101
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Naveca FG, Nascimento VAD, Souza VCD, Nunes BTD, Rodrigues DSG, Vasconcelos PFDC. Multiplexed reverse transcription real-time polymerase chain reaction for simultaneous detection of Mayaro, Oropouche, and Oropouche-like viruses. Mem Inst Oswaldo Cruz 2017; 112:510-513. [PMID: 28591313 PMCID: PMC5452489 DOI: 10.1590/0074-02760160062] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 06/29/2016] [Indexed: 11/24/2022] Open
Abstract
We describe a sensitive method for simultaneous detection of Oropouche and Oropouche-like viruses carrying the Oropouche S segment, as well as the Mayaro virus, using a multiplexed one-step reverse transcription real-time polymerase chain reaction (RT-qPCR). A chimeric plasmid containing both Mayaro and Oropouche targets was designed and evaluated for the in vitro production of transcribed RNA, which could be easily used as a non-infectious external control. To track false-negative results due to PCR inhibition or equipment malfunction, the MS2 bacteriophage was also included in the multiplex assay as an internal positive control. The specificity of the multiplex assay was evaluated by Primer-Blast analysis against the entire GenBank database, and further against a panel of 17 RNA arboviruses. The results indicated an accurate and highly sensitive assay with amplification efficiency greater than 98% for both targets, and a limit of detection between two and 20 copies per reaction. We believe that the assay described here will provide a tool for Mayaro and Oropouche virus detection, especially in areas where differential diagnosis of Dengue, Zika and Chikungunya viruses should be performed.
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Affiliation(s)
- Felipe Gomes Naveca
- Fundação Oswaldo Cruz-Fiocruz, Instituto Leônidas e Maria Deane, Manaus, AM, Brasil
| | | | | | - Bruno Tardelli Diniz Nunes
- Ministério da Saúde, Secretaria de Vigilância em Saúde, Instituto Evandro Chagas, Ananindeua, PA, Brasil
| | | | - Pedro Fernando da Costa Vasconcelos
- Ministério da Saúde, Secretaria de Vigilância em Saúde, Instituto Evandro Chagas, Ananindeua, PA, Brasil.,Unversidade do Estado do Pará, Belém, PA, Brasil
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102
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The Potential for Reassortment between Oropouche and Schmallenberg Orthobunyaviruses. Viruses 2017; 9:v9080220. [PMID: 28800086 PMCID: PMC5580477 DOI: 10.3390/v9080220] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 08/03/2017] [Accepted: 08/06/2017] [Indexed: 12/30/2022] Open
Abstract
A number of viruses within the Peribunyaviridae family are naturally occurring reassortants, a common phenomenon for segmented viruses. Using a minigenome-reporter and virus-like particle (VLP) production assay, we have accessed the potential of Oropouche virus (OROV), Schmallenberg virus (SBV), and other orthobunyaviruses within the Simbu serogroup to reassort. We found that the untranslated region (UTR) in the medium segment is a potential contributing factor for reassortment by the tested viruses. We demonstrate that for promoter activity to occur it was essential that the viral RNA polymerase (L) and nucleocapsid (N) proteins were from the same virus, reinforcing the hypothesis that the large and small segments that encode these proteins segregate together during genome reassortment. Our results indicate that, given the right epidemiological setting, reassortment between SBV and OROV would potentially be feasible and could contribute to the emergence of a new Simbu virus.
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103
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Dinçer E, Brinkmann A, Hekimoğlu O, Hacıoğlu S, Földes K, Karapınar Z, Polat PF, Oğuz B, Orunç Kılınç Ö, Hagedorn P, Özer N, Özkul A, Nitsche A, Ergünay K. Generic amplification and next generation sequencing reveal Crimean-Congo hemorrhagic fever virus AP92-like strain and distinct tick phleboviruses in Anatolia, Turkey. Parasit Vectors 2017; 10:335. [PMID: 28705183 PMCID: PMC5513282 DOI: 10.1186/s13071-017-2279-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/06/2017] [Indexed: 01/31/2023] Open
Abstract
Background Ticks are involved with the transmission of several viruses with significant health impact. As incidences of tick-borne viral infections are rising, several novel and divergent tick- associated viruses have recently been documented to exist and circulate worldwide. This study was performed as a cross-sectional screening for all major tick-borne viruses in several regions in Turkey. Next generation sequencing (NGS) was employed for virus genome characterization. Ticks were collected at 43 locations in 14 provinces across the Aegean, Thrace, Mediterranean, Black Sea, central, southern and eastern regions of Anatolia during 2014–2016. Following morphological identification, ticks were pooled and analysed via generic nucleic acid amplification of the viruses belonging to the genera Flavivirus, Nairovirus and Phlebovirus of the families Flaviviridae and Bunyaviridae, followed by sequencing and NGS in selected specimens. Results A total of 814 specimens, comprising 13 tick species, were collected and evaluated in 187 pools. Nairovirus and phlebovirus assays were positive in 6 (3.2%) and 48 (25.6%) pools. All nairovirus sequences were closely-related to the Crimean-Congo hemorrhagic fever virus (CCHFV) strain AP92 and formed a phylogenetically distinct cluster among related strains. Major portions of the CCHFV genomic segments were obtained via NGS. Phlebovirus sequencing revealed several tick-associated virus clades, including previously-characterized Antigone, Lesvos, KarMa and Bole tick viruses, as well as a novel clade. A wider host range for tick-associated virus strains has been observed. NGS provided near-complete sequences of the L genomic segments of Antigone and KarMa clades, as well as Antigone partial S segment. Co- infections of CCHFV and KarMa or novel phlebovirus clades were detected in 2.1% of the specimens. Conclusions Widespread circulation of various tick-associated phlebovirus clades were documented for the first time in Anatolia. Genomes of CCHFV AP92 strains were identified in previously unexplored locations. NGS provided the most detailed genomic characterization of the Antigone and KarMa viruses to date. The epidemiological and health-related consequences must be elucidated. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2279-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ender Dinçer
- Mersin University, Advanced Technology Education, Research and Application Center, 33110, Mersin, Turkey
| | - Annika Brinkmann
- Robert Koch Institute; Center for Biological Threats and Special Pathogens 1 (ZBS-1), 13353, Berlin, Germany
| | - Olcay Hekimoğlu
- Faculty of Science, Department of Biology, Division of Ecology, Hacettepe University, 06800, Ankara, Turkey
| | - Sabri Hacıoğlu
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, 06110, Ankara, Turkey
| | - Katalin Földes
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, 06110, Ankara, Turkey
| | - Zeynep Karapınar
- Faculty of Veterinary Medicine, Department of Virology, Yuzuncu Yil University, 65080, Van, Turkey
| | - Pelin Fatoş Polat
- Faculty of Veterinary Medicine, Department of Internal Medicine, Harran University, 63200,, Sanlıurfa, Turkey
| | - Bekir Oğuz
- Faculty of Veterinary Medicine, Department of Virology, Yuzuncu Yil University, 65080, Van, Turkey
| | | | - Peter Hagedorn
- Robert Koch Institute; Center for Biological Threats and Special Pathogens 1 (ZBS-1), 13353, Berlin, Germany
| | - Nurdan Özer
- Faculty of Science, Department of Biology, Division of Ecology, Hacettepe University, 06800, Ankara, Turkey
| | - Aykut Özkul
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, 06110, Ankara, Turkey
| | - Andreas Nitsche
- Robert Koch Institute; Center for Biological Threats and Special Pathogens 1 (ZBS-1), 13353, Berlin, Germany
| | - Koray Ergünay
- Robert Koch Institute; Center for Biological Threats and Special Pathogens 1 (ZBS-1), 13353, Berlin, Germany. .,Faculty of Medicine, Department of Medical Microbiology, Virology Unit, Hacettepe University, 06100, Ankara, Turkey.
