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Stegmüller S, Qi W, Torgerson PR, Fraefel C, Kubacki J. Hazard potential of Swiss Ixodes ricinus ticks: Virome composition and presence of selected bacterial and protozoan pathogens. PLoS One 2023; 18:e0290942. [PMID: 37956168 PMCID: PMC10642849 DOI: 10.1371/journal.pone.0290942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Ticks play an important role in transmitting many different emerging zoonotic pathogens that pose a significant threat to human and animal health. In Switzerland and abroad, the number of tick-borne diseases, in particular tick-borne encephalitis (TBE), has been increasing over the last few years. Thus, it remains essential to investigate the pathogen spectrum of ticks to rapidly detect emerging pathogens and initiate the necessary measures. To assess the risk of tick-borne diseases in different regions of Switzerland, we collected a total of 10'286 ticks from rural and urban areas in ten cantons in 2021 and 2022. Ticks were pooled according to species, developmental stage, gender, and collection site, and analyzed using next generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR). The metagenomic analysis revealed for the first time the presence of Alongshan virus (ALSV) in Swiss ticks. Interestingly, the pool-prevalence of ALSV was higher than that of tick-borne encephalitis virus (TBEV). Furthermore, several TBEV foci have been identified and pool prevalence of selected non-viral pathogens determined.
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Affiliation(s)
- Stefanie Stegmüller
- Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, Zurich, Switzerland
| | - Paul R. Torgerson
- Section of Epidemiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Cornel Fraefel
- Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Jakub Kubacki
- Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology (DIP), Vetsuisse Faculty, University of Bern, Bern, Switzerland
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2
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Qi YH, Ye ZX, Zhang CX, Chen JP, Li JM. Diversity of RNA viruses in agricultural insects. Comput Struct Biotechnol J 2023; 21:4312-4321. [PMID: 37711182 PMCID: PMC10497914 DOI: 10.1016/j.csbj.2023.08.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023] Open
Abstract
Recent advancements in next-generation sequencing (NGS) technology and bioinformatics tools have revealed a vast array of viral diversity in insects, particularly RNA viruses. However, our current understanding of insect RNA viruses has primarily focused on hematophagous insects due to their medical importance, while research on the viromes of agriculturally relevant insects remains limited. This comprehensive review aims to address the gap by providing an overview of the diversity of RNA viruses in agricultural pests and beneficial insects within the agricultural ecosystem. Based on the NCBI Virus Database, over eight hundred RNA viruses belonging to 39 viral families have been reported in more than three hundred agricultural insect species. These viruses are predominantly found in the insect orders of Hymenoptera, Hemiptera, Thysanoptera, Lepidoptera, Diptera, Coleoptera, and Orthoptera. These findings have significantly enriched our understanding of RNA viral diversity in agricultural insects. While further virome investigations are necessary to expand our knowledge to more insect species, it is crucial to explore the biological roles of these identified RNA viruses within insects in future studies. This review also highlights the limitations and challenges for the effective virus discovery through NGS and their potential solutions, which might facilitate for the development of innovative bioinformatic tools in the future.
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Affiliation(s)
- Yu-Hua Qi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zhuang-Xin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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3
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Fatehi S, Aikins M, Philips TW, Brown S, Zhu KY, Scully ED, Park Y. Characterization of Iflavirus in the Red Flour Beetle, Tribolium castaneum (Coleoptera; Tenebrionidae). INSECTS 2023; 14:220. [PMID: 36975905 PMCID: PMC10051554 DOI: 10.3390/insects14030220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Iflavirus is a group of viruses distributed mainly in arthropod species. We surveyed Tribolium castaneum iflavirus (TcIV) in different laboratory strains and in Sequence Read Archives (SRA) in GenBank. TcIV is highly specific to only T. castaneum and is not found in seven other Tenebrionid species, including the closely related species T. freemani. The same strains from different laboratories and different strains displayed largely different degrees of infections in the examination of 50 different lines by using Taqman-based quantitative PCR. We found that ~63% (27 out of 43 strains) of T. castaneum strains in different laboratories are positive for TcIV PCR with large degrees of variation, in the range of seven orders of magnitude, indicating that the TcIV is highly fluctuating depending on the rearing conditions. The TcIV was prevalent in the nervous system with low levels found in the gonad and gut. The transovarial transmission was supported in the experiment with surface-sterilized eggs. Interestingly, TcIV infection did not show observable pathogenicity. TcIV offers an opportunity to study the interaction between the virus and the immune system of this model beetle species.
