular pathogenesis between laboratory-adapted and field strain lyssavirus. This study therefore defines the first stem cell-derived ex-vivo model system to study rabies pathogenesis in human neurons. This new model system demonstrates the potential for enabling an increased understanding of molecular mechanisms in human rabies, which could lead to improved control methods.
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Affiliation(s)
- Vinod Sundaramoorthy
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Animal Health Laboratory (AAHL), East Geelong, VIC 3219, Australia; (V.S.); (N.G.); (R.J.F.); (D.G.); (J.B.)
| | - Nathan Godde
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Animal Health Laboratory (AAHL), East Geelong, VIC 3219, Australia; (V.S.); (N.G.); (R.J.F.); (D.G.); (J.B.)
| | - Ryan J. Farr
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Animal Health Laboratory (AAHL), East Geelong, VIC 3219, Australia; (V.S.); (N.G.); (R.J.F.); (D.G.); (J.B.)
| | - Diane Green
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Animal Health Laboratory (AAHL), East Geelong, VIC 3219, Australia; (V.S.); (N.G.); (R.J.F.); (D.G.); (J.B.)
| | - John M. Haynes
- Monash Institute of Pharmaceutical Sciences, 399 Royal Parade, Parkville, VIC 3052, Australia;
| | - John Bingham
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Animal Health Laboratory (AAHL), East Geelong, VIC 3219, Australia; (V.S.); (N.G.); (R.J.F.); (D.G.); (J.B.)
| | - Carmel M. O’Brien
- CSIRO Manufacturing, Research Way, Clayton, VIC 3168, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3168, Australia
| | - Megan Dearnley
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Animal Health Laboratory (AAHL), East Geelong, VIC 3219, Australia; (V.S.); (N.G.); (R.J.F.); (D.G.); (J.B.)
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4
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Gigante CM, Dettinger L, Powell JW, Seiders M, Condori REC, Griesser R, Okogi K, Carlos M, Pesko K, Breckenridge M, Simon EMM, Chu MYJV, Davis AD, Brunt SJ, Orciari L, Yager P, Carson WC, Hartloge C, Saliki JT, Sanchez S, Deldari M, Hsieh K, Wadhwa A, Wilkins K, Peredo VY, Rabideau P, Gruhn N, Cadet R, Isloor S, Nath SS, Joseph T, Gao J, Wallace R, Reynolds M, Olson VA, Li Y. Multi-site evaluation of the LN34 pan-lyssavirus real-time RT-PCR assay for post-mortem rabies diagnostics. PLoS One 2018; 13:e0197074. [PMID: 29768505 PMCID: PMC5955534 DOI: 10.1371/journal.pone.0197074] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/25/2018] [Indexed: 12/15/2022] Open
Abstract
Rabies is a fatal zoonotic disease that requires fast, accurate diagnosis to prevent disease in an exposed individual. The current gold standard for post-mortem diagnosis of human and animal rabies is the direct fluorescent antibody (DFA) test. While the DFA test has proven sensitive and reliable, it requires high quality antibody conjugates, a skilled technician, a fluorescence microscope and diagnostic specimen of sufficient quality. The LN34 pan-lyssavirus real-time RT-PCR assay represents a strong candidate for rabies post-mortem diagnostics due to its ability to detect RNA across the diverse Lyssavirus genus, its high sensitivity, its potential for use with deteriorated tissues, and its simple, easy to implement design. Here, we present data from a multi-site evaluation of the LN34 assay in 14 laboratories. A total of 2,978 samples (1,049 DFA positive) from Africa, the Americas, Asia, Europe, and the Middle East were tested. The LN34 assay exhibited low variability in repeatability and reproducibility studies and was capable of detecting viral RNA in fresh, frozen, archived, deteriorated and formalin-fixed brain tissue. The LN34 assay displayed high diagnostic specificity (99.68%) and sensitivity (99.90%) when compared to the DFA test, and no DFA positive samples were negative by the LN34 assay. The LN34 assay produced definitive findings for 80 samples that were inconclusive or untestable by DFA; 29 were positive. Five samples were inconclusive by the LN34 assay, and only one sample was inconclusive by both tests. Furthermore, use of the LN34 assay led to the identification of one false negative and 11 false positive DFA results. Together, these results demonstrate the reliability and robustness of the LN34 assay and support a role for the LN34 assay in improving rabies diagnostics and surveillance.
