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Assembly of plant virus agroinfectious clones using biological material or DNA synthesis. STAR Protoc 2022; 3:101716. [PMID: 36149792 PMCID: PMC9519601 DOI: 10.1016/j.xpro.2022.101716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/29/2022] [Accepted: 08/26/2022] [Indexed: 01/26/2023] Open
Abstract
Infectious clone technology is universally applied for biological characterization and engineering of viruses. This protocol describes procedures that implement synthetic biology advances for streamlined assembly of virus infectious clones. Here, I detail homology-based cloning using biological material, as well as SynViP assembly using type IIS restriction enzymes and chemically synthesized DNA fragments. The assembled virus clones are based on compact T-DNA binary vectors of the pLX series and are delivered to host plants by Agrobacterium-mediated inoculation. For complete details on the use and execution of this protocol, please refer to Pasin et al. (2017, 2018) and Pasin (2021).
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Transcriptomics Reveal Several Novel Viruses from Canegrubs (Coleoptera: Scarabaeidae) in Central Queensland, Australia. Viruses 2022; 14:v14030649. [PMID: 35337056 PMCID: PMC8949096 DOI: 10.3390/v14030649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/08/2022] [Accepted: 03/17/2022] [Indexed: 12/21/2022] Open
Abstract
Canegrubs (Coleoptera: Scarabaeidae) are major pests of sugarcane crops in Australia, but despite long-term and intensive research, no commercially viable biological control agents have been identified. We used the RNA-Seq approach to explore the viriomes of three different species of canegrubs from central Queensland, Australia to identify potential candidates for biological control. We identified six novel RNA viruses, characterized their genomes, and inferred their evolutionary relationships with other closely related viruses. These novel viruses showed similarity to other known members from picornaviruses, benyviruses, sobemoviruses, totiviruses, and reoviruses. The abundance of viral reads varied in these libraries; for example, Dermolepida albohirtum picorna-like virus (9696 nt) was built from 83,894 assembled reads while only 1350 reads mapped to Lepidiota negatoria beny-like virus (6371 nt). Future studies are essential to determine their natural incidence in different life stages of the host, biodiversity, geographical distributions, and potential as biological control agents for these important pests of sugarcane.
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Martinez-Mercado MA, de Jesús JLD, Galindo-Sánchez CE, Saavedra-Flores A, Carrillo-Tripp J. Novel viral RNA genomes of the vine mealybug Planococcus ficus. J Gen Virol 2022; 103. [PMID: 35259086 DOI: 10.1099/jgv.0.001717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The vine mealybug, Planococcus ficus (Signoret, 1875), is the most important insect pest in growing areas of the grapevine Vitis vinifera L. in several countries, including Mexico. In Mexico, Baja California (B.C.) is the region with the highest production of V. vinifera L. grapes for industrial purposes. Recently, the diversity of viruses infecting insects only (insect-specific viruses) has been broadly explored to elucidate further ecological viral-host interactions in many insect species, which in some cases has resulted in the application of virus-based biological control agents for insect pests. However, a survey of the Pl. ficus virome has not been done yet. In the present study, we pooled Pl. ficus individuals collected through different vineyards of Ensenada, B.C., Mexico and analysed them by meta-transcriptomics. Novel nearly complete genomes of five RNA viruses were retrieved. These viruses were related to the Iflaviridae and Reoviridae families, and to the Picornavirales and Tolivirales orders. A new isolate belonging to the Dicistroviridae family was also found. Phylogenetic analyses showed that these putative viral genomes group with viruses having hemipteran (including a mealybug species) or other insect hosts, or with viruses associated with insects. Our results suggest that the identified novel RNA viruses could be insect-specific viruses of Pl. ficus. This work is the first insight into the Pl. ficus virome; it guarantees further studies aimed to characterize those viruses with potential for application in biological control of this economically important insect.
