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Characterization of viruses in a tapeworm: phylogenetic position, vertical transmission, and transmission to the parasitized host. ISME JOURNAL 2020; 14:1755-1767. [PMID: 32286546 PMCID: PMC7305300 DOI: 10.1038/s41396-020-0642-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 12/19/2022]
Abstract
Parasitic flatworms (Neodermata) infect all vertebrates and represent a significant health and economic burden worldwide due to the debilitating diseases they cause. This study sheds light for the first time into the virome of a tapeworm by describing six novel RNA virus candidate species associated with Schistocephalus solidus, including three negative-strand RNA viruses (order Jingchuvirales, Mononegavirales, and Bunyavirales) and three double-stranded RNA viruses. Using in vitro culture of S. solidus, controlled experimental infections and field sampling, we demonstrate that five of these viruses are vertically transmitted, and persist throughout the S. solidus complex life cycle. Moreover, we show that one of the viruses, named Schistocephalus solidus rhabdovirus (SsRV1), is excreted by the parasite and transmitted to parasitized hosts indicating that it may impact S. solidus-host interactions. In addition, SsRV1 has a basal phylogenetic position relative to vertebrate rhabdoviruses suggesting that parasitic flatworms could have contributed to virus emergence. Viruses similar to four of the S. solidus viruses identified here were found in geographically distant S. solidus populations through data mining. Further studies are necessary to determine if flatworm viruses can replicate in parasitized hosts, how they contribute to parasite infection dynamics and if these viruses could be targeted for treatment of parasitic disease.
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Bejerman N, Acevedo RM, de Breuil S, Ruiz OA, Sansberro P, Dietzgen RG, Nome C, Debat H. Molecular characterization of a novel cytorhabdovirus with a unique genomic organization infecting yerba mate (Ilex paraguariensis) in Argentina. Arch Virol 2020; 165:1475-1479. [PMID: 32246285 DOI: 10.1007/s00705-020-04609-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/10/2020] [Indexed: 01/02/2023]
Abstract
The genome of a novel rhabdovirus was detected in yerba mate (Ilex paraguariensis St. Hil.). The newly identified virus, tentatively named "yerba mate virus A" (YmVA), has a genome of 14,961 nucleotides. Notably, eight open reading frames were identified in the antigenomic orientation of the negative-sense, single-stranded viral RNA, including two novel accessory genes, in the order 3'-N-P-3-4-M-G-L-8-5'. Sequence comparisons of the encoded proteins as well as phylogenetic analysis suggest that YmVA is a new member of the genus Cytorhabdovirus, family Rhabdoviridae. YmVA's unique genomic organization and phylogenetic relationships indicate that this virus likely represents a distinct evolutionary lineage among the cytorhabdoviruses.
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Affiliation(s)
- 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, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina.
| | - Raúl Maximiliano Acevedo
- Laboratorio de Biotecnología Aplicada y Genómica Funcional. Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (IBONE-CONICET), Universidad Nacional del Nordeste, W3402BKG, Corrientes, Argentina
| | - 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, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina
| | - Oscar A Ruiz
- INTECH (UNSAM-CONICET), Unidad de Biotecnología 1, B7130IWA, Chascomús, Argentina
| | - Pedro Sansberro
- Laboratorio de Biotecnología Aplicada y Genómica Funcional. Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (IBONE-CONICET), Universidad Nacional del Nordeste, W3402BKG, Corrientes, Argentina
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Claudia Nome
- 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, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina
| | - Humberto Debat
- 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, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina
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53
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Human Tibroviruses: Commensals or Lethal Pathogens? Viruses 2020; 12:v12030252. [PMID: 32106547 PMCID: PMC7150972 DOI: 10.3390/v12030252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 12/16/2022] Open
Abstract
Rhabdoviruses are a large and ecologically diverse family of negative-sense RNA viruses (Mononegavirales: Rhabdoviridae). These viruses are capable of infecting an unexpectedly wide variety of plants, vertebrates, and invertebrates distributed over all human-inhabited continents. However, only a few rhabdoviruses are known to infect humans: a ledantevirus (Le Dantec virus), several lyssaviruses (in particular, rabies virus), and several vesiculoviruses (e.g., Chandipura virus, vesicular stomatitis Indiana virus). Recently, several novel rhabdoviruses have been discovered in the blood of both healthy and severely ill individuals living in Central and Western Africa. These viruses—Bas-Congo virus, Ekpoma virus 1, and Ekpoma virus 2—are members of the little-understood rhabdoviral genus Tibrovirus. Other than the basic genomic architecture, tibroviruses bear little resemblance to well-studied rhabdoviruses such as rabies virus and vesicular stomatitis Indiana virus. These three human tibroviruses are quite divergent from each other, and each of them clusters closely with tibroviruses currently known only from biting midges or healthy cattle. Seroprevalence studies suggest that human tibrovirus infections may be common but are almost entirely unrecognized. The pathogenic potential of this diverse group of viruses remains unknown. Although certain tibroviruses may be benign and well-adapted to humans, others could be newly emerging and produce serious disease. Here, we review the current knowledge of tibroviruses and argue that assessing their impact on human health should be an urgent priority.
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Identification and characterization of a novel rhabdovirus infecting peach in China. Virus Res 2020; 280:197905. [PMID: 32105763 DOI: 10.1016/j.virusres.2020.197905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 02/23/2020] [Indexed: 02/08/2023]
Abstract
A novel negative-sense, single-stranded (ss) RNA virus was identified in peach trees by high-throughput sequencing, and named peach virus 1 (PeV1). The genome of PeV1 consists of 13,949 nucleotides (nt), and its organization is typical of rhabdoviruses with six open reading frames (ORFs) encoding deduced proteins N-P-P3-M-G-L on the antisense strand. These ORFs are separated by highly conserved intergenic sequences and flanked by complementary 3'-leader and 5'-trailer sequences. PeV1 shared highest complete genome (41.9%), N amino acid (43.6%), G amino acid (41.0%), and L amino acid (42.7%) identities with viruses which belong to the genus Alphanucleorhabdovirus, suggesting it may belong to a new species. This was further supported by phylogenetic analyses using amino acid sequences of N, G, and L proteins, in which this virus is always clustered with alphanucleorhabdoviruses. Collectively, results suggest that PeV1 is a member of a new alphanucleorhabdovirus species. Moreover, bioassays revealed that it could be transmitted through grafting. The findings expand our knowledge of peach-infecting viruses and alphanucleorhabdoviruses.
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55
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Temmam S, Chrétien D, Bigot T, Dufour E, Petres S, Desquesnes M, Devillers E, Dumarest M, Yousfi L, Jittapalapong S, Karnchanabanthoeng A, Chaisiri K, Gagnieur L, Cosson JF, Vayssier-Taussat M, Morand S, Moutailler S, Eloit M. Monitoring Silent Spillovers Before Emergence: A Pilot Study at the Tick/Human Interface in Thailand. Front Microbiol 2019; 10:2315. [PMID: 31681195 PMCID: PMC6812269 DOI: 10.3389/fmicb.2019.02315] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/23/2019] [Indexed: 01/16/2023] Open
Abstract
Emerging zoonoses caused by previously unknown agents are one of the most important challenges for human health because of their inherent inability to be predictable, conversely to emergences caused by previously known agents that could be targeted by routine surveillance programs. Emerging zoonotic infections either originate from increasing contacts between wildlife and human populations, or from the geographical expansion of hematophagous arthropods that act as vectors, this latter being more capable to impact large-scale human populations. While characterizing the viral communities from candidate vectors in high-risk geographical areas is a necessary initial step, the need to identify which viruses are able to spill over and those restricted to their hosts has recently emerged. We hypothesized that currently unknown tick-borne arboviruses could silently circulate in specific biotopes where mammals are highly exposed to tick bites, and implemented a strategy that combined high-throughput sequencing with broad-range serological techniques to both identify novel arboviruses and tick-specific viruses in a ticks/mammals interface in Thailand. The virome of Thai ticks belonging to the Rhipicephalus, Amblyomma, Dermacentor, Hyalomma, and Haemaphysalis genera identified numerous viruses, among which several viruses could be candidates for future emergence as regards to their phylogenetic relatedness with known tick-borne arboviruses. Luciferase immunoprecipitation system targeting external viral proteins of viruses identified among the Orthomyxoviridae, Phenuiviridae, Flaviviridae, Rhabdoviridae, and Chuviridae families was used to screen human and cattle Thai populations highly exposed to tick bites. Although no positive serum was detected for any of the six viruses selected, suggesting that these viruses are not infecting these vertebrates, or at very low prevalence (upper estimate 0.017% and 0.047% in humans and cattle, respectively), the virome of Thai ticks presents an extremely rich viral diversity, among which novel tick-borne arboviruses are probably hidden and could pose a public health concern if they emerge. The strategy developed in this pilot study, starting from the inventory of viral communities of hematophagous arthropods to end by the identification of viruses able (or likely unable) to infect vertebrates, is the first step in the prediction of putative new emergences and could easily be transposed to other reservoirs/vectors/susceptible hosts interfaces.
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Affiliation(s)
- Sarah Temmam
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Pathogen Discovery Laboratory, Paris, France
| | - Delphine Chrétien
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Pathogen Discovery Laboratory, Paris, France
| | - Thomas Bigot
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Pathogen Discovery Laboratory, Paris, France
- Institut Pasteur – Bioinformatics and Biostatistics Hub – Computational Biology Department, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Evelyne Dufour
- Institut Pasteur, Production and Purification of Recombinant Proteins Technological Platform – C2RT, Paris, France
| | - Stéphane Petres
- Institut Pasteur, Production and Purification of Recombinant Proteins Technological Platform – C2RT, Paris, France
| | - Marc Desquesnes
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR InterTryp, Bangkok, Thailand
- InterTryp, Institut de Recherche pour le Développement (IRD), CIRAD, University of Montpellier, Montpellier, France
- Department of Parasitology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Elodie Devillers
- UMR BIPAR, Animal Health Laboratory, ANSES, INRA, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - Marine Dumarest
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Pathogen Discovery Laboratory, Paris, France
| | - Léna Yousfi
- UMR BIPAR, Animal Health Laboratory, ANSES, INRA, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | | | | | | | - Léa Gagnieur
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Pathogen Discovery Laboratory, Paris, France
| | - Jean-François Cosson
- UMR BIPAR, Animal Health Laboratory, ANSES, INRA, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - Muriel Vayssier-Taussat
- UMR BIPAR, Animal Health Laboratory, ANSES, INRA, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - Serge Morand
- Institut des Sciences de l'Evolution, CNRS, CC065, Université Montpellier, Montpellier, France
- CIRAD ASTRE, Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Sara Moutailler
- UMR BIPAR, Animal Health Laboratory, ANSES, INRA, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - Marc Eloit
- Institut Pasteur, Biology of Infection Unit, Inserm U1117, Pathogen Discovery Laboratory, Paris, France
- National Veterinary School of Alfort, Paris-Est University, Maisons-Alfort, France
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56
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Hameed M, Liu K, Anwar MN, Wahaab A, Li C, Di D, Wang X, Khan S, Xu J, Li B, Nawaz M, Shao D, Qiu Y, Wei J, Ma Z. A viral metagenomic analysis reveals rich viral abundance and diversity in mosquitoes from pig farms. Transbound Emerg Dis 2019; 67:328-343. [PMID: 31512812 DOI: 10.1111/tbed.13355] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 08/02/2019] [Accepted: 09/03/2019] [Indexed: 12/14/2022]
Abstract
Mosquitoes harbour a diversity of viruses and are responsible for several mosquito-borne viral diseases of humans and animals, thereby leading to major public health concerns, and significant economic losses across the globe. Viral metagenomics offers a great opportunity for bulk analysis of viral genomes retrieved directly from environmental samples. In this study, we performed a viral metagenomic analysis of five pools of mosquitoes belonging to Aedes, Anopheles and Culex species, collected from different pig farms in the vicinity of Shanghai, China, to explore the viral community carried by mosquitoes. The resulting metagenomic data revealed that viral community in the mosquitoes was highly diverse and varied in abundance among pig farms, which comprised of more than 48 viral taxonomic families, specific to vertebrates, invertebrates, plants, fungi, bacteria and protozoa. In addition, a considerable number of viral reads were related to viruses that are not classified by host. The read sequences related to animal viruses included parvoviruses, anelloviruses, circoviruses, flavivirus, rhabdovirus and seadornaviruses, which might be taken up by mosquitoes from viremic animal hosts during blood feeding. Notably, sample G1 contained the most abundant sequence related to Banna virus, which is of public health interest because it causes encephalitis in humans. Furthermore, non-classified viruses also shared considerable virus sequences in all the samples, presumably belonging to unexplored virus category. Overall, the present study provides a comprehensive knowledge of diverse viral populations carried by mosquitoes at pig farms, which is a potential source of diseases for mammals including humans and animals. These viral metagenomic data are valuable for assessment of emerging and re-emerging viral epidemics.