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Affiliation(s)
- Crystal M. Gigante
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Lisa Dettinger
- Bureau of Laboratories, Pennsylvania Department of Health, Exton, Pennsylvania, United States of America
| | - James W. Powell
- Rabies Unit, Wisconsin State Laboratory of Hygiene, Madison, Wisconsin, United States of America
| | - Melanie Seiders
- Bureau of Laboratories, Pennsylvania Department of Health, Exton, Pennsylvania, United States of America
| | - Rene Edgar Condori Condori
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Richard Griesser
- Rabies Unit, Wisconsin State Laboratory of Hygiene, Madison, Wisconsin, United States of America
| | - Kenneth Okogi
- Rabies Laboratory, Center for Zoonotic and Vectorborne Diseases, Maryland Department of Health, Baltimore, Maryland, United States of America
| | - Maria Carlos
- Rabies Laboratory, Center for Zoonotic and Vectorborne Diseases, Maryland Department of Health, Baltimore, Maryland, United States of America
| | - Kendra Pesko
- Scientific Laboratory Division, New Mexico Department of Health, Santa Fe, New Mexico, United States of America
| | - Mike Breckenridge
- Scientific Laboratory Division, New Mexico Department of Health, Santa Fe, New Mexico, United States of America
| | - Edson Michael M. Simon
- Special Pathogens Laboratory, Department of Health, Research Institute for Tropical Medicine, Alabang Muntinlupa City, Manila, Philippines
| | - Maria Yna Joyce V. Chu
- Special Pathogens Laboratory, Department of Health, Research Institute for Tropical Medicine, Alabang Muntinlupa City, Manila, Philippines
| | - April D. Davis
- Rabies Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Scott J. Brunt
- Rabies Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Lillian Orciari
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Pamela Yager
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - William C. Carson
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Claire Hartloge
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jeremiah T. Saliki
- Athens Veterinary Diagnostic Laboratory, University of Georgia, Athens, Georgia, United States of America
| | - Susan Sanchez
- Athens Veterinary Diagnostic Laboratory, University of Georgia, Athens, Georgia, United States of America
| | - Mojgan Deldari
- California Department of Public Health, Sacramento, California, United States of America
| | - Kristina Hsieh
- California Department of Public Health, Sacramento, California, United States of America
| | - Ashutosh Wadhwa
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Kimberly Wilkins
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Veronica Yung Peredo
- Rabies section, Viral Disease, Public Health Institute of Chile, Santiago, Chile
| | - Patricia Rabideau
- Public Health Command Europe, Laboratory Sciences, Biological Analysis Division, Kirchberg Kaserne, Landstuhl, Germany
| | - Nina Gruhn
- Public Health Command Europe, Laboratory Sciences, Biological Analysis Division, Kirchberg Kaserne, Landstuhl, Germany
| | - Rolain Cadet
- Ministère de l’Agriculture, Port-au-Prince, Haiti
| | - Shrikrishna Isloor
- OIE Twinned KVAFSU-CVA-Crucell Rabies Diagnostic Laboratory, Deptartment of Veterinary Microbiology, Veterinary College, KVAFSU, Hebbal, Bangalore, India
| | - Sujith S. Nath
- OIE Twinned KVAFSU-CVA-Crucell Rabies Diagnostic Laboratory, Deptartment of Veterinary Microbiology, Veterinary College, KVAFSU, Hebbal, Bangalore, India
| | - Tomy Joseph
- Animal Health Centre, Ministry of Agriculture, Abbotsford, British Columbia, Canada
| | - Jinxin Gao
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Ryan Wallace
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Mary Reynolds
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Victoria A. Olson
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Yu Li
- Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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5
