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Eshak MIY, Rubbenstroth D, Beer M, Pfaff F. Diving deep into fish bornaviruses: Uncovering hidden diversity and transcriptional strategies through comprehensive data mining. Virus Evol 2023; 9:vead062. [PMID: 38028148 PMCID: PMC10645145 DOI: 10.1093/ve/vead062] [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: 08/23/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Recently, we discovered two novel orthobornaviruses in colubrid and viperid snakes using an in silico data-mining approach. Here, we present the results of a screening of more than 100,000 nucleic acid sequence datasets of fish samples from the Sequence Read Archive (SRA) for potential bornaviral sequences. We discovered the potentially complete genomes of seven bornavirids in datasets from osteichthyans and chondrichthyans. Four of these are likely to represent novel species within the genus Cultervirus, and we propose that one genome represents a novel genus within the family of Bornaviridae. Specifically, we identified sequences of Wǔhàn sharpbelly bornavirus in sequence data from the widely used grass carp liver and kidney cell lines L8824 and CIK, respectively. A complete genome of Murray-Darling carp bornavirus was identified in sequence data from a goldfish (Carassius auratus). The newly discovered little skate bornavirus, identified in the little skate (Leucoraja erinacea) dataset, contained a novel and unusual genomic architecture (N-Vp1-Vp2-X-P-G-M-L), as compared to other bornavirids. Its genome is thought to encode two additional open reading frames (tentatively named Vp1 and Vp2), which appear to represent ancient duplications of the gene encoding the viral glycoprotein (G). The datasets also provided insights into the possible transcriptional gradients of these bornavirids and revealed previously unknown splicing mechanisms.
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Affiliation(s)
- Mirette I Y Eshak
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Südufer 10, Greifswald—Insel Riems 17493, Germany
| | - Dennis Rubbenstroth
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Südufer 10, Greifswald—Insel Riems 17493, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Südufer 10, Greifswald—Insel Riems 17493, Germany
| | - Florian Pfaff
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Südufer 10, Greifswald—Insel Riems 17493, Germany
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2
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Blasdell KR, Davis SS, Voysey R, Bulach DM, Middleton D, Williams S, Harmsen MB, Weir RP, Crameri S, Walsh SJ, Peck GR, Tesh RB, Boyle DB, Melville LF, Walker PJ. Hayes Yard virus: a novel ephemerovirus isolated from a bull with severe clinical signs of bovine ephemeral fever is most closely related to Puchong virus. Vet Res 2020; 51:58. [PMID: 32349781 PMCID: PMC7191811 DOI: 10.1186/s13567-020-00781-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/06/2020] [Indexed: 01/05/2023] Open
Abstract
Bovine ephemeral fever is a vector-borne disease of ruminants that occurs in tropical and sub-tropical regions of Africa, Asia and Australia. The disease is caused by a rhabdovirus, bovine ephemeral fever virus (BEFV), which occurs as a single serotype globally. Although several other closely related ephemeroviruses have been isolated from cattle and/or arthropods, only kotonkan virus from Nigeria and (tentatively) Mavingoni virus from Mayotte Island in the Indian Ocean have been previously associated with febrile disease. Here, we report the isolation of a novel virus (Hayes Yard virus; HYV) from blood collected in February 2000 from a bull (Bos indicus) in the Northern Territory of Australia. The animal was suffering from a severe ephemeral fever-like illness with neurological involvement, including recumbency and paralysis, and was euthanised. Histological examination of spinal cord and lung tissue identified extensive haemorrhage in the dura mata with moderate perineuronal oedema and extensive emphysema. HYV displayed cone-shaped morphology, typical of rhabdoviruses, and was found to be most closely related antigenically to Puchong virus (PUCV), isolated in 1965 from mosquitoes in Malaysia. Analysis of complete genome sequences of HYV (15 025 nt) and PUCV (14 932 nt) indicated that each has a complex organisation (3' N-P-M-G-GNS-α1-α2-β-γ-L 5') and expression strategy, similar to that of BEFV. Based on an alignment of complete L protein sequences, HYV and PUCV cluster with other rhabdoviruses in the genus Ephemerovirus and appear to represent two new species. Neutralising antibody to HYV was also detected in a retrospective survey of cattle sera collected in the Northern Territory.
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Affiliation(s)
- Kim R Blasdell
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.
| | - Steven S Davis
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Darwin, NT, Australia.,Timor-Leste Office, Menzies School of Health Research, Dili, Timor-Leste
| | - Rhonda Voysey
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Dieter M Bulach
- Melbourne Bioinformatics, The University of Melbourne, Carlton, VIC, 3053, Australia
| | - Deborah Middleton
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Sinead Williams
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Margaret B Harmsen
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Darwin, NT, Australia
| | - Richard P Weir
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Darwin, NT, Australia
| | - Sandra Crameri
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Susan J Walsh
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Darwin, NT, Australia
| | - Grantley R Peck
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Robert B Tesh
- Center for Biodefense and Emerging Infectious Diseases, Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - David B Boyle
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Lorna F Melville
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Darwin, NT, Australia
| | - Peter J Walker
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.,School of Chemistry and Biomolecular Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
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3
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Vasilakis N, Tesh RB, Popov VL, Widen SG, Wood TG, Forrester NL, Gonzalez JP, Saluzzo JF, Alkhovsky S, Lam SK, Mackenzie JS, Walker PJ. Exploiting the Legacy of the Arbovirus Hunters. Viruses 2019; 11:E471. [PMID: 31126128 PMCID: PMC6563318 DOI: 10.3390/v11050471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 12/13/2022] Open
Abstract
In recent years, it has become evident that a generational gap has developed in the community of arbovirus research. This apparent gap is due to the dis-investment of training for the next generation of arbovirologists, which threatens to derail the rich history of virus discovery, field epidemiology, and understanding of the richness of diversity that surrounds us. On the other hand, new technologies have resulted in an explosion of virus discovery that is constantly redefining the virosphere and the evolutionary relationships between viruses. This paradox presents new challenges that may have immediate and disastrous consequences for public health when yet to be discovered arboviruses emerge. In this review we endeavor to bridge this gap by providing a historical context for the work being conducted today and provide continuity between the generations. To this end, we will provide a narrative of the thrill of scientific discovery and excitement and the challenges lying ahead.
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Affiliation(s)
- Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Robert B Tesh
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Vsevolod L Popov
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Steve G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston TX 77555, USA.
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston TX 77555, USA.
| | - Naomi L Forrester
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Jean Paul Gonzalez
- Center of Excellence for Emerging & Zoonotic Animal Disease, Kansas State University, Manhattan, KS 66502, USA.
| | | | - Sergey Alkhovsky
- Ivanovsky Institute of Virology, N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, 123098, 18 Gamaleya str., Moscow, Russia.
| | - Sai Kit Lam
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - John S Mackenzie
- Faculty of Medical Sciences, Curtin University, Perth, Western Australia 6102, Australia.
| | - Peter J Walker
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia.