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Affiliation(s)
- Muddassar Hameed
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Muhammad Naveed Anwar
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Abdul Wahaab
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Chenxi Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Di Di
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Xin Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Sawar Khan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Jinpeng Xu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Mohsin Nawaz
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Donghua Shao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai, PR China
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57
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Abstract
Vesicular stomatitis Indiana virus (VSIV) is a veterinary pathogen that is also used as a backbone for many oncolytic and vaccine strategies. In natural and therapeutic settings, viral infections like VSIV are sensed by the host, and as a result the host cells make proteins that can protect them from viruses. In the case of VSIV, these antiviral proteins constrain viral replication and protect most healthy tissues from virus infection. In order to understand how VSIV causes disease and how healthy tissues are protected from VSIV-based therapies, it is crucial that we identify the proteins that inhibit VSIV. Here, we show that TRIM69 is an antiviral defense that can potently and specifically block VSIV infection. Vesicular stomatitis Indiana virus (VSIV), formerly known as vesicular stomatitis virus (VSV) Indiana (VSVIND), is a model virus that is exceptionally sensitive to the inhibitory action of interferons (IFNs). Interferons induce an antiviral state by stimulating the expression of hundreds of interferon-stimulated genes (ISGs). These ISGs can constrain viral replication, limit tissue tropism, reduce pathogenicity, and inhibit viral transmission. Since VSIV is used as a backbone for multiple oncolytic and vaccine strategies, understanding how ISGs restrict VSIV not only helps in understanding VSIV-induced pathogenesis but also helps us evaluate and understand the safety and efficacy of VSIV-based therapies. Thus, there is a need to identify and characterize the ISGs that possess anti-VSIV activity. Using arrayed ISG expression screening, we identified TRIM69 as an ISG that potently inhibits VSIV. This inhibition was highly specific as multiple viruses, including influenza A virus, HIV-1, Rift Valley fever virus, and dengue virus, were unaffected by TRIM69. Indeed, just one amino acid substitution in VSIV can govern sensitivity/resistance to TRIM69. Furthermore, TRIM69 is highly divergent in human populations and exhibits signatures of positive selection that are consistent with this gene playing a key role in antiviral immunity. We propose that TRIM69 is an IFN-induced inhibitor of VSIV and speculate that TRIM69 could be important in limiting VSIV pathogenesis and might influence the specificity and/or efficacy of vesiculovirus-based therapies. IMPORTANCE Vesicular stomatitis Indiana virus (VSIV) is a veterinary pathogen that is also used as a backbone for many oncolytic and vaccine strategies. In natural and therapeutic settings, viral infections like VSIV are sensed by the host, and as a result the host cells make proteins that can protect them from viruses. In the case of VSIV, these antiviral proteins constrain viral replication and protect most healthy tissues from virus infection. In order to understand how VSIV causes disease and how healthy tissues are protected from VSIV-based therapies, it is crucial that we identify the proteins that inhibit VSIV. Here, we show that TRIM69 is an antiviral defense that can potently and specifically block VSIV infection.
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Emelianchik A, Rodrigues TCS, Subramaniam K, Nielsen O, Burek-Huntington KA, Rotstein D, Popov VL, Stone D, Waltzek TB. Characterization of a novel rhabdovirus isolated from a stranded harbour porpoise (Phocoena phocoena). Virus Res 2019; 273:197742. [PMID: 31499088 DOI: 10.1016/j.virusres.2019.197742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 11/28/2022]
Abstract
An adult male harbour porpoise (Phocoena phocoena) stranded off the coast of Alaska displaying poor body condition, scattered mild ulcerative dermatitis, and necrotizing balanoposthitis. Necropsy findings included severe verminous panniculitis, pneumonia, hepatitis, and enteritis. Histopathological examination of skin lesions revealed a pustular epidermitis and dermatitis, with ballooning degeneration of keratinocytes and occasional amphophilic intracytoplasmic inclusion bodies. A swab sample collected from the ulcerative penile lesions was processed for virus isolation resulting in cytopathic effects observed in primary beluga whale kidney (BWK) cells. Transmission electron microscopy revealed bullet-shaped virions budding from the cell surface of infected BWK cells consistent with a rhabdovirus. A cDNA library was prepared using RNA extracted from infected cell culture supernatant and sequenced on an Illumina MiSeq sequencer. The near-complete genome of a novel rhabdovirus was recovered. Genetic and phylogenetic analyses based on the complete L gene supported the harbour porpoise rhabdovirus (HPRV) as a new species. HPRV clustered phylogenetically with dolphin rhabdovirus (DRV) and this cetacean rhabdovirus clade was found to be the sister group to members of the genus Perhabdovirus that infect fish. A specific nested RT-PCR assay detected HPRV RNA in the epaxial musculature of the harbour porpoise. Our results are consistent with a previous hypothesis that cetacean rhabdoviruses may have arisen following a host jump from fish and suggest that DRV and HPRV represent separate species belonging in a new genus within the family Rhabdoviridae. Further research is needed to determine the health impact of HPRV in harbour porpoise populations, its prevalence, and route of transmission.
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Affiliation(s)
| | | | | | - Ole Nielsen
- Department of Fisheries & Oceans Canada, 501 University Crescent, Winnipeg, Manitoba, Canada
| | | | - David Rotstein
- Marine Mammal Pathology Services, 19117 Bloomfield Road, 20832, Olney, Maryland, USA
| | - Vsevolod L Popov
- Department of Pathology, University of Texas Medical Branch, 301 University Boulevard, 77555-0609, Galveston, Texas, USA
| | - David Stone
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, DT4 8UB, UK
| | - Thomas B Waltzek
- University of Florida, 2187 Mowry Road, 32611, Gainesville, Florida, USA.
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Gao Q, Xu WY, Yan T, Fang XD, Cao Q, Zhang ZJ, Ding ZH, Wang Y, Wang XB. Rescue of a plant cytorhabdovirus as versatile expression platforms for planthopper and cereal genomic studies. THE NEW PHYTOLOGIST 2019; 223:2120-2133. [PMID: 31059138 DOI: 10.1111/nph.15889] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/28/2019] [Indexed: 05/19/2023]
Abstract
Plant viruses have been used as rapid and cost-effective expression vectors for heterologous protein expression in genomic studies. However, delivering large or multiple foreign proteins in monocots and insect pests is challenging. Here, we recovered a recombinant plant cytorhabdovirus, Barley yellow striate mosaic virus (BYSMV), for use as a versatile expression platform in cereals and the small brown planthopper (SBPH, Laodelphax striatellus) insect vector. We engineered BYSMV vectors to provide versatile expression platforms for simultaneous expression of three foreign proteins in barley plants and SBPHs. Moreover, BYSMV vectors could express the c. 600-amino-acid β-glucuronidase (GUS) protein and a red fluorescent protein stably in systemically infected leaves and roots of cereals, including wheat, barley, foxtail millet, and maize plants. Moreover, we have demonstrated that BYSMV vectors can be used in barley to analyze biological functions of gibberellic acid (GA) biosynthesis genes. In a major technical advance, BYSMV vectors were developed for simultaneous delivery of CRISPR/Cas9 nuclease and single guide RNAs for genomic editing in Nicotiana benthamiana leaves. Taken together, our results provide considerable potential for rapid screening of functional proteins in cereals and planthoppers, and an efficient approach for developing other insect-transmitted negative-strand RNA viruses.
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Affiliation(s)
- Qiang Gao
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wen-Ya Xu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Teng Yan
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiao-Dong Fang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qing Cao
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhen-Jia Zhang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhi-Hang Ding
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ying Wang
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Xian-Bing Wang
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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60
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Ma H, Nandakumar S, Bae EH, Chin PJ, Khan AS. The Spodoptera frugiperda Sf9 cell line is a heterogeneous population of rhabdovirus-infected and virus-negative cells: Isolation and characterization of cell clones containing rhabdovirus X-gene variants and virus-negative cell clones. Virology 2019; 536:125-133. [PMID: 31494355 DOI: 10.1016/j.virol.2019.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 11/28/2022]
Abstract
The Sf9 cell line is broadly used for manufacturing baculovirus-expressed viral vaccines. We previously reported the presence of a novel, rhabdovirus in the Sf9 cell line, which contained a unique X gene (Sf-rhabdovirus; designated as X+ in this paper). These results were extended by other reports describing an Sf-rhabdovirus variant in Sf9 cells, which lacked 320 nucleotides encompassing the X-gene and adjacent intergenic region (designated as X- in this paper), and the development of an Sf-rhabdovirus negative cell line. Here, we report that the Sf9 cell line is a mixed-cell population, based upon isolation of cell clones with distinct phenotypes: Sf-rhabdovirus-negative, X+, and X-. We also show that Sf-rhabdovirus X+ and X- variants replicate independently in Sf-rhabdovirus-negative cells. These results shed light on the detection of different rhabdovirus variants by different laboratories using Sf9-derived cell clones and confirm that both X+ and X- viruses are infectious in rhabdovirus-negative Sf9 cells.
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Affiliation(s)
- Hailun Ma
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Subhiksha Nandakumar
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Eunhae H Bae
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Pei-Ju Chin
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Arifa S Khan
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA.
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Sequencing, genome analysis and prevalence of a cytorhabdovirus discovered in Carica papaya. PLoS One 2019; 14:e0215798. [PMID: 31220099 PMCID: PMC6586395 DOI: 10.1371/journal.pone.0215798] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/08/2019] [Indexed: 02/02/2023] Open
Abstract
The complete genome of a new rhabdovirus infecting papaya (Carica papaya L.) in Ecuador, named papaya virus E, was sequenced and characterized. The negative-sense single-stranded RNA genome consists of 13,469 nucleotides with six canonical open reading frames (ORFs) and two accessory short ORFs predicted between ORFs corresponding to P3 (movement protein) and M (matrix protein). Phylogenetic analyses using amino acid sequences from the nucleocapsid, glycoprotein and polymerase, grouped the virus with members of the genus Cytorhabdovirus, with rice stripe mosaic virus, yerba mate chlorosis-associated virus and Colocasia bobone disease-associated virus as closest relatives. The 3’ leader and 5’ trailer sequences were 144 and 167 nt long, respectively, containing partially complementary motifs. The motif 3’-AUUCUUUUUG-5’, conserved across rhabdoviruses, was identified in all but one intergenic regions; whereas the motif 3’-ACAAAAACACA-5’ was found in three intergenic junctions. This is the first complete genome sequence of a cytorhabdovirus infecting papaya. The virus was prevalent in commercial plantings of Los Ríos, the most important papaya producing province of Ecuador. Recently, the genome sequence of bean-associated cytorhabdovirus was reported. The genome is 97% identical to that of papaya virus E, indicating that both should be considered strains of the same virus.
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Popov VL, Tesh RB, Weaver SC, Vasilakis N. Electron Microscopy in Discovery of Novel and Emerging Viruses from the Collection of the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA). Viruses 2019; 11:v11050477. [PMID: 31130629 PMCID: PMC6563235 DOI: 10.3390/v11050477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/20/2019] [Accepted: 05/24/2019] [Indexed: 11/28/2022] Open
Abstract
Since the beginning of modern virology in the 1950s, transmission electron microscopy (TEM) has been an important and widely used technique for discovery, identification and characterization of new viruses. Using TEM, viruses can be differentiated by their ultrastructure: shape, size, intracellular location and for some viruses, by the ultrastructural cytopathic effects and/or specific structures forming in the host cell during their replication. Ultrastructural characteristics are usually sufficient for the identification of a virus to the family level. In this review, we summarize 25 years of experience in identification of novel viruses from the collection of the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA).
