1
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Koh C, Saleh MC. Translating mosquito viromes into vector management strategies. Trends Parasitol 2024; 40:10-20. [PMID: 38065789 DOI: 10.1016/j.pt.2023.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 01/06/2024]
Abstract
Mosquitoes are best known for transmitting human and animal viruses. However, they also harbour mosquito-specific viruses (MSVs) as part of their microbiota. These are a group of viruses whose diversity and prevalence overshadow their medically relevant counterparts. Although metagenomics sequencing has remarkably accelerated the discovery of these viruses, what we know about them is often limited to sequence information, leaving much of their fundamental biology to be explored. Understanding the biology and ecology of MSVs can enlighten our knowledge of virus-virus interactions and lead to new innovations in the management of mosquito-borne viral diseases. We retrace the history of their discovery and discuss research milestones that would line the path from mosquito virome knowledge to vector management strategies.
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Affiliation(s)
- Cassandra Koh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France.
| | - Maria-Carla Saleh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
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2
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Park JY, Sivasankar C, Kirthika P, Prabhu D, Lee JH. Non-Structural Protein-W61 as a Novel Target in Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV): An In-Vitro and In-Silico Study on Protein-Protein Interactions with Nucleoprotein and Viral Replication. Viruses 2023; 15:1963. [PMID: 37766369 PMCID: PMC10535573 DOI: 10.3390/v15091963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
The non-structural protein (NSs) and nucleoprotein (NP) of the severe fever with thrombocytopenia syndrome virus (SFTSV) encoded by the S segment are crucial for viral pathogenesis. They reside in viroplasm-like structures (VLS), but their interaction and their significance in viral propagation remain unclear. Here, we investigated the significance of the association between NSs and NP during viral infection through in-silico and in-vitro analyses. Through in-silico analysis, three possible binding sites were predicted, at positions C6S (Cystein at 6th position to Serine), W61Y (Tryptophan 61st to Tyrosine), and S207T (Serine 207th to Threonine), three mutants of NSs were developed by site-directed mutagenesis and tested for NP interaction by co-immunoprecipitation. NSsW61Y failed to interact with the nucleoprotein, which was substantiated by the conformational changes observed in the structural analyses. Additionally, molecular docking analysis corroborated that the NSW61Y mutant protein does not interact well compared to wild-type NSs. Over-expression of wild-type NSs in HeLa cells increased the SFTSV replication by five folds, but NSsW61Y exhibited 1.9-folds less viral replication than wild-type. We demonstrated that the W61Y alteration was implicated in the reduction of NSs-NP interaction and viral replication. Thus, the present study identified a critical NSs site, which could be targeted for development of therapeutic regimens against SFTSV.
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Affiliation(s)
- Ji-Young Park
- Department of Veterinary Public Health, College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea (P.K.)
| | - Chandran Sivasankar
- Department of Veterinary Public Health, College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea (P.K.)
| | - Perumalraja Kirthika
- Department of Veterinary Public Health, College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea (P.K.)
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Dhamodharan Prabhu
- Centre for Drug Discovery, Karpagam Academy of Higher Education, Coimbatore 641021, India;
| | - John Hwa Lee
- Department of Veterinary Public Health, College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea (P.K.)
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3
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Chen RX, Gong HY, Wang X, Sun MH, Ji YF, Tan SM, Chen JM, Shao JW, Liao M. Zoonotic Hantaviridae with Global Public Health Significance. Viruses 2023; 15:1705. [PMID: 37632047 PMCID: PMC10459939 DOI: 10.3390/v15081705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Hantaviridae currently encompasses seven genera and 53 species. Multiple hantaviruses such as Hantaan virus, Seoul virus, Dobrava-Belgrade virus, Puumala virus, Andes virus, and Sin Nombre virus are highly pathogenic to humans. They cause hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome or hantavirus pulmonary syndrome (HCPS/HPS) in many countries. Some hantaviruses infect wild or domestic animals without causing severe symptoms. Rodents, shrews, and bats are reservoirs of various mammalian hantaviruses. Recent years have witnessed significant advancements in the study of hantaviruses including genomics, taxonomy, evolution, replication, transmission, pathogenicity, control, and patient treatment. Additionally, new hantaviruses infecting bats, rodents, shrews, amphibians, and fish have been identified. This review compiles these advancements to aid researchers and the public in better recognizing this zoonotic virus family with global public health significance.