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104
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Patil BL, Dangwal M, Mishra R. Variability of Emaravirus Species Associated with Sterility Mosaic Disease of Pigeonpea in India Provides Evidence of Segment Reassortment. Viruses 2017; 9:E183. [PMID: 28696402 PMCID: PMC5537675 DOI: 10.3390/v9070183] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 11/16/2022] Open
Abstract
Sterility mosaic disease (SMD) of pigeonpea is a serious constraint for cultivation of pigeonpea in India and other South Asian countries. SMD of pigeonpea is associated with two distinct emaraviruses, Pigeonpea sterility mosaic virus 1 (PPSMV-1) and Pigeonpea sterility mosaic virus 2 (PPSMV-2), with genomes consisting of five and six negative-sense RNA segments, respectively. The recently published genome sequences of both PPSMV-1 and PPSMV-2 are from a single location, Patancheru from the state of Telangana in India. However, here we present the first report of sequence variability among 23 isolates of PPSMV-1 and PPSMV-2, collected from ten locations representing six states of India. Both PPSMV-1 and PPSMV-2 are shown to be present across India and to exhibit considerable sequence variability. Variability of RNA3 sequences was higher than the RNA4 sequences for both PPSMV-1 and PPSMV-2. Additionally, the sixth RNA segment (RNA6), previously reported to be associated with only PPSMV-2, is also associated with isolates of PPSMV-1. Multiplex reverse transcription PCR (RT-PCR) analyses show that PPSMV-1 and PPSMV-2 frequently occur as mixed infections. Further sequence analyses indicated the presence of reassortment of RNA4 between isolates of PPSMV-1 and PPSMV-2.
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Affiliation(s)
- Basavaprabhu L Patil
- ICAR-National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi 110012, India.
| | - Meenakshi Dangwal
- ICAR-National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi 110012, India.
| | - Ritesh Mishra
- ICAR-National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi 110012, India.
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105
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Wang J, Blasdell KR, Yin H, Walker PJ. A large-scale serological survey of Akabane virus infection in cattle, yak, sheep and goats in China. Vet Microbiol 2017; 207:7-12. [PMID: 28757043 DOI: 10.1016/j.vetmic.2017.05.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/17/2017] [Accepted: 05/17/2017] [Indexed: 11/19/2022]
Abstract
Akabane virus (AKAV) is a member of the Simbu serogroup, classified in the genus Orthobunyavirus, family Bunyaviridae. AKAV infection can cause abortion, stillbirth, and congenital arthrogryposis and hydranencephaly in cattle and sheep. The distribution and prevalence of AKAV infection in China is still unknown. A total of 2731 sera collected from 2006 to 2015 in 24 provinces of China from cattle, sheep, goats and yak were examined by serum neutralisation test. The overall seroprevalence rates for AKAV antibodies were 21.3% in cattle (471/2215) and 12.0% (17/142) in sheep or goats, and 0% in yak (0/374). The results indicated widespread AKAV infection in China among cattle and sheep but yak appear to have a low risk of infection. Using a selection of 50 AKAV-positive and 25 AKAV-negative cattle sera, neutralisation tests were also conducted to detect antibodies to several other Simbu serogroup bunyaviruses and closely related Leanyer virus. Although inconclusive, the data suggest that both Aino virus and Peaton virus, which have been reported previously in Japan and Korea, may also be present in cattle in China.
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Affiliation(s)
- Jidong Wang
- CSIRO Health & Biosecurity, Australian Animal Health Laboratory, Geelong 3200, Victoria, Australia; State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, Gansu, China
| | - Kim R Blasdell
- CSIRO Health & Biosecurity, Australian Animal Health Laboratory, Geelong 3200, Victoria, Australia
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, Gansu, China
| | - Peter J Walker
- CSIRO Health & Biosecurity, Australian Animal Health Laboratory, Geelong 3200, Victoria, Australia; School of Biological Sciences, The University of Queensland, St. Lucia 4072, Queensland, Australia.
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106
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Zhang J, Wang J, Wang L, Fu S, Li M, Zhao G, Zhu W, Wang D, Liang G. Molecular Characterization and Seroprevalence in Pigs of SC0806, a Cat Que Virus Isolated from Mosquitoes in Sichuan Province, China. Vector Borne Zoonotic Dis 2017; 15:423-31. [PMID: 26186514 DOI: 10.1089/vbz.2014.1767] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Simbu serogroup currently consists of a highly diverse group of related arboviruses that infect both humans and economically important livestock species. Cat Que virus (CQV), a Simbu serogroup virus of the genus Orthobunyavirus (family Bunyaviridae), was first isolated in 2004 from mosquitoes during surveillance of arbovirus activity in acute pediatric encephalitis in northern Vietnam. We report here the complete genome sequence of SC0806 isolated from mosquitoes (Culex tritaeniorhynchus) in Sichuan Province, China. Consistent with the genomic organization of Simbu serogroup viruses, the SC0806 genome comprises three RNA segments-a large (L) segment (6928 nucleotides) that encodes the 2261-amino-acid RNA-dependent RNA polymerase, a medium (M) segment (4481 nucleotides) that encodes the 1433-amino-acid polyprotein, and a small (S) segment (984 nucleotides) that encodes a 234-amino-acid nucleocapsid protein and a 95-amino-acid nonstructural protein. The respective lengths of the 5'-untranslated region (UTR) and 3'-UTR of L, M, and S are 56 and 86, 43 and 136, and 44 and 238 nucleotides. Sequence (nucleotide and deduced amino acid) comparison and phylogenetic analysis revealed that SC0806 was closely related to the reported Vietnam isolate CQV. This is the first time that CQV has been isolated in Sichuan Province, China. Anti-SC0806 immunoglobulin M (IgM) and IgG antibodies were found in pigs reared locally, indicating that CQV has formed a natural cycle in the local area. Surveillance of the distribution and pathogenicity of SC0806 should be strengthened.