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Deubelbeiss A, Zahno ML, Zanoni M, Bruegger D, Zanoni R. Real-Time RT-PCR for the Detection of Lyssavirus Species. J Vet Med 2014; 2014:476091. [PMID: 26464934 PMCID: PMC4590848 DOI: 10.1155/2014/476091] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/19/2014] [Accepted: 09/24/2014] [Indexed: 11/17/2022] Open
Abstract
The causative agents of rabies are single-stranded, negative-sense RNA viruses in the genus Lyssavirus of Rhabdoviridae, consisting of twelve classified and three as yet unclassified species including classical rabies virus (RABV). Highly neurotropic RABV causes rapidly progressive encephalomyelitis with nearly invariable fatal outcome. Rapid and reliable diagnosis of rabies is highly relevant for public and veterinary health. Due to growing variety of the genus Lyssavirus observed, the development of suitable molecular assays for diagnosis and differentiation is challenging. This work focused on the establishment of a suitable real-time RT-PCR technique for rabies diagnosis as a complement to fluorescent antibody test and rabies tissue culture infection test as gold standard for diagnosis and confirmation. The real-time RT-PCR was adapted with the goal to detect the whole spectrum of lyssavirus species, for nine of which synthesized DNA fragments were used. For the detection of species, seven probes were developed. Serial dilutions of the rabies virus strain CVS-11 showed a 100-fold higher sensitivity of real-time PCR compared to heminested RT-PCR. Using a panel of thirty-one lyssaviruses representing four species, the suitability of the protocol could be shown. Phylogenetic analysis of the sequences obtained by heminested PCR allowed correct classification of all viruses used.
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Affiliation(s)
- A. Deubelbeiss
- Institute of Virology and Immunology, 3012 Berne, Switzerland
| | - M.-L. Zahno
- Institute of Virology and Immunology, 3012 Berne, Switzerland
| | - M. Zanoni
- Institute of Virology and Immunology, 3012 Berne, Switzerland
| | - D. Bruegger
- Institute of Virology and Immunology, 3012 Berne, Switzerland
| | - R. Zanoni
- Institute of Virology and Immunology, 3012 Berne, Switzerland
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6
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Australian bat lyssavirus infection in two horses. Vet Microbiol 2014; 173:224-31. [PMID: 25195190 DOI: 10.1016/j.vetmic.2014.07.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/11/2014] [Accepted: 07/27/2014] [Indexed: 12/25/2022]
Abstract
In May 2013, the first cases of Australian bat lyssavirus infections in domestic animals were identified in Australia. Two horses (filly-H1 and gelding-H2) were infected with the Yellow-bellied sheathtail bat (YBST) variant of Australian bat lyssavirus (ABLV). The horses presented with neurological signs, pyrexia and progressing ataxia. Intra-cytoplasmic inclusion bodies (Negri bodies) were detected in some Purkinje neurons in haematoxylin and eosin (H&E) stained sections from the brain of one of the two infected horses (H2) by histological examination. A morphological diagnosis of sub-acute moderate non-suppurative, predominantly angiocentric, meningo-encephalomyelitis of viral aetiology was made. The presumptive diagnosis of ABLV infection was confirmed by the positive testing of the affected brain tissue from (H2) in a range of laboratory tests including fluorescent antibody test (FAT) and real-time PCR targeting the nucleocapsid (N) gene. Retrospective testing of the oral swab from (H1) in the real-time PCR also returned a positive result. The FAT and immunohistochemistry (IHC) revealed an abundance of ABLV antigen throughout the examined brain sections. ABLV was isolated from the brain (H2) and oral swab/saliva (H1) in the neuroblastoma cell line (MNA). Alignment of the genome sequence revealed a 97.7% identity with the YBST ABLV strain.