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Affiliation(s)
- Vsevolod L Popov
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Robert B Tesh
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Scott C Weaver
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
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Vasilakis N, Tesh RB, Popov VL, Widen SG, Wood TG, Forrester NL, Gonzalez JP, Saluzzo JF, Alkhovsky S, Lam SK, Mackenzie JS, Walker PJ. Exploiting the Legacy of the Arbovirus Hunters. Viruses 2019; 11:E471. [PMID: 31126128 PMCID: PMC6563318 DOI: 10.3390/v11050471] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 12/13/2022] Open
Abstract
In recent years, it has become evident that a generational gap has developed in the community of arbovirus research. This apparent gap is due to the dis-investment of training for the next generation of arbovirologists, which threatens to derail the rich history of virus discovery, field epidemiology, and understanding of the richness of diversity that surrounds us. On the other hand, new technologies have resulted in an explosion of virus discovery that is constantly redefining the virosphere and the evolutionary relationships between viruses. This paradox presents new challenges that may have immediate and disastrous consequences for public health when yet to be discovered arboviruses emerge. In this review we endeavor to bridge this gap by providing a historical context for the work being conducted today and provide continuity between the generations. To this end, we will provide a narrative of the thrill of scientific discovery and excitement and the challenges lying ahead.
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Affiliation(s)
- Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Robert B Tesh
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Vsevolod L Popov
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Steve G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston TX 77555, USA.
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston TX 77555, USA.
| | - Naomi L Forrester
- Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
- Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA.
| | - Jean Paul Gonzalez
- Center of Excellence for Emerging & Zoonotic Animal Disease, Kansas State University, Manhattan, KS 66502, USA.
| | | | - Sergey Alkhovsky
- Ivanovsky Institute of Virology, N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, 123098, 18 Gamaleya str., Moscow, Russia.
| | - Sai Kit Lam
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - John S Mackenzie
- Faculty of Medical Sciences, Curtin University, Perth, Western Australia 6102, Australia.
| | - Peter J Walker
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia.
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Gaafar YZA, Richert-Pöggeler KR, Maaß C, Vetten HJ, Ziebell H. Characterisation of a novel nucleorhabdovirus infecting alfalfa (Medicago sativa). Virol J 2019; 16:55. [PMID: 31036009 PMCID: PMC6489223 DOI: 10.1186/s12985-019-1147-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/19/2019] [Indexed: 12/22/2022] Open
Abstract
Background Nucleorhabdoviruses possess bacilliform particles which contain a single-stranded negative-sense RNA genome. They replicate and mature in the nucleus of infected cells. Together with viruses of three other genera of the family Rhabdoviridae, they are known to infect plants and can be transmitted by arthropod vectors, during vegetative propagation, or by mechanical means. In 2010, an alfalfa (Medicago sativa) plant showing virus-like symptoms was collected from Stadl-Paura, Austria and sent to Julius Kühn Institute for analysis. Methods Electron microscopy (EM) of leaf extracts from infected plants revealed the presence of rhabdovirus-like particles and was further used for ultrastructural analyses of infected plant tissue. Partially-purified preparations of rhabdovirus nucleocapsids were used for raising an antiserum. To determine the virus genome sequence, high throughput sequencing (HTS) was performed. RT-PCR primers were designed to confirm virus infection and to be used as a diagnostic tool. Results EM revealed bacilliform virions resembling those of plant-infecting rhabdoviruses. HTS of ribosomal RNA-depleted total RNA extracts revealed a consensus sequence consisting of 13,875 nucleotides (nt) and containing seven open reading frames (ORFs). Homology and phylogenetic analyses suggest that this virus isolate represents a new species of the genus Nucleorhabdovirus (family Rhabdoviridae). Since the virus originated from an alfalfa plant in Austria, the name alfalfa-associated nucleorhabdovirus (AaNV) is proposed. Viroplasms (Vp) and budding virions were observed in the nuclei of infected cells by EM, thus confirming its taxonomic assignment based on sequence data. Conclusions In this study, we identified and characterised a new nucleorhabdovirus from alfalfa. It shared only 39.8% nucleotide sequence identity with its closest known relative, black currant-associated rhabdovirus 1. The virus contains an additional open reading frame (accessory gene) with unknown function, located between the matrix protein and the glycoprotein genes. Serological and molecular diagnostic assays were designed for future screening of field samples. Further studies are needed to identify other natural hosts and potential vectors. Electronic supplementary material The online version of this article (10.1186/s12985-019-1147-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yahya Z A Gaafar
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Katja R Richert-Pöggeler
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Christina Maaß
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany
| | | | - Heiko Ziebell
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104, Braunschweig, Germany.
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65
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Caì Y, Yú S, Jangra RK, Postnikova EN, Wada J, Tesh RB, Whelan SPJ, Lauck M, Wiley MR, Finch CL, Radoshitzky SR, O’Connor DH, Palacios G, Chandran K, Chiu CY, Kuhn JH. Human, Nonhuman Primate, and Bat Cells Are Broadly Susceptible to Tibrovirus Particle Cell Entry. Front Microbiol 2019; 10:856. [PMID: 31105663 PMCID: PMC6499107 DOI: 10.3389/fmicb.2019.00856] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/03/2019] [Indexed: 12/23/2022] Open
Abstract
In 2012, the genome of a novel rhabdovirus, Bas-Congo virus (BASV), was discovered in the acute-phase serum of a Congolese patient with presumed viral hemorrhagic fever. In the absence of a replicating virus isolate, fulfilling Koch's postulates to determine whether BASV is indeed a human virus and/or pathogen has been impossible. However, experiments with vesiculoviral particles pseudotyped with Bas-Congo glycoprotein suggested that BASV particles can enter cells from multiple animals, including humans. In 2015, genomes of two related viruses, Ekpoma virus 1 (EKV-1) and Ekpoma virus 2 (EKV-2), were detected in human sera in Nigeria. Isolates could not be obtained. Phylogenetic analyses led to the classification of BASV, EKV-1, and EKV-2 in the same genus, Tibrovirus, together with five biting midge-borne rhabdoviruses [i.e., Beatrice Hill virus (BHV), Bivens Arm virus (BAV), Coastal Plains virus (CPV), Sweetwater Branch virus (SWBV), and Tibrogargan virus (TIBV)] not known to infect humans. Using individual recombinant vesiculoviruses expressing the glycoproteins of all eight known tibroviruses and more than 75 cell lines representing different animal species, we demonstrate that the glycoproteins of all tibroviruses can mediate vesiculovirus particle entry into human, bat, nonhuman primate, cotton rat, boa constrictor, and Asian tiger mosquito cells. Using four of five isolated authentic tibroviruses (i.e., BAV, CPV, SWBV, and TIBV), our experiments indicate that many cell types may be partially resistant to tibrovirus replication after virion cell entry. Consequently, experimental data solely obtained from experiments using tibrovirus surrogate systems (e.g., vesiculoviral pseudotypes, recombinant vesiculoviruses) cannot be used to predict whether BASV, or any other tibrovirus, infects humans.
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Affiliation(s)
- Yíngyún Caì
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Shuǐqìng Yú
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Rohit K. Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Elena N. Postnikova
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Robert B. Tesh
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, The University of Texas Medical Branch, Galveston, TX, United States
| | - Sean P. J. Whelan
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, United States
| | - Michael Lauck
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, WI, United States
| | - Michael R. Wiley
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Courtney L. Finch
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Sheli R. Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, WI, United States
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Charles Y. Chiu
- Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, United States
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
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The First Complete Genome Sequence of a Novel Tetrastichus brontispae RNA Virus-1 (TbRV-1). Viruses 2019; 11:v11030257. [PMID: 30871248 PMCID: PMC6466307 DOI: 10.3390/v11030257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/09/2019] [Accepted: 03/10/2019] [Indexed: 11/17/2022] Open
Abstract
The complete sequence of a novel RNA virus isolated from Tetrastichus brontispae (TbRV-1) was determined to be 12,239 nucleotides in length with five non-overlapping, linearly arranged coding sequences (CDS), potentially encoding nucleoproteins, hypothetical proteins, matrix proteins, glycoproteins, and RNA-dependent RNA polymerases. Sequence analysis indicated that the RNA-dependent RNA polymerase of TbRV-1 shares a 65% nucleotide and 67% amino acid sequence identity with Hubei dimarhabdovirus 2, suggesting that TbRV-1 is a member of the dimarhabdovirus supergroup. This corresponded to the result of the phylogenetic analysis. The affiliation of TbRV-1 with members of the family Rhabdoviridae was further validated by similar transcription termination motifs (GGAACUUUUUUU) to the Drosophila sigmavirus. The prevalence of TbRV-1 in all tissues suggested that the virus was constitutive of, and not specific to, any wasp tissue. To our knowledge, this is the first report on the complete genome sequence of a dimarhabdovirus in parasitoids.
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Alves-Freitas DMT, Pinheiro-Lima B, Faria JC, Lacorte C, Ribeiro SG, Melo FL. Double-Stranded RNA High-Throughput Sequencing Reveals a New Cytorhabdovirus in a Bean Golden Mosaic Virus-Resistant Common Bean Transgenic Line. Viruses 2019; 11:E90. [PMID: 30669683 PMCID: PMC6357046 DOI: 10.3390/v11010090] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
Using double-strand RNA (dsRNA) high-throughput sequencing, we identified five RNA viruses in a bean golden mosaic virus (BGMV)-resistant common bean transgenic line with symptoms of viral infection. Four of the identified viruses had already been described as infecting common bean (cowpea mild mottle virus, bean rugose mosaic virus, Phaseolus vulgaris alphaendornavirus 1, and Phaseolus vulgaris alphaendornavirus 2) and one is a putative new plant rhabdovirus (genus Cytorhabdovirus), tentatively named bean-associated cytorhabdovirus (BaCV). The BaCV genome presented all five open reading frames (ORFs) found in most rhabdoviruses: nucleoprotein (N) (ORF1) (451 amino acids, aa), phosphoprotein (P) (ORF2) (445 aa), matrix (M) (ORF4) (287 aa), glycoprotein (G) (ORF5) (520 aa), and an RNA-dependent RNA polymerase (L) (ORF6) (114 aa), as well as a putative movement protein (P3) (ORF3) (189 aa) and the hypothetical small protein P4. The predicted BaCV proteins were compared to homologous proteins from the closest cytorhabdoviruses, and a low level of sequence identity (15⁻39%) was observed. The phylogenetic analysis shows that BaCV clustered with yerba mate chlorosis-associated virus (YmCaV) and rice stripe mosaic virus (RSMV). Overall, our results provide strong evidence that BaCV is indeed a new virus species in the genus Cytorhabdovirus (family Rhabdoviridae), the first rhabdovirus to be identified infecting common bean.
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Affiliation(s)
| | - Bruna Pinheiro-Lima
- Embrapa Recursos Genéticos e Biotecnologia, 70.770-917 Brasília, Brazil.
- Departamento de Biologia Celular, Universidade de Brasília, 70910-900 Brasília, Brazil.
| | | | - Cristiano Lacorte
- Embrapa Recursos Genéticos e Biotecnologia, 70.770-917 Brasília, Brazil.
| | - Simone G Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, 70.770-917 Brasília, Brazil.
| | - Fernando L Melo
- Departamento de Biologia Celular, Universidade de Brasília, 70910-900 Brasília, Brazil.
- Departamento de Fitopatologia, Universidade de Brasília, 70910-900 Brasília, Brazil.
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Ortega V, Stone JA, Contreras EM, Iorio RM, Aguilar HC. Addicted to sugar: roles of glycans in the order Mononegavirales. Glycobiology 2019; 29:2-21. [PMID: 29878112 PMCID: PMC6291800 DOI: 10.1093/glycob/cwy053] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/29/2018] [Accepted: 06/05/2018] [Indexed: 12/25/2022] Open
Abstract
Glycosylation is a biologically important protein modification process by which a carbohydrate chain is enzymatically added to a protein at a specific amino acid residue. This process plays roles in many cellular functions, including intracellular trafficking, cell-cell signaling, protein folding and receptor binding. While glycosylation is a common host cell process, it is utilized by many pathogens as well. Protein glycosylation is widely employed by viruses for both host invasion and evasion of host immune responses. Thus better understanding of viral glycosylation functions has potential applications for improved antiviral therapeutic and vaccine development. Here, we summarize our current knowledge on the broad biological functions of glycans for the Mononegavirales, an order of enveloped negative-sense single-stranded RNA viruses of high medical importance that includes Ebola, rabies, measles and Nipah viruses. We discuss glycobiological findings by genera in alphabetical order within each of eight Mononegavirales families, namely, the bornaviruses, filoviruses, mymonaviruses, nyamiviruses, paramyxoviruses, pneumoviruses, rhabdoviruses and sunviruses.