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Affiliation(s)
- Soheila Fatehi
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
| | - Michael Aikins
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
| | - Thomas W. Philips
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
| | - Susan Brown
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Kun Yan Zhu
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
| | - Erin D. Scully
- Stored Product Insect and Engineering Research Unit, USDA-ARS-CGAHR, Manhattan, KS 66502, USA
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
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4
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da Silva LA, Basso MF, Ribeiro BM. A novel picorna-like virus identified in the cotton boll weevil Anthonomus grandis (Coleoptera: Curculionidae). Arch Virol 2023; 168:29. [PMID: 36598610 DOI: 10.1007/s00705-022-05672-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/27/2022] [Indexed: 01/05/2023]
Abstract
The cotton boll weevil (CBW; Anthonomus grandis; Coleoptera: Curculionidae) is considered the major insect pest of cotton, causing considerable losses in yield and fiber quality. An increase in the boll weevil population due to increasingly inefficient chemical control measures is of great concernamong cotton producers. The absence of conventional or transgenic cultivars with minimal resistance to CBW has stimulated the search for new molecular and biological tools for efficient control of this insect pest. In this study, we used a metagenomic approach based on RNA deep sequencing to investigate the presence of viruses and coding viral RNA in apparently healthy native adult CBW insects collected from cotton crops in Mato Grosso state, Brazil. Using an Illumina HiSeq 2000 paired-end platform, 138,798 virus-related reads were obtained, and a consensus sequence of a putative new virus, 10,632 nucleotides in length, was assembled. The sequences of the 5' and 3' untranslated regions (UTRs) were determined by rapid amplification of cDNA ends (RACE), followed by Nanopore sequencing. The complete genome sequence included a 5'-UTR (1,158 nucleotides), a 3'-UTR (561 nucleotides), and a single ORF of 8,913 nucleotides encoding a large polyprotein. Sequence analysis of the putative polyprotein showed several regions with high sequence similarity to structural and non-structural proteins of viruses of the family Iflaviridae. Pairwise alignments of polyprotein amino acid sequences showed the highest sequence identity (32.13%) to a partial polyprotein sequence of a putative iflavirus (QKN89051.1) found in samples from wild zoo birds in China. Phylogenetic analysis based on full polyprotein sequences of different iflaviruses indicated that this new picorna-like virus is most closely related to iflaviruses found in lepidopteran insects, and it was therefore tentatively named "Anthonomus grandis iflavirus 1" (AgIV-1). This is, to our knowledge, the first complete viral genome sequence found in CBW, and it could provide a basis for further studies about the infectivity and transmission of this virus and its possible association with symptoms or acute disease. AgIV-1 could potentially be used to develop biological or molecular tools, such as a viral vector to carry interfering RNA molecules for CBW control.
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Affiliation(s)
- Leonardo Assis da Silva
- Laboratory of Baculovirus, Cell Biology Department, University of Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, CEP 70910-900, Brazil
| | - Marcos Fernando Basso
- BIOMOL/BIOTEC Laboratory, Mato Grosso Cotton Institute (IMAmt), Rondonópolis, MT, 78740-970, Brazil
| | - Bergmann Morais Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, CEP 70910-900, Brazil.