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7
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Fischer M, Freuling CM, Müller T, Wegelt A, Kooi EA, Rasmussen TB, Voller K, Marston DA, Fooks AR, Beer M, Hoffmann B. Molecular double-check strategy for the identification and characterization of European Lyssaviruses. J Virol Methods 2014; 203:23-32. [PMID: 24681051 DOI: 10.1016/j.jviromet.2014.03.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 03/14/2014] [Accepted: 03/18/2014] [Indexed: 10/25/2022]
Abstract
The "gold standard" for post-mortem rabies diagnosis is the direct fluorescent antibody test (FAT). However, in the case of ante-mortem non-neural sample material or decomposed tissues, the FAT reaches its limit, and the use of molecular techniques can be advantageous. In this study, we developed and validated a reverse transcription PCR cascade protocol feasible for the classification of samples, even those for which there is no epidemiological background knowledge. This study emphasises on the most relevant European lyssaviruses. In a first step, two independent N- and L-gene based pan-lyssavirus intercalating dye assays are performed in a double-check application to increase the method's diagnostic safety. For the second step, characterization of the lyssavirus positive samples via two independent multiplex PCR-systems was performed. Both assays were probe-based, species-specific multiplex PCR-systems for Rabies virus, European bat lyssavirus type 1 and 2 as well as Bokeloh bat lyssavirus. All assays were validated successfully with a comprehensive panel of lyssavirus positive samples, as well as negative material from various host species. This double-check strategy allows for both safe and sensitive screening, detection and characterization of all lyssavirus species of humans and animals, as well as the rapid identification of currently unknown lyssaviruses in bats in Europe.
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Affiliation(s)
- Melina Fischer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Conrad M Freuling
- Institute of Molecular Biology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Thomas Müller
- Institute of Molecular Biology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Anne Wegelt
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Engbert A Kooi
- Central Veterinary Institute of Wageningen UR, Houtribweg 39, NL-8221 RA Lelystad, The Netherlands
| | - Thomas B Rasmussen
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark
| | - Katja Voller
- Animal Health & Veterinary Laboratories Agency (AHVLA, Weybridge), New Haw, Addlestone, Surrey KT15 3NB, United Kingdom
| | - Denise A Marston
- Animal Health & Veterinary Laboratories Agency (AHVLA, Weybridge), New Haw, Addlestone, Surrey KT15 3NB, United Kingdom
| | - Anthony R Fooks
- Animal Health & Veterinary Laboratories Agency (AHVLA, Weybridge), New Haw, Addlestone, Surrey KT15 3NB, United Kingdom; Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, Merseyside L69 7BE, United Kingdom
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany.
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8
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Differentiation of the seven major lyssavirus species by oligonucleotide microarray. J Clin Microbiol 2011; 50:619-25. [PMID: 22189108 DOI: 10.1128/jcm.00848-11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
An oligonucleotide microarray, LyssaChip, has been developed and verified as a highly specific diagnostic tool for differentiation of the 7 major lyssavirus species. As with conventional typing microarray methods, the LyssaChip relies on sequence differences in the 371-nucleotide region coding for the nucleoprotein. This region was amplified using nested reverse transcription-PCR primers that bind to the 7 major lyssaviruses. The LyssaChip includes 57 pairs of species typing and corresponding control oligonucleotide probes (oligoprobes) immobilized on glass slides, and it can analyze 12 samples on a single slide within 8 h. Analysis of 111 clinical brain specimens (65 from animals with suspected rabies submitted to the laboratory and 46 of butchered dog brain tissues collected from restaurants) showed that the chip method was 100% sensitive and highly consistent with the "gold standard," a fluorescent antibody test (FAT). The chip method could detect rabies virus in highly decayed brain tissues, whereas the FAT did not, and therefore the chip test may be more applicable to highly decayed brain tissues than the FAT. LyssaChip may provide a convenient and inexpensive alternative for diagnosis and differentiation of rabies and rabies-related diseases.