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Affiliation(s)
- Victoria Ortega
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Jacquelyn A Stone
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - Erik M Contreras
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Ronald M Iorio
- Department of Microbiology and Physiological Systems and Program in Immunology and Microbiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hector C Aguilar
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
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Ibrahim A, Odon V, Kormelink R. Plant Viruses in Plant Molecular Pharming: Toward the Use of Enveloped Viruses. FRONTIERS IN PLANT SCIENCE 2019; 10:803. [PMID: 31275344 PMCID: PMC6594412 DOI: 10.3389/fpls.2019.00803] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/04/2019] [Indexed: 05/03/2023]
Abstract
Plant molecular pharming has emerged as a reliable platform for recombinant protein expression providing a safe and low-cost alternative to bacterial and mammalian cells-based systems. Simultaneously, plant viruses have evolved from pathogens to molecular tools for recombinant protein expression, chimaeric viral vaccine production, and lately, as nanoagents for drug delivery. This review summarizes the genesis of viral vectors and agroinfection, the development of non-enveloped viruses for various biotechnological applications, and the on-going research on enveloped plant viruses.
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Abstract
Rhabdoviruses are enveloped viruses with a negative-sense single strand RNA genome and are widespread among a great variety of organisms. In their membrane, they have a single glycoprotein (G) that mediates both virus attachment to cellular receptors and fusion between viral and endosomal membranes allowing viral genome release in the cytoplasm. We present structural and cellular aspects of Rhabdovirus entry into their host cell with a focus on vesicular stomatitis virus (VSV) and rabies virus (RABV) for which the early events of the viral cycle have been extensively studied. Recent data have shown that the only VSV receptors are the members of the LDL-R family. This is in contrast with RABV for which multiple receptors belonging to unrelated families have been identified. Despite having different receptors, after attachment, rhabdovirus internalization occurs through clathrin-mediated endocytosis (CME) in an actin-dependent manner. There are still debates about the exact endocytic pathway of VSV in the cell and on RABV transport in the neuronal axon. In any case, fusion is triggered in the endosomal vesicle via a low-pH induced structural rearrangement of G from its pre- to its postfusion conformation. Vesiculovirus G is one of the best characterized fusion glycoproteins as the previously reported crystal structures of the pre- and postfusion states have been recently completed by those of intermediates during the structural transition. Understanding the entry pathway of rhabdoviruses may have strong impact in biotechnologies as, for example, VSV G is used for pseudotyping lentiviruses to promote efficient transduction, and VSV is a promising oncolytic virus.
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Vasilakis N, Tesh RB, Widen SG, Mirchandani D, Walker PJ. Genomic characterisation of Cuiaba and Charleville viruses: arboviruses (family Rhabdoviridae, genus Sripuvirus) infecting reptiles and amphibians. Virus Genes 2018; 55:87-94. [PMID: 30511209 DOI: 10.1007/s11262-018-1620-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/23/2018] [Indexed: 11/25/2022]
Abstract
Viruses in the family Rhabdoviridae are ecologically very diverse, infecting mammals, birds, reptiles, fish, plants and a wide range of other terrestrial and aquatic invertebrates. The genus Sripuvirus currently comprises five viruses that appear to circulate in transmission cycles involving reptiles and sandflies. Here, we report an analysis of the complete coding sequences of Cuiaba virus (CUIV), isolated from an amphibian (Bufo marinus) collected in Brazil, and Charleville virus (CHVV), isolated from sandflies (Phlebotomus sp.) and lizards (Gehyra australis), collected in Australia. CUIV and CHVV cluster phylogenetically with the sripuviruses in maximum likelihood trees generated from complete L protein (RdRp) sequences. They also share with sripuviruses unique features in genome organisation, including an additional gene (U1) between the matrix protein (M) gene and glycoprotein (G) gene, and an alternative long open reading frame near the start of the G ORF that encodes a predicted transmembrane protein. In view of their phylogenetic relationships, similar genome organisations and similar ecological characteristics, we propose the assignment of CUIV and CHVV as novel members of the genus Sripuvirus.
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Affiliation(s)
- Nikos Vasilakis
- Department of Pathology, Center for Biodefence and Emerging Infectious Diseases, The University of Texas Medical Branch, Galveston, TX, USA
- Center for Tropical Diseases, The University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infection and Immunity, The University of Texas Medical Branch, Galveston, TX, USA
| | - Robert B Tesh
- Department of Pathology, Center for Biodefence and Emerging Infectious Diseases, The University of Texas Medical Branch, Galveston, TX, USA
- Center for Tropical Diseases, The University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infection and Immunity, The University of Texas Medical Branch, Galveston, TX, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Divya Mirchandani
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Peter J Walker
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, Australia.
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Wille M, Eden JS, Shi M, Klaassen M, Hurt AC, Holmes EC. Virus-virus interactions and host ecology are associated with RNA virome structure in wild birds. Mol Ecol 2018; 27:5263-5278. [PMID: 30375075 PMCID: PMC6312746 DOI: 10.1111/mec.14918] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/11/2018] [Accepted: 10/18/2018] [Indexed: 12/13/2022]
Abstract
Little is known about the factors that shape the ecology of RNA viruses in nature. Wild birds are an important case in point, as other than influenza A virus, avian samples are rarely tested for viruses, especially in the absence of overt disease. Using bulk RNA-sequencing ("meta-transcriptomics"), we revealed the viral diversity present in Australian wild birds through the lens of the ecological factors that may determine virome structure and abundance. A meta-transcriptomic analysis of four Anseriformes (waterfowl) and Charadriiformes (shorebird) species sampled in temperate and arid Australia revealed the presence of 27 RNA virus genomes, 18 of which represent newly described species. The viruses identified included a previously described gammacoronavirus and influenza A viruses. Additionally, we identified novel virus species from the families Astroviridae, Caliciviridae, Reoviridae, Rhabdoviridae, Picobirnaviridae and Picornaviridae. We noted differences in virome structure that reflected underlying differences in location and influenza A infection status. Red-necked Avocets (Recurvirostra novaehollandiae) from Australia's arid interior possessed the greatest viral diversity and abundance, markedly higher than individuals sampled in temperate Australia. In Ruddy Turnstones (Arenaria interpres) and dabbling ducks (Anas spp.), viral abundance and diversity were higher and more similar in hosts that were positive for influenza A infection compared to those that were negative for this virus, despite samples being collected on the same day and from the same location. This study highlights the extent and diversity of RNA viruses in wild birds and lays the foundation for understanding the factors that determine virome structure in wild populations.
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Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.,The Westmead Institute for Medical Research, Centre for Virus Research, Sydney, New South Wales, Australia
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
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73
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Sadeghi M, Altan E, Deng X, Barker CM, Fang Y, Coffey LL, Delwart E. Virome of > 12 thousand Culex mosquitoes from throughout California. Virology 2018; 523:74-88. [DOI: 10.1016/j.virol.2018.07.029] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 12/25/2022]
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Hutchings RSG, Hutchings RW, Menezes IS, Motta MDA, Sallum MAM. Mosquitoes (Diptera: Culicidae) From the Northwestern Brazilian Amazon: Araçá River. JOURNAL OF MEDICAL ENTOMOLOGY 2018; 55:1188-1209. [PMID: 29767750 DOI: 10.1093/jme/tjy065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Indexed: 06/08/2023]
Abstract
The mosquito fauna (Diptera: Culicidae) from two remote localities along the Araçá River, within the Municipality of Barcelos, towards the northern border of the Brazilian State of Amazonas, were sampled using CDC, Shannon, Malaise, and Suspended traps, along with net sweeping and immature collections. During June 2010, 111 collections yielded more than 23,500 mosquitoes distributed in 15 genera, representing 119 different species, together with eight morphospecies, which may represent undescribed new taxa. Among the species collected, there is one new distributional record for Brazil and nine new distributional records for the State of Amazonas. With the highest number of species, the genus Culex Linnaeus also had the largest number of individuals followed by Aedes Meigen with the second highest number of species. The most abundant species was Culex (Melanoconion) gnomatos Sallum, Hutchings & Ferreira followed by Culex (Melanoconion) portesi Senevet & Abonnenc, Culex (Culex) mollis Dyar & Knab, Aedes (Ochlerotatus) fulvus (Wiedemann), Culex (Melanoconion) pedroi Sirivanakarn & Belkin, Culex (Melanoconion) crybda Dyar, Aedes (Ochlerotatus) nubilus (Theobald), and Anopheles (Anopheles) peryassui Dyar & Knab. The epidemiological implications of mosquito species found are discussed and are compared with other mosquito inventories from the Amazon region. As the first standardized mosquito inventory of the Araçá River, with the identification of 127 species level taxa, the number of mosquito species which have been collected along the northern tributaries of the middle Rio Negro Basin (i.e., Padauari and Araçá Rivers) increased significantly.
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Affiliation(s)
- Rosa Sá Gomes Hutchings
- Laboratório de Bionomia e Sistemática de Culicidae, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, Manaus, AM, Brazil
| | - Roger William Hutchings
- Laboratório de Bionomia e Sistemática de Culicidae, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, Manaus, AM, Brazil
| | - Isis Sá Menezes
- Laboratório de Bionomia e Sistemática de Culicidae, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, Manaus, AM, Brazil
| | - Monique de Albuquerque Motta
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, Rio de Janeiro, RJ, Brazil
| | - Maria Anice Mureb Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Av. Doutor Arnaldo, São Paulo, SP, Brazil
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Aedes Anphevirus: an Insect-Specific Virus Distributed Worldwide in Aedes aegypti Mosquitoes That Has Complex Interplays with Wolbachia and Dengue Virus Infection in Cells. J Virol 2018; 92:JVI.00224-18. [PMID: 29950416 DOI: 10.1128/jvi.00224-18] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/30/2018] [Indexed: 01/21/2023] Open
Abstract
Insect-specific viruses (ISVs) of the yellow fever mosquito Aedes aegypti have been demonstrated to modulate transmission of arboviruses such as dengue virus (DENV) and West Nile virus by the mosquito. The diversity and composition of the virome of A. aegypti, however, remains poorly understood. In this study, we characterized Aedes anphevirus (AeAV), a negative-sense RNA virus from the order Mononegavirales AeAV identified from Aedes cell lines was infectious to both A. aegypti and Aedes albopictus cells but not to three mammalian cell lines. To understand the incidence and genetic diversity of AeAV, we assembled 17 coding-complete and two partial genomes of AeAV from available transcriptome sequencing (RNA-Seq) data. AeAV appears to transmit vertically and be present in laboratory colonies, wild-caught mosquitoes, and cell lines worldwide. Phylogenetic analysis of AeAV strains indicates that as the A. aegypti mosquito has expanded into the Americas and Asia-Pacific, AeAV has evolved into monophyletic African, American, and Asia-Pacific lineages. The endosymbiotic bacterium Wolbachia pipientis restricts positive-sense RNA viruses in A. aegypti Reanalysis of a small RNA library of A. aegypti cells coinfected with AeAV and Wolbachia produces an abundant RNA interference (RNAi) response consistent with persistent virus replication. We found Wolbachia enhances replication of AeAV compared to a tetracycline-cleared cell line, and AeAV modestly reduces DENV replication in vitro The results from our study improve understanding of the diversity and evolution of the virome of A. aegypti and adds to previous evidence that shows Wolbachia does not restrict a range of negative-strand RNA viruses.IMPORTANCE The mosquito Aedes aegypti transmits a number of arthropod-borne viruses (arboviruses), such as dengue virus and Zika virus. Mosquitoes also harbor insect-specific viruses that may affect replication of pathogenic arboviruses in their body. Currently, however, there are only a few insect-specific viruses described from A. aegypti in the literature. Here, we characterize a novel negative-strand virus, AeAV. Meta-analysis of A. aegypti samples showed that it is present in A. aegypti mosquitoes worldwide and is vertically transmitted. Wolbachia-transinfected mosquitoes are currently being used in biocontrol, as they effectively block transmission of several positive-sense RNA viruses in mosquitoes. Our results demonstrate that Wolbachia enhances the replication of AeAV and modestly reduces dengue virus replication in a cell line model. This study expands our understanding of the virome in A. aegypti as well as providing insight into the complexity of the Wolbachia virus restriction phenotype.