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Affiliation(s)
- Jiake Zhang
- 1 Sichuan Center for Disease Control and Prevention , Chengdu, Sichuan, China
| | - Jinglin Wang
- 2 State Key Laboratory for Infectious Disease Prevention and Control, Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention , Chinese Center for Disease Control and Prevention, Beijing, China .,3 Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Hangzhou, China
| | - Lihua Wang
- 2 State Key Laboratory for Infectious Disease Prevention and Control, Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention , Chinese Center for Disease Control and Prevention, Beijing, China .,3 Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Hangzhou, China
| | - Shihong Fu
- 2 State Key Laboratory for Infectious Disease Prevention and Control, Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention , Chinese Center for Disease Control and Prevention, Beijing, China .,3 Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Hangzhou, China
| | - Minghua Li
- 2 State Key Laboratory for Infectious Disease Prevention and Control, Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention , Chinese Center for Disease Control and Prevention, Beijing, China .,3 Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Hangzhou, China
| | - Guoyan Zhao
- 4 Washington University , St. Louis, Missouri
| | - Wuyang Zhu
- 2 State Key Laboratory for Infectious Disease Prevention and Control, Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention , Chinese Center for Disease Control and Prevention, Beijing, China .,3 Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Hangzhou, China
| | - David Wang
- 4 Washington University , St. Louis, Missouri
| | - Guodong Liang
- 2 State Key Laboratory for Infectious Disease Prevention and Control, Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention , Chinese Center for Disease Control and Prevention, Beijing, China .,3 Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Hangzhou, China
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107
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de Souza Luna LK, Rodrigues AH, Santos RIM, Sesti-Costa R, Criado MF, Martins RB, Silva ML, Delcaro LS, Proença-Modena JL, Figueiredo LTM, Acrani GO, Arruda E. Oropouche virus is detected in peripheral blood leukocytes from patients. J Med Virol 2017; 89:1108-1111. [PMID: 27787907 DOI: 10.1002/jmv.24722] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2016] [Indexed: 11/05/2022]
Abstract
Oropouche virus (OROV) is a frequent cause of arboviral febrile disease in the Amazon. The present report describes studies done in two patients, one of them; the first OROV human case acquired outside of the Amazon, which have revealed for the first time the presence of OROV in peripheral blood leukocytes. This novel finding raises important issues regarding pathogenesis of human infections and may offer a new tool, for the rapid diagnosis of this neglected infection. J. Med. Virol. 89:1108-1111, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Luciano Kleber de Souza Luna
- Department of Cell and Molecular Biology, Virology Research Center, Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Alcir Humberto Rodrigues
- Department of Cell and Molecular Biology, Virology Research Center, Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Rodrigo Ivo Marques Santos
- Department of Cell and Molecular Biology, Virology Research Center, Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Renata Sesti-Costa
- Department of Biochemistry and Immunology, University of Sao Paulo School of Medicine, Ribeirao Preto, São Paulo, Brazil
| | - Miriã Ferreira Criado
- Department of Cell and Molecular Biology, Virology Research Center, Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Ronaldo B Martins
- Department of Cell and Molecular Biology, Virology Research Center, Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Maria Lúcia Silva
- Department of Cell and Molecular Biology, Virology Research Center, Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Luana Sella Delcaro
- Department of Internal Medicine, Virology Research Center, University of Sao Paulo School of Medicine, Ribeirao Preto, São Paulo, Brazil
| | - Jose Luiz Proença-Modena
- Department of Cell and Molecular Biology, Virology Research Center, Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Luiz Tadeu Moraes Figueiredo
- Department of Internal Medicine, Virology Research Center, University of Sao Paulo School of Medicine, Ribeirao Preto, São Paulo, Brazil
| | - Gustavo Olszanski Acrani
- Department of Cell and Molecular Biology, Virology Research Center, Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Eurico Arruda
- Department of Cell and Molecular Biology, Virology Research Center, Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, São Paulo, Brazil
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108
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Travassos da Rosa JF, de Souza WM, Pinheiro FDP, Figueiredo ML, Cardoso JF, Acrani GO, Nunes MRT. Oropouche Virus: Clinical, Epidemiological, and Molecular Aspects of a Neglected Orthobunyavirus. Am J Trop Med Hyg 2017; 96:1019-1030. [PMID: 28167595 PMCID: PMC5417190 DOI: 10.4269/ajtmh.16-0672] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
AbstractOropouche virus (OROV) is an important cause of arboviral illness in Latin American countries, more specifically in the Amazon region of Brazil, Venezuela and Peru, as well as in other countries such as Panama. In the past decades, the clinical, epidemiological, pathological, and molecular aspects of OROV have been published and provide the basis for a better understanding of this important human pathogen. Here, we describe the milestones in a comprehensive review of OROV epidemiology, pathogenesis, and molecular biology, including a description of the first isolation of the virus, the outbreaks during the past six decades, clinical aspects of OROV infection, diagnostic methods, genome and genetic traits, evolution, and viral dispersal.
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Affiliation(s)
| | - William Marciel de Souza
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland.,Virology Research Center, School of Medicine of Ribeirao Preto of University of São Paulo, São Paulo, Brazil
| | | | - Mário Luiz Figueiredo
- Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | | | | | - Márcio Roberto Teixeira Nunes
- Evandro Chagas Institute, Ministry of Health, Pará, Brazil.,Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas
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109
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Pereira A, Figueira L, Nunes M, Esteves A, Cotão AJ, Vieira ML, Maia C, Campino L, Parreira R. Multiple Phlebovirus (Bunyaviridae) genetic groups detected in Rhipicephalus , Hyalomma and Dermacentor ticks from southern Portugal. Ticks Tick Borne Dis 2017; 8:45-52. [DOI: 10.1016/j.ttbdis.2016.09.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 09/23/2016] [Accepted: 09/23/2016] [Indexed: 01/22/2023]
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110
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Pyke AT, Warrilow D. Archival Collections are Important in the Study of the Biology, Diversity, and Evolution of Arboviruses. Evol Bioinform Online 2016; 12:27-30. [PMID: 27688704 PMCID: PMC5024791 DOI: 10.4137/ebo.s40569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/16/2016] [Accepted: 08/17/2016] [Indexed: 11/05/2022] Open
Abstract
Historically, classifications of arboviruses were based on serological techniques. Hence, collections of arbovirus isolates have been central to this process by providing the antigenic reagents for these methods. However, with increasing concern about biosafety and security, the introduction of molecular biology techniques has led to greater emphasis on the storage of nucleic acid sequence data over the maintenance of archival material. In this commentary, we provide examples of where archival collections provide an important source of genetic material to assist in confirming the authenticity of reference strains and vaccine stocks, to clarify taxonomic relationships particularly when isolates of the same virus species have been collected across a wide expanse of time and space, for future phenotypic analysis, to determine the historical diversity of strains, and to understand the mechanisms leading to changes in genome structure and virus evolution.