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Affiliation(s)
- Miguel A Martinez-Mercado
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Baja California 22860, Mexico
| | - José Luis Duarte de Jesús
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Baja California 22860, Mexico
| | - Clara E Galindo-Sánchez
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Baja California 22860, Mexico
| | - Anaid Saavedra-Flores
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Baja California 22860, Mexico
| | - Jimena Carrillo-Tripp
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Baja California 22860, Mexico
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4
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Chen J, DeGrandi-Hoffman G, Ratti V, Kang Y. Review on mathematical modeling of honeybee population dynamics. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:9606-9650. [PMID: 34814360 DOI: 10.3934/mbe.2021471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Honeybees have an irreplaceable position in agricultural production and the stabilization of natural ecosystems. Unfortunately, honeybee populations have been declining globally. Parasites, diseases, poor nutrition, pesticides, and climate changes contribute greatly to the global crisis of honeybee colony losses. Mathematical models have been used to provide useful insights on potential factors and important processes for improving the survival rate of colonies. In this review, we present various mathematical tractable models from different aspects: 1) simple bee-only models with features such as age segmentation, food collection, and nutrient absorption; 2) models of bees with other species such as parasites and/or pathogens; and 3) models of bees affected by pesticide exposure. We aim to review those mathematical models to emphasize the power of mathematical modeling in helping us understand honeybee population dynamics and its related ecological communities. We also provide a review of computational models such as VARROAPOP and BEEHAVE that describe the bee population dynamics in environments that include factors such as temperature, rainfall, light, distance and quality of food, and their effects on colony growth and survival. In addition, we propose a future outlook on important directions regarding mathematical modeling of honeybees. We particularly encourage collaborations between mathematicians and biologists so that mathematical models could be more useful through validation with experimental data.
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Affiliation(s)
- Jun Chen
- Simon A. Levin Mathematical and Computational Modeling Sciences Center, Arizona State University, 1031 Palm Walk, Tempe AZ 85281, USA
| | - Gloria DeGrandi-Hoffman
- Carl Hayden Bee Research Center, United States Department of Agriculture-Agricultural Research Service, 2000 East Allen Road, Tucson AZ 85719, USA
| | - Vardayani Ratti
- Department of Mathematics and Statistics, California State University, Chico, 400 W. First Street, Chico CA 95929-0560, USA
| | - Yun Kang
- Sciences and Mathematics Faculty, College of Integrative Sciences and Arts, Arizona State University, 6073 S. Backus Mall, Mesa AZ 85212, USA
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Watanabe K, Yoshiyama M, Akiduki G, Yokoi K, Hoshida H, Kayukawa T, Kimura K, Hatakeyama M. A simple method for ex vivo honey bee cell culture capable of in vitro gene expression analysis. PLoS One 2021; 16:e0257770. [PMID: 34555120 PMCID: PMC8460014 DOI: 10.1371/journal.pone.0257770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/09/2021] [Indexed: 01/29/2023] Open
Abstract
Cultured cells are a very powerful tool for investigating biological events in vitro; therefore, cell lines have been established not only in model insect species, but also in non-model species. However, there are few reports on the establishment of stable cell lines and development of systems to introduce genes into the cultured cells of the honey bee (Apis mellifera). We describe a simple ex vivo cell culture system for the honey bee. Hemocyte cells obtained from third and fourth instar larvae were cultured in commercial Grace’s insect medium or MGM-450 insect medium for more than two weeks maintaining a normal morphology without deterioration. After an expression plasmid vector bearing the enhanced green fluorescent protein (egfp) gene driven by the immediate early 2 (IE2) viral promoter was transfected into cells, EGFP fluorescence was detected in cells for more than one week from one day after transfection. Furthermore, double-stranded RNA corresponding to a part of the egfp gene was successfully introduced into cells and interfered with egfp gene expression. A convenient and reproducible method for an ex vivo cell culture that is fully practicable for gene expression assays was established for the honey bee.