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76
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Hao F, Wu M, Li G. Molecular Characterization and Geographic Distribution of a Mymonavirus in the Population of Botrytis cinerea. Viruses 2018; 10:E432. [PMID: 30111764 PMCID: PMC6116283 DOI: 10.3390/v10080432] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/12/2018] [Accepted: 08/14/2018] [Indexed: 01/10/2023] Open
Abstract
Here, we characterized a negative single-stranded (-ss)RNA mycovirus, Botrytis cinerea mymonavirus 1 (BcMyV1), isolated from the phytopathogenic fungus Botrytis cinerea. The genome of BcMyV1 is 7863 nt in length, possessing three open reading frames (ORF1⁻3). The ORF1 encodes a large polypeptide containing a conserved mononegaviral RNA-dependent RNA polymerase (RdRp) domain showing homology to the protein L of mymonaviruses, whereas the possible functions of the remaining two ORFs are still unknown. The internal cDNA sequence (10-7829) of BcMyV1 was 97.9% identical to the full-length cDNA sequence of Sclerotinia sclerotiorum negative stranded RNA virus 7 (SsNSRV7), a virus-like contig obtained from Sclerotinia sclerotiorum metatranscriptomes, indicating BcMyV1 should be a strain of SsNSRV7. Phylogenetic analysis based on RdRp domains showed that BcMyV1 was clustered with the viruses in the family Mymonaviridae, suggesting it is a member of Mymonaviridae. BcMyV1 may be widely distributed in regions where B. cinerea occurs in China and even over the world, although it infected only 0.8% of tested B. cinerea strains.
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Affiliation(s)
- Fangmin Hao
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Mingde Wu
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Guoqing Li
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
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77
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Discovery and high prevalence of Phasi Charoen-like virus in field-captured Aedes aegypti in South China. Virology 2018; 523:35-40. [PMID: 30077072 DOI: 10.1016/j.virol.2018.07.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 01/20/2023]
Abstract
Arboviruses have caused significant global health concerns during the past decade. In this regard, continuous viral surveillance is essential to timely identify emerging arboviruses and other novel viruses. Here, a novel isolate of Phasi Charoen-like virus (PCLV Zhanjiang01) was identified from field-captured Aedes aegypti mosquitoes in Zhanjiang by next generation sequencing. Phylogenetic analysis suggested that PCLV Zhanjiang01 belonged to the genus Phasivirus in the family Phenuiviridae. The presence of PCLV in three batches of Aedes aegypti confirmed its high prevalence in nature. Further detection of PCLV in progenies and adult males suggested vertical transmission in mosquitoes. In parallel, PCLV was detected from multiple organs indicating its broad tissue distribution in the infected mosquitoes. To the best of our knowledge, this is the first report of PCLV in China. Our results expanded the global biogeographic distribution of PCLV. Further investigations of PCLV on the arboviral transmission and control strategies are warranted.
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78
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Chabi-Jesus C, Ramos-González PL, Tassi AD, Guerra-Peraza O, Kitajima EW, Harakava R, Beserra JEA, Salaroli RB, Freitas-Astúa J. Identification and Characterization of Citrus Chlorotic Spot Virus, a New Dichorhavirus Associated with Citrus Leprosis-Like Symptoms. PLANT DISEASE 2018; 102:1588-1598. [PMID: 30673423 DOI: 10.1094/pdis-09-17-1425-re] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Local chlorotic spots resembling early lesions characteristic of citrus leprosis (CL) were observed in leaves of two sweet orange (Citrus sinensis L.) trees in Teresina, State of Piauí, Brazil, in early 2017. However, despite the similarities, these spots were generally larger than those of a typical CL and showed rare or no necrosis symptoms. In symptomatic tissues, transmission electron microscopy revealed the presence of viroplasms in the nuclei of the infected parenchymal cells and rod-shaped particles with an average size of approximately 40 × 100 nm, resembling those typically observed during infection by dichorhaviruses. A bipartite genome of the putative novel virus, tentatively named citrus chlorotic spot virus (CiCSV) (RNA1 = 6,518 nucleotides [nt] and RNA2 = 5,987 nt), revealed the highest nucleotide sequence identity values with the dichorhaviruses coffee ringspot virus strain Lavras (73.8%), citrus leprosis virus N strain Ibi1 (58.6%), and orchid fleck virus strain So (56.9%). In addition to citrus, CiCSV was also found in local chlorotic lesions on leaves of the ornamental plant beach hibiscus (Talipariti tiliaceum (L.) Fryxell). Morphological characterization of mites recovered from the infected plants revealed at least two different types of Brevipalpus. One of them corresponds to Brevipalpus yothersi. The other is slightly different from B. yothersi mites but comprises traits that possibly place it as another species. A mix of the two mite types collected on beach hibiscus successfully transmitted CiCSV to arabidopsis plants but additional work is required to verify whether both types of flat mite may act as viral vectors. The current study reveals a newly described dichorhavirus associated with a citrus disease in the northeastern region of Brazil.
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Affiliation(s)
- C Chabi-Jesus
- Instituto Biológico, São Paulo, SP, Brazil; and PPG Microbiologia Agrícola ESALQ/USP, Piracicaba, SP, Brazil
| | | | - A D Tassi
- LFN/ESALQ/USP, 13418-900 Piracicaba, SP, Brazil
| | - O Guerra-Peraza
- Instituto Biológico, São Paulo; and Citrus Research & Education Center, University of Florida
| | | | | | | | | | - J Freitas-Astúa
- Instituto Biológico, São Paulo; and Embrapa Mandioca e Fruticultura, Cruz das Almas, BA, Brazil
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Maurice NA, Luka PD, Maurice MN, Ngbede EO, Zhakom PN, Mshelbwala PP, Tekki IS, Udoh UAH, Inyang UA, Ekanem NJ, Ifut OJ, Okewole PA, Shamaki D, Lombin LH. RABIES IN A SET OF EIGHT-WEEK OLD PUPPIES IN NIGERIA: THE NEED FOR REVIEW OF CURRENT DOG ANTIRABIES VACCINATION SCHEDULE. Afr J Infect Dis 2018; 12:72-77. [PMID: 30109290 PMCID: PMC6085740 DOI: 10.21010/ajid.v12i2.12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 11/23/2022] Open
Abstract
Background: Rabies is endemic in Nigeria with clinical cases reported mainly in dogs and occasionally in livestock from all the geo-ecological zones of the country. Detection of rabies virus antigen in puppies at the age of five to ten weeks and in apparently healthy dogs shedding the virus in their saliva have been reported in some parts of Nigeria. Material and Method: This report describes a clinical rabies in a set of eight weeks old puppies confirmed by antigen detection using the direct fluorescent antibody test (DFAT), the direct rapid immunohistochemical test (DRIT), and RT-PCR. Results: it was positive for all test used including the RT-PCR which amplified at 750 bp from the gel electrophoresis. Conclusion: Occurrence of rabies in puppies of this age, within which they are acquired and owned by other unsuspecting members of the public, is of grave public health consequences. People that love puppies, especially children, who are fond of carrying and playing with them, are also faced with the risk of exposure to rabies. Consequently, review of the existing dog antirabies vaccination schedule at twelve weeks of age in Nigeria, is recommended to ensure effective immunization of this age group of dogs and for the overall safety of the vulnerable members of the public.
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Affiliation(s)
- Nanven Abraham Maurice
- Department of Diagnostic and Extension, National Veterinary Research Institute, Uyo Laboratory, Akwa Ibom State, Nigeria
| | - Pam Dachung Luka
- Biotechnology Division, National Veterinary Research Institute, Vom. Plateau State, Nigeria
| | - Magdalene Nanven Maurice
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria, Kaduna State, Nigeria
| | - Emmanuel Ochefije Ngbede
- Department of Pathology and Microbiology, College of Veterinary Medicine, University of Agriculture, Makurdi, Benue State. Nigeria
| | - Ponfa Nden Zhakom
- Rabies Laboratory, National Veterinary Research Institute, Vom., Plateau State, Nigeria
| | - Philip Paul Mshelbwala
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Abuja, Nigeria
| | - Ishaya Sini Tekki
- Department of Pathology and Microbiology, College of Veterinary Medicine, University of Agriculture, Makurdi, Benue State. Nigeria
| | - Utibe-Abasi Hilary Udoh
- Department of Animal Science, Faculty of Agriculture, University of Uyo, Akwa Ibom State, Nigeria
| | - Udoh Akpan Inyang
- Department of Animal Science, Faculty of Agriculture, University of Uyo, Akwa Ibom State, Nigeria
| | - Nsika Joseph Ekanem
- Department of Animal Science, Faculty of Agriculture, University of Uyo, Akwa Ibom State, Nigeria
| | - Okon John Ifut
- Department of Animal Science, Faculty of Agriculture, University of Uyo, Akwa Ibom State, Nigeria
| | - Philip A Okewole
- Department of Diagnostic and Extension, National Veterinary Research Institute, Uyo Laboratory, Akwa Ibom State, Nigeria
| | - David Shamaki
- Department of Diagnostic and Extension, National Veterinary Research Institute, Uyo Laboratory, Akwa Ibom State, Nigeria
| | - Lami Hanatu Lombin
- Faculty of Veterinary Medicine, University of Jos, Plateau State Nigeria
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Wang L, He H, Wang S, Chen X, Qiu D, Kondo H, Guo L. Evidence for a novel negative-stranded RNA mycovirus isolated from the plant pathogenic fungus Fusarium graminearum. Virology 2018; 518:232-240. [PMID: 29549785 DOI: 10.1016/j.virol.2018.03.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/26/2018] [Accepted: 03/07/2018] [Indexed: 10/24/2022]
Abstract
Here we describe a novel (-)ssRNA mycovirus, Fusarium graminearum negative-stranded RNA virus 1 (FgNSRV-1), isolated from Fusarium graminearum strain HN1. The genome of FgNSRV-1 is 9072 nucleotides in length, with five discontinuous but linear ORFs (ORF I-V). Phylogenetic analysis based on entire L polymerase sequences indicated that FgNSRV-1 is related to the (-)ssRNA mycovirus Sclerotinia sclerotiorum negative-stranded RNA virus 1 (SsNSRV-1), and other mycoviruses. Our data suggest that FgNSRV-1 can be classified into the family Mymonaviridae, order Mononegavirales. Putative enveloped virion-like structures with filamentous morphology similar to SsNSRV-1 were observed in virion preparation samples. The L proteins of FgNSRV-1, and other fungal mononegaviruses, were found to be related to L protein-like sequences in some fungal genome, supporting the hypothesis that there is coevolution occurring between mycoviruses and fungi. Besides, clearing the virus from the infected host fungus resulted in no discernable phenotypic change.
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Affiliation(s)
- Luan Wang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hao He
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shuangchao Wang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoguang Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dewen Qiu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hideki Kondo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Okayama 710-0046, Japan.
| | - Lihua Guo
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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81
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Liu Y, Du Z, Wang H, Zhang S, Cao M, Wang X. Identification and Characterization of Wheat Yellow Striate Virus, a Novel Leafhopper-Transmitted Nucleorhabdovirus Infecting Wheat. Front Microbiol 2018; 9:468. [PMID: 29593700 PMCID: PMC5861215 DOI: 10.3389/fmicb.2018.00468] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 02/28/2018] [Indexed: 11/13/2022] Open
Abstract
A new wheat viral disease was found in China. Bullet-shaped viral particles within the nucleus of the infected wheat leave cells, which possessed 180-210 nm length and 35-40 nm width, were observed under transmission electron microscopy. A putative wheat-infecting rhabdovirus vectored by the leafhopper Psammotettix alienus was identified and tentatively named wheat yellow striate virus (WYSV). The full-length nucleotide sequence of WYSV was determined using transcriptome sequencing and RACE analysis of both wheat samples and leafhoppers P. alienus. The negative-sense RNA genome of WYSV contains 14,486 nucleotides (nt) and seven open reading frames (ORFs) encode deduced proteins in the order N-P-P3-M-P6-G-L on the antisense strand. In addition, WYSV genome has a 76-nt 3' leader RNA and a 258-nt 5' trailer, and the ORFs are separated by conserved intergenic sequences. The entire genome sequence shares 58.1 and 57.7% nucleotide sequence identity with two strains of rice yellow stunt virus (RYSV-A and RYSV-B) genomes, respectively. The highest amino acid sequence identity was 63.8% between the L proteins of the WYSV and RYSV-B, but the lowest was 29.5% between the P6 proteins of these viruses. Phylogenetic analysis firmly established WYSV as a new member of the genus Nucleorhabdovirus. Collectively, this study provided evidence that WYSV is likely the first nucleorhabdovirus described infecting wheat via leafhopper P. alienus transmission.