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Affiliation(s)
- Alyssa T Pyke
- Public Health Virology Laboratory, Forensic and Scientific Services, Queensland Health, Archerfield, Queensland, Australia
| | - David Warrilow
- Public Health Virology Laboratory, Forensic and Scientific Services, Queensland Health, Archerfield, Queensland, Australia
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111
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Kim JA, Kim WK, No JS, Lee SH, Lee SY, Kim JH, Kho JH, Lee D, Song DH, Gu SH, Jeong ST, Park MS, Kim HC, Klein TA, Song JW. Genetic Diversity and Reassortment of Hantaan Virus Tripartite RNA Genomes in Nature, the Republic of Korea. PLoS Negl Trop Dis 2016; 10:e0004650. [PMID: 27315053 PMCID: PMC4912082 DOI: 10.1371/journal.pntd.0004650] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 03/30/2016] [Indexed: 11/19/2022] Open
Abstract
Background Hantaan virus (HTNV), a negative sense tripartite RNA virus of the Family Bunyaviridae, is the most prevalent hantavirus in the Republic of Korea (ROK). It is the causative agent of Hemorrhagic Fever with Renal Syndrome (HFRS) in humans and maintained in the striped field mouse, Apodemus agrarius, the primary zoonotic host. Clinical HFRS cases have been reported commonly in HFRS-endemic areas of Gyeonggi province. Recently, the death of a member of the ROK military from Gangwon province due to HFRS prompted an investigation of the epidemiology and distribution of hantaviruses in Gangwon and Gyeonggi provinces that border the demilitarized zone separating North and South Korea. Methodology and Principal Findings To elucidate the geographic distribution and molecular diversity of HTNV, whole genome sequences of HTNV Large (L), Medium (M), and Small (S) segments were acquired from lung tissues of A. agrarius captured from 2003–2014. Consistent with the clinical incidence of HFRS established by the Korea Centers for Disease Control & Prevention (KCDC), the prevalence of HTNV in naturally infected mice in Gangwon province was lower than for Gyeonggi province. Whole genomic sequences of 34 HTNV strains were identified and a phylogenetic analysis showed geographic diversity of the virus in the limited areas. Reassortment analysis first suggested an occurrence of genetic exchange of HTNV genomes in nature, ROK. Conclusion/Significance This study is the first report to demonstrate the molecular prevalence of HTNV in Gangwon province. Whole genome sequencing of HTNV showed well-supported geographic lineages and the molecular diversity in the northern region of ROK due to a natural reassortment of HTNV genomes. These observations contribute to a better understanding of the genetic diversity and molecular evolution of hantaviruses. Also, the full-length of HTNV tripartite genomes will provide a database for phylogeographic analysis of spatial and temporal outbreaks of hantavirus infection. Hemorrhagic Fever with Renal Syndrome (HFRS) and Hantavirus Pulmonary Syndrome (HPS) are endemic zoonotic infectious diseases caused by hantaviruses that belong to the Family Bunyaviridae containing negative-sense tripartite RNA genomes. Hantaviruses pose a critical emerging public health threat, with up to 200,000 clinical cases reported annually worldwide with 1–36% case fatality rates. In humans, hantavirus-borne diseases are contracted by the inhalation of viruses aerosolized from rodent excreta. However, there is no effective therapeutic or vaccine to prevent from the disease. Whole genome sequences of Hantaan virus (HTNV) were acquired from lung tissues of Apodemus agrarius captured in HFRS-endemic areas of the Republic of Korea (ROK). Phylogenetic analyses demonstrated that sequences of the HTNV tripartite genomes clustered geographically, showing broad diversity of HTNV throughout the areas surveyed. Reassortment analysis first suggested a natural occurrence of the HTNV genetic exchange in the ROK. These observations contribute to a better understanding of the genetic diversity and molecular evolution of hantaviruses in HFRS-endemic regions. The complete sequences of HTNV genomes will provide a database for the phylogeographic analysis and surveillance of endemic hantavirus-borne diseases.
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Affiliation(s)
- Jeong-Ah Kim
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Won-keun Kim
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Jin Sun No
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Seung-Ho Lee
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Sook-Young Lee
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Ji Hye Kim
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Jeong Hoon Kho
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Daesang Lee
- Agency for Defense Development, Yuseong-gu, Daejeon, Republic of Korea
| | - Dong Hyun Song
- Agency for Defense Development, Yuseong-gu, Daejeon, Republic of Korea
| | - Se Hun Gu
- Agency for Defense Development, Yuseong-gu, Daejeon, Republic of Korea
| | - Seong Tae Jeong
- Agency for Defense Development, Yuseong-gu, Daejeon, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, College of Medicine, Institute for Viral Diseases, Korea University, Seoul, Republic of Korea
| | - Heung-Chul Kim
- 168th Multifunctional Medical Battalion, 65th Medical Brigade, Unit 15247, 5th Medical Detachment, Yongsan Army Garrison, Seoul, Republic of Korea
| | - Terry A. Klein
- 65th Medical Brigade, Unit 15281, Public Health Command District-Korea, Yongsan Army Garrison, Seoul, Republic of Korea
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
- * E-mail:
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112
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Kuhn JH, Wiley MR, Rodriguez SE, Bào Y, Prieto K, Travassos da Rosa APA, Guzman H, Savji N, Ladner JT, Tesh RB, Wada J, Jahrling PB, Bente DA, Palacios G. Genomic Characterization of the Genus Nairovirus (Family Bunyaviridae). Viruses 2016; 8:E164. [PMID: 27294949 PMCID: PMC4926184 DOI: 10.3390/v8060164] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 05/25/2016] [Accepted: 05/26/2016] [Indexed: 12/21/2022] Open
Abstract
Nairovirus, one of five bunyaviral genera, includes seven species. Genomic sequence information is limited for members of the Dera Ghazi Khan, Hughes, Qalyub, Sakhalin, and Thiafora nairovirus species. We used next-generation sequencing and historical virus-culture samples to determine 14 complete and nine coding-complete nairoviral genome sequences to further characterize these species. Previously unsequenced viruses include Abu Mina, Clo Mor, Great Saltee, Hughes, Raza, Sakhalin, Soldado, and Tillamook viruses. In addition, we present genomic sequence information on additional isolates of previously sequenced Avalon, Dugbe, Sapphire II, and Zirqa viruses. Finally, we identify Tunis virus, previously thought to be a phlebovirus, as an isolate of Abu Hammad virus. Phylogenetic analyses indicate the need for reassignment of Sapphire II virus to Dera Ghazi Khan nairovirus and reassignment of Hazara, Tofla, and Nairobi sheep disease viruses to novel species. We also propose new species for the Kasokero group (Kasokero, Leopards Hill, Yogue viruses), the Ketarah group (Gossas, Issyk-kul, Keterah/soft tick viruses) and the Burana group (Wēnzhōu tick virus, Huángpí tick virus 1, Tǎchéng tick virus 1). Our analyses emphasize the sister relationship of nairoviruses and arenaviruses, and indicate that several nairo-like viruses (Shāyáng spider virus 1, Xīnzhōu spider virus, Sānxiá water strider virus 1, South Bay virus, Wǔhàn millipede virus 2) require establishment of novel genera in a larger nairovirus-arenavirus supergroup.
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Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
| | - Michael R Wiley
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Sergio E Rodriguez
- Galveston National Laboratory, Institute for Human Infection and Immunity, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Yīmíng Bào
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Karla Prieto
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Amelia P A Travassos da Rosa
- Galveston National Laboratory, Institute for Human Infection and Immunity, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Hilda Guzman
- Galveston National Laboratory, Institute for Human Infection and Immunity, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Nazir Savji
- School of Medicine, New York University, New York, NY 10016, USA.
| | - Jason T Ladner
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
| | - Robert B Tesh
- Galveston National Laboratory, Institute for Human Infection and Immunity, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
| | - Peter B Jahrling
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
| | - Dennis A Bente
- Galveston National Laboratory, Institute for Human Infection and Immunity, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA.
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113
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de Breuil S, Cañizares J, Blanca JM, Bejerman N, Trucco V, Giolitti F, Ziarsolo P, Lenardon S. Analysis of the coding-complete genomic sequence of groundnut ringspot virus suggests a common ancestor with tomato chlorotic spot virus. Arch Virol 2016; 161:2311-6. [PMID: 27260536 DOI: 10.1007/s00705-016-2912-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/24/2016] [Indexed: 11/29/2022]
Abstract
Groundnut ringspot virus (GRSV) and tomato chlorotic spot virus (TCSV) share biological and serological properties, so their identification is carried out by molecular methods. Their genomes consist of three segmented RNAs: L, M and S. The finding of a reassortant between these two viruses may complicate correct virus identification and requires the characterization of the complete genome. Therefore, we present for the first time the complete sequences of all the genes encoded by a GRSV isolate. The high level of sequence similarity between GRSV and TCSV (over 90 % identity) observed in the genes and proteins encoded in the M RNA support previous results indicating that these viruses probably have a common ancestor.