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4
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Amarasinghe GK, Bào Y, Basler CF, Bavari S, Beer M, Bejerman N, Blasdell KR, Bochnowski A, Briese T, Bukreyev A, Calisher CH, Chandran K, Collins PL, Dietzgen RG, Dolnik O, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Fang Q, Formenty P, Fouchier RAM, Ghedin E, Harding RM, Hewson R, Higgins CM, Hong J, Horie M, James AP, Jiāng D, Kobinger GP, Kondo H, Kurath G, Lamb RA, Lee B, Leroy EM, Li M, Maisner A, Mühlberger E, Netesov SV, Nowotny N, Patterson JL, Payne SL, Paweska JT, Pearson MN, Randall RE, Revill PA, Rima BK, Rota P, Rubbenstroth D, Schwemmle M, Smither SJ, Song Q, Stone DM, Takada A, Terregino C, Tesh RB, Tomonaga K, Tordo N, Towner JS, Vasilakis N, Volchkov VE, Wahl-Jensen V, Walker PJ, Wang B, Wang D, Wang F, Wang LF, Werren JH, Whitfield AE, Yan Z, Ye G, Kuhn JH. Taxonomy of the order Mononegavirales: update 2017. Arch Virol 2017; 162:2493-2504. [PMID: 28389807 PMCID: PMC5831667 DOI: 10.1007/s00705-017-3311-7] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 02/26/2017] [Indexed: 12/11/2022]
Abstract
In 2017, the order Mononegavirales was expanded by the inclusion of a total of 69 novel species. Five new rhabdovirus genera and one new nyamivirus genus were established to harbor 41 of these species, whereas the remaining new species were assigned to already established genera. Furthermore, non-Latinized binomial species names replaced all paramyxovirus and pneumovirus species names, thereby accomplishing application of binomial species names throughout the entire order. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yīmíng Bào
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Nicolás Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Kim R Blasdell
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Alisa Bochnowski
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Alexander Bukreyev
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Charles H Calisher
- Arthropod-Borne and Infectious Diseases Laboratory, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Peter L Collins
- Respiratory Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | | | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Qi Fang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhèjiāng University, Hángzhōu, China
| | | | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Robert M Harding
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Roger Hewson
- Public Health England, Porton Down, Wiltshire, Salisbury, UK
| | - Colleen M Higgins
- Institute of Applied Ecology, School of Science, Auckland University of Technology, Auckland, New Zealand
- AUT Roche Diagnostic Laboratory, Auckland University of Technology, Auckland, New Zealand
| | - Jian Hong
- Analysis Center of Agrobiology and Environmental Sciences and Institute of Agrobiology and Environmental Sciences, Zhèjiāng University, Hángzhōu, China
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Anthony P James
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology of Húběi Province, College of Plant Science and Technology, Huázhōng Agricultural University, Wǔhàn, China
| | - Gary P Kobinger
- Department of Microbiology, Immunology and Infectious Diseases Université Laval, Quebec City, Canada
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, Washington, USA
| | - Robert A Lamb
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Howard Hughes Medical Institute, Northwestern University, Evanston, IL, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric M Leroy
- Centre International de Recherches Médicales de Franceville, Institut de Recherche pour le Développement, Franceville, Gabon
| | - Ming Li
- Institute of Applied Ecology, School of Science, Auckland University of Technology, Auckland, New Zealand
- AUT Roche Diagnostic Laboratory, Auckland University of Technology, Auckland, New Zealand
| | - Andrea Maisner
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Elke Mühlberger
- Department of Microbiology and, National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine, Vienna, Austria
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Jean L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Susan L Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Janusz T Paweska
- Center for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, Gauteng, South Africa
| | - Michael N Pearson
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Rick E Randall
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Scotland, UK
| | - Peter A Revill
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
- Victorian Infectious Diseases Reference Laboratory, Doherty Institute of Infection and Immunity, Melbourne, Victoria, Australia
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dennis Rubbenstroth
- Institute for Virology, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Schwemmle
- Institute for Virology, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sophie J Smither
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, UK
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Ayato Takada
- Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Calogero Terregino
- Istituto Zooprofilattico Sperimentale delle Venezie, Department of Comparative Biomedical Sciences, National/OIE Reference Laboratory for Newcastle Disease and Avian Influenza, FAO Reference Centre for Animal Influenza and Newcastle Disease, OIE Collaborating Centre for Diseases at the Human-Animal Interface, Legnaro, Padova, Italy
| | - Robert B Tesh
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Keizo Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur, Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV and CCHFV, Paris, France
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Viktor E Volchkov
- Molecular Basis of Viral Pathogenicity, CIRIINSERM U1111 - CNRS UMR5308, Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Victoria Wahl-Jensen
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Biological Sciences, University of Queensland, St. Lucia, QLD, Australia
| | - Beibei Wang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhèjiāng University, Hángzhōu, China
| | - David Wang
- Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Fei Wang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhèjiāng University, Hángzhōu, China
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, USA
| | | | - Zhichao Yan
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhèjiāng University, Hángzhōu, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhèjiāng University, Hángzhōu, China
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA.
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5
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Gubala A, Walsh S, McAllister J, Weir R, Davis S, Melville L, Mitchell I, Bulach D, Gauci P, Skvortsov A, Boyle D. Identification of very small open reading frames in the genomes of Holmes Jungle virus, Ord River virus, and Wongabel virus of the genus Hapavirus, family Rhabdoviridae. Evol Bioinform Online 2017; 13:1176934317713484. [PMID: 28747815 PMCID: PMC5510769 DOI: 10.1177/1176934317713484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/05/2017] [Indexed: 12/11/2022] Open
Abstract
Viruses of the family Rhabdoviridae infect a broad range of hosts from a variety of ecological and geographical niches, including vertebrates, arthropods, and plants. The arthropod-transmitted members of this family display considerable genetic diversity and remarkable genomic flexibility that enable coding for various accessory proteins in different locations of the genome. Here, we describe the genome of Holmes Jungle virus, isolated from Culex annulirostris mosquitoes collected in northern Australia, and make detailed comparisons with the closely related Ord River and Wongabel viruses, with a focus on identifying very small open reading frames (smORFs) in their genomes. This is the first systematic prediction of smORFs in rhabdoviruses, emphasising the intricacy of the rhabdovirus genome and the knowledge gaps. We speculate that these smORFs may be of importance to the life cycle of the virus in the arthropod vector.
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Affiliation(s)
- Aneta Gubala
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Susan Walsh
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Jane McAllister
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Richard Weir
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Steven Davis
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Lorna Melville
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Ian Mitchell
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Dieter Bulach
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC, Australia
| | - Penny Gauci
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Alex Skvortsov
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - David Boyle
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC, Australia
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6
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Simo Tchetgna HD, Nakoune E, Selekon B, Gessain A, Manuguerra JC, Kazanji M, Berthet N. Molecular Characterization of the Kamese Virus, an Unassigned Rhabdovirus, Isolated from Culex pruina in the Central African Republic. Vector Borne Zoonotic Dis 2017; 17:447-451. [PMID: 28350284 DOI: 10.1089/vbz.2016.2068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Rhabdoviridae is one of the most diversified families of RNA viruses whose members infect a wide range of plants, animals, and arthropods. The members of this family are classified into 13 genera and >150 unassigned viruses. Here, we sequenced the complete genome of a rhabdovirus belonging to the Hart Park serogroup, the Kamese virus (KAMV), isolated in 1977 from Culex pruina in the Central African Republic. The genomic sequence showed an organization typical of rhabdoviruses with additional genes in the P-M and G-L intergenic regions, as already reported for the Hart Park serogroup. Our Kamese strain (ArB9074) had 98% and 78.8% nucleotide sequence similarity with the prototypes of the KAMV and Mossuril virus isolated in Uganda and Mozambique in two different Culex species, respectively. Moreover, the protein sequences had 98-100% amino acid similarity with the prototype of the KAMV, except for an additional gene (U3) that showed a divergence of 6%. These molecular data show that our strain of the KAMV is genetically close to the Culex annuliorus strain that was circulating in Uganda in 1967. However, this study suggests the need to improve our knowledge of the KAMV to better understand its behavior, its life cycle, and its potential reservoirs.