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5
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Sosa-Gómez DR, Morgado FS, Corrêa RFT, Silva LA, Ardisson-Araújo DMP, Rodrigues BMP, Oliveira EE, Aguiar RWS, Ribeiro BM. Entomopathogenic Viruses in the Neotropics: Current Status and Recently Discovered Species. NEOTROPICAL ENTOMOLOGY 2020; 49:315-331. [PMID: 32358711 DOI: 10.1007/s13744-020-00770-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/03/2020] [Indexed: 06/11/2023]
Abstract
The market for biological control of insect pests in the world and in Brazil has grown in recent years due to the unwanted ecological and human health impacts of chemical insecticides. Therefore, research on biological control agents for pest management has also increased. For instance, insect viruses have been used to protect crops and forests around the world for decades. Among insect viruses, the baculoviruses are the most studied and used viral biocontrol agent. More than 700 species of insects have been found to be naturally infected by baculoviruses, with 90% isolated from lepidopteran insects. In this review, some basic aspects of baculovirus infection in vivo and in vitro infection, gene content, viral replication will be discussed. Furthermore, we provide examples of the use of insect viruses for biological pest control and recently characterized baculoviruses in Brazil.
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Affiliation(s)
- D R Sosa-Gómez
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Soja, Londrina, PR, Brasil
| | - F S Morgado
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - R F T Corrêa
- Depto de Biotecnologia, Univ Federal de Tocantins, Gurupi, TO, Brasil
| | - L A Silva
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - D M P Ardisson-Araújo
- Depto de Bioquímica e Biologia Molecular, Univ Federal de Santa Maria, Santa Maria, RS, Brasil
| | - B M P Rodrigues
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - E E Oliveira
- Depto de Entomologia, Univ Federal de Viçosa, Viçosa, MG, Brasil
| | - R W S Aguiar
- Depto de Biotecnologia, Univ Federal de Tocantins, Gurupi, TO, Brasil
| | - B M Ribeiro
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil.
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6
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Carballo A, Williams T, Murillo R, Caballero P. Iflavirus Covert Infection Increases Susceptibility to Nucleopolyhedrovirus Disease in Spodoptera exigua. Viruses 2020; 12:E509. [PMID: 32380682 PMCID: PMC7290388 DOI: 10.3390/v12050509] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 01/04/2023] Open
Abstract
Naturally occurring covert infections in lepidopteran populations can involve multiple viruses with potentially different transmission strategies. In this study, we characterized covert infection by two RNA viruses, Spodoptera exigua iflavirus 1 (SeIV-1) and Spodoptera exigua iflavirus 2 (SeIV-2) (family Iflaviridae) that naturally infect populations of Spodoptera exigua, and examined their influence on susceptibility to patent disease by the nucleopolyhedrovirus Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) (family Baculoviridae). The abundance of SeIV-1 genomes increased up to ten-thousand-fold across insect developmental stages after surface contamination of host eggs with a mixture of SeIV-1 and SeIV-2 particles, whereas the abundance of SeIV-2 remained constant across all developmental stages. Low levels of SeIV-2 infection were detected in all groups of insects, including those that hatched from surface-decontaminated egg masses. SeIV-1 infection resulted in reduced larval weight gain, and an unbalanced sex ratio, whereas larval developmental time, pupal weight, and adult emergence and fecundity were not significantly affected in infected adults. The inoculation of S. exigua egg masses with iflavirus, followed by a subsequent infection with SeMNPV, resulted in an additive effect on larval mortality. The 50% lethal concentration (LC50) of SeMNPV was reduced nearly 4-fold and the mean time to death was faster by 12 h in iflavirus-treated insects. These results suggest that inapparent iflavirus infections may be able to modulate the host response to a new pathogen, a finding that has particular relevance to the use of SeMNPV as the basis for biological pest control products.
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Affiliation(s)
- Arkaitz Carballo
- Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra, 31006 Pamplona, Spain; (A.C.); (P.C.)