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Affiliation(s)
- Rui-Xu Chen
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (R.-X.C.); (H.-Y.G.); (X.W.); (M.-H.S.); (Y.-F.J.); (S.-M.T.)
| | - Huan-Yu Gong
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (R.-X.C.); (H.-Y.G.); (X.W.); (M.-H.S.); (Y.-F.J.); (S.-M.T.)
| | - Xiu Wang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (R.-X.C.); (H.-Y.G.); (X.W.); (M.-H.S.); (Y.-F.J.); (S.-M.T.)
| | - Ming-Hui Sun
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (R.-X.C.); (H.-Y.G.); (X.W.); (M.-H.S.); (Y.-F.J.); (S.-M.T.)
| | - Yu-Fei Ji
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (R.-X.C.); (H.-Y.G.); (X.W.); (M.-H.S.); (Y.-F.J.); (S.-M.T.)
| | - Su-Mei Tan
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (R.-X.C.); (H.-Y.G.); (X.W.); (M.-H.S.); (Y.-F.J.); (S.-M.T.)
| | - Ji-Ming Chen
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (R.-X.C.); (H.-Y.G.); (X.W.); (M.-H.S.); (Y.-F.J.); (S.-M.T.)
| | - Jian-Wei Shao
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (R.-X.C.); (H.-Y.G.); (X.W.); (M.-H.S.); (Y.-F.J.); (S.-M.T.)
| | - Ming Liao
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510230, China
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4
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Park JY, Hewawaduge C, Sivasankar C, Lloren KKS, Oh B, So MY, Lee JH. An mRNA-Based Multiple Antigenic Gene Expression System Delivered by Engineered Salmonella for Severe Fever with Thrombocytopenia Syndrome and Assessment of Its Immunogenicity and Protection Using a Human DC-SIGN-Transduced Mouse Model. Pharmaceutics 2023; 15:pharmaceutics15051339. [PMID: 37242581 DOI: 10.3390/pharmaceutics15051339] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/14/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Currently, there are no commercial vaccines or therapeutics against severe fever with thrombocytopenia syndrome (SFTS) virus. This study explored an engineered Salmonella as a vaccine carrier to deliver a eukaryotic self-mRNA replicating vector, pJHL204. This vector expresses multiple SFTS virus antigenic genes for the nucleocapsid protein (NP), glycoprotein precursor (Gn/Gc), and nonstructural protein (NS) to induce host immune responses. The engineered constructs were designed and validated through 3D structure modeling. Western blot and qRT-PCR analyses of transformed HEK293T cells confirmed the delivery and expression of the vaccine antigens. Significantly, mice immunized with these constructs demonstrated a cell-mediated and humoral response as balanced Th1/Th2 immunity. The JOL2424 and JOL2425 delivering NP and Gn/Gc generated strong immunoglobulin IgG and IgM antibodies and high neutralizing titers. To further examine the immunogenicity and protection, we utilized a human DC-SIGN receptor transduced mouse model for SFTS virus infection by an adeno-associated viral vector system. Among the SFTSV antigen constructs, the construct with full-length NP and Gn/Gc and the construct with NP and selected Gn/Gc epitopes induced robust cellular and humoral immune responses. These were followed by adequate protection based on viral titer reduction and reduced histopathological lesions in the spleen and liver. In conclusion, these data indicate that recombinant attenuated Salmonella JOL2424 and JOL2425 delivering NP and Gn/Gc antigens of SFTSV are promising vaccine candidates that induce strong humoral and cellular immune responses and protection against SFTSV. Moreover, the data proved that the hDC-SIGN transduced mice as a worthy tool for immunogenicity study for SFTSV.
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Affiliation(s)
- Ji-Young Park
- Department of Veterinary Public Health, College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - Chamith Hewawaduge
- Department of Veterinary Public Health, College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - Chandran Sivasankar
- Department of Veterinary Public Health, College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - Khristine Kaith S Lloren
- Department of Veterinary Public Health, College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - Byungkwan Oh
- Department of Veterinary Pathology, College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - Mi Young So
- Department of Veterinary Public Health, College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - John Hwa Lee
- Department of Veterinary Public Health, College of Veterinary Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
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5
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Simmonds P, Adriaenssens EM, Zerbini FM, Abrescia NGA, Aiewsakun P, Alfenas-Zerbini P, Bao Y, Barylski J, Drosten C, Duffy S, Duprex WP, Dutilh BE, Elena SF, García ML, Junglen S, Katzourakis A, Koonin EV, Krupovic M, Kuhn JH, Lambert AJ, Lefkowitz EJ, Łobocka M, Lood C, Mahony J, Meier-Kolthoff JP, Mushegian AR, Oksanen HM, Poranen MM, Reyes-Muñoz A, Robertson DL, Roux S, Rubino L, Sabanadzovic S, Siddell S, Skern T, Smith DB, Sullivan MB, Suzuki N, Turner D, Van Doorslaer K, Vandamme AM, Varsani A, Vasilakis N. Four principles to establish a universal virus taxonomy. PLoS Biol 2023; 21:e3001922. [PMID: 36780432 PMCID: PMC9925010 DOI: 10.1371/journal.pbio.3001922] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.