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Affiliation(s)
| | - Emmanuel Nakoune
- 2 Virology Department, Institut Pasteur de Bangui , Bangui, Central African Republic
| | - Benjamin Selekon
- 2 Virology Department, Institut Pasteur de Bangui , Bangui, Central African Republic
| | - Antoine Gessain
- 3 Epidemiology and Physiopathology of Oncogenic Viruses, Institut Pasteur , Paris, France .,4 Centre National de Recherche Scientifique (CNRS) UMR3569 , Paris, France
| | - Jean-Claude Manuguerra
- 5 Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur , Paris, France
| | - Mirdad Kazanji
- 2 Virology Department, Institut Pasteur de Bangui , Bangui, Central African Republic
| | - Nicolas Berthet
- 1 Centre International de Recherches Médicales de Franceville (CIRMF) , Franceville, Gabon .,4 Centre National de Recherche Scientifique (CNRS) UMR3569 , Paris, France .,5 Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur , Paris, France
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7
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Contreras MA, Eastwood G, Guzman H, Popov V, Savit C, Uribe S, Kramer LD, Wood TG, Widen SG, Fish D, Tesh RB, Vasilakis N, Walker PJ. Almendravirus: A Proposed New Genus of Rhabdoviruses Isolated from Mosquitoes in Tropical Regions of the Americas. Am J Trop Med Hyg 2016; 96:100-109. [PMID: 27799634 DOI: 10.4269/ajtmh.16-0403] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/27/2016] [Indexed: 01/10/2023] Open
Abstract
The Rhabdoviridae is a diverse family of negative-sense single-stranded RNA viruses, many of which infect vertebrate hosts and are transmitted by hematophagous arthropods. Others appear to be arthropod specific, circulating only within arthropod populations. Herein, we report the isolation and characterization of three novel viruses from mosquitoes collected from the Americas. Coot Bay virus was isolated from Anopheles quadrimaculatus mosquitoes collected in the Everglades National Park, Florida; Rio Chico virus was isolated from Anopheles triannulatus mosquitoes collected in Panama; and Balsa virus was isolated from two pools of Culex erraticus mosquitoes collected in Colombia. Sequence analysis indicated that the viruses share a similar genome organization to Arboretum virus and Puerto Almendras virus that had previously been isolated from mosquitoes collected in Peru. Each genome features the five canonical rhabdovirus structural protein genes as well as a gene encoding a class 1A viroporin-like protein (U1) located between the G and L genes (3'-N-P-M-G-U1-L-5'). Phylogenetic analysis of complete L protein sequences indicated that all five viruses cluster in a unique clade that is relatively deeply rooted in the ancestry of animal rhabdoviruses. The failure of all viruses in this clade to grow in newborn mice or vertebrate cells in culture suggests that they may be poorly adapted to replication in vertebrates.
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Affiliation(s)
- Maria Angelica Contreras
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Sede de Investigacion Universitaria (SIU), Universidad de Antioquia, Medellin, Colombia.,Grupo de Investigacion en Sistematica Molecular (GSM), Facultad de Ciencias, Universidad Nacional de Colombia, Medellin, Colombia
| | - Gillian Eastwood
- Griffin Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Hilda Guzman
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas
| | - Vsevolod Popov
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas
| | - Chelsea Savit
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Sandra Uribe
- Grupo de Investigacion en Sistematica Molecular (GSM), Facultad de Ciencias, Universidad Nacional de Colombia, Medellin, Colombia
| | - Laura D Kramer
- Griffin Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
| | - Durland Fish
- Yale School of Public Health, New Haven, Connecticut
| | - Robert B Tesh
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas
| | - Nikos Vasilakis
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases, Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas.
| | - Peter J Walker
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Australia. .,School of Biological Sciences, University of Queensland, St Lucia, Australia
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8
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Charles J, Firth AE, Loroño-Pino MA, Garcia-Rejon JE, Farfan-Ale JA, Lipkin WI, Blitvich BJ, Briese T. Merida virus, a putative novel rhabdovirus discovered in Culex and Ochlerotatus spp. mosquitoes in the Yucatan Peninsula of Mexico. J Gen Virol 2016; 97:977-987. [PMID: 26868915 DOI: 10.1099/jgv.0.000424] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sequences corresponding to a putative, novel rhabdovirus [designated Merida virus (MERDV)] were initially detected in a pool of Culex quinquefasciatus collected in the Yucatan Peninsula of Mexico. The entire genome was sequenced, revealing 11 798 nt and five major ORFs, which encode the nucleoprotein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G) and RNA-dependent RNA polymerase (L). The deduced amino acid sequences of the N, G and L proteins have no more than 24, 38 and 43 % identity, respectively, to the corresponding sequences of all other known rhabdoviruses, whereas those of the P and M proteins have no significant identity with any sequences in GenBank and their identity is only suggested based on their genome position. Using specific reverse transcription-PCR assays established from the genome sequence, 27 571 C. quinquefasciatus which had been sorted in 728 pools were screened to assess the prevalence of MERDV in nature and 25 pools were found positive. The minimal infection rate (calculated as the number of positive mosquito pools per 1000 mosquitoes tested) was 0.9, and similar for both females and males. Screening another 140 pools of 5484 mosquitoes belonging to four other genera identified positive pools of Ochlerotatus spp. mosquitoes, indicating that the host range is not restricted to C. quinquefasciatus. Attempts to isolate MERDV in C6/36 and Vero cells were unsuccessful. In summary, we provide evidence that a previously undescribed rhabdovirus occurs in mosquitoes in Mexico.
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Affiliation(s)
- Jermilia Charles
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Maria A Loroño-Pino
- Laboratorio de Arbovirología, Centro de Investigaciones Regionales Dr Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Julian E Garcia-Rejon
- Laboratorio de Arbovirología, Centro de Investigaciones Regionales Dr Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Jose A Farfan-Ale
- Laboratorio de Arbovirología, Centro de Investigaciones Regionales Dr Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Bradley J Blitvich
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
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9
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Bodewes R, Ruiz-Gonzalez A, Schürch AC, Osterhaus AD, Smits SL. Novel divergent rhabdovirus in feces of red fox, Spain. Emerg Infect Dis 2015; 20:2172-4. [PMID: 25419624 PMCID: PMC4257811 DOI: 10.3201/eid2012.140236] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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10
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Sakai K, Hagiwara K, Omatsu T, Hamasaki C, Kuwata R, Shimoda H, Suzuki K, Endoh D, Nagata N, Nagai M, Katayama Y, Oba M, Kurane I, Saijo M, Morikawa S, Mizutani T, Maeda K. Isolation and characterization of a novel Rhabdovirus from a wild boar (Sus scrofa) in Japan. Vet Microbiol 2015; 179:197-203. [PMID: 26116524 DOI: 10.1016/j.vetmic.2015.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 01/29/2023]
Abstract
A novel rhabdovirus was isolated from the serum of a healthy Japanese wild boar (Sus scrofa leucomystax) and identified using the rapid determination system for viral nucleic acid sequences (RDV), next-generation sequencing, and electron microscopy. The virus was tentatively named wild boar rhabdovirus 1 (WBRV1). Phylogenetic analysis of the entire genome sequence indicated that WBRV1 is closely related to Tupaia rhabdovirus (TRV), which was isolated from cultured cells of hepatocellular carcinoma tissue of tree shrew. TRV has not been assigned to any genus of Rhabdoviridae till date. Analysis of the L gene indicated that WBRV1 belongs to the genus Vesiculovirus. These observations suggest that both TRV and WBRV1 belong to a new genus of Rhabdoviridae. Next-generation genome sequencing of WBRV1 revealed 5 open reading frames of 1329, 765, 627, 1629, and 6336 bases in length. The WBRV1 gene sequences are similar to those of other rhabdoviruses. Epizootiological analysis of a population of wild boars in Wakayama prefecture in Japan indicated that 6.5% were positive for the WBRV1 gene and 52% were positive for WBRV1-neutralizing antibodies. Furthermore, such viral neutralizing antibodies were found in domestic pigs in another prefecture. WBRV1 was inoculated intranasally and intraperitoneally into SCID and BALB/c mice and viral RNA was detected in SCID mice, suggesting that WBRV1 can replicate in immunocompromised mice. These results indicate this novel virus is endemic in wild animals and livestock in Japan.