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Affiliation(s)
- Soledad de Breuil
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, X5020ICA, Córdoba, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB, CABA, Argentina.
| | - Joaquín Cañizares
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de Valencia (COMAV-UPV), Camino de Vera s/n, 46022, Valencia, Spain
| | - José Miguel Blanca
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de Valencia (COMAV-UPV), Camino de Vera s/n, 46022, Valencia, Spain
| | - Nicolás Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, X5020ICA, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB, CABA, Argentina
| | - Verónica Trucco
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, X5020ICA, Córdoba, Argentina
| | - Fabián Giolitti
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, X5020ICA, Córdoba, Argentina
| | - Peio Ziarsolo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de Valencia (COMAV-UPV), Camino de Vera s/n, 46022, Valencia, Spain
| | - Sergio Lenardon
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, X5020ICA, Córdoba, Argentina
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114
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Walker PJ, Widen SG, Wood TG, Guzman H, Tesh RB, Vasilakis N. A Global Genomic Characterization of Nairoviruses Identifies Nine Discrete Genogroups with Distinctive Structural Characteristics and Host-Vector Associations. Am J Trop Med Hyg 2016; 94:1107-1122. [PMID: 26903607 PMCID: PMC4856612 DOI: 10.4269/ajtmh.15-0917] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/13/2016] [Indexed: 01/08/2023] Open
Abstract
Nairoviruses are primarily tick-borne bunyaviruses, some of which are known to cause mild-to-severe febrile illness in humans or livestock. We describe the genome sequences of 11 poorly characterized nairoviruses that have ecological associations with either birds (Farallon, Punta Salinas, Sapphire II, Zirqa, Avalon, Clo Mor, Taggert, and Abu Hammad viruses), rodents (Qalyub and Bandia viruses), or camels (Dera Ghazi Khan virus). Global phylogenetic analyses of proteins encoded in the L, M, and S RNA segments of these and 20 other available nairovirus genomes identified nine well-supported genogroups (Nairobi sheep disease, Thiafora, Sakhalin, Keterah, Qalyub, Kasokero, Dera Ghazi Khan, Hughes, and Tamdy). Genogroup-specific structural variations were evident, particularly in the M segment encoding a polyprotein from which virion envelope glycoproteins (Gn and Gc) are generated by proteolytic processing. Structural variations include the extension, abbreviation, or absence sequences encoding an O-glycosylated mucin-like protein in the N-terminal domain, distinctive patterns of conserved cysteine residues in the GP38-like domain, insertion of sequences encoding a double-membrane-spanning protein (NSm) between the Gn and Gc domains, and the presence of an alternative long open reading frame encoding a viroporin-like transmembrane protein (Gx). We also observed strong genogroup-specific associations with categories of hosts and tick vectors.
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Affiliation(s)
- Peter J. Walker
- *Address correspondence to Peter J. Walker, CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, Victoria, 3220, Australia. E-mail:
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115
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Hontz RD, Guevara C, Halsey ES, Silvas J, Santiago FW, Widen SG, Wood TG, Casanova W, Vasilakis N, Watts DM, Kochel TJ, Ebihara H, Aguilar PV. Itaya virus, a Novel Orthobunyavirus Associated with Human Febrile Illness, Peru. Emerg Infect Dis 2016; 21:781-8. [PMID: 25898901 PMCID: PMC4412221 DOI: 10.3201/eid2105.141368] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Analysis of uncharacterized bunyavirus isolates identified a possible reassortant virus. Our genetic analyses of uncharacterized bunyaviruses isolated in Peru identified a possible reassortant virus containing small and large gene segment sequences closely related to the Caraparu virus and a medium gene segment sequence potentially derived from an unidentified group C orthobunyavirus. Neutralization tests confirmed serologic distinction among the newly identified virus and the prototype and Caraparu strains. This virus, named Itaya, was isolated in 1999 and 2006 from febrile patients in the cities of Iquitos and Yurimaguas in Peru. The geographic distance between the 2 cases suggests that the Itaya virus could be widely distributed throughout the Amazon basin in northeastern Peru. Identification of a new Orthobunyavirus species that causes febrile disease in humans reinforces the need to expand viral disease surveillance in tropical regions of South America.
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116
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Hover S, King B, Hall B, Loundras EA, Taqi H, Daly J, Dallas M, Peers C, Schnettler E, McKimmie C, Kohl A, Barr JN, Mankouri J. Modulation of Potassium Channels Inhibits Bunyavirus Infection. J Biol Chem 2015; 291:3411-22. [PMID: 26677217 PMCID: PMC4751384 DOI: 10.1074/jbc.m115.692673] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Indexed: 11/06/2022] Open
Abstract
Bunyaviruses are considered to be emerging pathogens facilitated by the segmented nature of their genome that allows reassortment between different species to generate novel viruses with altered pathogenicity. Bunyaviruses are transmitted via a diverse range of arthropod vectors, as well as rodents, and have established a global disease range with massive importance in healthcare, animal welfare, and economics. There are no vaccines or anti-viral therapies available to treat human bunyavirus infections and so development of new anti-viral strategies is urgently required. Bunyamwera virus (BUNV; genus Orthobunyavirus) is the model bunyavirus, sharing aspects of its molecular and cellular biology with all Bunyaviridae family members. Here, we show for the first time that BUNV activates and requires cellular potassium (K(+)) channels to infect cells. Time of addition assays using K(+) channel modulating agents demonstrated that K(+) channel function is critical to events shortly after virus entry but prior to viral RNA synthesis/replication. A similar K(+) channel dependence was identified for other bunyaviruses namely Schmallenberg virus (Orthobunyavirus) as well as the more distantly related Hazara virus (Nairovirus). Using a rational pharmacological screening regimen, two-pore domain K(+) channels (K2P) were identified as the K(+) channel family mediating BUNV K(+) channel dependence. As several K2P channel modulators are currently in clinical use, our work suggests they may represent a new and safe drug class for the treatment of potentially lethal bunyavirus disease.
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Affiliation(s)
- Samantha Hover
- From the School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT
| | - Barnabas King
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH
| | - Bradley Hall
- From the School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT
| | - Eleni-Anna Loundras
- From the School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT
| | - Hussah Taqi
- From the School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT
| | - Janet Daly
- Veterinary Medicine and Science, University of Nottingham, Nottingham NG7 2RD
| | - Mark Dallas
- School of Pharmacy, University of Reading, Reading RG6 6AP, and
| | - Chris Peers
- From the School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT
| | - Esther Schnettler
- MRC-University of Glasgow Centre for Virus Research, Scotland, Glasgow G61 1QH, United Kingdom
| | - Clive McKimmie
- MRC-University of Glasgow Centre for Virus Research, Scotland, Glasgow G61 1QH, United Kingdom
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Scotland, Glasgow G61 1QH, United Kingdom
| | - John N Barr
- From the School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT,
| | - Jamel Mankouri
- From the School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT,
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117
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Shchetinin AM, Lvov DK, Deriabin PG, Botikov AG, Gitelman AK, Kuhn JH, Alkhovsky SV. Genetic and Phylogenetic Characterization of Tataguine and Witwatersrand Viruses and Other Orthobunyaviruses of the Anopheles A, Capim, Guamá, Koongol, Mapputta, Tete, and Turlock Serogroups. Viruses 2015; 7:5987-6008. [PMID: 26610546 PMCID: PMC4664991 DOI: 10.3390/v7112918] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/22/2015] [Accepted: 11/07/2015] [Indexed: 01/12/2023] Open
Abstract
The family Bunyaviridae has more than 530 members that are distributed among five genera or remain to be classified. The genus Orthobunyavirus is the most diverse bunyaviral genus with more than 220 viruses that have been assigned to more than 18 serogroups based on serological cross-reactions and limited molecular-biological characterization. Sequence information for all three orthobunyaviral genome segments is only available for viruses belonging to the Bunyamwera, Bwamba/Pongola, California encephalitis, Gamboa, Group C, Mapputta, Nyando, and Simbu serogroups. Here we present coding-complete sequences for all three genome segments of 15 orthobunyaviruses belonging to the Anopheles A, Capim, Guamá, Kongool, Tete, and Turlock serogroups, and of two unclassified bunyaviruses previously not known to be orthobunyaviruses (Tataguine and Witwatersrand viruses). Using those sequence data, we established the most comprehensive phylogeny of the Orthobunyavirus genus to date, now covering 15 serogroups. Our results emphasize the high genetic diversity of orthobunyaviruses and reveal that the presence of the small nonstructural protein (NSs)-encoding open reading frame is not as common in orthobunyavirus genomes as previously thought.
