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Hesketh-Best PJ, Fowler PD, Odogwu NM, Milbrath MO, Schroeder DC. Sacbrood viruses and select Lake Sinai virus variants dominated Apis mellifera colonies symptomatic for European foulbrood. Microbiol Spectr 2024; 12:e0065624. [PMID: 38980019 PMCID: PMC11302354 DOI: 10.1128/spectrum.00656-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/05/2024] [Indexed: 07/10/2024] Open
Abstract
European foulbrood (EFB) is a prevalent disease in the European honey bee (Apis mellifera) in the United States, which can lead to colony decline and collapse. The bacterial components of EFB are well-studied, but the diversity of viral infections within infected colonies has not been explored. In this study, we use meta-transcriptomics sequencing of 12 honey bee hives, symptomatic (+, n = 6) and asymptomatic (-, n = 6) for EFB, to investigate viral infection associated with the disease. We assembled 41 viral genomes, belonging to three families (Iflaviridae, Dicistroviridae, and Sinhaliviridae), all previously reported in honey bees, including Lake Sinai virus, deformed wing virus, sacbrood virus, Black queen cell virus, and Israeli acute paralysis virus. In colonies with severe EFB, we observed a higher occurrence of viral genomes (34 genomes) in contrast to fewer recovered from healthy colonies (seven genomes) and a complete absence of Dicistroviridae genomes.We observed specific Lake Sinai virus clades associated exclusively with EFB + or EFB - colonies, in addition to EFB-afflicted colonies that exhibited an increase in relative abundance of sacbrood viruses. Multivariate analyses highlighted that a combination of site and EFB disease status influenced RNA virome composition, while EFB status alone did not significantly impact it, presenting a challenge for comparisons between colonies kept in different yards. These findings contribute to the understanding of viral dynamics in honey bee colonies compromised by EFB and underscore the need for future investigations to consider viral composition when investigating EFB.IMPORTANCEThis study on the viromes of honey bee colonies affected by European foulbrood (EFB) sheds light on the dynamics of viral populations in bee colonies in the context of a prevalent bacterial brood disease. The identification of distinct Lake Sinai virus and sacbrood virus clades associated with colonies affected by severe EFB suggests a potential connection between viral composition and disease status, emphasizing the need for further investigation into the role of viruses during EFB infection. The observed increase in sacbrood viruses during EFB infection suggests a potential viral dysbiosis, with potential implications for honey bee brood health. These findings contribute valuable insights related to beekeeping practices, offering a foundation for future research aimed at understanding and mitigating the impact of bacterial and viral infection in commercial honey bee operations and the management of EFB.
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Affiliation(s)
- Poppy J. Hesketh-Best
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter D. Fowler
- Department of Comparative Medicine and Integrative Biology, Michigan State University, East Lansing, Michigan, USA
| | - Nkechi M. Odogwu
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Meghan O. Milbrath
- Department of Entomology, Michigan State University, Pollinator Performance Center, Lansing, Michigan, USA
| | - Declan C. Schroeder
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
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2
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Ryder D, Stone D, Minardi D, Riley A, Avant J, Cross L, Soeffker M, Davidson D, Newman A, Thomson P, Darby C, van Aerle R. De novo assembly and annotation of the Patagonian toothfish (Dissostichus eleginoides) genome. BMC Genomics 2024; 25:233. [PMID: 38438840 PMCID: PMC10910785 DOI: 10.1186/s12864-024-10141-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Patagonian toothfish (Dissostichus eleginoides) is an economically and ecologically important fish species in the family Nototheniidae. Juveniles occupy progressively deeper waters as they mature and grow, and adults have been caught as deep as 2500 m, living on or in just above the southern shelves and slopes around the sub-Antarctic islands of the Southern Ocean. As apex predators, they are a key part of the food web, feeding on a variety of prey, including krill, squid, and other fish. Despite its importance, genomic sequence data, which could be used for more accurate dating of the divergence between Patagonian and Antarctic toothfish, or establish whether it shares adaptations to temperature with fish living in more polar or equatorial climes, has so far been limited. RESULTS A high-quality D. eleginoides genome was generated using a combination of Illumina, PacBio and Omni-C sequencing technologies. To aid the genome annotation, the transcriptome derived from a variety of toothfish tissues was also generated using both short and long read sequencing methods. The final genome assembly was 797.8 Mb with a N50 scaffold length of 3.5 Mb. Approximately 31.7% of the genome consisted of repetitive elements. A total of 35,543 putative protein-coding regions were identified, of which 50% have been functionally annotated. Transcriptomics analysis showed that approximately 64% of the predicted genes (22,617 genes) were found to be expressed in the tissues sampled. Comparative genomics analysis revealed that the anti-freeze glycoprotein (AFGP) locus of D. eleginoides does not contain any AFGP proteins compared to the same locus in the Antarctic toothfish (Dissostichus mawsoni). This is in agreement with previously published results looking at hybridization signals and confirms that Patagonian toothfish do not possess AFGP coding sequences in their genome. CONCLUSIONS We have assembled and annotated the Patagonian toothfish genome, which will provide a valuable genetic resource for ecological and evolutionary studies on this and other closely related species.