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Affiliation(s)
- Kouji Sakai
- Department of Virology 3, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Katsuro Hagiwara
- Virus Unit, School of Veterinary Medicine, Rakuno Gakuen University, 582 Midorimachi, Bunkyodai, Ebetsu, Hokkaido 069-8501, Japan
| | - Tsutomu Omatsu
- Research and Education center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Chinami Hamasaki
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
| | - Ryusei Kuwata
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
| | - Hiroshi Shimoda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan
| | - Kazuo Suzuki
- Hikiiwa Park Center, 1629 Inari-cho, Tanabe 646-0051, Japan
| | - Daiji Endoh
- Department of Veterinary Radiology, School of Veterinary Medicine, Rakuno Gakuen University, 582 Midorimachi, Bunkyodai, Ebetsu-shi 069-8501, Japan
| | - Noriyo Nagata
- Department of Pathology, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Makoto Nagai
- Research and Education center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Yukie Katayama
- Research and Education center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Mami Oba
- Research and Education center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Ichiro Kurane
- Department of Virology 1, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Masayuki Saijo
- Department of Virology 1, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Shigeru Morikawa
- Department of Veterinary Science, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 162-8640, Japan
| | - Tetsuya Mizutani
- Research and Education center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.
| | - Ken Maeda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8515, Japan.
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11
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Roy A, Stone AL, Shao J, Otero-Colina G, Wei G, Choudhary N, Achor D, Levy L, Nakhla MK, Hartung JS, Schneider WL, Brlansky RH. Identification and Molecular Characterization of Nuclear Citrus leprosis virus, a Member of the Proposed Dichorhavirus Genus Infecting Multiple Citrus Species in Mexico. PHYTOPATHOLOGY 2015; 105:564-75. [PMID: 25423071 DOI: 10.1094/phyto-09-14-0245-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Citrus leprosis is one of the most destructive diseases of Citrus spp. and is associated with two unrelated virus groups that produce particles primarily in either the cytoplasm or nucleus of infected plant cells. Symptoms of leprosis, including chlorotic spots surrounded by yellow haloes on leaves and necrotic spots on twigs and fruit, were observed on leprosis-affected mandarin and navel sweet orange trees in the state of Querétaro, Mexico. Serological and molecular assays showed that the cytoplasmic types of Citrus leprosis virus (CiLV-C) often associated with leprosis symptomatic tissues were absent. However, using transmission electron microscopy, bullet-shaped rhabdovirus-like virions were observed in the nuclei and cytoplasm of the citrus leprosis-infected leaf tissues. An analysis of small RNA populations from symptomatic tissue was carried out to determine the genome sequence of the rhabdovirus-like particles observed in the citrus leprosis samples. The complete genome sequence showed that the nuclear type of CiLV (CiLV-N) present in the samples consisted of two negative-sense RNAs: 6,268-nucleotide (nt)-long RNA1 and 5,847-nt-long RNA2, excluding the poly(A) tails. CiLV-N had a genome organization identical to that of Orchid fleck virus (OFV), with the exception of shorter 5' untranslated regions in RNA1 (53 versus 205 nt) and RNA2 (34 versus 182 nt). Phylogenetic trees constructed with the amino acid sequences of the nucleocapsid (N) and glycoproteins (G) and the RNA polymerase (L protein) showed that CiLV-N clusters with OFV. Furthermore, phylogenetic analyses of N protein established CiLV-N as a member of the proposed genus Dichorhavirus. Reverse-transcription polymerase chain reaction primers for the detection of CiLV-N were designed based on the sequence of the N gene and the assay was optimized and tested to detect the presence of CiLV-N in both diseased and symptom-free plants.
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Affiliation(s)
- Avijit Roy
- First, sixth, seventh, and twelfth authors: University of Florida, IFAS, Plant Pathology Department, Citrus Research and Education Center, 700 Experiment Station Road, Lake Alfred, FL; second and eleventh authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit (FDWSRU), Fort Detrick, MD; third and tenth authors: USDA-ARS, Molecular Plant Pathology Laboratory (MPPL), Beltsville, MD; fourth author: Colegio de Postgraduados, Campus Montecillo, Texcoco, Edo. De Mex., CP 56230, México; fifth and ninth authors: USDA-Animal and Plant Health Inspection Service (APHIS)-Plant Protection and Quarantine (PPQ)-Center for Plant Health Science and Technology (CSIRO), Beltsville, MD; and eighth author: USDA-APHIS-PPQ-CPHST, Riverdale, MD
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12
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Walker PJ, Firth C, Widen SG, Blasdell KR, Guzman H, Wood TG, Paradkar PN, Holmes EC, Tesh RB, Vasilakis N. Evolution of genome size and complexity in the rhabdoviridae. PLoS Pathog 2015; 11:e1004664. [PMID: 25679389 PMCID: PMC4334499 DOI: 10.1371/journal.ppat.1004664] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 01/06/2015] [Indexed: 12/14/2022] Open
Abstract
RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3' to 5' direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae.
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Affiliation(s)
- Peter J. Walker
- CSIRO Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
- * E-mail:
| | - Cadhla Firth
- CSIRO Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Steven G. Widen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kim R. Blasdell
- CSIRO Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Hilda Guzman
- Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, Center for Tropical Diseases, and Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Thomas G. Wood
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Prasad N. Paradkar
- CSIRO Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Robert B. Tesh
- Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, Center for Tropical Diseases, and Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Nikos Vasilakis
- Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, Center for Tropical Diseases, and Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, Texas, United States of America
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13
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Gauci PJ, McAllister J, Mitchell IR, Boyle DB, Bulach DM, Weir RP, Melville LF, Gubala AJ. Genomic characterisation of three Mapputta group viruses, a serogroup of Australian and Papua New Guinean bunyaviruses associated with human disease. PLoS One 2015; 10:e0116561. [PMID: 25588016 PMCID: PMC4294684 DOI: 10.1371/journal.pone.0116561] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 12/11/2014] [Indexed: 01/19/2023] Open
Abstract
The Mapputta serogroup tentatively contains the mosquito-associated viruses Mapputta, Maprik, Trubanaman and Gan Gan. Interestingly, this serogroup has previously been associated with an acute epidemic polyarthritis-like illness in humans; however, there has been no ensuing genetic characterisation. Here we report the complete genome sequences of Mapputta and Maprik viruses, and a new Mapputta group candidate, Buffalo Creek virus, previously isolated from mosquitoes and detected by serology in a hospitalised patient. Phylogenetic analyses indicate that the group is one of the earliest diverged groups within the genus Orthobunyavirus of the family Bunyaviridae. Analyses show that these three viruses are related to the recently sequenced Australian bunyaviruses from mosquitoes, Salt Ash and Murrumbidgee. A notable feature of the Mapputta group viruses is the absence of the NSs (non-structural) ORF commonly found on the S segment of other orthobunyaviruses. Viruses of the Mapputta group have been isolated from geographically diverse regions ranging from tropical Papua New Guinea to the semi-arid climate of south-eastern Australia. The relevance of this group to human health in the region merits further investigation.