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Affiliation(s)
- Kazuyo Watanabe
- Insect Gene Function Research Unit, Division of Insect Sciences, Institute of Agrobiological Sciences, NARO, Owashi, Tsukuba, Japan
| | - Mikio Yoshiyama
- Animal Genetics Unit, Division of Animal Breeding and Reproduction Research, Institute of Livestock and Grassland Science, NARO, Ikenodai, Tsukuba, Japan
| | - Gaku Akiduki
- Insect Pest Management Group, Division of Agro-Environment Research, Kyushu Okinawa Agricultural Research Center, NARO, Koshi, Kumamoto, Japan
| | - Kakeru Yokoi
- Insect Genome Research and Engineering Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, NARO, Owashi, Tsukuba, Japan
| | - Hiroko Hoshida
- Insect Genome Research and Engineering Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, NARO, Owashi, Tsukuba, Japan
| | - Takumi Kayukawa
- Insect Gene Function Research Unit, Division of Insect Sciences, Institute of Agrobiological Sciences, NARO, Owashi, Tsukuba, Japan
| | - Kiyoshi Kimura
- Animal Genetics Unit, Division of Animal Breeding and Reproduction Research, Institute of Livestock and Grassland Science, NARO, Ikenodai, Tsukuba, Japan
| | - Masatsugu Hatakeyama
- Insect Genome Research and Engineering Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, NARO, Owashi, Tsukuba, Japan
- * E-mail:
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6
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McMenamin AJ, Parekh F, Lawrence V, Flenniken ML. Investigating Virus-Host Interactions in Cultured Primary Honey Bee Cells. INSECTS 2021; 12:653. [PMID: 34357313 PMCID: PMC8329929 DOI: 10.3390/insects12070653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/10/2021] [Accepted: 07/13/2021] [Indexed: 12/23/2022]
Abstract
Honey bee (Apis mellifera) health is impacted by viral infections at the colony, individual bee, and cellular levels. To investigate honey bee antiviral defense mechanisms at the cellular level we further developed the use of cultured primary cells, derived from either larvae or pupae, and demonstrated that these cells could be infected with a panel of viruses, including common honey bee infecting viruses (i.e., sacbrood virus (SBV) and deformed wing virus (DWV)) and an insect model virus, Flock House virus (FHV). Virus abundances were quantified over the course of infection. The production of infectious virions in cultured honey bee pupal cells was demonstrated by determining that naïve cells became infected after the transfer of deformed wing virus or Flock House virus from infected cell cultures. Initial characterization of the honey bee antiviral immune responses at the cellular level indicated that there were virus-specific responses, which included increased expression of bee antiviral protein-1 (GenBank: MF116383) in SBV-infected pupal cells and increased expression of argonaute-2 and dicer-like in FHV-infected hemocytes and pupal cells. Additional studies are required to further elucidate virus-specific honey bee antiviral defense mechanisms. The continued use of cultured primary honey bee cells for studies that involve multiple viruses will address this knowledge gap.
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Affiliation(s)
- Alexander J. McMenamin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (A.J.M.); (F.P.); (V.L.)
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA
| | - Fenali Parekh
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (A.J.M.); (F.P.); (V.L.)
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA
| | - Verena Lawrence
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (A.J.M.); (F.P.); (V.L.)
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA
| | - Michelle L. Flenniken
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (A.J.M.); (F.P.); (V.L.)
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA
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7
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DeGrandi-Hoffman G, Corby-Harris V, Chen Y, Graham H, Chambers M, Watkins deJong E, Ziolkowski N, Kang Y, Gage S, Deeter M, Simone-Finstrom M, de Guzman L. Can supplementary pollen feeding reduce varroa mite and virus levels and improve honey bee colony survival? EXPERIMENTAL & APPLIED ACAROLOGY 2020; 82:455-473. [PMID: 33125599 PMCID: PMC7686192 DOI: 10.1007/s10493-020-00562-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/17/2020] [Indexed: 06/11/2023]
Abstract
Varroa destructor is an ectoparasitic mite of immature and adult honey bees that can transmit several single-stranded RNA viruses to its host. Varroa reproduce in brood cells, and mite populations increase as colonies produce brood in spring and summer. Mite numbers also can sharply rise, particularly in the fall, by the migration of varroa into hives on foragers. Colonies with high levels of varroa and viruses often die over the winter. Feeding colonies pollen might keep virus levels low and improve survival because of the positive effects of pollen on immunity and colony growth. We compared varroa and virus levels and overwinter survival in colonies with (fed) and without (unfed) supplemental pollen. We also measured the frequency of capturing foragers with mites (FWM) at colony entrances to determine its relationship to varroa and virus levels. Colonies fed supplemental pollen were larger than unfed colonies and survived longer. Varroa populations and levels of Deformed wing virus (DWV) rose throughout the season, and were similar between fed and unfed colonies. The growth of varroa populations was correlated with FWM in fed and unfed colonies, and significantly affected DWV levels. Increasing frequencies of FWM and the effects on varroa populations might reduce the positive influence of supplemental pollen on immune function. However, pollen feeding can stimulate colony growth and this can improve colony survival.