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Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - F. Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Nicola G. A. Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences—BRTA, Derio, Spain
- Basque Foundation for Science, IKERBASQUE, Bilbao, Spain
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jakub Barylski
- Department of Molecular Virology, Adam Mickiewicz University, Poznan, Poland
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt University, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - W. Paul Duprex
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University, Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Valencia, Spain
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Maria Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, La Plata, Argentina
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt University, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Aris Katzourakis
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Amy J. Lambert
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Elliot J. Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Cédric Lood
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics and Databases, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, Virginia, United States of America
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Minna M. Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Alejandro Reyes-Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Stuart Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Tim Skern
- Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Donald B. Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Matthew B. Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, Ohio, United States of America
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Dann Turner
- School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and University of Arizona Cancer Center, Tucson, Arizona, United States of America
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America
| | - Nikos Vasilakis
- Department of Pathology, Center of Vector-Borne and Zoonotic Diseases, Institute for Human Infection and Immunity and World Reference Center for Emerging Viruses and Arboviruses, The University of Texas Medical Branch, Galveston, Texas, United States of America
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6
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Highly adaptive
Phenuiviridae
with biomedical importance in multiple fields. J Med Virol 2022; 94:2388-2401. [DOI: 10.1002/jmv.27618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/24/2021] [Accepted: 01/21/2022] [Indexed: 11/07/2022]
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Koka H, Lutomiah J, Langat S, Koskei E, Nyunja A, Mutisya J, Mulwa F, Owaka S, Ofula V, Konongoi S, Eyase F, Sang R. Evidence of circulation of Orthobunyaviruses in diverse mosquito species in Kwale County, Kenya. Virol J 2021; 18:204. [PMID: 34641884 PMCID: PMC8507213 DOI: 10.1186/s12985-021-01670-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/16/2021] [Indexed: 12/05/2022] Open
Abstract
Background Arbovirus surveillance and recurrence of outbreaks in Kenya continues to reveal the re-emergence of viruses of public health importance. This calls for sustained efforts in early detection and characterization of these agents to avert future potential outbreaks. Methods A larval survey was carried out in three different sites in Kwale County, Vanga, Jego and Lunga Lunga. All containers in every accessible household and compound were sampled for immature mosquitoes. In addition, adult mosquitoes were also sampled using CO2-baited CDC light traps and BG-Sentinel traps in the three sites and also in Tsuini. The mosquitoes were knocked down using trimethylamine and stored in a liquid nitrogen shipper for transportation to the laboratory where they were identified to species, pooled and homogenized ready for testing. Results A total of 366 houses and 1730 containers were inspected. The House Index (HI), Container Index (CI) and Breateau Index (BI) for Vanga Island were (3%: 0.66: 3.66) respectively. In Jego, a rural site, the HI, CI and BI were (2.4%: 0.48: 2.4) respectively. In Lunga Lunga, a site in an urban area, the HI, CI and BI were (22.03%: 3.97: 29.7) respectively. The indices suggest that this region is at risk of arbovirus transmission given they were above the WHO threshold (CI > 1, HI > 1% and BI > 5). The most productive containers were the concrete tanks (44.4%), plastic tank (22.2%), claypot (13.3%), plastic drums (8.9%), plastic basins (4%), jerricans (1.2%) and buckets (0.3%). Over 20,200 adult mosquitoes were collected using CDC light traps, and over 9,200 using BG- sentinel traps. These mosquitoes were screened for viruses by inoculating in Vero cells. Eleven Orthobunyavirus isolates were obtained from pools of Ae. pembaensis (4), Ae. tricholabis (1), Cx. quinquefasciatus (3), Culex spp. (1) and Cx. zombaensis (2). Five of the Orthobunyaviruses were sequenced and four of these were determined to be Bunyamwera viruses while one isolate was found to be Nyando virus. One isolate remained unidentified. Conclusions These results indicate circulation of Orthobunyaviruses known to cause diverse grades of febrile illness with rash in humans in this region and highlights the need for continued monitoring and surveillance to avert outbreaks.
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Affiliation(s)
- Hellen Koka
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya.
| | - Joel Lutomiah
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Solomon Langat
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Edith Koskei
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Albert Nyunja
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - James Mutisya
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Francis Mulwa
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Samuel Owaka
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Victor Ofula
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Samson Konongoi
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
| | - Fredrick Eyase
- US Army Medical Research Directorate - Kenya, P. O. Box 606-00621, Nairobi, Kenya
| | - Rosemary Sang
- Centre for Virus Research, Kenya Medical Research Institute, P. O. Box 54628-00200, Nairobi, Kenya
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8
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The virome of German bats: comparing virus discovery approaches. Sci Rep 2021; 11:7430. [PMID: 33795699 PMCID: PMC8016945 DOI: 10.1038/s41598-021-86435-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
Bats are known to be reservoirs of several highly pathogenic viruses. Hence, the interest in bat virus discovery has been increasing rapidly over the last decade. So far, most studies have focused on a single type of virus detection method, either PCR, virus isolation or virome sequencing. Here we present a comprehensive approach in virus discovery, using all three discovery methods on samples from the same bats. By family-specific PCR screening we found sequences of paramyxoviruses, adenoviruses, herpesviruses and one coronavirus. By cell culture we isolated a novel bat adenovirus and bat orthoreovirus. Virome sequencing revealed viral sequences of ten different virus families and orders: three bat nairoviruses, three phenuiviruses, one orbivirus, one rotavirus, one orthoreovirus, one mononegavirus, five parvoviruses, seven picornaviruses, three retroviruses, one totivirus and two thymoviruses were discovered. Of all viruses identified by family-specific PCR in the original samples, none was found by metagenomic sequencing. Vice versa, none of the viruses found by the metagenomic virome approach was detected by family-specific PCRs targeting the same family. The discrepancy of detected viruses by different detection approaches suggests that a combined approach using different detection methods is necessary for virus discovery studies.