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Affiliation(s)
- David Ryder
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK.
| | - David Stone
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Diana Minardi
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Ainsley Riley
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Justin Avant
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Lisa Cross
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Marta Soeffker
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
- Collaborative Centre for Sustainable Use of the Seas, University of East Anglia, Norwich, UK
| | | | | | | | - Chris Darby
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
| | - Ronny van Aerle
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Lowestoft, Suffolk, UK
- Centre for Sustainable Aquaculture Futures , University of Exeter, Exeter, UK
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3
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Lamas ZS, Chen Y, Evans JD. Case Report: Emerging Losses of Managed Honey Bee Colonies. BIOLOGY 2024; 13:117. [PMID: 38392335 PMCID: PMC10887003 DOI: 10.3390/biology13020117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024]
Abstract
United States commercial beekeepers prepare honey bee colonies for almond pollination in California each year in late January to early February. This represents the largest managed pollination event in the world and involves more than half of all U.S. honey bee colonies. In winter 2023, numerous colonies in Florida, which were graded as suitable for almonds (larger than ten frames of bees), dwindled suddenly or altogether died within several weeks, just prior to movement for almonds. The timing of these losses and the resulting morbidity caused severe economic harm to affected operations. This study reports interviews with affected stakeholders, their economic harm, and analyses of pathogens and parasites found in their colonies.
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Affiliation(s)
- Zachary S Lamas
- USDA-ARS Bee Research Lab, BARC-East Bldg. 306, Beltsville, MD 20705, USA
| | - Yanping Chen
- USDA-ARS Bee Research Lab, BARC-East Bldg. 306, Beltsville, MD 20705, USA
| | - Jay D Evans
- USDA-ARS Bee Research Lab, BARC-East Bldg. 306, Beltsville, MD 20705, USA
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4
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Hodoameda P, Ebel GD, Mukhopadhyay S, Clem RJ. Extreme infectious titer variability in individual Aedes aegypti mosquitoes infected with Sindbis virus is associated with both differences in virus population structure and dramatic disparities in specific infectivity. PLoS Pathog 2024; 20:e1012047. [PMID: 38412195 PMCID: PMC10923411 DOI: 10.1371/journal.ppat.1012047] [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: 07/15/2023] [Revised: 03/08/2024] [Accepted: 02/13/2024] [Indexed: 02/29/2024] Open
Abstract
Variability in how individuals respond to pathogens is a hallmark of infectious disease, yet the basis for individual variation in host response is often poorly understood. The titer of infectious virus among individual mosquitoes infected with arboviruses is frequently observed to vary by several orders of magnitude in a single experiment, even when the mosquitoes are highly inbred. To better understand the basis for this titer variation, we sequenced populations of Sindbis virus (SINV) obtained from individual infected Aedes aegypti mosquitoes that, despite being from a highly inbred laboratory colony, differed in their titers of infectious virus by approximately 10,000-fold. We observed genetic differences between these virus populations that indicated the virus present in the midguts of low titer mosquitoes was less fit than that of high titer mosquitoes, possibly due to founder effects that occurred during midgut infection. Furthermore, we found dramatic differences in the specific infectivity or SI (the ratio of infectious units/viral genome equivalents) between these virus populations, with the SI of low titer mosquitoes being up to 10,000-fold lower than that of high titer mosquitoes. Despite having similar amounts of viral genomes, low titer mosquitoes appeared to contain less viral particles, suggesting that viral genomes were packaged into virions less efficiently than in high titer mosquitoes. Finally, antibiotic treatment, which has been shown to suppress mosquito antiviral immunity, caused an increase in SI. Our results indicate that the extreme variation that is observed in SINV infectious titer between individual Ae. aegypti mosquitoes is due to both genetic differences between virus populations and to differences in the proportion of genomes that are packaged into infectious particles.