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Affiliation(s)
| | | | | | | | | | | | | | - Yun Kang
- Arizona State University, Tempe, AZ, USA
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Erez T, Chejanovsky N. Infection of a Lepidopteran Cell Line with Deformed Wing Virus. Viruses 2020; 12:E739. [PMID: 32659903 PMCID: PMC7412015 DOI: 10.3390/v12070739] [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: 05/14/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 12/19/2022] Open
Abstract
Many attempts to develop a reliable cell cultured-based system to study honey bee virus infections have encountered substantial difficulties. We investigated the ability of a cell line from a heterologous insect to sustain infection by a honey bee virus. For this purpose, we infected the Lepidopteran hemocytic cell line (P1) with Deformed wing virus (DWV). The genomic copies of DWV increased upon infection, as monitored by quantitative RT-PCR. Moreover, a tagged-primer-based RT-PCR analysis showed the presence of DWV negative-sense RNA in the cells, indicating virus replication. However, the DWV from infected cells was mildly infectious to P1 cells. Similar results were obtained when the virus was injected into Apis mellifera pupae. Thus, though the virus yields from the infected cells appeared to be very low, we show for the first time that DWV can replicate in a heterologous cell line. Given the availability of many other insect cell lines, our study paves the way for future exploration in this direction. In the absence of adequate A. mellifera cell lines, exploring the ability of alternative cell lines to enable honey bee virus infections could provide the means to study and understand the viral infectious cycle at the cellular level and facilitate obtaining purified isolates of these viruses.
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Affiliation(s)
| | - Nor Chejanovsky
- Department of Entomology Institute of Plant Protection, Agricultural Research Organization, Rishon Lezion 7528809, Israel;
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Yañez O, Piot N, Dalmon A, de Miranda JR, Chantawannakul P, Panziera D, Amiri E, Smagghe G, Schroeder D, Chejanovsky N. Bee Viruses: Routes of Infection in Hymenoptera. Front Microbiol 2020; 11:943. [PMID: 32547504 PMCID: PMC7270585 DOI: 10.3389/fmicb.2020.00943] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/20/2020] [Indexed: 11/13/2022] Open
Abstract
Numerous studies have recently reported on the discovery of bee viruses in different arthropod species and their possible transmission routes, vastly increasing our understanding of these viruses and their distribution. Here, we review the current literature on the recent advances in understanding the transmission of viruses, both on the presence of bee viruses in Apis and non-Apis bee species and on the discovery of previously unknown bee viruses. The natural transmission of bee viruses will be discussed among different bee species and other insects. Finally, the research potential of in vivo (host organisms) and in vitro (cell lines) serial passages of bee viruses is discussed, from the perspective of the host-virus landscape changes and potential transmission routes for emerging bee virus infections.