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Affiliation(s)
- Penelope J. Gauci
- Land Division, Defence Science & Technology Organisation, Fishermans Bend, Victoria, Australia
- * E-mail:
| | - Jane McAllister
- Land Division, Defence Science & Technology Organisation, Fishermans Bend, Victoria, Australia
| | - Ian R. Mitchell
- Land Division, Defence Science & Technology Organisation, Fishermans Bend, Victoria, Australia
| | - David B. Boyle
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation, Geelong, Victoria, Australia
| | - Dieter M. Bulach
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation, Geelong, Victoria, Australia
| | - Richard P. Weir
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Berrimah, Northern Territory, Australia
| | - Lorna F. Melville
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Berrimah, Northern Territory, Australia
| | - Aneta J. Gubala
- Land Division, Defence Science & Technology Organisation, Fishermans Bend, Victoria, Australia
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14
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Bodewes R, Ruiz-Gonzalez A, Schürch AC, Osterhaus AD, Smits SL. Novel Divergent Rhabdovirus in Feces of Red Fox, Spain. Emerg Infect Dis 2014. [DOI: 10.3201/eid2013.140236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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15
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Wongabel rhabdovirus accessory protein U3 targets the SWI/SNF chromatin remodeling complex. J Virol 2014; 89:1377-88. [PMID: 25392228 DOI: 10.1128/jvi.02010-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
UNLABELLED Wongabel virus (WONV) is an arthropod-borne rhabdovirus that infects birds. It is one of the growing array of rhabdoviruses with complex genomes that encode multiple accessory proteins of unknown function. In addition to the five canonical rhabdovirus structural protein genes (N, P, M, G, and L), the 13.2-kb negative-sense single-stranded RNA (ssRNA) WONV genome contains five uncharacterized accessory genes, one overlapping the N gene (Nx or U4), three located between the P and M genes (U1 to U3), and a fifth one overlapping the G gene (Gx or U5). Here we show that WONV U3 is expressed during infection in insect and mammalian cells and is required for efficient viral replication. A yeast two-hybrid screen against a mosquito cell cDNA library identified that WONV U3 interacts with the 83-amino-acid (aa) C-terminal domain of SNF5, a component of the SWI/SNF chromatin remodeling complex. The interaction was confirmed by affinity chromatography, and nuclear colocalization was established by confocal microscopy. Gene expression studies showed that SNF5 transcripts are upregulated during infection of mosquito cells with WONV, as well as West Nile virus (Flaviviridae) and bovine ephemeral fever virus (Rhabdoviridae), and that SNF5 knockdown results in increased WONV replication. WONV U3 also inhibits SNF5-regulated expression of the cytokine gene CSF1. The data suggest that WONV U3 targets the SWI/SNF complex to block the host response to infection. IMPORTANCE The rhabdoviruses comprise a large family of RNA viruses infecting plants, vertebrates, and invertebrates. In addition to the major structural proteins (N, P, M, G, and L), many rhabdoviruses encode a diverse array of accessory proteins of largely unknown function. Understanding the role of these proteins may reveal much about host-pathogen interactions in infected cells. Here we examine accessory protein U3 of Wongabel virus, an arthropod-borne rhabdovirus that infects birds. We show that U3 enters the nucleus and interacts with SNF5, a component of the chromatin remodeling complex that is upregulated in response to infection and restricts viral replication. We also show that U3 inhibits SNF5-regulated expression of the cytokine colony-stimulating factor 1 (CSF1), suggesting that it targets the chromatin remodeling complex to block the host response to infection. This study appears to provide the first evidence of a virus targeting SNF5 to inhibit host gene expression.
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16
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Xiburema Virus, a Hitherto Undescribed Virus within the Family Rhabdoviridae Isolated in the Brazilian Amazon Region. GENOME ANNOUNCEMENTS 2014; 2:2/3/e00454-14. [PMID: 24948755 PMCID: PMC4064021 DOI: 10.1128/genomea.00454-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the first complete open reading frame (ORF) genome sequence of Xiburema virus (XIBV), that of strain BE AR362159, isolated from mosquitoes (Sabethes intermedius) in Sena Madureira, Acre state, northern Brazil. All genes showed similarities with those belonging to members of the family Rhabdoviridae.
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17
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Bovine ephemeral fever rhabdovirus α1 protein has viroporin-like properties and binds importin β1 and importin 7. J Virol 2013; 88:1591-603. [PMID: 24257609 DOI: 10.1128/jvi.01812-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bovine ephemeral fever virus (BEFV) is an arthropod-borne rhabdovirus that is classified as the type species of the genus Ephemerovirus. In addition to the five canonical rhabdovirus structural proteins (N, P, M, G, and L), the large and complex BEFV genome contains several open reading frames (ORFs) between the G and L genes (α1, α2/α3, β, and γ) encoding proteins of unknown function. We show that the 10.5-kDa BEFV α1 protein is expressed in infected cells and, consistent with previous predictions based on its structure, has the properties of a viroporin. Expression of a BEFV α1-maltose binding protein (MBP) fusion protein in Escherichia coli was observed to inhibit cell growth and increase membrane permeability to hygromycin B. Increased membrane permeability was also observed in BEFV-infected mammalian cells (but not cells infected with an α1-deficient BEFV strain) and in cells expressing a BEFV α1-green fluorescent protein (GFP) fusion protein, which was shown by confocal microscopy to localize to the Golgi complex. Furthermore, the predicted C-terminal cytoplasmic domain of α1, which contains a strong nuclear localization signal (NLS), was translocated to the nucleus when expressed independently, and in an affinity chromatography assay employing a GFP trap, the full-length α1 was observed to interact specifically with importin β1 and importin 7 but not with importin α3. These data suggest that, in addition to its function as a viroporin, BEFV α1 may modulate components of nuclear trafficking pathways, but the specific role thereof remains unclear. Although rhabdovirus accessory genes occur commonly among arthropod-borne rhabdoviruses, little is known of their functions. Here, we demonstrate that the BEFV α1 ORF encodes a protein which has the structural and functional characteristics of a viroporin. We show that α1 localizes in the Golgi complex and increases cellular permeability. We also show that BEFV α1 binds importin β1 and importin 7, suggesting that it may have a yet unknown role in modulating nuclear trafficking. This is the first functional analysis of an ephemerovirus accessory protein and of a rhabdovirus viroporin.
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Allison AB, Mead DG, Palacios GF, Tesh RB, Holmes EC. Gene duplication and phylogeography of North American members of the Hart Park serogroup of avian rhabdoviruses. Virology 2013; 448:284-92. [PMID: 24314659 PMCID: PMC3873333 DOI: 10.1016/j.virol.2013.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 06/11/2013] [Accepted: 10/17/2013] [Indexed: 12/28/2022]
Abstract
Flanders virus (FLAV) and Hart Park virus (HPV) are rhabdoviruses that circulate in mosquito–bird cycles in the eastern and western United States, respectively, and constitute the only two North American representatives of the Hart Park serogroup. Previously, it was suggested that FLAV is unique among the rhabdoviruses in that it contains two pseudogenes located between the P and M genes, while the cognate sequence for HPV has been lacking. Herein, we demonstrate that FLAV and HPV do not contain pseudogenes in this region, but encode three small functional proteins designated as U1–U3 that apparently arose by gene duplication. To further investigate the U1–U3 region, we conducted the first large-scale evolutionary analysis of a member of the Hart Park serogroup by analyzing over 100 spatially and temporally distinct FLAV isolates. Our phylogeographic analysis demonstrates that although FLAV appears to be slowly evolving, phylogenetically divergent lineages co-circulate sympatrically. Flanders virus (FLAV) does not contain pseudogenes as previously reported. The FLAV U1–U3 proteins arose by gene duplication. The SH protein of FLAV is tentatively expressed by coupled translation. Distinct lineages of FLAV circulate sympatrically in the United States. Histone H4 and cyclophilin A are apparently incorporated into FLAV particles.