- Departamento de Biotecnología, Agronomía y Alimentos, Universidad Pública de Navarra, 31006 Pamplona, Spain
| | | | - Rosa Murillo
- Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra, 31006 Pamplona, Spain; (A.C.); (P.C.)
- Departamento de Biotecnología, Agronomía y Alimentos, Universidad Pública de Navarra, 31006 Pamplona, Spain
| | - Primitivo Caballero
- Institute for Multidisciplinary Research in Applied Biology, Universidad Pública de Navarra, 31006 Pamplona, Spain; (A.C.); (P.C.)
- Departamento de Biotecnología, Agronomía y Alimentos, Universidad Pública de Navarra, 31006 Pamplona, Spain
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7
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Shi SL, Xia RX. Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa. Viruses 2019; 11:E1087. [PMID: 31766648 PMCID: PMC6950266 DOI: 10.3390/v11121087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/17/2019] [Accepted: 11/20/2019] [Indexed: 12/12/2022] Open
Abstract
All iflavirus members belong to the unique genus, Iflavirus, of the family, Iflaviridae. The host taxa and sequence identities of these viruses are diverse. A codon usage bias, maintained by a balance between selection, mutation, and genetic drift, exists in a wide variety of organisms. We characterized the codon usage patterns of 44 iflavirus genomes that were isolated from the classes, Insecta, Arachnida, Mammalia, and Malacostraca. Iflaviruses lack a strong codon usage bias when they are evaluated using an effective number of codons. The odds ratios of the majority of dinucleotides are within the normal range. However, the dinucleotides at the 1st-2nd codon positions are more biased than those at the 2nd-3rd codon positions. Plots of effective numbers of codons, relative neutrality analysis, and PR2 bias analysis all indicate that selection pressure dominates mutations in shaping codon usage patterns in the family, Iflaviridae. When these viruses were grouped into their host taxa, we found that the indices, including the nucleotide composition, effective number of codons, relative synonymous codon usage, and the influencing factors behind the codon usage patterns, all show that there are non-significant differences between the six host-taxa-groups. Our results disagree with our assumption that diverse viruses should possess diverse codon usage patterns, suggesting that the nucleotide composition and codon usage in the family, Iflaviridae, are not host taxa-specific signatures.
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Affiliation(s)
| | - Run-Xi Xia
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China;
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8
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Santos D, Mingels L, Vogel E, Wang L, Christiaens O, Cappelle K, Wynant N, Gansemans Y, Van Nieuwerburgh F, Smagghe G, Swevers L, Vanden Broeck J. Generation of Virus- and dsRNA-Derived siRNAs with Species-Dependent Length in Insects. Viruses 2019; 11:v11080738. [PMID: 31405199 PMCID: PMC6723321 DOI: 10.3390/v11080738] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 01/01/2023] Open
Abstract
Double-stranded RNA (dsRNA) molecules of viral origin trigger a post-transcriptional gene-silencing mechanism called RNA interference (RNAi). Specifically, virally derived dsRNA is recognized and cleaved by the enzyme Dicer2 into short interfering RNAs (siRNAs), which further direct sequence-specific RNA silencing, ultimately silencing replication of the virus. Notably, RNAi can also be artificially triggered by the delivery of gene-specific dsRNA, thereby leading to endogenous gene silencing. This is a widely used technology that holds great potential to contribute to novel pest control strategies. In this regard, research efforts have been set to find methods to efficiently trigger RNAi in the field. In this article, we demonstrate the generation of dsRNA- and/or virus-derived siRNAs—the main RNAi effectors—in six insect species belonging to five economically important orders (Lepidoptera, Orthoptera, Hymenoptera, Coleoptera, and Diptera). In addition, we describe that the siRNA length distribution is species-dependent. Taken together, our results reveal interspecies variability in the (antiviral) RNAi mechanism in insects and show promise to contribute to future research on (viral-based) RNAi-triggering mechanisms in this class of animals.