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9
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Kapuscinski ML, Bergren NA, Russell BJ, Lee JS, Borland EM, Hartman DA, King DC, Hughes HR, Burkhalter KL, Kading RC, Stenglein MD. Genomic characterization of 99 viruses from the bunyavirus families Nairoviridae, Peribunyaviridae, and Phenuiviridae, including 35 previously unsequenced viruses. PLoS Pathog 2021; 17:e1009315. [PMID: 33647063 PMCID: PMC7951987 DOI: 10.1371/journal.ppat.1009315] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 03/11/2021] [Accepted: 01/13/2021] [Indexed: 11/30/2022] Open
Abstract
Bunyaviruses (Negarnaviricota: Bunyavirales) are a large and diverse group of viruses that include important human, veterinary, and plant pathogens. The rapid characterization of known and new emerging pathogens depends on the availability of comprehensive reference sequence databases that can be used to match unknowns, infer evolutionary relationships and pathogenic potential, and make response decisions in an evidence-based manner. In this study, we determined the coding-complete genome sequences of 99 bunyaviruses in the Centers for Disease Control and Prevention's Arbovirus Reference Collection, focusing on orthonairoviruses (family Nairoviridae), orthobunyaviruses (Peribunyaviridae), and phleboviruses (Phenuiviridae) that either completely or partially lacked genome sequences. These viruses had been collected over 66 years from 27 countries from vertebrates and arthropods representing 37 genera. Many of the viruses had been characterized serologically and through experimental infection of animals but were isolated in the pre-sequencing era. We took advantage of our unusually large sample size to systematically evaluate genomic characteristics of these viruses, including reassortment, and co-infection. We corroborated our findings using several independent molecular and virologic approaches, including Sanger sequencing of 197 genome segments, and plaque isolation of viruses from putative co-infected virus stocks. This study contributes to the described genetic diversity of bunyaviruses and will enhance the capacity to characterize emerging human pathogenic bunyaviruses.
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Affiliation(s)
- Marylee L. Kapuscinski
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Nicholas A. Bergren
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Brandy J. Russell
- Arboviral Diseases Branch, Division of Vector Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Justin S. Lee
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Erin M. Borland
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Daniel A. Hartman
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - David C. King
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Holly R. Hughes
- Arboviral Diseases Branch, Division of Vector Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Kristen L. Burkhalter
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
- Arboviral Diseases Branch, Division of Vector Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Rebekah C. Kading
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Mark D. Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
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10
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A Look into Bunyavirales Genomes: Functions of Non-Structural (NS) Proteins. Viruses 2021; 13:v13020314. [PMID: 33670641 PMCID: PMC7922539 DOI: 10.3390/v13020314] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/12/2021] [Accepted: 02/16/2021] [Indexed: 12/13/2022] Open
Abstract
In 2016, the Bunyavirales order was established by the International Committee on Taxonomy of Viruses (ICTV) to incorporate the increasing number of related viruses across 13 viral families. While diverse, four of the families (Peribunyaviridae, Nairoviridae, Hantaviridae, and Phenuiviridae) contain known human pathogens and share a similar tri-segmented, negative-sense RNA genomic organization. In addition to the nucleoprotein and envelope glycoproteins encoded by the small and medium segments, respectively, many of the viruses in these families also encode for non-structural (NS) NSs and NSm proteins. The NSs of Phenuiviridae is the most extensively studied as a host interferon antagonist, functioning through a variety of mechanisms seen throughout the other three families. In addition, functions impacting cellular apoptosis, chromatin organization, and transcriptional activities, to name a few, are possessed by NSs across the families. Peribunyaviridae, Nairoviridae, and Phenuiviridae also encode an NSm, although less extensively studied than NSs, that has roles in antagonizing immune responses, promoting viral assembly and infectivity, and even maintenance of infection in host mosquito vectors. Overall, the similar and divergent roles of NS proteins of these human pathogenic Bunyavirales are of particular interest in understanding disease progression, viral pathogenesis, and developing strategies for interventions and treatments.
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11
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Kuhn JH. Virus Taxonomy. ENCYCLOPEDIA OF VIROLOGY 2021. [PMCID: PMC7157452 DOI: 10.1016/b978-0-12-809633-8.21231-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Virus taxonomy is the classification of viruses into categories called taxa and the development and implementation of a standardized nomenclature for taxa. Whereas virus taxonomy has been a niche subspecialty over many decades, the field has recently gained importance due to the exponentially increasing number of new viruses discovered by next-generation sequencing methods. The expanded known global virome and associated viral genome sequence space gradually morph virus taxonomy from a phenotype-based and inherently subjective process, focussing on shared or distinct, often arbitrarily chosen biophysical characteristics of virions to a significant subspecialty of systematic evolutionary biology. Indeed, current virus classification is increasingly performed using ever more complex phylogenetic approaches that move researchers closer to a rudimentary understanding of the origin, evolution, relatedness, and diversification of viruses over eons.