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Affiliation(s)
- Alexey M Shchetinin
- D.I. Ivanovsky Institute of Virology, Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098, Moscow, Russia.
| | - Dmitry K Lvov
- D.I. Ivanovsky Institute of Virology, Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098, Moscow, Russia.
| | - Petr G Deriabin
- D.I. Ivanovsky Institute of Virology, Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098, Moscow, Russia.
| | - Andrey G Botikov
- D.I. Ivanovsky Institute of Virology, Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098, Moscow, Russia.
| | - Asya K Gitelman
- D.I. Ivanovsky Institute of Virology, Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098, Moscow, Russia.
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Sergey V Alkhovsky
- D.I. Ivanovsky Institute of Virology, Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098, Moscow, Russia.
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118
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Gilbertson RL, Batuman O, Webster CG, Adkins S. Role of the Insect SupervectorsBemisia tabaciandFrankliniella occidentalisin the Emergence and Global Spread of Plant Viruses. Annu Rev Virol 2015; 2:67-93. [DOI: 10.1146/annurev-virology-031413-085410] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Robert L. Gilbertson
- Department of Plant Pathology, University of California, Davis, California 95616; ,
| | - Ozgur Batuman
- Department of Plant Pathology, University of California, Davis, California 95616; ,
| | - Craig G. Webster
- US Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida 34945; ,
| | - Scott Adkins
- US Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida 34945; ,
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119
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Wiley CA, Bhardwaj N, Ross TM, Bissel SJ. Emerging Infections of CNS: Avian Influenza A Virus, Rift Valley Fever Virus and Human Parechovirus. Brain Pathol 2015; 25:634-50. [PMID: 26276027 PMCID: PMC4538697 DOI: 10.1111/bpa.12281] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 06/22/2015] [Indexed: 11/28/2022] Open
Abstract
History is replete with emergent pandemic infections that have decimated the human population. Given the shear mass of humans that now crowd the earth, there is every reason to suspect history will repeat itself. We describe three RNA viruses that have recently emerged in the human population to mediate severe neurological disease. These new diseases are results of new mutations in the infectious agents or new exposure pathways to the agents or both. To appreciate their pathogenesis, we summarize the essential virology and immune response to each agent. Infection is described in the context of known host defenses. Once the viruses evade immune defenses and enter central nervous system (CNS) cells, they rapidly co-opt host RNA processing to a cataclysmic extent. It is not clear why the brain is particularly susceptible to RNA viruses; but perhaps because of its tremendous dependence on RNA processing for physiological functioning, classical mechanisms of host defense (eg, interferon disruption of viral replication) are diminished or not available. Effectiveness of immunity, immunization and pharmacological therapies is reviewed to contextualize the scope of the public health challenge. Unfortunately, vaccines that confer protection from systemic disease do not necessarily confer protection for the brain after exposure through unconventional routes.
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Affiliation(s)
| | - Nitin Bhardwaj
- Department of Infectious Diseases and MicrobiologyUniversity of PittsburghPittsburghPA
- Present address:
Sanofi Pasteur1755 Steeles Avenue WestTorontoOntarioCanadaM2R 3T4
| | - Ted M. Ross
- Center for Vaccine DevelopmentUniversity of GeorgiaAthensGA
- Department of Infectious DiseasesUniversity of GeorgiaAthensGA
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120
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Palacios G, Wiley MR, Travassos da Rosa APA, Guzman H, Quiroz E, Savji N, Carrera JP, Bussetti AV, Ladner JT, Ian Lipkin W, Tesh RB. Characterization of the Punta Toro species complex (genus Phlebovirus, family Bunyaviridae). J Gen Virol 2015; 96:2079-2085. [PMID: 25934793 DOI: 10.1099/vir.0.000170] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Punta Toro virus (PTV), a member of the PTV complex, is a relatively common causative agent of febrile illness in Panama that is often misdiagnosed as 'dengue' or 'influenza'. Currently, only two named members make up this species complex, PTV and Buenaventura virus (BUEV). Genomic and antigenic characterization of 17 members of the PTV complex, nine of which were isolated from human acute febrile illness cases, reveals that this species complex is composed of six distant viruses. We propose to add four additional new viruses, designated Leticia virus, Cocle virus, Campana virus and Capira virus.
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Affiliation(s)
- Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases, Frederick, MD, USA
| | - Michael R Wiley
- Center for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases, Frederick, MD, USA
| | - Amelia P A Travassos da Rosa
- Center for Biodefense and Emerging Infectious Diseases, Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hilda Guzman
- Center for Biodefense and Emerging Infectious Diseases, Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Evelia Quiroz
- Department of Virology and Biotechnology Research, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Department of Microbiology, University of Panama, Panama City, Panama
| | - Nazir Savji
- School of Medicine, New York University, New York, NY, USA
| | - Jean-Paul Carrera
- Department of Virology and Biotechnology Research, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- School of Medicine, Columbus University, Panama City, Panama
| | | | - Jason T Ladner
- Center for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases, Frederick, MD, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Robert B Tesh
- Center for Biodefense and Emerging Infectious Diseases, Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
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121
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Tilston-Lunel NL, Hughes J, Acrani GO, da Silva DEA, Azevedo RSS, Rodrigues SG, Vasconcelos PFC, Nunes MRT, Elliott RM. Genetic analysis of members of the species Oropouche virus and identification of a novel M segment sequence. J Gen Virol 2015; 96:1636-50. [PMID: 25735305 PMCID: PMC4635451 DOI: 10.1099/vir.0.000108] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Oropouche virus (OROV) is a public health threat in South America, and in particular in northern Brazil, causing frequent outbreaks of febrile illness. Using a combination of deep sequencing and Sanger sequencing approaches, we determined the complete genome sequences of eight clinical isolates that were obtained from patient sera during an Oropouche fever outbreak in Amapa state, northern Brazil, in 2009. We also report the complete genome sequences of two OROV reassortants isolatd from two marmosets in Minas Gerais state, south-east Brazil, in 2012 that contained a novel M genome segment. Interestingly, all 10 isolates possessed a 947 nt S segment that lacked 11 residues in the S-segment 3′ UTR compared with the recently redetermined Brazilian prototype OROV strain BeAn19991. OROV maybe circulating more widely in Brazil and in the non-human primate population than previously appreciated, and the identification of yet another reassortant highlights the importance of bunyavirus surveillance in South America.