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Affiliation(s)
- Dulce Santos
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, 3000 Leuven, Belgium.
| | - Lina Mingels
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, 3000 Leuven, Belgium
| | - Elise Vogel
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, 3000 Leuven, Belgium
| | - Luoluo Wang
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Olivier Christiaens
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Kaat Cappelle
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Niels Wynant
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, 3000 Leuven, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology Group, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", 15310 Athens, Greece
| | - Jozef Vanden Broeck
- Research Group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, 3000 Leuven, Belgium
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9
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Dos Santos ER, Trentin LB, Ecker A, Silva LA, Borges M, Mowery JD, Ribeiro BM, Harrison RL, Ardisson-Araújo DMP. An iflavirus found in stink bugs (Hemiptera: Pentatomidae) of four different species. Virology 2019; 534:72-79. [PMID: 31207441 DOI: 10.1016/j.virol.2019.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 11/29/2022]
Abstract
An analysis of transcriptomes from the antennae of the three South American stink bugs (Euschistus heros, Chinavia ubica, and Dichelops melacanthus) revealed the presence of picorna-like virus genome-length RNAs with high sequence identity to the genome of Halyomorpha halys virus (HhV), originally discovered in the transcriptome of the brown marmorated stink bug, Halyomorpha halys. Features of the genome, phylogenetic relationships to other viruses, and the appearances of virus-like particles isolated from host stink bugs all confirm that these viruses are iflaviruses and isolates of an undescribed species. Iflavirus RNAs were present at high levels (40%-90% of transcriptome reads) in the stink bug antennal transcriptomes. In whole-insect transcriptomes of H. halys, HhV reads were >500-fold more abundant in adults than in nymphs. We identified from field population a subject of species E. heros infected by this iflavirus. The results of the analysis suggest that these iflaviruses are able to produce large quantities of their RNAs without causing any obvious pathology to their hosts.
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Affiliation(s)
- Ethiane R Dos Santos
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, 97105-900, Brazil.
| | - Luana B Trentin
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, 97105-900, Brazil.
| | - Assis Ecker
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, 97105-900, Brazil.
| | - Leonardo A Silva
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasilia, DF, 70910-900, Brazil.
| | - Miguel Borges
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, 70.770-917, Brazil.
| | - Joseph D Mowery
- Electron and Confocal Microscopy Unit, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, MD, 20705, USA.
| | - Bergmann M Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasilia, DF, 70910-900, Brazil.
| | - Robert L Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, MD, 20705, USA.
| | - Daniel M P Ardisson-Araújo
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, 97105-900, Brazil.
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10
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Dhaygude K, Johansson H, Kulmuni J, Sundström L. Genome organization and molecular characterization of the three Formica exsecta viruses-FeV1, FeV2 and FeV4. PeerJ 2019; 6:e6216. [PMID: 30809424 PMCID: PMC6387575 DOI: 10.7717/peerj.6216] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/05/2018] [Indexed: 12/12/2022] Open
Abstract
We present the genome organization and molecular characterization of the three Formica exsecta viruses, along with ORF predictions, and functional annotation of genes. The Formica exsecta virus-4 (FeV4; GenBank ID: MF287670) is a newly discovered negative-sense single-stranded RNA virus representing the first identified member of order Mononegavirales in ants, whereas the Formica exsecta virus-1 (FeV1; GenBank ID: KF500001), and the Formica exsecta virus-2 (FeV2; GenBank ID: KF500002) are positive single-stranded RNA viruses initially identified (but not characterized) in our earlier study. The new virus FeV4 was found by re-analyzing data from a study published earlier. The Formica exsecta virus-4 genome is 9,866 bp in size, with an overall G + C content of 44.92%, and containing five predicted open reading frames (ORFs). Our bioinformatics analysis indicates that gaps are absent and the ORFs are complete, which based on our comparative genomics analysis suggests that the genomes are complete. Following the characterization, we validate virus infection for FeV1, FeV2 and FeV4 for the first time in field-collected worker ants. Some colonies were infected by multiple viruses, and the viruses were observed to infect all castes, and multiple life stages of workers and queens. Finally, highly similar viruses were expressed in adult workers and queens of six other Formica species: F. fusca, F. pressilabris, F. pratensis, F. aquilonia, F. truncorum and F. cinerea. This research indicates that viruses can be shared between ant species, but further studies on viral transmission are needed to understand viral infection pathways.