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Affiliation(s)
- Yan Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenzhen Du
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Song Zhang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, China
| | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Identification of Novel Viruses in Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis Ticks. mSphere 2018; 3:mSphere00614-17. [PMID: 29564401 PMCID: PMC5853492 DOI: 10.1128/msphere.00614-17] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 01/29/2018] [Indexed: 12/21/2022] Open
Abstract
Ticks carry a wide range of known human and animal pathogens and are postulated to carry others with the potential to cause disease. Here we report a discovery effort wherein unbiased high-throughput sequencing was used to characterize the virome of 2,021 ticks, including Ixodes scapularis (n = 1,138), Amblyomma americanum (n = 720), and Dermacentor variabilis (n = 163), collected in New York, Connecticut, and Virginia in 2015 and 2016. We identified 33 viruses, including 24 putative novel viral species. The most frequently detected viruses were phylogenetically related to members of the Bunyaviridae and Rhabdoviridae families, as well as the recently proposed Chuviridae. Our work expands our understanding of tick viromes and underscores the high viral diversity that is present in ticks. IMPORTANCE The incidence of tick-borne disease is increasing, driven by rapid geographical expansion of ticks and the discovery of new tick-associated pathogens. The examination of the tick microbiome is essential in order to understand the relationship between microbes and their tick hosts and to facilitate the identification of new tick-borne pathogens. Genomic analyses using unbiased high-throughput sequencing platforms have proven valuable for investigations of tick bacterial diversity, but the examination of tick viromes has historically not been well explored. By performing a comprehensive virome analysis of the three primary tick species associated with human disease in the United States, we gained substantial insight into tick virome diversity and can begin to assess a potential role of these viruses in the tick life cycle.
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83
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Walker PJ, Blasdell KR, Calisher CH, Dietzgen RG, Kondo H, Kurath G, Longdon B, Stone DM, Tesh RB, Tordo N, Vasilakis N, Whitfield AE, Ictv Report Consortium. ICTV Virus Taxonomy Profile: Rhabdoviridae. J Gen Virol 2018; 99:447-448. [PMID: 29465028 DOI: 10.1099/jgv.0.001020] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The family Rhabdoviridae comprises viruses with negative-sense (-) single-stranded RNA genomes of 10.8-16.1 kb. Virions are typically enveloped with bullet-shaped or bacilliform morphology but can also be non-enveloped filaments. Rhabdoviruses infect plants and animals including mammals, birds, reptiles and fish, as well as arthropods which serve as single hosts or act as biological vectors for transmission to animals or plants. Rhabdoviruses include important pathogens of humans, livestock, fish and agricultural crops. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of Rhabdoviridae, which is available at www.ictv.global/report/rhabdoviridae.
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Affiliation(s)
- Peter J Walker
- School of Biological Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Kim R Blasdell
- CSIRO Health and Biosecurity, Geelong, VIC 3220, Australia
| | | | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Gael Kurath
- Western Fisheries Research Center, Seattle, WA 98115, USA
| | - Ben Longdon
- Department of Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, DT4 8UB, UK
| | - Robert B Tesh
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Noël Tordo
- Institut Pasteur de Guinée, Gamal Abdel Nasser University, Conakry, Guinea
| | - Nikos Vasilakis
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Anna E Whitfield
- Department of Plant Pathology, Kansas State University, Manhattan KS 66506, USA
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84
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Lelli D, Prosperi A, Moreno A, Chiapponi C, Gibellini AM, De Benedictis P, Leopardi S, Sozzi E, Lavazza A. Isolation of a novel Rhabdovirus from an insectivorous bat (Pipistrellus kuhlii) in Italy. Virol J 2018; 15:37. [PMID: 29454370 PMCID: PMC5816388 DOI: 10.1186/s12985-018-0949-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/08/2018] [Indexed: 12/27/2022] Open
Abstract
Background Rhabdoviridae is one of the most ecologically diverse families of RNA viruses which can infect a wide range of vertebrates and invertebrates. Bats, among mammals, are pointed to harbor a significantly higher proportion of unknown or emerging viruses with zoonotic potential. Herein, we report the isolation of a novel rhabdovirus, detected in the framework of a virological survey on bats implemented in North Italy. Methods Virus isolation and identification were performed on samples of 635 bats by using cell cultures, negative staining electron microscopy and PCRs for different viruses. NGS was commonly performed on cell culture supernatants showing cytopathic effect or in case of samples resulted positive by at least one of the PCRs included in the diagnostic protocol. Results A rhabdovirus was isolated from different organs of a Pipistrellus kuhlii. Virus identification was obtained by electron microscopy and NGS sequencing. The complete genome size was 11,774 nt comprised 5 genes, encoding the canonical rhabdovirus structural proteins, and an additional transcriptional unit (U1) encoding a hypothetical small protein (157aa) (3’-N-P-M-G-U1-L-5′). The genome organization and phylogenetic analysis suggest that the new virus, named Vaprio virus (VAPV), belongs to the recently established genus Ledantevirus (subgroup B) and it is highly divergent to its closest known relative, Le Dantec virus (LDV) (human, 1965 Senegal). A specific RT-PCR amplifying a 350 bp fragment of the ORF 6 gene, encoding for L protein, was developed and used to test retrospectively a subset of 76 bats coming from the same area and period, revealing two more VAPV positive bats. Conclusions VAPV is a novel isolate of chiropteran rhabdovirus. Genome organization and phylogenetic analyses demonstrated that VAPV should be considered a novel species within the genus Ledantevirus for which viral ecology and disease associations should be investigated.
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Affiliation(s)
- Davide Lelli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Via Bianchi 9 -, 25124, Brescia, Italy.
| | - Alice Prosperi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Via Bianchi 9 -, 25124, Brescia, Italy
| | - Ana Moreno
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Via Bianchi 9 -, 25124, Brescia, Italy
| | - Chiara Chiapponi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Via Bianchi 9 -, 25124, Brescia, Italy
| | - Anna Maria Gibellini
- Wildlife Rehabilitation Center WWF of Valpredina via Pioda n.1, 24060 Cenate Sopra (BG), Bergamo, Italy
| | - Paola De Benedictis
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVE), Viale dell'Università, 10 - 35020 Legnaro (PD), Padova, Italy
| | - Stefania Leopardi
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVE), Viale dell'Università, 10 - 35020 Legnaro (PD), Padova, Italy
| | - Enrica Sozzi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Via Bianchi 9 -, 25124, Brescia, Italy
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Via Bianchi 9 -, 25124, Brescia, Italy
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85
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Økland AL, Skoge RH, Nylund A. The complete genome sequence of CrRV-Ch01, a new member of the family Rhabdoviridae in the parasitic copepod Caligus rogercresseyi present on farmed Atlantic salmon (Salmo salar) in Chile. Arch Virol 2018; 163:1657-1661. [PMID: 29445987 PMCID: PMC5958147 DOI: 10.1007/s00705-018-3768-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/01/2018] [Indexed: 11/25/2022]
Abstract
We have determined the complete genome sequence of a new rhabdovirus, tentatively named Caligus rogercresseyi rhabdovirus Ch01 (CrRV-Ch01), which was found in the parasite Caligus rogercresseyi, present on farmed Atlantic salmon (Salmo salar) in Chile. The genome encodes the five canonical rhabdovirus proteins in addition to an unknown protein, in the order N-P-M-U (unknown)-G-L. Phylogenetic analysis showed that the virus clusters with two rhabdoviruses (Lepeophtheirus salmonis rhabdovirus No9 and Lepeophtheirus salmonis rhabdovirus No127) obtained from another parasitic caligid, Lepeophtheirus salmonis, present on farmed Atlantic salmon on the west coast of Norway.
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Affiliation(s)
| | | | - Are Nylund
- Department of Biology, University of Bergen, 5020, Bergen, Norway
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86
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Abstract
Ticks are important vectors for the transmission of pathogens including viruses. The viruses carried by ticks also known as tick-borne viruses (TBVs), contain a large group of viruses with diverse genetic properties and are concluded in two orders, nine families, and at least 12 genera. Some members of the TBVs are notorious agents causing severe diseases with high mortality rates in humans and livestock, while some others may pose risks to public health that are still unclear to us. Herein, we review the current knowledge of TBVs with emphases on the history of virus isolation and identification, tick vectors, and potential pathogenicity to humans and animals, including assigned species as well as the recently discovered and unassigned species. All these will promote our understanding of the diversity of TBVs, and will facilitate the further investigation of TBVs in association with both ticks and vertebrate hosts.
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Affiliation(s)
- Junming Shi
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Fei Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Shu Shen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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87
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McNair K, Aziz RK, Pusch GD, Overbeek R, Dutilh BE, Edwards R. Phage Genome Annotation Using the RAST Pipeline. Methods Mol Biol 2018; 1681:231-238. [PMID: 29134599 DOI: 10.1007/978-1-4939-7343-9_17] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Phages are complex biomolecular machineries that have to survive in a bacterial world. Phage genomes show many adaptations to their lifestyle such as shorter genes, reduced capacity for redundant DNA sequences, and the inclusion of tRNAs in their genomes. In addition, phages are not free-living, they require a host for replication and survival. These unique adaptations provide challenges for the bioinformatics analysis of phage genomes. In particular, ORF calling, genome annotation, noncoding RNA (ncRNA) identification, and the identification of transposons and insertions are all complicated in phage genome analysis. We provide a road map through the phage genome annotation pipeline, and discuss the challenges and solutions for phage genome annotation as we have implemented in the rapid annotation using subsystems (RAST) pipeline.
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Affiliation(s)
- Katelyn McNair
- Computational Sciences Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Ramy Karam Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.,Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL, 60439, USA
| | - Gordon D Pusch
- Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL, 60439, USA
| | - Ross Overbeek
- Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL, 60439, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584, Utrecht, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525, Nijmegen, The Netherlands
| | - Robert Edwards
- Computational Sciences Research Center, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA. .,Departments of Biology and Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA.
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88
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Levin S, Galbraith D, Sela N, Erez T, Grozinger CM, Chejanovsky N. Presence of Apis Rhabdovirus-1 in Populations of Pollinators and Their Parasites from Two Continents. Front Microbiol 2017; 8:2482. [PMID: 29312191 PMCID: PMC5732965 DOI: 10.3389/fmicb.2017.02482] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 11/29/2017] [Indexed: 01/05/2023] Open
Abstract
The viral ecology of bee communities is complex, where viruses are readily shared among co-foraging bee species. Additionally, in honey bees (Apis mellifera), many viruses are transmitted - and their impacts exacerbated - by the parasitic Varroa destructor mite. Thus far, the viruses found to be shared across bee species and transmitted by V. destructor mites are positive-sense single-stranded RNA viruses. Recently, a negative-sense RNA enveloped virus, Apis rhabdovirus-1 (ARV-1), was found in A. mellifera honey bees in Africa, Europe, and islands in the Pacific. Here, we describe the identification - using a metagenomics approach - of ARV-1 in two bee species (A. mellifera and Bombus impatiens) and in V. destructor mites from populations collected in the United States and Israel. We confirmed the presence of ARV-1 in pools of A. mellifera, B. impatiens, and V. destructor from Israeli and U.S. populations by RT-PCR and found that it can reach high titers in individual honey bees and mites (107-108 viral genomic copies per individual). To estimate the prevalence of ARV-1 in honey bee populations, we screened 104 honey bee colonies across Israel, with 21 testing ARV-1-positive. Tagged-primer-mediated RT-PCR analysis detected the presence of the positive-sense ARV-1 RNA in A. mellifera and V. destructor, indicating that ARV-1 replicates in both hosts. This is the first report of the presence of ARV-1 in B. impatiens and of the replication of a rhabdovirus in A. mellifera and V. destructor. Our data suggest that Varroa mites could act as an ARV-1 vector; however, the presence of ARV-1 in B. impatiens (which are not parasitized by Varroa) suggests that it may not require the mite for transmission and ARV-1 may be shared among co-foraging bee species. Given that ARV-1 is found in non-Apis bee species, and because "ARV" is used for the Adelaide River virus, we propose that this virus should be called bee rhabdovirus 1 and abbreviated BRV-1. These results greatly expand our understanding of the diversity of viruses that can infect bee communities, though further analysis is required to determine how infection with this virus impacts these different hosts.