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Affiliation(s)
- Andrew B Allison
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
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19
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Ghedin E, Rogers MB, Widen SG, Guzman H, Travassos da Rosa APA, Wood TG, Fitch A, Popov V, Holmes EC, Walker PJ, Vasilakis N, Tesh RB. Kolente virus, a rhabdovirus species isolated from ticks and bats in the Republic of Guinea. J Gen Virol 2013; 94:2609-2615. [PMID: 24062532 DOI: 10.1099/vir.0.055939-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Kolente virus (KOLEV) is a rhabdovirus originally isolated from ticks and a bat in Guinea, West Africa, in 1985. Although tests at the time of isolation suggested that KOLEV is a novel rhabdovirus, it has remained largely uncharacterized. We assembled the complete genome sequence of the prototype strain DakAr K7292, which was found to encode the five canonical rhabdovirus structural proteins (N, P, M, G and L) with alternative ORFs (>180 nt) in the P and L genes. Serologically, KOLEV exhibited a weak antigenic relationship with Barur and Fukuoka viruses in the Kern Canyon group. Phylogenetic analysis revealed that KOLEV represents a distinct and divergent lineage that shows no clear relationship to any rhabdovirus except Oita virus, although with limited phylogenetic resolution. In summary, KOLEV represents a novel species in the family Rhabdoviridae.
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Affiliation(s)
- Elodie Ghedin
- Center for Vaccine Research, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Matthew B Rogers
- Center for Vaccine Research, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hilda Guzman
- Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Amelia P A Travassos da Rosa
- Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Adam Fitch
- Center for Vaccine Research, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Vsevolod Popov
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.,Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA.,Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Edward C Holmes
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.,Sydney Emerging Infections & Biosecurity Institute, School of Biological Sciences and Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Peter J Walker
- CSIRO Animal, Food and Health Sciences, Australian Animal Health Laboratory, Geelong, VIC 3220, Australia
| | - Nikos Vasilakis
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.,Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA.,Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Robert B Tesh
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.,Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA.,Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
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20
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Vasilakis N, Widen S, Mayer SV, Seymour R, Wood TG, Popov V, Guzman H, Travassos da Rosa APA, Ghedin E, Holmes EC, Walker PJ, Tesh RB. Niakha virus: a novel member of the family Rhabdoviridae isolated from phlebotomine sandflies in Senegal. Virology 2013; 444:80-9. [PMID: 23773405 DOI: 10.1016/j.virol.2013.05.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 05/21/2013] [Accepted: 05/22/2013] [Indexed: 01/18/2023]
Abstract
Members of the family Rhabdoviridae have been assigned to eight genera but many remain unassigned. Rhabdoviruses have a remarkably diverse host range that includes terrestrial and marine animals, invertebrates and plants. Transmission of some rhabdoviruses often requires an arthropod vector, such as mosquitoes, midges, sandflies, ticks, aphids and leafhoppers, in which they replicate. Herein we characterize Niakha virus (NIAV), a previously uncharacterized rhabdovirus isolated from phebotomine sandflies in Senegal. Analysis of the 11,124 nt genome sequence indicates that it encodes the five common rhabdovirus proteins with alternative ORFs in the M, G and L genes. Phylogenetic analysis of the L protein indicate that NIAV's closest relative is Oak Vale rhabdovirus, although in this analysis NIAV is still so phylogenetically distinct that it might be classified as distinct from the eight currently recognized Rhabdoviridae genera. This observation highlights the vast, and yet not fully recognized diversity, of this family.
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Affiliation(s)
- Nikos Vasilakis
- Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, Galveston, TX 77555-0609, USA.
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21
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Yu C, Hernandez T, Zheng H, Yau SC, Huang HH, He RL, Yang J, Yau SST. Real time classification of viruses in 12 dimensions. PLoS One 2013; 8:e64328. [PMID: 23717598 PMCID: PMC3661469 DOI: 10.1371/journal.pone.0064328] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 04/12/2013] [Indexed: 11/18/2022] Open
Abstract
The International Committee on Taxonomy of Viruses authorizes and organizes the taxonomic classification of viruses. Thus far, the detailed classifications for all viruses are neither complete nor free from dispute. For example, the current missing label rates in GenBank are 12.1% for family label and 30.0% for genus label. Using the proposed Natural Vector representation, all 2,044 single-segment referenced viral genomes in GenBank can be embedded in [Formula: see text]. Unlike other approaches, this allows us to determine phylogenetic relations for all viruses at any level (e.g., Baltimore class, family, subfamily, genus, and species) in real time. Additionally, the proposed graphical representation for virus phylogeny provides a visualization of the distribution of viruses in [Formula: see text]. Unlike the commonly used tree visualization methods which suffer from uniqueness and existence problems, our representation always exists and is unique. This approach is successfully used to predict and correct viral classification information, as well as to identify viral origins; e.g. a recent public health threat, the West Nile virus, is closer to the Japanese encephalitis antigenic complex based on our visualization. Based on cross-validation results, the accuracy rates of our predictions are as high as 98.2% for Baltimore class labels, 96.6% for family labels, 99.7% for subfamily labels and 97.2% for genus labels.
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Affiliation(s)
- Chenglong Yu
- Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Troy Hernandez
- Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Hui Zheng
- Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Shek-Chung Yau
- Information Technology Services Center, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Hsin-Hsiung Huang
- Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Rong Lucy He
- Department of Biological Sciences, Chicago State University, Chicago, Illinois, United States of America
| | - Jie Yang
- Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Stephen S.-T. Yau
- Department of Mathematical Sciences, Tsinghua University, Beijing, P. R. China
- * E-mail:
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22
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Blasdell KR, Voysey R, Bulach DM, Trinidad L, Tesh RB, Boyle DB, Walker PJ. Malakal virus from Africa and Kimberley virus from Australia are geographic variants of a widely distributed ephemerovirus. Virology 2012; 433:236-44. [DOI: 10.1016/j.virol.2012.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 08/01/2012] [Accepted: 08/03/2012] [Indexed: 02/05/2023]
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23
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Grard G, Fair JN, Lee D, Slikas E, Steffen I, Muyembe JJ, Sittler T, Veeraraghavan N, Ruby JG, Wang C, Makuwa M, Mulembakani P, Tesh RB, Mazet J, Rimoin AW, Taylor T, Schneider BS, Simmons G, Delwart E, Wolfe ND, Chiu CY, Leroy EM. A novel rhabdovirus associated with acute hemorrhagic fever in central Africa. PLoS Pathog 2012; 8:e1002924. [PMID: 23028323 PMCID: PMC3460624 DOI: 10.1371/journal.ppat.1002924] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 08/08/2012] [Indexed: 12/01/2022] Open
Abstract
Deep sequencing was used to discover a novel rhabdovirus (Bas-Congo virus, or BASV) associated with a 2009 outbreak of 3 human cases of acute hemorrhagic fever in Mangala village, Democratic Republic of Congo (DRC), Africa. The cases, presenting over a 3-week period, were characterized by abrupt disease onset, high fever, mucosal hemorrhage, and, in two patients, death within 3 days. BASV was detected in an acute serum sample from the lone survivor at a concentration of 1.09×106 RNA copies/mL, and 98.2% of the genome was subsequently de novo assembled from ∼140 million sequence reads. Phylogenetic analysis revealed that BASV is highly divergent and shares less than 34% amino acid identity with any other rhabdovirus. High convalescent neutralizing antibody titers of >1∶1000 were detected in the survivor and an asymptomatic nurse directly caring for him, both of whom were health care workers, suggesting the potential for human-to-human transmission of BASV. The natural animal reservoir host or arthropod vector and precise mode of transmission for the virus remain unclear. BASV is an emerging human pathogen associated with acute hemorrhagic fever in Africa. We used deep sequencing, a method for generating millions of DNA sequence reads from clinical samples, to discover a novel rhabdovirus (Bas-Congo virus, or BASV) associated with a 2009 outbreak of 3 human cases of acute hemorrhagic fever in Mangala village, Democratic Republic of Congo (DRC), Africa. The cases, presenting over a 3-week period, were characterized by abrupt disease onset, high fever, bloody vomiting and diarrhea, and, in two patients, death within 3 days. BASV was present in the blood of the lone survivor at a concentration of over a million copies per milliliter. The genome of BASV, assembled from over 140 million sequence reads, reveals that it is very different from any other rhabdovirus. The lone survivor and a nurse caring for him (with no symptoms), both health care workers, were found to have high levels of antibodies to BASV, indicating that they both had been infected by the virus. Although the source of the virus remains unclear, our study findings suggest that BASV may be spread by human-to-human contact and is an emerging pathogen associated with acute hemorrhagic fever in Africa.