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Affiliation(s)
- Kishor Dhaygude
- Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Helena Johansson
- Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jonna Kulmuni
- Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Liselotte Sundström
- Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, Hanko, Finland
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11
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Dong Y, Chao J, Liu J, Rice A, Holdbrook R, Liu Y, Xu P. Characterization of a novel RNA virus from Nesidiocoris tenuis related to members of the genus Iflavirus. Arch Virol 2017; 163:571-574. [PMID: 29101538 DOI: 10.1007/s00705-017-3622-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/26/2017] [Indexed: 01/10/2023]
Abstract
The complete genome of a novel virus from Nesidiocoris tenuis was determined by RNA-seq and rapid amplification of cDNA ends. This virus has a single-stranded RNA genome of 10633 nucleotides (nt) in length, not including the poly(A) tail, and contains two putative open reading frames (ORFs). ORF1 encodes a polypeptide of 1320 amino acids (aa) with a predicted molecular mass of 147.92 kDa and theoretical isoelectric point (pI) of 6.96. ORF2 encodes a polypeptide of 1728 aa with a predicted molecular mass of 197.09 kDa and pI of 6.73. Phylogenetic analysis with the deduced aa sequences of the conserved RNA dependent RNA polymerase domain as well as whole genome nt sequences indicated that the virus clusters with viruses classified within the genus Iflavirus, with a high bootstrap value in the maximum-likelihood and neighbor-joining trees. However, this virus has a distinct genome structure with two ORFs, iflaviruses normally having one, suggesting the virus might be a prototype of a new genus. We named the virus isolate Nesidiocoris tenuis virus 1 (NtV-1). The prevalence of NtV-1 infection in wild samples of N. tenuis was at a low level (7.32%, 6 positive in 82 samples), suggesting a possible harmful effect to its host.
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Affiliation(s)
- Yonghao Dong
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, P.R. China.,College of Plant Protection, Shandong Agricultural University, Taian, P.R. China
| | - Jiangtao Chao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, P.R. China
| | - Jinyan Liu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, P.R. China
| | - Annabel Rice
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Robert Holdbrook
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Yongjie Liu
- College of Plant Protection, Shandong Agricultural University, Taian, P.R. China
| | - Pengjun Xu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, P.R. China. .,Lancaster Environment Centre, Lancaster University, Lancaster, UK.
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12
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Yuan H, Xu P, Yang X, Graham RI, Wilson K, Wu K. Characterization of a novel member of genus Iflavirus in Helicoverpa armigera. J Invertebr Pathol 2017; 144:65-73. [PMID: 28163012 DOI: 10.1016/j.jip.2017.01.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 01/16/2017] [Accepted: 01/19/2017] [Indexed: 01/27/2023]
Abstract
The cotton bollworm, Helicoverpa armigera, is one of the most important agricultural pests of many economic crops worldwide. Herein, we found a novel single-strand RNA virus by RNA-Seq and Polymerase Chain Reaction (PCR) method in H. armigera named Helicoverpa armigera iflavirus (HaIV), which possessed a genome with 10,017 nucleotides in length and contained a single large open reading frame (ORF) encoding a putative polyprotein of 3021 amino acids with a predicted molecular mass of 344.16kDa and a theoretical isoelectric point (pI) of 6.45. The deduced amino acid sequence showed highest similarity (61.0%) with the protein of Lymantria dispar Iflavirus 1. Phylogenetic analysis with putative RdRp amino acid sequences indicated that the virus clustered with members of the genus Iflavirus. The virus was mainly distributed in the fat body of its host and was found to be capable of both horizontal and vertical transmission. The efficiency of perorally horizontal transmission was dose dependent (100% infection rate with a viral dose of 108copies/μl) while vertical transmission efficiency was found to be relatively low (<28.57%). These results suggest that we have found a novel member of genus Iflavirus in H. armigera.