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Abstract
Bats have been gaining attention as potential reservoir hosts of numerous viruses pathogenic to animals and man. Issyk-Kul virus, a member of the family Nairoviridae, was first isolated in the 1970s from vespertilionid bats in Central Asia. Issyk-Kul virus has been described as human-pathogenic virus, causing febrile outbreaks in humans with headaches, myalgia and nausea. Here we describe the detection of a novel strain of Issyk-Kul virus from Eptesicus nilssonii in Germany. This finding indicates for the first time the prevalence of these zoonotic viruses in Europe.
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13
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Dutuze MF, Ingabire A, Gafarasi I, Uwituze S, Nzayirambaho M, Christofferson RC. Identification of Bunyamwera and Possible Other Orthobunyavirus Infections and Disease in Cattle during a Rift Valley Fever Outbreak in Rwanda in 2018. Am J Trop Med Hyg 2020; 103:183-189. [PMID: 32314686 PMCID: PMC7356447 DOI: 10.4269/ajtmh.19-0596] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In 2018, a large outbreak of Rift Valley fever (RVF)–like illness in cattle in Rwanda and surrounding countries was reported. From this outbreak, sera samples from 157 cows and 28 goats suspected to be cases of RVF were tested to confirm or determine the etiology of the disease. Specifically, the hypothesis that orthobunyaviruses—Bunyamwera virus (BUNV), Batai virus (BATV), and Ngari virus (NRIV)—were co-circulating and contributed to RVF-like disease was tested. Using reverse transcriptase-polymerase chain reaction (RT-PCR), RVFV RNA was detected in approximately 30% of acutely ill animals, but in all cases of hemorrhagic disease. Seven cows with experienced abortion had positive amplification and visualization by gel electrophoresis of all three segments of either BUNV or BATV, and three of these were suggested to be coinfected with BUNV and BATV. On sequencing, five of these seven cows were conclusively positive for BUNV. However, in several other animals, sequencing was successful for some but not all segments of targeted viruses BUNV and BATV. In addition, there was evidence of RVFV–orthobunyavirus coinfection, through RT-PCR/gel electrophoresis and subsequent Sanger sequencing. In no cases were we able to definitely identify the specific coinfecting viral species. This is the first time evidence for orthobunyavirus circulation has been molecularly confirmed in Rwanda. Furthermore, RT-PCR results suggest that BUNV and BATV may coinfect cattle and that RVFV-infected animals may be coinfected with other orthobunyaviruses. Finally, we confirm that BUNV and, perhaps, other orthobunyaviruses were co-circulating with RVFV and contributed to the burden of disease attributed to RVFV in Rwanda.
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Affiliation(s)
- Marie Fausta Dutuze
- College of Agriculture and Animal Sciences and Veterinary Medicine, University of Rwanda, Kigali, Rwanda.,School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana
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14
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Berčič RL, Bányai K, Růžek D, Fehér E, Domán M, Danielová V, Bakonyi T, Nowotny N. Phylogenetic Analysis of Lednice Orthobunyavirus. Microorganisms 2019; 7:microorganisms7100447. [PMID: 31614950 PMCID: PMC6843640 DOI: 10.3390/microorganisms7100447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 11/16/2022] Open
Abstract
Lednice virus (LEDV) has been detected in Culex modestus mosquitoes in several European countries within the last six decades. In this study, phylogenetic analyses of the complete genome segments confirm that LEDV belongs to the Turlock orthobunyavirus (Orthobunyavirus, Peribunyaviridae) species and is closely related to Umbre, Turlock, and Kedah viruses.
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Affiliation(s)
- Rebeka Lucijana Berčič
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Hungária krt. 23-25, 1143 Budapest, Hungary.
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, 1143 Budapest, Hungary.
| | - Daniel Růžek
- Department of Virology, Veterinary Research Institute, Hudcova 296, 621 00 Brno, Czech Republic.
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.
| | - Enikő Fehér
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, 1143 Budapest, Hungary.
| | - Marianna Domán
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, 1143 Budapest, Hungary.
| | - Vlasta Danielová
- National Institute of Public Health, Centre of Epidemiology and Microbiology, Šrobárova 48, 10042 Prague, Czech Republic.
| | - Tamás Bakonyi
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Hungária krt. 23-25, 1143 Budapest, Hungary.
| | - Norbert Nowotny
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Building 14, Dubai Healthcare, Dubai, UAE.