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Affiliation(s)
- Natasha L Tilston-Lunel
- 1MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK 2Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, Scotland, UK
| | - Joseph Hughes
- 1MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
| | - Gustavo Olszanski Acrani
- 1MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK 3Department of Cell and Molecular Biology, University of Sao Paulo School of Medicine, 3900, Av Bandeirantes, Ribeirão Preto, SP 14049-900, Brazil
| | - Daisy E A da Silva
- 4Center for Technological Innovation, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Raimunda S S Azevedo
- 5Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Sueli G Rodrigues
- 5Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Pedro F C Vasconcelos
- 5Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Marcio R T Nunes
- 4Center for Technological Innovation, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Richard M Elliott
- 1MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
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122
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Webster CG, Frantz G, Reitz SR, Funderburk JE, Mellinger HC, McAvoy E, Turechek WW, Marshall SH, Tantiwanich Y, McGrath MT, Daughtrey ML, Adkins S. Emergence of Groundnut ringspot virus and Tomato chlorotic spot virus in Vegetables in Florida and the Southeastern United States. PHYTOPATHOLOGY 2015; 105:388-398. [PMID: 25317844 DOI: 10.1094/phyto-06-14-0172-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Groundnut ringspot virus (GRSV) and Tomato chlorotic spot virus (TCSV) are two emerging tospoviruses in Florida. In a survey of the southeastern United States, GRSV and TCSV were frequently detected in solanaceous crops and weeds with tospovirus-like symptoms in south Florida, and occurred sympatrically with Tomato spotted wilt virus (TSWV) in tomato and pepper in south Florida. TSWV was the only tospovirus detected in other survey locations, with the exceptions of GRSV from tomato (Solanum lycopersicum) in South Carolina and New York, both of which are first reports. Impatiens (Impatiens walleriana) and lettuce (Lactuca sativa) were the only non-solanaceous GRSV and/or TCSV hosts identified in experimental host range studies. Little genetic diversity was observed in GRSV and TCSV sequences, likely due to the recent introductions of both viruses. All GRSV isolates characterized were reassortants with the TCSV M RNA. In laboratory transmission studies, Frankliniella schultzei was a more efficient vector of GRSV than F. occidentalis. TCSV was acquired more efficiently than GRSV by F. occidentalis but upon acquisition, transmission frequencies were similar. Further spread of GRSV and TCSV in the United States is possible and detection of mixed infections highlights the opportunity for additional reassortment of tospovirus genomic RNAs.
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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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124
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Bunyavirus-vector interactions. Viruses 2014; 6:4373-97. [PMID: 25402172 PMCID: PMC4246228 DOI: 10.3390/v6114373] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/30/2014] [Accepted: 11/04/2014] [Indexed: 01/23/2023] Open
Abstract
The Bunyaviridae family is comprised of more than 350 viruses, of which many within the Hantavirus, Orthobunyavirus, Nairovirus, Tospovirus, and Phlebovirus genera are significant human or agricultural pathogens. The viruses within the Orthobunyavirus, Nairovirus, and Phlebovirus genera are transmitted by hematophagous arthropods, such as mosquitoes, midges, flies, and ticks, and their associated arthropods not only serve as vectors but also as virus reservoirs in many cases. This review presents an overview of several important emerging or re-emerging bunyaviruses and describes what is known about bunyavirus-vector interactions based on epidemiological, ultrastructural, and genetic studies of members of this virus family.
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125
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Weber M, Weber F. RIG-I-like receptors and negative-strand RNA viruses: RLRly bird catches some worms. Cytokine Growth Factor Rev 2014; 25:621-8. [PMID: 24894317 PMCID: PMC7108359 DOI: 10.1016/j.cytogfr.2014.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 05/12/2014] [Indexed: 12/16/2022]
Abstract
Negative strand RNA viruses with a nonsegmented genome (ns-NSVs) or a segmented genome (s-NSVs) are an important source of human and animal diseases. Survival of the host from those infections is critically dependent on rapidly reacting innate immune responses. Two cytoplasmic RNA helicases, RIG-I and MDA5 (collectively termed RIG-I-like receptors, RLRs), are essential for recognizing virus-specific RNA structures to initiate a signalling cascade, resulting in the production of the antiviral type I interferons. Here, we will review the current knowledge and views on RLR agonists, RLR signalling, and the wide variety of countermeasures ns-NSVs and s-NSVs have evolved. Specific aspects include the consequences of genome segmentation for RLR activation and a discussion on the physiological ligands of RLRs.
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Affiliation(s)
- Michaela Weber
- Institute for Virology, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Friedemann Weber
- Institute for Virology, Philipps-University Marburg, D-35043 Marburg, Germany.
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126
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Abstract
Orthobunyaviruses, which have small, tripartite, negative-sense RNA genomes and structurally simple virions composed of just four proteins, can have devastating effects on human health and well-being, either by causing disease in humans or by causing disease in livestock and crops. In this Review, I describe the recent genetic and structural advances that have revealed important insights into the composition of orthobunyavirus virions, viral transcription and replication and viral interactions with the host innate immune response. Lastly, I highlight outstanding questions and areas of future research.
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Affiliation(s)
- Richard M Elliott
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, UK
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127
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Alimonti J, Leung A, Jones S, Gren J, Qiu X, Fernando L, Balcewich B, Wong G, Ströher U, Grolla A, Strong J, Kobinger G. Evaluation of transmission risks associated with in vivo replication of several high containment pathogens in a biosafety level 4 laboratory. Sci Rep 2014; 4:5824. [PMID: 25059478 PMCID: PMC5376055 DOI: 10.1038/srep05824] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 07/01/2014] [Indexed: 01/05/2023] Open
Abstract
Containment level 4 (CL4) laboratories studying biosafety level 4 viruses are under strict regulations to conduct nonhuman primate (NHP) studies in compliance of both animal welfare and biosafety requirements. NHPs housed in open-barred cages raise concerns about cross-contamination between animals, and accidental exposure of personnel to infectious materials. To address these concerns, two NHP experiments were performed. One examined the simultaneous infection of 6 groups of NHPs with 6 different viruses (Machupo, Junin, Rift Valley Fever, Crimean-Congo Hemorrhagic Fever, Nipah and Hendra viruses). Washing personnel between handling each NHP group, floor to ceiling biobubble with HEPA filter, and plexiglass between cages were employed for partial primary containment. The second experiment employed no primary containment around open barred cages with Ebola virus infected NHPs 0.3 meters from naïve NHPs. Viral antigen-specific ELISAs, qRT-PCR and TCID50 infectious assays were utilized to determine antibody levels and viral loads. No transmission of virus to neighbouring NHPs was observed suggesting limited containment protocols are sufficient for multi-viral CL4 experiments within one room. The results support the concept that Ebola virus infection is self-contained in NHPs infected intramuscularly, at least in the present experimental conditions, and is not transmitted to naïve NHPs via an airborne route.