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Affiliation(s)
- He Yuan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Pengjun Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, PR China
| | - Xianming Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Robert I Graham
- Crop and Environment Sciences, Harper Adams University, Edgmond, Shropshire TF10 8NB, UK
| | - Kenneth Wilson
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Kongming Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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13
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Putative RNA viral sequences detected in an Ixodes scapularis-derived cell line. Ticks Tick Borne Dis 2017; 8:103-111. [DOI: 10.1016/j.ttbdis.2016.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 09/30/2016] [Accepted: 10/11/2016] [Indexed: 11/22/2022]
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14
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Abbà S, Galetto L, Vallino M, Rossi M, Turina M, Sicard A, Marzachì C. Genome sequence, prevalence and quantification of the first iflavirus identified in a phytoplasma insect vector. Arch Virol 2016; 162:799-809. [PMID: 27888410 DOI: 10.1007/s00705-016-3158-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/18/2016] [Indexed: 01/29/2023]
Abstract
The leafhopper Euscelidius variegatus is a natural vector of chrysanthemum yellows phytoplasma (CY) and an efficient vector of flavescence dorée phytoplasma (FD) under laboratory conditions. During a transcriptome sequencing (RNA-seq) project aimed at investigating the interactions between the insect and the two phytoplasmas, a 10,616-nucleotide-long contig with high sequence similarity to known picorna-like viruses was identified among the assembled insect transcripts. The discovery came totally unexpected, because insects from the laboratory colony did not show any evident symptom that could be related to the presence of a virus. The amino acid sequence, the shape and size of viral particles, and the results of phylogenetic analysis suggest that this virus, named Euscelidius variegatus virus 1 (EVV-1), can be considered a new member of a new species in the genus Iflavirus. EVV-1 was detected in all of the tested insects from the laboratory colony used for RNA-seq, both in phytoplasma-exposed and in non-exposed insects, but the viral load measured in FD-exposed samples was significantly lower than that in non-exposed insects. This result suggests the possible existence of an intriguing cross-talk among insects, endogenous bacteria, and viruses. The identification of two other E. variegatus laboratory colonies that were free of EVV-1 could represent the key to addressing some basic virological issues, e.g., viral replication and transmission mechanisms, and offer the opportunity to use infectious clones to express heterologous genes in the leafhopper and manipulate the expression of endogenous genes by promoting virus-induced gene silencing.
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Affiliation(s)
- Simona Abbà
- Institute for Sustainable Plant Protection, National Research Council of Italy, IPSP-CNR, Strada delle Cacce 73, 10135, Turin, Italy.
| | - Luciana Galetto
- Institute for Sustainable Plant Protection, National Research Council of Italy, IPSP-CNR, Strada delle Cacce 73, 10135, Turin, Italy
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy, IPSP-CNR, Strada delle Cacce 73, 10135, Turin, Italy
| | - Marika Rossi
- Institute for Sustainable Plant Protection, National Research Council of Italy, IPSP-CNR, Strada delle Cacce 73, 10135, Turin, Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy, IPSP-CNR, Strada delle Cacce 73, 10135, Turin, Italy
| | - Anne Sicard
- Department of Environmental Science, Policy and Management, University of California, 130 Mulford Hall, Berkeley, CA, 94720, USA
| | - Cristina Marzachì
- Institute for Sustainable Plant Protection, National Research Council of Italy, IPSP-CNR, Strada delle Cacce 73, 10135, Turin, Italy
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