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Affiliation(s)
- Orlando Yañez
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Niels Piot
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Anne Dalmon
- INRAE, Unité de Recherche Abeilles et Environnement, Avignon, France
| | | | - Panuwan Chantawannakul
- Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Delphine Panziera
- General Zoology, Institute for Biology, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany
- Halle-Jena-Leipzig, German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Esmaeil Amiri
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, United States
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Declan Schroeder
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Nor Chejanovsky
- Entomology Department, Institute of Plant Protection, The Volcani Center, Rishon LeZion, Israel
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10
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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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11
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Yang X, Xu P, Yuan H, Graham RI, Wilson K, Wu K. Discovery and characterization of a novel picorna-like RNA virus in the cotton bollworm Helicoverpa armigera. J Invertebr Pathol 2019; 160:1-7. [DOI: 10.1016/j.jip.2018.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 11/02/2018] [Accepted: 11/14/2018] [Indexed: 11/26/2022]
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12
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Roberts JMK, Anderson DL, Durr PA. Metagenomic analysis of Varroa-free Australian honey bees (Apis mellifera) shows a diverse Picornavirales virome. J Gen Virol 2018; 99:818-826. [PMID: 29749926 DOI: 10.1099/jgv.0.001073] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The viral landscape of the honey bee (Apismellifera) has changed as a consequence of the global spread of the parasitic mite Varroa destructor and accompanying virulent strains of the iflavirus deformed wing virus (DWV), which the mite vectors. The presence of DWV in honey bee populations is known to influence the occurrence of other viruses, suggesting that the current known virome of A. mellifera may be undercharacterized. Here we tested this hypothesis by examining the honey bee virome in Australia, which is uniquely free of parasitic mites or DWV. Using a high-throughput sequencing (HTS) approach, we examined the RNA virome from nine pools of A. mellifera across Australia. In addition to previously reported honey bee viruses, several other insect viruses were detected, including strains related to aphid lethal paralysis virus (ALPV) and Rhopalosiphum padi virus (RhPV), which have recently been identified as infecting honey bees in the USA, as well as several other viruses recently found in Drosophila spp. A further 42 putative novel insect virus genomes spanning the order Picornavirales were assembled, which significantly increases the known viral diversity in A. mellifera. Among these novel genomes, we identified several that were similar (but different) to key A. mellifera viruses, such as DWV, that warrant further investigation. We propose that A. mellifera may be preferentially infected with viruses of the order Picornavirales and that a diverse population of these viruses may be representative of a Varroa-free landscape.
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Affiliation(s)
- John M K Roberts
- Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, 2601, Australia
| | - Denis L Anderson
- Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, 2601, Australia
- ADFCA, Research and Development Division, Al Ain, UAE
| | - Peter A Durr
- CSIRO, Australian Animal Health Laboratory, Geelong, Victoria, 3219, Australia
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DeGrandi-Hoffman G, Ahumada F, Graham H. Are Dispersal Mechanisms Changing the Host-Parasite Relationship and Increasing the Virulence of Varroa destructor (Mesostigmata: Varroidae) in Managed Honey Bee (Hymenoptera: Apidae) Colonies? ENVIRONMENTAL ENTOMOLOGY 2017; 46:737-746. [PMID: 28486589 DOI: 10.1093/ee/nvx077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Indexed: 06/07/2023]
Abstract
Varroa (Varroa destructor Anderson and Trueman) are a serious pest of European honey bees (Apis mellifera L.), and difficult to control in managed colonies. In our 11-mo longitudinal study, we applied multiple miticide treatments, yet mite numbers remained high and colony losses exceeded 55%. High mortality from varroa in managed apiaries is a departure from the effects of the mite in feral colonies where bees and varroa can coexist. Differences in mite survival strategies and dispersal mechanisms may be contributing factors. In feral colonies, mites can disperse through swarming. In managed apiaries, where swarming is reduced, mites disperse on foragers robbing or drifting from infested hives. Using a honey bee-varroa population model, we show that yearly swarming curtails varroa population growth, enabling colony survival for >5 yr. Without swarming, colonies collapsed by the third year. To disperse, varroa must attach to foragers that then enter other hives. We hypothesize that stress from parasitism and virus infection combined with effects that viruses have on cognitive function may contribute to forager drift and mite and virus dispersal. We also hypothesize that drifting foragers with mites can measurably increase mite populations. Simulations initialized with field data indicate that low levels of drifting foragers with mites can create sharp increases in mite populations in the fall and heavily infested colonies in the spring. We suggest new research directions to investigate factors leading to mite dispersal on foragers, and mite management strategies with consideration of varroa as a migratory pest.