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Affiliation(s)
- Judie Alimonti
- 1] Special Pathogens Program, Public Health Agency of Canada, 1015 Arlington St., Winnipeg. Manitoba [2]
| | - Anders Leung
- 1] Special Pathogens Program, Public Health Agency of Canada, 1015 Arlington St., Winnipeg. Manitoba [2]
| | - Shane Jones
- Special Pathogens Program, Public Health Agency of Canada, 1015 Arlington St., Winnipeg. Manitoba
| | - Jason Gren
- Containment Services, Public Health Agency of Canada, 1015 Arlington St., Winnipeg. Manitoba
| | - Xiangguo Qiu
- Special Pathogens Program, Public Health Agency of Canada, 1015 Arlington St., Winnipeg. Manitoba
| | - Lisa Fernando
- Special Pathogens Program, Public Health Agency of Canada, 1015 Arlington St., Winnipeg. Manitoba
| | - Brittany Balcewich
- Bioforensics Assay Development and Diagnostics; Public Health Agency of Canada, 1015 Arlington St., Winnipeg. Manitoba
| | - Gary Wong
- 1] Special Pathogens Program, Public Health Agency of Canada, 1015 Arlington St., Winnipeg. Manitoba [2] Departments of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Ute Ströher
- 1] Special Pathogens Program, Public Health Agency of Canada, 1015 Arlington St., Winnipeg. Manitoba [2]
| | - Allen Grolla
- Special Pathogens Program, Public Health Agency of Canada, 1015 Arlington St., Winnipeg. Manitoba
| | - James Strong
- 1] Special Pathogens Program, Public Health Agency of Canada, 1015 Arlington St., Winnipeg. Manitoba [2] Departments of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada [3] Departments of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Gary Kobinger
- 1] Special Pathogens Program, Public Health Agency of Canada, 1015 Arlington St., Winnipeg. Manitoba [2] Departments of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada [3] Departments of Immunology, University of Manitoba, Winnipeg, MB, Canada [4] Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
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128
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Next-generation sequencing of southern African Crimean-Congo haemorrhagic fever virus isolates reveals a high frequency of M segment reassortment. Epidemiol Infect 2014; 142:1952-62. [PMID: 24786748 DOI: 10.1017/s0950268814000818] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Crimean Congo haemorrhagic fever virus (CCHFV) is a bunyavirus with a single-stranded RNA genome consisting of three segments (S, M, L), coding for the nucleocapsid protein, envelope glycoproteins and RNA polymerase, respectively. To date only five complete genome sequences are available from southern African isolates. Complete genome sequences were generated for 10 southern African CCHFV isolates using next-generation sequencing techniques. The maximum-likelihood method was used to generate tree topologies for 15 southern African plus 26 geographically distinct complete sequences from GenBank. M segment reassortment was identified in 10/15 southern African isolates by incongruencies in grouping compared to the S and L segments. These reassortant M segments cluster with isolates from Asia/Middle East, while the S and L segments cluster with strains from South/West Africa. The CCHFV M segment shows a high level of genetic diversity, while the S and L segments appear to co-evolve. The reason for the high frequency of M segment reassortment is not known. It has previously been suggested that M segment reassortment results in a virus with high fitness but a clear role in increased pathogenicity has yet to be shown.
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129
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Genomic characterization of group C Orthobunyavirus reference strains and recent South American clinical isolates. PLoS One 2014; 9:e92114. [PMID: 24633174 PMCID: PMC3954874 DOI: 10.1371/journal.pone.0092114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 02/17/2014] [Indexed: 11/19/2022] Open
Abstract
Group C orthobunyaviruses (family Bunyaviridae, genus Orthobunyavirus), discovered in the 1950s, are vector-borne human pathogens in the Americas. Currently there is a gap in genomic information for group C viruses. In this study, we obtained complete coding region sequences of reference strains of Caraparu (CARV), Oriboca (ORIV), Marituba (MTBV) and Madrid (MADV) viruses, and five clinical isolates from Peru and Bolivia, using an unbiased de novo approach consisting of random reverse transcription, random anchored PCR amplification, and high throughput pyrosequencing. The small, medium, and large segments encode for a 235 amino acid nucleocapsid protein, an approximately 1430 amino acid surface glycoprotein polyprotein precursor, and a 2248 amino acid RNA-dependent RNA polymerase, respectively. Additionally, the S segment encodes for an 83 amino acid non-structural protein, although this protein is truncated or silenced in some isolates. Phylogenetically, three clinical isolates clustered with CARV, one clustered with MTBV, and one isolate appeared to be a reassortant or a genetic drift resulted from the high variability of the medium segment which was also seen in a few other orthobunyaviruses. These data represent the first complete coding region sequences for this serocomplex of pathogenic orthobunyaviruses. The genome-wide phylogeny of reference strains is consistent with the antigenic properties of the viruses reported in the original serological studies conducted in the 1960s. Comparative analysis of conserved protein regions across group C virus strains and the other orthobunyavirus groups revealed that these group C viruses contain characteristic domains of potential structural and functional significance. Our results provide the basis for the developments of diagnostics, further genetic analyses, and future epidemiologic studies of group C viruses.
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130
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Ladner JT, Savji N, Lofts L, Travassos da Rosa A, Wiley MR, Gestole MC, Rosen GE, Guzman H, Vasconcelos PFC, Nunes MRT, J Kochel T, Lipkin WI, Tesh RB, Palacios G. Genomic and phylogenetic characterization of viruses included in the Manzanilla and Oropouche species complexes of the genus Orthobunyavirus, family Bunyaviridae. J Gen Virol 2014; 95:1055-1066. [PMID: 24558222 DOI: 10.1099/vir.0.061309-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A thorough characterization of the genetic diversity of viruses present in vector and vertebrate host populations is essential for the early detection of and response to emerging pathogenic viruses, yet genetic characterization of many important viral groups remains incomplete. The Simbu serogroup of the genus Orthobunyavirus, family Bunyaviridae, is an example. The Simbu serogroup currently consists of a highly diverse group of related arboviruses that infect both humans and economically important livestock species. Here, we report complete genome sequences for 11 viruses within this group, with a focus on the large and poorly characterized Manzanilla and Oropouche species complexes. Phylogenetic and pairwise divergence analyses indicated the presence of high levels of genetic diversity within these two species complexes, on a par with that seen among the five other species complexes in the Simbu serogroup. Based on previously reported divergence thresholds between species, the data suggested that these two complexes should actually be divided into at least five species. Together these five species formed a distinct phylogenetic clade apart from the rest of the Simbu serogroup. Pairwise sequence divergences among viruses of this clade and viruses in other Simbu serogroup species complexes were similar to levels of divergence among the other orthobunyavirus serogroups. The genetic data also suggested relatively high levels of natural reassortment, with three potential reassortment events present, including two well-supported events involving viruses known to infect humans.
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Affiliation(s)
- Jason T Ladner
- Center for Genomic Sciences, United States Army Medical Institute for Infectious Disease, Frederick, MD, USA
| | - Nazir Savji
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Loreen Lofts
- Center for Genomic Sciences, United States Army Medical Institute for Infectious Disease, Frederick, MD, USA
| | - Amelia Travassos da Rosa
- Center for Biodefense and Emerging Infectious Diseases, Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Michael R Wiley
- Center for Genomic Sciences, United States Army Medical Institute for Infectious Disease, Frederick, MD, USA
| | - Marie C Gestole
- Center for Genomic Sciences, United States Army Medical Institute for Infectious Disease, Frederick, MD, USA
| | - Gail E Rosen
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Hilda Guzman
- Center for Biodefense and Emerging Infectious Diseases, Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pedro F C Vasconcelos
- Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Marcio R T Nunes
- Virology Department, Naval Medical Research Unit Six, Lima, Peru
| | - Tadeusz J Kochel
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Robert B Tesh
- Center for Biodefense and Emerging Infectious Diseases, Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Gustavo Palacios
- Center for Genomic Sciences, United States Army Medical Institute for Infectious Disease, Frederick, MD, USA
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131
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Calisher CH, Tesh RB. Two misleading words in reports of virus discovery: little things mean a lot. Arch Virol 2014; 159:2189-91. [PMID: 24532301 DOI: 10.1007/s00705-014-2008-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 01/26/2014] [Indexed: 10/25/2022]
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, Fort Collins, CO, 80523-1690, USA,
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