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Affiliation(s)
- Sofia Levin
- Department of Entomology, Institute of Plant Protection, Agricultural Research Organization, Rishon LeZion, Israel
- Faculty of Agricultural, Food and the Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - David Galbraith
- Department of Entomology – Center for Pollinator Research – Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Noa Sela
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization, Rishon LeZion, Israel
| | - Tal Erez
- Department of Entomology, Institute of Plant Protection, Agricultural Research Organization, Rishon LeZion, Israel
| | - Christina M. Grozinger
- Department of Entomology – Center for Pollinator Research – Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Nor Chejanovsky
- Department of Entomology, Institute of Plant Protection, Agricultural Research Organization, Rishon LeZion, Israel
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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89
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Xu L, Wu J, Jiang T, Qin S, Xia L, Li X, He B, Tu C. Molecular detection and sequence characterization of diverse rhabdoviruses in bats, China. Virus Res 2017; 244:208-212. [PMID: 29196194 PMCID: PMC7114522 DOI: 10.1016/j.virusres.2017.11.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/23/2017] [Accepted: 11/27/2017] [Indexed: 11/22/2022]
Abstract
Three new rhabdoviruses were detected in bats, China. JHBV and BXBV found in Rhinolophus bats could be new members of the genus Vesiculovirus. Four strains of YJBV detected in Hipposideros larvatus formed a new lineage.
The Rhabdoviridae is among the most diverse families of RNA viruses and currently classified into 18 genera with some rhabdoviruses lethal to humans and other animals. Herein, we describe genetic characterization of three novel rhabdoviruses from bats in China. Of these, two viruses (Jinghong bat virus and Benxi bat virus) found in Rhinolophus bats showed a phylogenetic relationship with vesiculoviruses, and sequence analyses indicate that they represent two new species within the genus Vesiculovirus. The remaining Yangjiang bat virus found in Hipposideros larvatus bats were only distantly related to currently known rhabdoviruses.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Jianmin Wu
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Tinglei Jiang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
| | - Shaomin Qin
- Guangxi Key Laboratory of Veterinary Biotechnology, Guangxi Veterinary Research Institute, Nanning, Guangxi, China
| | - Lele Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Xingyu Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Biao He
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, Jilin, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, Jiangsu, China.
| | - Changchun Tu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, Jilin, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, Jiangsu, China.
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90
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Geisler C, Jarvis DL. Adventitious viruses in insect cell lines used for recombinant protein expression. Protein Expr Purif 2017; 144:25-32. [PMID: 29133148 DOI: 10.1016/j.pep.2017.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/08/2017] [Indexed: 11/16/2022]
Abstract
Insect cells are widely used for recombinant protein expression, typically as hosts for recombinant baculovirus vectors, but also for plasmid-mediated transient transfection or stable genetic transformation. Insect cells are used to express proteins for research, as well as to manufacture biologicals for human and veterinary medicine. Recently, several insect cell lines used for recombinant protein expression were found to be persistently infected with adventitious viruses. This has raised questions about how these infections might affect research performed using those cell lines. Furthermore, these findings raised serious concerns about the safety of biologicals produced using those cell lines. In response, new insect cell lines lacking adventitious viruses have been isolated for use as improved research tools and safer biological manufacturing platforms. Here, we review the scientific and patent literature on adventitious viruses found in insect cell lines, affected cell lines, and new virus-free cell lines.
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Affiliation(s)
| | - Donald L Jarvis
- GlycoBac LLC, 1938 Harney Street, Laramie, WY 82072, USA; University of Wyoming, Department of Molecular Biology, 1000 E. University Avenue, Laramie, WY 82071, USA
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91
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de Lara Pinto AZ, Santos de Carvalho M, de Melo FL, Ribeiro ALM, Morais Ribeiro B, Dezengrini Slhessarenko R. Novel viruses in salivary glands of mosquitoes from sylvatic Cerrado, Midwestern Brazil. PLoS One 2017; 12:e0187429. [PMID: 29117239 PMCID: PMC5678729 DOI: 10.1371/journal.pone.0187429] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 10/19/2017] [Indexed: 12/22/2022] Open
Abstract
Viruses may represent the most diverse microorganisms on Earth. Novel viruses and variants continue to emerge. Mosquitoes are the most dangerous animals to humankind. This study aimed at identifying viral RNA diversity in salivary glands of mosquitoes captured in a sylvatic area of Cerrado at the Chapada dos Guimarães National Park, Mato Grosso, Brazil. In total, 66 Culicinae mosquitoes belonging to 16 species comprised 9 pools, subjected to viral RNA extraction, double-strand cDNA synthesis, random amplification and high-throughput sequencing, revealing the presence of seven insect-specific viruses, six of which represent new species of Rhabdoviridae (Lobeira virus), Chuviridae (Cumbaru and Croada viruses), Totiviridae (Murici virus) and Partitiviridae (Araticum and Angico viruses). In addition, two mosquito pools presented Kaiowa virus sequences that had already been reported in South Pantanal, Brazil. These findings amplify the understanding of viral diversity in wild-type Culicinae. Insect-specific viruses may present a broader diversity than previously imagined and future studies may address their possible role in mosquito vector competence.
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Affiliation(s)
- Andressa Zelenski de Lara Pinto
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Michellen Santos de Carvalho
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Fernando Lucas de Melo
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Ana Lúcia Maria Ribeiro
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Bergmann Morais Ribeiro
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Renata Dezengrini Slhessarenko
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
- * E-mail:
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92
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Detection and characterization of a novel rhabdovirus in Aedes cantans mosquitoes and evidence for a mosquito-associated new genus in the family Rhabdoviridae. INFECTION GENETICS AND EVOLUTION 2017; 55:260-268. [PMID: 28943405 DOI: 10.1016/j.meegid.2017.09.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/18/2017] [Accepted: 09/20/2017] [Indexed: 12/27/2022]
Abstract
Thanks to recent advances in random amplification technologies, metagenomic surveillance expanded the number of novel, often unclassified viruses within the family Rhabdoviridae. Using a vector-enabled metagenomic (VEM) tool, we identified a novel rhabdovirus in Aedes cantans mosquitoes collected from Germany provisionally named Ohlsdorf virus (OHSDV). The OHSDV genome encodes the canonical rhabdovirus structural proteins (N, P, M, G and L) with alternative ORF in the P gene. Sequence analysis indicated that OHSDV exhibits a similar genome organization and characteristics compared to other mosquito-associated rhabdoviruses (Riverside virus, Tongilchon virus and North Creek virus). Complete L protein based phylogeny revealed that all four viruses share a common ancestor and form a deeply rooted and divergent monophyletic group within the dimarhabdovirus supergroup and define a new genus, tentatively named Ohlsdorfvirus. Although the Ohlsdorfvirus clade is basal within the dimarhabdovirus supergroup phylogeny that includes genera of arthropod-borne rhabdoviruses, it remains unknown if viruses in the proposed new genus are vector-borne pathogens. The observed spatiotemporal distribution in mosquitoes suggests that members of the proposed genus Ohlsdorfvirus are geographically restricted/separated. These findings increase the current knowledge of the genetic diversity, classification and evolution of this virus family. Further studies are needed to determine the host range, transmission route and the evolutionary relationships of these mosquito-associated viruses with those infecting vertebrates.
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93
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Remnant EJ, Shi M, Buchmann G, Blacquière T, Holmes EC, Beekman M, Ashe A. A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations. J Virol 2017; 91:e00158-17. [PMID: 28515299 PMCID: PMC5533899 DOI: 10.1128/jvi.00158-17] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/26/2017] [Indexed: 01/16/2023] Open
Abstract
Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees (Apis mellifera) has changed dramatically since the emergence of the parasitic mite Varroa destructor, which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity. To capture the viral diversity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa This analysis revealed seven novel viruses isolated from honey bees sampled globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically diverse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral diversity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management.IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been described in honey bees, with most belonging to the order Picornavirales Collapsing Varroa-infected colonies are often overwhelmed with high levels of picornaviruses. To examine the underlying viral diversity in honey bees, we employed viral metatranscriptomics analyses on three geographically diverse Varroa-resistant populations from Europe, Africa, and the Pacific. We describe seven novel viruses from a range of diverse viral families, including two viruses that are present in all three locations. In honey bees, small RNA sequences indicate that these viruses are processed by Dicer and the RNA interference pathway, whereas Varroa mites produce strikingly novel small RNA patterns. This work increases the number and diversity of known honey bee viruses and will ultimately contribute to improved disease management in our most important agricultural pollinator.
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Affiliation(s)
- Emily J Remnant
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Mang Shi
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Gabriele Buchmann
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | | | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
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94
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High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia. J Virol 2017. [PMID: 28637756 DOI: 10.1128/jvi.00680-17] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mosquitoes harbor a high diversity of RNA viruses, including many that impact human health. Despite a growing effort to describe the extent and nature of the mosquito virome, little is known about how these viruses persist, spread, and interact with both their hosts and other microbes. To address this issue we performed a metatranscriptomics analysis of 12 Western Australian mosquito populations structured by species and geographic location. Our results identified the complete genomes of 24 species of RNA viruses from a diverse range of viral families and orders, among which 19 are newly described. Comparisons of viromes revealed a striking difference between the two mosquito genera, with viromes of mosquitoes of the Aedes genus exhibiting substantially less diversity and lower abundances than those of mosquitoes of the Culex genus, within which the viral abundance reached 16.87% of the total non-rRNA. In addition, there was little overlap in viral diversity between the two genera, although the viromes were very similar among the three Culex species studied, suggesting that the host taxon plays a major role in structuring virus diversity. In contrast, we found no evidence that geographic location played a major role in shaping RNA virus diversity, and several viruses discovered here exhibited high similarity (95 to 98% nucleotide identity) to those from Indonesia and China. Finally, using abundance-level and phylogenetic relationships, we were able to distinguish potential mosquito viruses from those present in coinfecting bacteria, fungi, and protists. In sum, our metatranscriptomics approach provides important insights into the ecology of mosquito RNA viruses.IMPORTANCE Studies of virus ecology have generally focused on individual viral species. However, recent advances in bulk RNA sequencing make it possible to utilize metatranscriptomic approaches to reveal both complete virus diversity and the relative abundance of these viruses. We used such a metatranscriptomic approach to determine key aspects of the ecology of mosquito viruses in Western Australia. Our results show that RNA viruses are some of the most important components of the mosquito transcriptome, and we identified 19 new virus species from a diverse set of virus families. A key result was that host genetic background plays a more important role in shaping virus diversity than sampling location, with Culex species harboring more viruses at higher abundance than those from Aedes mosquitoes.
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95
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Ramos-González PL, Chabi-Jesus C, Guerra-Peraza O, Tassi AD, Kitajima EW, Harakava R, Salaroli RB, Freitas-Astúa J. Citrus leprosis virus N: A New Dichorhavirus Causing Citrus Leprosis Disease. PHYTOPATHOLOGY 2017; 107:963-976. [PMID: 28398876 DOI: 10.1094/phyto-02-17-0042-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Citrus leprosis (CL) is a viral disease endemic to the Western Hemisphere that produces local necrotic and chlorotic lesions on leaves, branches, and fruit and causes serious yield reduction in citrus orchards. Samples of sweet orange (Citrus × sinensis) trees showing CL symptoms were collected during a survey in noncommercial citrus areas in the southeast region of Brazil in 2013 to 2016. Transmission electron microscopy analyses of foliar lesions confirmed the presence of rod-like viral particles commonly associated with CL in the nucleus and cytoplasm of infected cells. However, every attempt to identify these particles by reverse-transcription polymerase chain reaction tests failed, even though all described primers for the detection of known CL-causing cileviruses and dichorhaviruses were used. Next-generation sequencing of total RNA extracts from three symptomatic samples revealed the genome of distinct, although highly related (>92% nucleotide sequence identity), viruses whose genetic organization is similar to that of dichorhaviruses. The genome sequence of these viruses showed <62% nucleotide sequence identity with those of orchid fleck virus and coffee ringspot virus. Globally, the deduced amino acid sequences of the open reading frames they encode share 32.7 to 63.8% identity with the proteins of the dichorhavirids. Mites collected from both the naturally infected citrus trees and those used for the transmission of one of the characterized isolates to Arabidopsis plants were anatomically recognized as Brevipalpus phoenicis sensu stricto. Molecular and biological features indicate that the identified viruses belong to a new species of CL-associated dichorhavirus, which we propose to call Citrus leprosis N dichorhavirus. Our results, while emphasizing the increasing diversity of viruses causing CL disease, lead to a reevaluation of the nomenclature of those viruses assigned to the genus Dichorhavirus. In this regard, a comprehensive discussion is presented.