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15
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Evaluation of an Indirect Enzyme-Linked Immunosorbent Assay Based on Recombinant Baculovirus-Expressed Rift Valley Fever Virus Nucleoprotein as the Diagnostic Antigen. J Clin Microbiol 2019; 57:JCM.01058-19. [PMID: 31366690 DOI: 10.1128/jcm.01058-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 07/26/2019] [Indexed: 01/09/2023] Open
Abstract
The increasing risk of Rift Valley fever virus (RVFV) infection as a global veterinary and public health threat demands the development of safe and accurate diagnostic tests. The aim of this study was to assess the suitability of a baculovirus expression system to produce recombinant RVFV nucleoprotein (N) for use as serodiagnostic antigen in an indirect enzyme-linked immunosorbent assay (ELISA). The ability of the recombinant N antigen to detect RVFV antibody responses was evaluated in ELISA format using antisera from sheep and cattle experimentally infected with two genetically distinct wild-type RVFV strains and sera from indigenous sheep and goat populations exposed to natural RVFV field infection in The Gambia. The recombinant N exhibited specific reactivity with the N-specific monoclonal antibody and various hyperimmune serum samples from ruminants. The indirect ELISA detected N-specific antibody responses in animals with 100% sensitivity compared to the plaque reduction neutralization test (6 to 21 days postinfection) and with 97% and 100% specificity in sheep and cattle, respectively. There was a high level of correlation between the indirect N ELISA and the virus neutralization test for sheep sera (R 2 = 0.75; 95% confidence interval [CI] = 0.73 to 0.92) and cattle sera (R 2 = 0.80; 95% CI = 0.67 to 0.97); in addition, the N-specific ELISA detected RVFV seroprevalence levels of 26.1% and 54.3% in indigenous sheep and goats, respectively, in The Gambia. The high specificity and correlation with the virus neutralization test support the idea of the feasibility of using the recombinant baculovirus-expressed RVFV N-based indirect ELISA to assess RVFV seroprevalence in livestock in areas of endemicity and nonendemicity.
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16
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Calisher CH, Briese T, Brister JR, Charrel RN, Dürrwald R, Ebihara H, Fulhorst CF, Gāo GF, Groschup MH, Haddow AD, Hyndman TH, Junglen S, Klempa B, Klingström J, Kropinski AM, Krupovic M, LaBeaud AD, Maes P, Nowotny N, Nunes MRT, Payne SL, Radoshitzky SR, Rubbenstroth D, Sabanadzovic S, Sasaya T, Stenglein MD, Varsani A, Wahl V, Weaver SC, Zerbini FM, Vasilakis N, Kuhn JH. Strengthening the Interaction of the Virology Community with the International Committee on Taxonomy of Viruses (ICTV) by Linking Virus Names and Their Abbreviations to Virus Species. Syst Biol 2019; 68:828-839. [PMID: 30597118 PMCID: PMC6701456 DOI: 10.1093/sysbio/syy087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 12/16/2018] [Accepted: 11/19/2018] [Indexed: 01/09/2023] Open
Abstract
The International Committee on Taxonomy of Viruses (ICTV) is tasked with classifying viruses into taxa (phyla to species) and devising taxon names. Virus names and virus name abbreviations are currently not within the ICTV's official remit and are not regulated by an official entity. Many scientists, medical/veterinary professionals, and regulatory agencies do not address evolutionary questions nor are they concerned with the hierarchical organization of the viral world, and therefore, have limited use for ICTV-devised taxa. Instead, these professionals look to the ICTV as an expert point source that provides the most current taxonomic affiliations of viruses of interests to facilitate document writing. These needs are currently unmet as an ICTV-supported, easily searchable database that includes all published virus names and abbreviations linked to their taxa is not available. In addition, in stark contrast to other biological taxonomic frameworks, virus taxonomy currently permits individual species to have several members. Consequently, confusion emerges among those who are not aware of the difference between taxa and viruses, and because certain well-known viruses cannot be located in ICTV publications or be linked to their species. In addition, the number of duplicate names and abbreviations has increased dramatically in the literature. To solve this conundrum, the ICTV could mandate listing all viruses of established species and all reported unclassified viruses in forthcoming online ICTV Reports and create a searchable webpage using this information. The International Union of Microbiology Societies could also consider changing the mandate of the ICTV to include the nomenclature of all viruses in addition to taxon considerations. With such a mandate expansion, official virus names and virus name abbreviations could be catalogued and virus nomenclature could be standardized. As a result, the ICTV would become an even more useful resource for all stakeholders in virology.