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9
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Moore PR, Jansen CC, Graham GC, Smith IL, Craig SB. Emerging tropical diseases in Australia. Part 3. Australian bat lyssavirus. ANNALS OF TROPICAL MEDICINE AND PARASITOLOGY 2011; 104:613-21. [PMID: 21144181 DOI: 10.1179/136485910x12851868779948] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Since its discovery in a juvenile black flying fox (Pteropus alecto) in 1996, Australian bat lyssavirus (ABLV) has become the cause of a potentially important emerging disease for health authorities in Australia, with two human deaths (one in 1996 and one in 1998) attributed to the virus in the north-eastern state of Queensland. In Australia, the virus has been isolated from all four species of flying fox found on the mainland (i.e. P. alecto, P. scapulatus, P. poliocephalus and P. conspicillatus) as well as a single species of insectivorous bat (Saccolaimus flaviventris). Australian bat lyssavirus belongs to the Lyssavirus genus and is closely related, genetically, to the type strain of Rabies virus (RABV). Clinically, patients infected with ABLV have displayed the 'classical' symptoms of rabies and a similar disease course. This similarity has led to the belief that the infection and dissemination of ABLV in the body follows the same pathways as those followed by RABV. Following the two ABLV-related deaths in Queensland, protocols based on the World Health Organization's guidelines for RABV prophylaxis were implemented and, presumably in consequence, no human infection with ABLV has been recorded since 1998. ABLV will, however, probably always have an important part to play in the health of Australians as the density of the human population in Australia and, consequently, the level of interaction between humans and flying foxes increase.
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Affiliation(s)
- P R Moore
- Public Health Virology, Queensland Health Forensic and Scientific Services, P.O. Box 594, Archerfield, Queensland, 4108, Australia.
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10
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Hoffmann B, Freuling CM, Wakeley PR, Rasmussen TB, Leech S, Fooks AR, Beer M, Müller T. Improved safety for molecular diagnosis of classical rabies viruses by use of a TaqMan real-time reverse transcription-PCR "double check" strategy. J Clin Microbiol 2010; 48:3970-8. [PMID: 20739489 PMCID: PMC3020878 DOI: 10.1128/jcm.00612-10] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 04/29/2010] [Accepted: 08/18/2010] [Indexed: 11/20/2022] Open
Abstract
To improve the diagnosis of classical rabies virus with molecular methods, a validated, ready-to-use, real-time reverse transcription-PCR (RT-PCR) assay was developed. In a first step, primers and 6-carboxyfluorescien-labeled TaqMan probes specific for rabies virus were selected from the consensus sequence of the nucleoprotein gene of 203 different rabies virus sequences derived from GenBank. The selected primer-probe combination was highly specific and sensitive. During validation using a sample set of rabies virus strains from the virus archives of the Friedrich-Loeffler-Institut (FLI; Germany), the Veterinary Laboratories Agency (VLA; United Kingdom), and the DTU National Veterinary Institute (Lindholm, Denmark), covering the global diversity of rabies virus lineages, it was shown that both the newly developed assay and a previously described one had some detection failures. This was overcome by a combined assay that detected all samples as positive. In addition, the introduction of labeled positive controls (LPC) increased the diagnostic safety of the single as well as the combined assay. Based on the newly developed, alternative assay for the detection of rabies virus and the application of LPCs, an improved diagnostic sensitivity and reliability can be ascertained for postmortem and intra vitam real-time RT-PCR analyses in rabies reference laboratories.
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Affiliation(s)
- B Hoffmann
- Institute of Diagnostic Virology, Südufer 10, 17493 Greifswald-Insel Riems, Germany.
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Wacharapluesadee S, Hemachudha T. Ante- and post-mortem diagnosis of rabies using nucleic acid-amplification tests. Expert Rev Mol Diagn 2010; 10:207-18. [PMID: 20214539 DOI: 10.1586/erm.09.85] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Sensitivity, specificity and short turn-around time nucleic acid-amplification tests (NATs) have been steadily improving. NATs have been employed in the diagnosis of rabies to distinct different strains, as well as to identify new lyssaviruses. NATs have advantages over traditional methods, such as the direct fluorescence antibody test. They can be applied to fluid samples and brain tissue that is substantially decomposed. NATs can be used as an alternative method for confirmation or exclusion of the diagnosis in a suspected rabies patient. Real-time PCR methods are more favored than conventional reverse-transcription PCR methods by several laboratories. Second-round PCR, either nested or heminested, has been used for ante-mortem diagnosis to detect low levels of RNA. This review the details obstacles in making a diagnosis, how to properly utilize NATs (sample preparation, nucleic amplification techniques, amplification targets and primer design); and interprets the results obtained in recent studies.