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Affiliation(s)
| | | | - Henry Graham
- Carl Hayden Bee Research Center, USDA-ARS, 2000 East Allen Rd., Tucson, AZ 85719
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14
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Kolliopoulou A, Taning CNT, Smagghe G, Swevers L. Viral Delivery of dsRNA for Control of Insect Agricultural Pests and Vectors of Human Disease: Prospects and Challenges. Front Physiol 2017; 8:399. [PMID: 28659820 PMCID: PMC5469917 DOI: 10.3389/fphys.2017.00399] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/26/2017] [Indexed: 12/12/2022] Open
Abstract
RNAi is applied as a new and safe method for pest control in agriculture but efficiency and specificity of delivery of dsRNA trigger remains a critical issue. Various agents have been proposed to augment dsRNA delivery, such as engineered micro-organisms and synthetic nanoparticles, but the use of viruses has received relatively little attention. Here we present a critical view of the potential of the use of recombinant viruses for efficient and specific delivery of dsRNA. First of all, it requires the availability of plasmid-based reverse genetics systems for virus production, of which an overview is presented. For RNA viruses, their application seems to be straightforward since dsRNA is produced as an intermediate molecule during viral replication, but DNA viruses also have potential through the production of RNA hairpins after transcription. However, application of recombinant virus for dsRNA delivery may not be straightforward in many cases, since viruses can encode RNAi suppressors, and virus-induced silencing effects can be determined by the properties of the encoded RNAi suppressor. An alternative is virus-like particles that retain the efficiency and specificity determinants of natural virions but have encapsidated non-replicating RNA. Finally, the use of viruses raises important safety issues which need to be addressed before application can proceed.
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Affiliation(s)
- Anna Kolliopoulou
- Insect Molecular Genetics and Biotechnology Research Group, Institute of Biosciences and Applications, NCSR “Demokritos,”Aghia Paraskevi, Greece
| | - Clauvis N. T. Taning
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent UniversityGhent, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent UniversityGhent, Belgium
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology Research Group, Institute of Biosciences and Applications, NCSR “Demokritos,”Aghia Paraskevi, Greece
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15
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Maciel-Vergara G, Ros VID. Viruses of insects reared for food and feed. J Invertebr Pathol 2017; 147:60-75. [PMID: 28189501 DOI: 10.1016/j.jip.2017.01.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 01/26/2017] [Accepted: 01/31/2017] [Indexed: 02/07/2023]
Abstract
The use of insects as food for humans or as feed for animals is an alternative for the increasing high demand for meat and has various environmental and social advantages over the traditional intensive production of livestock. Mass rearing of insects, under insect farming conditions or even in industrial settings, can be the key for a change in the way natural resources are utilized in order to produce meat, animal protein and a list of other valuable animal products. However, because insect mass rearing technology is relatively new, little is known about the different factors that determine the quality and yield of the production process. Obtaining such knowledge is crucial for the success of insect-based product development. One of the issues that is likely to compromise the success of insect rearing is the outbreak of insect diseases. In particular, viral diseases can be devastating for the productivity and the quality of mass rearing systems. Prevention and management of viral diseases imply the understanding of the different factors that interact in insect mass rearing. This publication provides an overview of the known viruses in insects most commonly reared for food and feed. Nowadays with large-scale sequencing techniques, new viruses are rapidly being discovered. We discuss factors affecting the emergence of viruses in mass rearing systems, along with virus transmission routes. Finally we provide an overview of the wide range of measures available to prevent and manage virus outbreaks in mass rearing systems, ranging from simple sanitation methods to highly sophisticated methods including RNAi and transgenics.