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Affiliation(s)
- Gilda Grard
- Viral Emergent Diseases unit, Centre International de Recherches Médicales de Franceville, Franceville, Gabon
- MIVEGEC, UMR (IRD 224 - CNRS 5290 - UM1 - UM2), Institut de Recherche pour le Développement, Montpellier, France
| | - Joseph N. Fair
- Global Viral Forecasting, Incorporated, San Francisco, California, United States of America
| | - Deanna Lee
- Department of Laboratory Medicine, University of California, San Francisco, California, United States of America
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Elizabeth Slikas
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Imke Steffen
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Jean-Jacques Muyembe
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Taylor Sittler
- Department of Laboratory Medicine, University of California, San Francisco, California, United States of America
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Narayanan Veeraraghavan
- Department of Laboratory Medicine, University of California, San Francisco, California, United States of America
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - J. Graham Ruby
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Department of Biochemistry, University of California, San Francisco, California, United States of America
| | - Chunlin Wang
- Department of Biochemistry, Stanford University, Stanford, California, United States of America
| | - Maria Makuwa
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Prime Mulembakani
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Robert B. Tesh
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jonna Mazet
- Department of Epidemiology, University of California at Davis, Davis, California, United States of America
| | - Anne W. Rimoin
- Department of Epidemiology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Travis Taylor
- Global Viral Forecasting, Incorporated, San Francisco, California, United States of America
| | - Bradley S. Schneider
- Global Viral Forecasting, Incorporated, San Francisco, California, United States of America
| | - Graham Simmons
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Nathan D. Wolfe
- Global Viral Forecasting, Incorporated, San Francisco, California, United States of America
| | - Charles Y. Chiu
- Department of Laboratory Medicine, University of California, San Francisco, California, United States of America
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (CYC); (EML)
| | - Eric M. Leroy
- Viral Emergent Diseases unit, Centre International de Recherches Médicales de Franceville, Franceville, Gabon
- MIVEGEC, UMR (IRD 224 - CNRS 5290 - UM1 - UM2), Institut de Recherche pour le Développement, Montpellier, France
- * E-mail: (CYC); (EML)
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Kotonkan and Obodhiang viruses: African ephemeroviruses with large and complex genomes. Virology 2012; 425:143-53. [DOI: 10.1016/j.virol.2012.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 01/04/2012] [Accepted: 01/06/2012] [Indexed: 11/24/2022]
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25
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Wellehan JFX, Pessier AP, Archer LL, Childress AL, Jacobson ER, Tesh RB. Initial sequence characterization of the rhabdoviruses of squamate reptiles, including a novel rhabdovirus from a caiman lizard (Dracaena guianensis). Vet Microbiol 2012; 158:274-9. [PMID: 22397930 DOI: 10.1016/j.vetmic.2012.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 01/25/2012] [Accepted: 02/13/2012] [Indexed: 11/25/2022]
Abstract
Rhabdoviruses infect a variety of hosts, including non-avian reptiles. Consensus PCR techniques were used to obtain partial RNA-dependent RNA polymerase gene sequence from five rhabdoviruses of South American lizards; Marco, Chaco, Timbo, Sena Madureira, and a rhabdovirus from a caiman lizard (Dracaena guianensis). The caiman lizard rhabdovirus formed inclusions in erythrocytes, which may be a route for infecting hematophagous insects. This is the first information on behavior of a rhabdovirus in squamates. We also obtained sequence from two rhabdoviruses of Australian lizards, confirming previous Charleville virus sequence and finding that, unlike a previous sequence report but in agreement with serologic reports, Almpiwar virus is clearly distinct from Charleville virus. Bayesian and maximum likelihood phylogenetic analysis revealed that most known rhabdoviruses of squamates cluster in the Almpiwar subgroup. The exception is Marco virus, which is found in the Hart Park group.
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Affiliation(s)
- James F X Wellehan
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA.
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Walker PJ, Dietzgen RG, Joubert DA, Blasdell KR. Rhabdovirus accessory genes. Virus Res 2011; 162:110-25. [PMID: 21933691 PMCID: PMC7114375 DOI: 10.1016/j.virusres.2011.09.004] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 09/02/2011] [Accepted: 09/04/2011] [Indexed: 12/16/2022]
Abstract
The Rhabdoviridae is one of the most ecologically diverse families of RNA viruses with members infecting a wide range of organisms including placental mammals, marsupials, birds, reptiles, fish, insects and plants. The availability of complete nucleotide sequences for an increasing number of rhabdoviruses has revealed that their ecological diversity is reflected in the diversity and complexity of their genomes. The five canonical rhabdovirus structural protein genes (N, P, M, G and L) that are shared by all rhabdoviruses are overprinted, overlapped and interspersed with a multitude of novel and diverse accessory genes. Although not essential for replication in cell culture, several of these genes have been shown to have roles associated with pathogenesis and apoptosis in animals, and cell-to-cell movement in plants. Others appear to be secreted or have the characteristics of membrane-anchored glycoproteins or viroporins. However, most encode proteins of unknown function that are unrelated to any other known proteins. Understanding the roles of these accessory genes and the strategies by which rhabdoviruses use them to engage, divert and re-direct cellular processes will not only present opportunities to develop new anti-viral therapies but may also reveal aspects of cellar function that have broader significance in biology, agriculture and medicine.
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Affiliation(s)
- Peter J Walker
- CSIRO Livestock Industries, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC 3220, Australia.
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27
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Barnard RT, Hall RA, Gould EA. Expecting the unexpected: nucleic acid-based diagnosis and discovery of emerging viruses. Expert Rev Mol Diagn 2011; 11:409-23. [PMID: 21545258 PMCID: PMC7103685 DOI: 10.1586/erm.11.24] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Extrapolation from recent disease history suggests that changes in the global environment, including virus, vector and human behavior, will continue to influence the spectrum of viruses to which humans are exposed. In this article, these environmental changes will be enumerated, and their potential impact on target-focused, nucleic acid-based diagnostic tests will be considered, followed by a presentation of some emerging technological responses.
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Affiliation(s)
- Ross Thomas Barnard
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, Australia.
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28
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Quan PL, Williams DT, Johansen CA, Jain K, Petrosov A, Diviney SM, Tashmukhamedova A, Hutchison SK, Tesh RB, Mackenzie JS, Briese T, Lipkin WI. Genetic characterization of K13965, a strain of Oak Vale virus from Western Australia. Virus Res 2011; 160:206-13. [PMID: 21740935 DOI: 10.1016/j.virusres.2011.06.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/17/2011] [Accepted: 06/21/2011] [Indexed: 10/18/2022]
Abstract
K13965, an uncharacterized virus, was isolated in 1993 from Anopheles annulipes mosquitoes collected in the Kimberley region of northern Western Australia. Here, we report its genomic sequence, identify it as a rhabdovirus, and characterize its phylogenetic relationships. The genome comprises a P' (C) and SH protein similar to the recently characterized Tupaia and Durham viruses, and shows overlap between G and L genes. Comparison of K13965 genome sequence to other rhabdoviruses identified K13965 as a strain of the unclassified Australian Oak Vale rhabdovirus, whose complete genome sequence we also determined. Phylogenetic analysis of N and L sequences indicated genetic relationship to a recently proposed Sandjima virus clade, although the Oak Vale virus sequences form a branch separate from the African members of that group.