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Affiliation(s)
- Charles H Calisher
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, 3195 Rampart Rd., Delivery Code 1690, Foothills Campus, Fort Collins, CO 80523-1692, USA
| | - Thomas Briese
- Department of Epidemiology, Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 St., New York, NY 10032, USA
| | - J Rodney Brister
- National Center for Biotechnology, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 27102, USA
| | - Rémi N Charrel
- Unité des Virus Emergents (Faculté de Médecine, Université Aix-Marseille—IRD 190—Inserm 1207—IHU Méditerranée Infection), Marseille, France
| | - Ralf Dürrwald
- Department of Infectious Diseases, Robert Koch-Institut, Postfach 65 02 61, D-13302 Berlin, Germany
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Guggenheim Building, 18th Floor, 200 First St. SW, Rochester, MN 55905, USA
| | - Charles F Fulhorst
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0609, USA
| | - George Fú Gāo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd., Changping District, Beijing 102206, China
| | - Martin H Groschup
- Institut für Virusdiagnostik, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Andrew D Haddow
- Department of Virology, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Timothy H Hyndman
- College of Veterinary Medicine, School of Veterinary and Life Sciences, Murdoch University, 90 South St., Murdoch, Western Australia 6150, Australia
| | - Sandra Junglen
- Institute of Virology, Charité Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Germany
- Deutsches Zentrum für Infektionsforschung, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Boris Klempa
- Biomedicínske centrum, Virologický ústav, Slovenská Akadémia Vied, Dúbravská cesta 9, 845 05 Bratislava, Slovakia
| | - Jonas Klingström
- Centre for Infectious Medicine, Institutionen för Medicin, Huddinge, Karolinska Institutet, C2:94, Karolinska Universitetssjukhuset, 141 86 Stockholm, Sweden
| | - Andrew M Kropinski
- Department of Food Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department of Pathobiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Mart Krupovic
- Departement of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
| | - A Desiree LaBeaud
- Division of Infectious Diseases, Department of Pediatrics, Stanford University School of Medicine, 300 Pasteur Dr., G312, Stanford, CA, 94305 USA
| | - Piet Maes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Zoonotic Infectious Diseases unit, Herestraat 49 box 1040, BE3000 Leuven, Belgium
| | - Norbert Nowotny
- Institute of Virology, Department of Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Building 14, Dubai Healthcare City, P.O. Box 505055, Dubai, United Arab Emirates
| | - Márcio Roberto Teixeira Nunes
- Evandro Chagas Institute, Brazilian Ministry of Health, Rodovia Br-316, Km 7 s/n, Levilândia, Ananindeua, Pará, 67030-000, Brazil
| | - Susan L Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Veterinary Medical Sciences Building, 400 Raymond Stotzer Parkway, Texas A&M University 4467, College Station, TX 77843, USA
| | - Sheli R Radoshitzky
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA
| | - Dennis Rubbenstroth
- Institut für Virusdiagnostik, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
- Institut für Virologie, Universitätsklinikum Freiburg, Hermann-Herder-Straße 11, 79104 Freiburg, Germany
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 402 Dorman Hall, Box 9655, Mississippi State, MS 39762, USA
| | - Takahide Sasaya
- Department of Planning and Coordination, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517, Japan
| | - Mark D Stenglein
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523 USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 727 E. Tyler St., P.O. Box 876101, Tempe, AZ 85287-6101, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, Frederick, MD 27102, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, Institute for Human Infections and Immunity, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO and National Institute of Science and Technology for Plant-Pest Interactions, Universidade Federal de Viçosa, Av. P.H. Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - Nikos Vasilakis
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, Center for Tropical Diseases, Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, B-8200 Research Plaza, Fort Detrick, Frederick, MD 27102, USA
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17
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Grossi-Soyster EN, Lee J, King CH, LaBeaud AD. The influence of raw milk exposures on Rift Valley fever virus transmission. PLoS Negl Trop Dis 2019; 13:e0007258. [PMID: 30893298 PMCID: PMC6443189 DOI: 10.1371/journal.pntd.0007258] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/01/2019] [Accepted: 02/23/2019] [Indexed: 02/07/2023] Open
Abstract
Rift Valley fever virus (RVFV) is a zoonotic phlebovirus that can be transmitted to humans or livestock by mosquitoes or through direct contact with contaminated bodily fluids and tissues. Exposure to bodily fluids and tissues varies by types of behaviors engaged for occupational tasks, homestead responsibilities, or use in dietary or therapeutic capacities. While previous studies have included milk exposures in their analyses, their primary focus on livestock exposures has been on animal handling, breeding, and slaughter. We analyzed data from multiple field surveys in Kenya with the aim of associating RVFV infection to raw milk exposures from common animal species. Of those with evidence of prior RVFV infection by serology (n = 267), 77.2% engaged in milking livestock compared to 32.0% for 3,956 co-local seronegative individuals (p < 0.001), and 86.5% of seropositive individuals consumed raw milk compared to 33.4% seronegative individuals (p < 0.001). Individuals who milked and also consumed raw milk had greater odds of RVFV exposure than individuals whose only contact to raw milk was through milking. Increased risks were associated with exposure to milk sourced from cows (p < 0.001), sheep (p < 0.001), and goats (p < 0.001), but not camels (p = 0.98 for consuming, p = 0.21 for milking). Our data suggest that exposure to raw milk may contribute to a significant number of cases of RVFV, especially during outbreaks and in endemic areas, and that some animal species may be associated with a higher risk for RVFV exposure. Livestock trade is regulated to limit RVFV spread from endemic areas, yet further interventions designed to fully understand the risk of RVFV exposure from raw milk are imperative.