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Affiliation(s)
- Gabriela Maciel-Vergara
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
| | - Vera I D Ros
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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16
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Cornman RS. Available Genetic Data Do Not Support Adaptation of Tobacco Ringspot Virus to an Arthropod Host. mBio 2017; 8:e01875-16. [PMID: 28119469 PMCID: PMC5263245 DOI: 10.1128/mbio.01875-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Robert S Cornman
- US Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
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17
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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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18
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Liu S, Vijayendran D, Chen Y, Bonning BC. Aphis Glycines Virus 2, a Novel Insect Virus with a Unique Genome Structure. Viruses 2016; 8:E315. [PMID: 27869772 PMCID: PMC5127029 DOI: 10.3390/v8110315] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 10/27/2016] [Accepted: 11/08/2016] [Indexed: 12/14/2022] Open
Abstract
The invasive soybean aphid, Aphis glycines, is a major pest in soybeans, resulting in substantial economic loss. We analyzed the A. glycines transcriptome to identify sequences derived from viruses of A. glycines. We identified sequences derived from a novel virus named Aphis glycines virus 2 (ApGlV2). The assembled virus genome sequence was confirmed by reverse transcription polymerase chain reaction (RT-PCR) and Sanger sequencing, conserved domains were characterized, and distribution, and transmission examined. This virus has a positive sense, single-stranded RNA genome of ~4850 nt that encodes three proteins. The RNA-dependent RNA polymerase (RdRp) of ApGlV2 is a permuted RdRp similar to those of some tetraviruses, while the capsid protein is structurally similar to the capsid proteins of plant sobemoviruses. ApGlV2 also encodes a larger minor capsid protein, which is translated by a readthrough mechanism. ApGlV2 appears to be widespread in A. glycines populations and to persistently infect aphids with a 100% vertical transmission rate. ApGlV2 is susceptible to the antiviral RNA interference (RNAi) pathway. This virus, with its unique genome structure with both plant- and insect-virus characteristics, is of particular interest from an evolutionary standpoint.
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Affiliation(s)
- Sijun Liu
- Department of Entomology, Iowa State University, Ames, IA 50011, USA.
| | | | - Yuting Chen
- Department of Entomology, Iowa State University, Ames, IA 50011, USA.
| | - Bryony C Bonning
- Department of Entomology, Iowa State University, Ames, IA 50011, USA.
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19
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McMahon DP, Natsopoulou ME, Doublet V, Fürst M, Weging S, Brown MJF, Gogol-Döring A, Paxton RJ. Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Proc Biol Sci 2016; 283:20160811. [PMID: 27358367 PMCID: PMC4936039 DOI: 10.1098/rspb.2016.0811] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/03/2016] [Indexed: 01/29/2023] Open
Abstract
Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.
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Affiliation(s)
- Dino P McMahon
- School of Biological Sciences, MBC, Queen's University Belfast, Belfast BT9 7BL, UK Institute of Biology, Free University Berlin, Schwendenerstrasse 1, 14195 Berlin, Germany Department for Materials and Environment, BAM Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205 Berlin, Germany
| | - Myrsini E Natsopoulou
- Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
| | - Vincent Doublet
- Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Matthias Fürst
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 OEX, UK IST Austria (Institute of Science and Technology Austria), 3400 Klosterneuburg, Austria
| | - Silvio Weging
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Mark J F Brown
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 OEX, UK
| | - Andreas Gogol-Döring
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Robert J Paxton
- School of Biological Sciences, MBC, Queen's University Belfast, Belfast BT9 7BL, UK Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
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20
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Carrillo-Tripp J, Dolezal AG, Goblirsch MJ, Miller WA, Toth AL, Bonning BC. In vivo and in vitro infection dynamics of honey bee viruses. Sci Rep 2016; 6:22265. [PMID: 26923109 PMCID: PMC4770293 DOI: 10.1038/srep22265] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/10/2016] [Indexed: 12/20/2022] Open
Abstract
The honey bee (Apis mellifera) is commonly infected by multiple viruses. We developed an experimental system for the study of such mixed viral infections in newly emerged honey bees and in the cell line AmE-711, derived from honey bee embryos. When inoculating a mixture of iflavirids [sacbrood bee virus (SBV), deformed wing virus (DWV)] and dicistrovirids [Israeli acute paralysis virus (IAPV), black queen cell virus (BQCV)] in both live bee and cell culture assays, IAPV replicated to higher levels than other viruses despite the fact that SBV was the major component of the inoculum mixture. When a different virus mix composed mainly of the dicistrovirid Kashmir bee virus (KBV) was tested in cell culture, the outcome was a rapid increase in KBV but not IAPV. We also sequenced the complete genome of an isolate of DWV that covertly infects the AmE-711 cell line, and found that this virus does not prevent IAPV and KBV from accumulating to high levels and causing cytopathic effects. These results indicate that different mechanisms of virus-host interaction affect virus dynamics, including complex virus-virus interactions, superinfections, specific virus saturation limits in cells and virus specialization for different cell types.