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Affiliation(s)
- Supaporn Wacharapluesadee
- WHO Collaborating Centre for Research and Training on Viral Zoonoses, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand, 10330.
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12
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Fooks AR, Johnson N, Freuling CM, Wakeley PR, Banyard AC, McElhinney LM, Marston DA, Dastjerdi A, Wright E, Weiss RA, Müller T. Emerging technologies for the detection of rabies virus: challenges and hopes in the 21st century. PLoS Negl Trop Dis 2009; 3:e530. [PMID: 19787037 PMCID: PMC2745658 DOI: 10.1371/journal.pntd.0000530] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The diagnosis of rabies is routinely based on clinical and epidemiological information, especially when exposures are reported in rabies-endemic countries. Diagnostic tests using conventional assays that appear to be negative, even when undertaken late in the disease and despite the clinical diagnosis, have a tendency, at times, to be unreliable. These tests are rarely optimal and entirely dependent on the nature and quality of the sample supplied. In the course of the past three decades, the application of molecular biology has aided in the development of tests that result in a more rapid detection of rabies virus. These tests enable viral strain identification from clinical specimens. Currently, there are a number of molecular tests that can be used to complement conventional tests in rabies diagnosis. Indeed the challenges in the 21st century for the development of rabies diagnostics are not of a technical nature; these tests are available now. The challenges in the 21st century for diagnostic test developers are two-fold: firstly, to achieve internationally accepted validation of a test that will then lead to its acceptance by organisations globally. Secondly, the areas of the world where such tests are needed are mainly in developing regions where financial and logistical barriers prevent their implementation. Although developing countries with a poor healthcare infrastructure recognise that molecular-based diagnostic assays will be unaffordable for routine use, the cost/benefit ratio should still be measured. Adoption of rapid and affordable rabies diagnostic tests for use in developing countries highlights the importance of sharing and transferring technology through laboratory twinning between the developed and the developing countries. Importantly for developing countries, the benefit of molecular methods as tools is the capability for a differential diagnosis of human diseases that present with similar clinical symptoms. Antemortem testing for human rabies is now possible using molecular techniques. These barriers are not insurmountable and it is our expectation that if such tests are accepted and implemented where they are most needed, they will provide substantial improvements for rabies diagnosis and surveillance. The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis.
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Affiliation(s)
- Anthony R. Fooks
- Rabies and Wildlife Zoonoses Group, Veterinary Laboratories Agency (VLA, Weybridge), WHO Collaborating Centre for the Characterisation of Rabies and Rabies-related Viruses, New Haw, Addlestone, United Kingdom
| | - Nicholas Johnson
- Rabies and Wildlife Zoonoses Group, Veterinary Laboratories Agency (VLA, Weybridge), WHO Collaborating Centre for the Characterisation of Rabies and Rabies-related Viruses, New Haw, Addlestone, United Kingdom
| | - Conrad M. Freuling
- Friedrich-Loeffler-Institute, Federal Research Institute of Animal Health, Wusterhausen, Germany
| | - Philip R. Wakeley
- Rabies and Wildlife Zoonoses Group, Veterinary Laboratories Agency (VLA, Weybridge), WHO Collaborating Centre for the Characterisation of Rabies and Rabies-related Viruses, New Haw, Addlestone, United Kingdom
| | - Ashley C. Banyard
- Rabies and Wildlife Zoonoses Group, Veterinary Laboratories Agency (VLA, Weybridge), WHO Collaborating Centre for the Characterisation of Rabies and Rabies-related Viruses, New Haw, Addlestone, United Kingdom
| | - Lorraine M. McElhinney
- Rabies and Wildlife Zoonoses Group, Veterinary Laboratories Agency (VLA, Weybridge), WHO Collaborating Centre for the Characterisation of Rabies and Rabies-related Viruses, New Haw, Addlestone, United Kingdom