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Affiliation(s)
- Pedro Luis Ramos-González
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
| | - Camila Chabi-Jesus
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
| | - Orlene Guerra-Peraza
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
| | - Aline Daniele Tassi
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
| | - Elliot Watanabe Kitajima
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
| | - Ricardo Harakava
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
| | - Renato Barbosa Salaroli
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
| | - Juliana Freitas-Astúa
- First, second, third, sixth, and eighth authors: Lab. Bioquímica Fitopatológica, Instituto Biológico, São Paulo 04014-002, Brazil; second, fourth, fifth, and seventh authors: Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo 13418-900, Brazil; third author: Citrus Research & Education Center, University of Florida, Lake Alfred 33850; and eighth author: Embrapa Mandioca e Fruticultura, Cruz das Almas, Bahia 44380-000, Brazil
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96
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Amarasinghe GK, Bào Y, Basler CF, Bavari S, Beer M, Bejerman N, Blasdell KR, Bochnowski A, Briese T, Bukreyev A, Calisher CH, Chandran K, Collins PL, Dietzgen RG, Dolnik O, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Fang Q, Formenty P, Fouchier RAM, Ghedin E, Harding RM, Hewson R, Higgins CM, Hong J, Horie M, James AP, Jiāng D, Kobinger GP, Kondo H, Kurath G, Lamb RA, Lee B, Leroy EM, Li M, Maisner A, Mühlberger E, Netesov SV, Nowotny N, Patterson JL, Payne SL, Paweska JT, Pearson MN, Randall RE, Revill PA, Rima BK, Rota P, Rubbenstroth D, Schwemmle M, Smither SJ, Song Q, Stone DM, Takada A, Terregino C, Tesh RB, Tomonaga K, Tordo N, Towner JS, Vasilakis N, Volchkov VE, Wahl-Jensen V, Walker PJ, Wang B, Wang D, Wang F, Wang LF, Werren JH, Whitfield AE, Yan Z, Ye G, Kuhn JH. Taxonomy of the order Mononegavirales: update 2017. Arch Virol 2017; 162:2493-2504. [PMID: 28389807 PMCID: PMC5831667 DOI: 10.1007/s00705-017-3311-7] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 02/26/2017] [Indexed: 12/11/2022]
Abstract
In 2017, the order Mononegavirales was expanded by the inclusion of a total of 69 novel species. Five new rhabdovirus genera and one new nyamivirus genus were established to harbor 41 of these species, whereas the remaining new species were assigned to already established genera. Furthermore, non-Latinized binomial species names replaced all paramyxovirus and pneumovirus species names, thereby accomplishing application of binomial species names throughout the entire order. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yīmíng Bào
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Nicolás Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Kim R Blasdell
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria, Australia
| | - Alisa Bochnowski
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Alexander Bukreyev
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Charles H Calisher
- Arthropod-Borne and Infectious Diseases Laboratory, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Peter L Collins
- Respiratory Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | | | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Qi Fang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhèjiāng University, Hángzhōu, China
| | | | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Robert M Harding
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Roger Hewson
- Public Health England, Porton Down, Wiltshire, Salisbury, UK
| | - Colleen M Higgins
- Institute of Applied Ecology, School of Science, Auckland University of Technology, Auckland, New Zealand
- AUT Roche Diagnostic Laboratory, Auckland University of Technology, Auckland, New Zealand
| | - Jian Hong
- Analysis Center of Agrobiology and Environmental Sciences and Institute of Agrobiology and Environmental Sciences, Zhèjiāng University, Hángzhōu, China
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Anthony P James
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology of Húběi Province, College of Plant Science and Technology, Huázhōng Agricultural University, Wǔhàn, China
| | - Gary P Kobinger
- Department of Microbiology, Immunology and Infectious Diseases Université Laval, Quebec City, Canada
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, Washington, USA
| | - Robert A Lamb
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Howard Hughes Medical Institute, Northwestern University, Evanston, IL, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric M Leroy
- Centre International de Recherches Médicales de Franceville, Institut de Recherche pour le Développement, Franceville, Gabon
| | - Ming Li
- Institute of Applied Ecology, School of Science, Auckland University of Technology, Auckland, New Zealand
- AUT Roche Diagnostic Laboratory, Auckland University of Technology, Auckland, New Zealand
| | - Andrea Maisner
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Elke Mühlberger
- Department of Microbiology and, National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine, Vienna, Austria
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Jean L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Susan L Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Janusz T Paweska
- Center for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, Gauteng, South Africa
| | - Michael N Pearson
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Rick E Randall
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Scotland, UK
| | - Peter A Revill
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
- Victorian Infectious Diseases Reference Laboratory, Doherty Institute of Infection and Immunity, Melbourne, Victoria, Australia
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dennis Rubbenstroth
- Institute for Virology, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Schwemmle
- Institute for Virology, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sophie J Smither
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire, UK
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Ayato Takada
- Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Calogero Terregino
- Istituto Zooprofilattico Sperimentale delle Venezie, Department of Comparative Biomedical Sciences, National/OIE Reference Laboratory for Newcastle Disease and Avian Influenza, FAO Reference Centre for Animal Influenza and Newcastle Disease, OIE Collaborating Centre for Diseases at the Human-Animal Interface, Legnaro, Padova, Italy
| | - Robert B Tesh
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Keizo Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur, Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV and CCHFV, Paris, France
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Viktor E Volchkov
- Molecular Basis of Viral Pathogenicity, CIRIINSERM U1111 - CNRS UMR5308, Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Victoria Wahl-Jensen
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Biological Sciences, University of Queensland, St. Lucia, QLD, Australia
| | - Beibei Wang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhèjiāng University, Hángzhōu, China
| | - David Wang
- Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Fei Wang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhèjiāng University, Hángzhōu, China
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, USA
| | | | - Zhichao Yan
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhèjiāng University, Hángzhōu, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhèjiāng University, Hángzhōu, China
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA.
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97
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Kuno G, Mackenzie JS, Junglen S, Hubálek Z, Plyusnin A, Gubler DJ. Vertebrate Reservoirs of Arboviruses: Myth, Synonym of Amplifier, or Reality? Viruses 2017; 9:E185. [PMID: 28703771 PMCID: PMC5537677 DOI: 10.3390/v9070185] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/10/2017] [Accepted: 07/10/2017] [Indexed: 02/07/2023] Open
Abstract
The rapid succession of the pandemic of arbovirus diseases, such as dengue, West Nile fever, chikungunya, and Zika fever, has intensified research on these and other arbovirus diseases worldwide. Investigating the unique mode of vector-borne transmission requires a clear understanding of the roles of vertebrates. One major obstacle to this understanding is the ambiguity of the arbovirus definition originally established by the World Health Organization. The paucity of pertinent information on arbovirus transmission at the time contributed to the notion that vertebrates played the role of reservoir in the arbovirus transmission cycle. Because this notion is a salient feature of the arbovirus definition, it is important to reexamine its validity. This review addresses controversial issues concerning vertebrate reservoirs and their role in arbovirus persistence in nature, examines the genesis of the problem from a historical perspective, discusses various unresolved issues from multiple points of view, assesses the present status of the notion in light of current knowledge, and provides options for a solution to resolve the issue.
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Affiliation(s)
- Goro Kuno
- Formerly at the Division of Vector-Borne Infectious Diseases, Centers for Control and Prevention, Fort Collins, CO, USA.
| | - John S Mackenzie
- Faculty of Medical Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
- Division of Microbiology & Infectious Diseases, PathWest, Nedlands, Western Australia 6009.
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Helmut-Ruska-Haus, Chariteplatz 1, 10117 Berlin, Germany.
| | - Zdeněk Hubálek
- Institute of Vertebrate Biology, Academy of Sciences of Czech Republic, 60365 Brno, Czech Republic.
| | - Alexander Plyusnin
- Department of Virology, University of Helsinki, Haartmaninkatu 3, University of Helsinki, 00014 Helsinki, Finland.
| | - Duane J Gubler
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd., Singapore 169857 Singapore.
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98
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Goldberg TL, Bennett AJ, Kityo R, Kuhn JH, Chapman CA. Kanyawara Virus: A Novel Rhabdovirus Infecting Newly Discovered Nycteribiid Bat Flies Infesting Previously Unknown Pteropodid Bats in Uganda. Sci Rep 2017; 7:5287. [PMID: 28706276 PMCID: PMC5509700 DOI: 10.1038/s41598-017-05236-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 05/25/2017] [Indexed: 12/21/2022] Open
Abstract
Bats are natural reservoir hosts of highly virulent pathogens such as Marburg virus, Nipah virus, and SARS coronavirus. However, little is known about the role of bat ectoparasites in transmitting and maintaining such viruses. The intricate relationship between bats and their ectoparasites suggests that ectoparasites might serve as viral vectors, but evidence to date is scant. Bat flies, in particular, are highly specialized obligate hematophagous ectoparasites that incidentally bite humans. Using next-generation sequencing, we discovered a novel ledantevirus (mononegaviral family Rhabdoviridae, genus Ledantevirus) in nycteribiid bat flies infesting pteropodid bats in western Uganda. Mitochondrial DNA analyses revealed that both the bat flies and their bat hosts belong to putative new species. The coding-complete genome of the new virus, named Kanyawara virus (KYAV), is only distantly related to that of its closest known relative, Mount Elgon bat virus, and was found at high titers in bat flies but not in blood or on mucosal surfaces of host bats. Viral genome analysis indicates unusually low CpG dinucleotide depletion in KYAV compared to other ledanteviruses and rhabdovirus groups, with KYAV displaying values similar to rhabdoviruses of arthropods. Our findings highlight the possibility of a yet-to-be-discovered diversity of potentially pathogenic viruses in bat ectoparasites.
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Affiliation(s)
- Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
- Global Health Institute, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
- Department of Zoology, Makerere University, Kampala, Uganda.
| | - Andrew J Bennett
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Robert Kityo
- Department of Zoology, Makerere University, Kampala, Uganda
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, 21702, USA
| | - Colin A Chapman
- Department of Zoology, Makerere University, Kampala, Uganda
- Department of Anthropology and School of Environment, McGill University, Montreal, Quebec, H3A 2T7, Canada
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99
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Gubala A, Walsh S, McAllister J, Weir R, Davis S, Melville L, Mitchell I, Bulach D, Gauci P, Skvortsov A, Boyle D. Identification of very small open reading frames in the genomes of Holmes Jungle virus, Ord River virus, and Wongabel virus of the genus Hapavirus, family Rhabdoviridae. Evol Bioinform Online 2017; 13:1176934317713484. [PMID: 28747815 PMCID: PMC5510769 DOI: 10.1177/1176934317713484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/05/2017] [Indexed: 12/11/2022] Open
Abstract
Viruses of the family Rhabdoviridae infect a broad range of hosts from a variety of ecological and geographical niches, including vertebrates, arthropods, and plants. The arthropod-transmitted members of this family display considerable genetic diversity and remarkable genomic flexibility that enable coding for various accessory proteins in different locations of the genome. Here, we describe the genome of Holmes Jungle virus, isolated from Culex annulirostris mosquitoes collected in northern Australia, and make detailed comparisons with the closely related Ord River and Wongabel viruses, with a focus on identifying very small open reading frames (smORFs) in their genomes. This is the first systematic prediction of smORFs in rhabdoviruses, emphasising the intricacy of the rhabdovirus genome and the knowledge gaps. We speculate that these smORFs may be of importance to the life cycle of the virus in the arthropod vector.
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Affiliation(s)
- Aneta Gubala
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Susan Walsh
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Jane McAllister
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Richard Weir
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Steven Davis
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Lorna Melville
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Ian Mitchell
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Dieter Bulach
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC, Australia
| | - Penny Gauci
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Alex Skvortsov
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - David Boyle
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC, Australia
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Ryabov EV. Invertebrate RNA virus diversity from a taxonomic point of view. J Invertebr Pathol 2017; 147:37-50. [PMID: 27793741 PMCID: PMC7094257 DOI: 10.1016/j.jip.2016.10.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 10/03/2016] [Accepted: 10/14/2016] [Indexed: 02/04/2023]
Abstract
Invertebrates are hosts to diverse RNA viruses that have all possible types of encapsidated genomes (positive, negative and ambisense single stranded RNA genomes, or a double stranded RNA genome). These viruses also differ markedly in virion morphology and genome structure. Invertebrate RNA viruses are present in three out of four currently recognized orders of RNA viruses: Mononegavirales, Nidovirales, and Picornavirales, and 10 out of 37 RNA virus families that have yet to be assigned to an order. This mini-review describes general properties of the taxonomic groups, which include invertebrate RNA viruses on the basis of their current classification by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Eugene V Ryabov
- ER Healthcare Consulting Ltd., Poundgate Lane, Coventry CV4 8HJ, United Kingdom.
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