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Affiliation(s)
- Jimena Carrillo-Tripp
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Adam G. Dolezal
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | | | - W. Allen Miller
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Amy L. Toth
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Department of Entomology, Iowa State University, Ames, IA 50011, USA
| | - Bryony C. Bonning
- Department of Entomology, Iowa State University, Ames, IA 50011, USA
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21
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Kerr CH, Wang QS, Keatings K, Khong A, Allan D, Yip CK, Foster LJ, Jan E. The 5' untranslated region of a novel infectious molecular clone of the dicistrovirus cricket paralysis virus modulates infection. J Virol 2015; 89:5919-34. [PMID: 25810541 PMCID: PMC4442438 DOI: 10.1128/jvi.00463-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 03/12/2015] [Indexed: 02/05/2023] Open
Abstract
UNLABELLED Dicistroviridae are a family of RNA viruses that possesses a single-stranded positive-sense RNA genome containing two distinct open reading frames (ORFs), each preceded by an internal ribosome entry site that drives translation of the viral structural and nonstructural proteins, respectively. The type species, Cricket paralysis virus (CrPV), has served as a model for studying host-virus interactions; however, investigations into the molecular mechanisms of CrPV and other dicistroviruses have been limited as an established infectious clone was elusive. Here, we report the construction of an infectious molecular clone of CrPV. Transfection of in vitro-transcribed RNA from the CrPV clone into Drosophila Schneider line 2 (S2) cells resulted in cytopathic effects, viral RNA accumulation, detection of negative-sense viral RNA, and expression of viral proteins. Transmission electron microscopy, viral titers, and immunofluorescence-coupled transwell assays demonstrated that infectious viral particles are released from transfected cells. In contrast, mutant clones containing stop codons in either ORF decreased virus infectivity. Injection of adult Drosophila flies with virus derived from CrPV clones but not UV-inactivated clones resulted in mortality. Molecular analysis of the CrPV clone revealed a 196-nucleotide duplication within its 5' untranslated region (UTR) that stimulated translation of reporter constructs. In cells infected with the CrPV clone, the duplication inhibited viral infectivity yet did not affect viral translation or RNA accumulation, suggesting an effect on viral packaging or entry. The generation of the CrPV infectious clone provides a powerful tool for investigating the viral life cycle and pathogenesis of dicistroviruses and may further understanding of fundamental host-virus interactions in insect cells. IMPORTANCE Dicistroviridae, which are RNA viruses that infect arthropods, have served as a model to gain insights into fundamental host-virus interactions in insect cells. Further insights into the viral molecular mechanisms are hampered due to a lack of an established infectious clone. We report the construction of the first infectious clone of the dicistrovirus, cricket paralysis virus (CrPV). We show that transfection of the CrPV clone RNA into Drosophila cells led to production of infectious particles that resemble natural CrPV virions and result in cytopathic effects and expression of CrPV proteins and RNA in infected cells. The CrPV clone should provide insights into the dicistrovirus life cycle and host-virus interactions in insect cells. Using this clone, we find that a 196-nucleotide duplication within the 5' untranslated region of the CrPV clone increased viral translation in reporter constructs but decreased virus infectivity, thus revealing a balance that interplays between viral translation and replication.
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Affiliation(s)
- Craig H Kerr
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Qing S Wang
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathleen Keatings
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anthony Khong
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Douglas Allan
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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