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Affiliation(s)
- Phenix-Lan Quan
- Center for Infection and Immunity, Columbia University, New York, NY 10032, USA
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29
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Genomic analysis of four human metapneumovirus prototypes. Virus Res 2011; 160:200-5. [PMID: 21740936 DOI: 10.1016/j.virusres.2011.06.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 06/18/2011] [Accepted: 06/21/2011] [Indexed: 11/22/2022]
Abstract
Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in children. We determined the complete genome sequence of four strains of HMPV representing each of the four lineages. These sequences were compared with published HMPV genome sequences. Most genes were conserved between the genetic lineages (79.5-99.6%), though nucleotide diversity was greater than amino acid diversity, suggesting functional constraints on mutation. However, the SH and G open reading frames were more variable (mean 76.4% and 59.0% aa identity, respectively), with mostly nonsynonymous changes, suggesting selective pressure on the SH and G proteins. Gene-start regions were largely conserved between genes and viruses, while gene-end sequences were conserved between viruses but not between genes. The SH-G and G-L intergenic regions were extremely long (∼200 nt) and have no defined function, yet were highly conserved within major groups. These findings highlight broadly conserved regions of the HMPV genome and suggest unidentified biological roles for SH and G.
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Gubala A, Davis S, Weir R, Melville L, Cowled C, Boyle D. Tibrogargan and Coastal Plains rhabdoviruses: genomic characterization, evolution of novel genes and seroprevalence in Australian livestock. J Gen Virol 2011; 92:2160-2170. [PMID: 21593274 DOI: 10.1099/vir.0.026120-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tibrogargan virus (TIBV) and Coastal Plains virus (CPV) were isolated from cattle in Australia and TIBV has also been isolated from the biting midge Culicoides brevitarsis. Complete genomic sequencing revealed that the viruses share a novel genome structure within the family Rhabdoviridae, each virus containing two additional putative genes between the matrix protein (M) and glycoprotein (G) genes and one between the G and viral RNA polymerase (L) genes. The predicted novel protein products are highly diverged at the sequence level but demonstrate clear conservation of secondary structure elements, suggesting conservation of biological functions. Phylogenetic analyses showed that TIBV and CPV form an independent group within the 'dimarhabdovirus supergroup'. Although no disease has been observed in association with these viruses, antibodies were detected at high prevalence in cattle and buffalo in northern Australia, indicating the need for disease monitoring and further study of this distinctive group of viruses.
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Affiliation(s)
- Aneta Gubala
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Livestock Industries, Australian Animal Health Laboratory, Geelong, Victoria, Australia
- Human Protection and Performance Division, Defence Science and Technology Organisation, Melbourne, Australia
- School of Chemistry and Molecular Sciences, University of Queensland, St Lucia, Queensland, Australia
- Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease, Brisbane, Queensland, Australia
| | - Steven Davis
- Northern Territory Department of Resources, Berrimah Veterinary Laboratories, Berrimah, Northern Territory, Australia
| | - Richard Weir
- Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease, Brisbane, Queensland, Australia
- Northern Territory Department of Resources, Berrimah Veterinary Laboratories, Berrimah, Northern Territory, Australia
| | - Lorna Melville
- Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease, Brisbane, Queensland, Australia
- Northern Territory Department of Resources, Berrimah Veterinary Laboratories, Berrimah, Northern Territory, Australia
| | - Chris Cowled
- Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease, Brisbane, Queensland, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Livestock Industries, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - David Boyle
- Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease, Brisbane, Queensland, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Livestock Industries, Australian Animal Health Laboratory, Geelong, Victoria, Australia
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31
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Allison AB, Palacios G, Travassos da Rosa A, Popov VL, Lu L, Xiao SY, DeToy K, Briese T, Lipkin WI, Keel MK, Stallknecht DE, Bishop GR, Tesh RB. Characterization of Durham virus, a novel rhabdovirus that encodes both a C and SH protein. Virus Res 2010; 155:112-22. [PMID: 20863863 DOI: 10.1016/j.virusres.2010.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 09/10/2010] [Accepted: 09/14/2010] [Indexed: 11/18/2022]
Abstract
The family Rhabdoviridae is a diverse group of non-segmented, negative-sense RNA viruses that are distributed worldwide and infect a wide range of hosts including vertebrates, invertebrates, and plants. Of the 114 currently recognized vertebrate rhabdoviruses, relatively few have been well characterized at both the antigenic and genetic level; hence, the phylogenetic relationships between many of the vertebrate rhabdoviruses remain unknown. The present report describes a novel rhabdovirus isolated from the brain of a moribund American coot (Fulica americana) that exhibited neurological signs when found in Durham County, North Carolina, in 2005. Antigenic characterization of the virus revealed that it was serologically unrelated to 68 other known vertebrate rhabdoviruses. Genomic sequencing of the virus indicated that it shared the highest identity to Tupaia rhabdovirus (TUPV), and as only previously observed in TUPV, the genome encoded a putative C protein in an overlapping open reading frame (ORF) of the phosphoprotein gene and a small hydrophobic (SH) protein located in a novel ORF between the matrix and glycoprotein genes. Phylogenetic analysis of partial amino acid sequences of the nucleoprotein and polymerase protein indicated that, in addition to TUPV, the virus was most closely related to avian and small mammal rhabdoviruses from Africa and North America. In this report, we present the morphological, pathological, antigenic, and genetic characterization of the new virus, tentatively named Durham virus (DURV), and discuss its potential evolutionary relationship to other vertebrate rhabdoviruses.
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Affiliation(s)
- A B Allison
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, United States.
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32
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Gubala A, Davis S, Weir R, Melville L, Cowled C, Walker P, Boyle D. Ngaingan virus, a macropod-associated rhabdovirus, contains a second glycoprotein gene and seven novel open reading frames. Virology 2010; 399:98-108. [PMID: 20089287 DOI: 10.1016/j.virol.2009.12.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 11/16/2009] [Accepted: 12/14/2009] [Indexed: 11/30/2022]
Abstract
Ngaingan virus (NGAV) was isolated from a pool of biting midges that were collected in the tropics of northern Australia. Reported here is the full-length sequence of the NGAV genome, which, at over 15.7 kb, is the largest in any rhabdovirus described to date and contains 13 genes, the highest number of genes observed in any (-) ssRNA virus. Seven of these putative genes show no significant homology to known proteins. Like viruses in the genus Ephemerovirus, NGAV possesses a second glycoprotein gene (G(NS)). Phylogenetic analyses, however, place NGAV within the yet to be classified "Hart Park" group containing Wongabel and Flanders viruses, which do not contain a second glycoprotein gene. Screening of various animal sera from northern Australia has indicated that NGAV is currently circulating in macropods (wallabies, wallaroos and kangaroos), highlighting the need for further studies to determine its potential to cause disease in these species.
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Affiliation(s)
- Aneta Gubala
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, Victoria, Australia; School of Chemistry and Molecular Sciences, University of Queensland, St. Lucia, Queensland, Australia; Human Protection and Performance Division, Defence Science and Technology Organisation, Melbourne, Australia; Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease, Brisbane, Queensland, Australia.
| | - Steven Davis
- Northern Territory Department of Regional Development, Primary Industry, Fisheries and Resources, Berrimah Veterinary Laboratories, Berrimah, Northern Territory, Australia
| | - Richard Weir
- Northern Territory Department of Regional Development, Primary Industry, Fisheries and Resources, Berrimah Veterinary Laboratories, Berrimah, Northern Territory, Australia; Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease, Brisbane, Queensland, Australia
| | - Lorna Melville
- Northern Territory Department of Regional Development, Primary Industry, Fisheries and Resources, Berrimah Veterinary Laboratories, Berrimah, Northern Territory, Australia; Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease, Brisbane, Queensland, Australia
| | - Chris Cowled
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, Victoria, Australia; Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease, Brisbane, Queensland, Australia
| | - Peter Walker
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - David Boyle
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Geelong, Victoria, Australia; Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease, Brisbane, Queensland, Australia
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