| | - Denise A. Marston
- Rabies and Wildlife Zoonoses Group, Veterinary Laboratories Agency (VLA, Weybridge), WHO Collaborating Centre for the Characterisation of Rabies and Rabies-related Viruses, New Haw, Addlestone, United Kingdom
| | - Akbar Dastjerdi
- Rabies and Wildlife Zoonoses Group, Veterinary Laboratories Agency (VLA, Weybridge), WHO Collaborating Centre for the Characterisation of Rabies and Rabies-related Viruses, New Haw, Addlestone, United Kingdom
| | - Edward Wright
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Robin A. Weiss
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Thomas Müller
- Friedrich-Loeffler-Institute, Federal Research Institute of Animal Health, Wusterhausen, Germany
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13
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Philbey AW, Kirkland PD, Ross AD, Field HE, Srivastava M, Davis RJ, Love RJ. Infection with Menangle virus in flying foxes (Pteropus spp.) in Australia. Aust Vet J 2009; 86:449-54. [PMID: 18959537 DOI: 10.1111/j.1751-0813.2008.00361.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To examine flying foxes (Pteropus spp.) for evidence of infection with Menangle virus. DESIGN Clustered non-random sampling for serology, virus isolation and electron microscopy (EM). PROCEDURE Serum samples were collected from 306 Pteropus spp. in northern and eastern Australia and tested for antibodies against Menangle virus (MenV) using a virus neutralisation test (VNT). Virus isolation was attempted from tissues and faeces collected from 215 Pteropus spp. in New South Wales. Faecal samples from 68 individual Pteropus spp. and four pools of faeces were examined by transmission EM following routine negative staining and immunogold labelling. RESULTS Neutralising antibodies (VNT titres > or = 8) against MenV were detected in 46% of black flying foxes (P. alecto), 41% of grey-headed flying foxes (P. poliocephalus), 25% of spectacled flying foxes (P. conspicillatus) and 1% of little red flying foxes (P. scapulatus) in Australia. Positive sera included samples collected from P. poliocephalus in a colony adjacent to a piggery that had experienced reproductive disease caused by MenV. Virus-like particles were observed by EM in faeces from Pteropus spp. and reactivity was detected in pooled faeces and urine by immunogold EM using sera from sows that had been exposed to MenV. Attempts to isolate the virus from the faeces and tissues from Pteropus spp. were unsuccessful. CONCLUSION Serological evidence of infection with MenV was detected in Pteropus spp. in Australia. Although virus-like particles were detected in faeces, no viruses were isolated from faeces, urine or tissues of Pteropus spp.
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Affiliation(s)
- A W Philbey
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle NSW, Australia.
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Development of a TaqMan real-time RT-PCR assay for the detection of rabies virus. J Virol Methods 2008; 151:317-320. [DOI: 10.1016/j.jviromet.2008.05.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 04/17/2008] [Accepted: 05/08/2008] [Indexed: 11/23/2022]
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Abstract
Various technological developments have revitalized the approaches employed to study the disease of rabies. In particular, reverse genetics has facilitated the generation of novel viruses used to improve our understanding of the fundamental aspects of rabies virus (RABV) biology and pathogenicity and yielded novel constructs potentially useful as vaccines against rabies and other diseases. Other techniques such as high throughput methods to examine the impact of rabies virus infection on host cell gene expression and two hybrid systems to explore detailed protein-protein interactions also contribute substantially to our understanding of virus-host interactions. This review summarizes much of the increased knowledge about rabies that has resulted from such studies but acknowledges that this is still insufficient to allow rational attempts at curing those who present with clinical disease.
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Affiliation(s)
- Susan A Nadin-Davis
- Centre of Expertise for Rabies, Ottawa Laboratory (Fallowfield), Canadian Food Inspection Agency, Ottawa, ON, Canada
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