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Affiliation(s)
- Elysse N. Grossi-Soyster
- Department of Pediatrics, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, United States of America
- * E-mail:
| | - Justin Lee
- Quantitative Sciences Unit, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Charles H. King
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, United States of America
| | - A. Desiree LaBeaud
- Department of Pediatrics, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, United States of America
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18
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Bergren NA, Kading RC. The Ecological Significance and Implications of Transovarial Transmission among the Vector-Borne Bunyaviruses: A Review. INSECTS 2018; 9:E173. [PMID: 30486417 PMCID: PMC6315607 DOI: 10.3390/insects9040173] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/12/2018] [Accepted: 11/21/2018] [Indexed: 11/20/2022]
Abstract
Transovarial transmission (TOT) is a widespread and efficient process through which pathogens can be passed between generations of arthropod vectors. Many species within the order Bunyavirales utilize TOT as a means of persisting within the environment when classical horizontal transmission is not possible due to ecological constraints. The purpose of this review is to summarize previous findings regarding the ecological significance of TOT among viruses in the order Bunyavirales and identify the gaps in knowledge regarding this important mechanism of arboviral maintenance.
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Affiliation(s)
- Nicholas A Bergren
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - Rebekah C Kading
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
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19
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Tangudu CS, Charles J, Blitvich BJ. Evidence that Lokern virus (family Peribunyaviridae) is a reassortant that acquired its small and large genome segments from Main Drain virus and its medium genome segment from an undiscovered virus. Virol J 2018; 15:122. [PMID: 30081908 PMCID: PMC6080421 DOI: 10.1186/s12985-018-1031-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/25/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lokern virus (LOKV) is a poorly characterized arthropod-borne virus belonging to the genus Orthobunyavirus (family Peribunyaviridae). All viruses in this genus have tripartite, single-stranded, negative-sense RNA genomes, and the three RNA segments are designated as small, (S), medium (M) and large (L). A 559 nt. region of the M RNA segment of LOKV has been sequenced and there are no sequence data available for its S or L RNA segments. The purpose of this study was to sequence the genome of LOKV. METHODS The genome of LOKV was fully sequenced by unbiased high-throughput sequencing, 5' and 3' rapid amplification of cDNA ends, reverse transcription-polymerase chain reaction and Sanger sequencing. RESULTS The S and L RNA segments of LOKV consist of 952 and 6864 nt. respectively and both have 99.0% nucleotide identity with the corresponding regions of Main Drain virus (MDV). In contrast, the 4450-nt. M RNA segment has only 59.0% nucleotide identity with the corresponding region of MDV and no more than 72.7% nucleotide identity with all other M RNA segment sequences in the Genbank database. Phylogenetic data support these findings. CONCLUSIONS This study provides evidence that LOKV is a natural reassortant that acquired its S and L RNA segments from MDV and its M RNA segment from an undiscovered, and possibly extinct, virus. The availability of complete genome sequence data facilitates the accurate detection, identification and diagnosis of viruses and viral infections, and this is especially true for viruses with segmented genomes because it can be difficult or even impossible to differentiate between reassortants and their precursors when incomplete sequence data are available.
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Affiliation(s)
- Chandra S Tangudu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jermilia Charles
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Bradley J Blitvich
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA. .,2116 Veterinary Medicine, Iowa State University, Ames, Iowa, 50011, USA.
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20
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Simmonds P, Aiewsakun P. Virus classification - where do you draw the line? Arch Virol 2018; 163:2037-2046. [PMID: 30039318 PMCID: PMC6096723 DOI: 10.1007/s00705-018-3938-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 11/23/2022]
Abstract
High-throughput sequencing (HTS) and its use in recovering and assembling novel virus sequences from environmental, human clinical, veterinary and plant samples has unearthed a vast new catalogue of viruses. Their classification, known by their sequences alone, sets a major challenge to traditional virus taxonomy, especially at the family and species levels, which have been historically based largely on descriptive taxon definitions. These typically entail some knowledge of their phenotypic properties, including replication strategies, virion structure and clinical and epidemiological features, such as host range, geographical distribution and disease outcomes. Little to no information on these attributes is available, however, for viruses identified in metagenomic datasets. If such viruses are to be included in virus taxonomy, their assignments will have to be guided largely or entirely by metrics of genetic relatedness. The immediate problem here is that the International Committee on Taxonomy of Viruses (ICTV), an organisation that authorises the taxonomic classification of viruses, provides little or no guidance on how similar or how divergent viruses must be in order to be considered members of new species or new families. We have recently developed a method for scoring genomic (dis)similarity between viruses (Genome Relationships Applied to Virus Taxonomy - GRAViTy) among the eukaryotic and prokaryotic viruses currently classified by the ICTV. At the family and genus levels, we found large-scale consistency between genetic relationships and their taxonomic assignments for eukaryotic viruses of all genome configurations and genome sizes. Family assignments of prokaryotic viruses have, however, been made at a quite different genetic level, and groupings currently classified as sub-families are a much better match to the eukaryotic virus family level. These findings support the ongoing reorganisation of bacteriophage taxonomy by the ICTV Phage Study Group. A rapid and objective means to explore metagenomic viral diversity and make evidence-based assignments for such viruses at each taxonomic layer is essential. Analysis of sequences by GRAViTy provides evidence that family (and genus) assignments of currently classified viruses are largely underpinned by genomic relatedness, and these features could serve as a guide towards an evidence-based classification of metagenomic viruses in the future.
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Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY UK
| | - Pakorn Aiewsakun
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY UK
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, 10400 Thailand
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