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Affiliation(s)
- Peter Hodoameda
- Division of Biology, Kansas State University, Manhattan, Kansas United States of America
| | - Gregory D. Ebel
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado United States of America
| | - Suchetana Mukhopadhyay
- Department of Biology, Indiana University, Bloomington, Indiana United States of America
| | - Rollie J. Clem
- Division of Biology, Kansas State University, Manhattan, Kansas United States of America
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Eliash N, Suenaga M, Mikheyev AS. Vector-virus interaction affects viral loads and co-occurrence. BMC Biol 2022; 20:284. [PMID: 36527054 PMCID: PMC9758805 DOI: 10.1186/s12915-022-01463-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 11/10/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Vector-borne viral diseases threaten human and wildlife worldwide. Vectors are often viewed as a passive syringe injecting the virus. However, to survive, replicate and spread, viruses must manipulate vector biology. While most vector-borne viral research focuses on vectors transmitting a single virus, in reality, vectors often carry diverse viruses. Yet how viruses affect the vectors remains poorly understood. Here, we focused on the varroa mite (Varroa destructor), an emergent parasite that can carry over 20 honey bee viruses, and has been responsible for colony collapses worldwide, as well as changes in global viral populations. Co-evolution of the varroa and the viral community makes it possible to investigate whether viruses affect vector gene expression and whether these interactions affect viral epidemiology. RESULTS Using a large set of available varroa transcriptomes, we identified how abundances of individual viruses affect the vector's transcriptional network. We found no evidence of competition between viruses, but rather that some virus abundances are positively correlated. Furthermore, viruses that are found together interact with the vector's gene co-expression modules in similar ways, suggesting that interactions with the vector affect viral epidemiology. We experimentally validated this observation by silencing candidate genes using RNAi and found that the reduction in varroa gene expression was accompanied by a change in viral load. CONCLUSIONS Combined, the meta-transcriptomic analysis and experimental results shed light on the mechanism by which viruses interact with each other and with their vector to shape the disease course.
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Affiliation(s)
- Nurit Eliash
- grid.18098.380000 0004 1937 0562Shamir Research Institute, University of Haifa, Katzrin, Israel ,grid.250464.10000 0000 9805 2626Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, Okinawa, 904-0495 Japan
| | - Miyuki Suenaga
- grid.250464.10000 0000 9805 2626Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, Okinawa, 904-0495 Japan
| | - Alexander S. Mikheyev
- grid.250464.10000 0000 9805 2626Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, Okinawa, 904-0495 Japan ,grid.1001.00000 0001 2180 7477Australian National University, Canberra, ACT, 2600 Australia
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6
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Paxton RJ, Schäfer MO, Nazzi F, Zanni V, Annoscia D, Marroni F, Bigot D, Laws-Quinn ER, Panziera D, Jenkins C, Shafiey H. Epidemiology of a major honey bee pathogen, deformed wing virus: potential worldwide replacement of genotype A by genotype B. Int J Parasitol Parasites Wildl 2022; 18:157-171. [PMID: 35592272 PMCID: PMC9112108 DOI: 10.1016/j.ijppaw.2022.04.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/16/2022] [Accepted: 04/29/2022] [Indexed: 01/10/2023]
Abstract
The western honey bee (Apis mellifera) is of major economic and ecological importance, with elevated rates of colony losses in temperate regions over the last two decades thought to be largely caused by the exotic ectoparasitic mite Varroa destructor and deformed wing virus (DWV), which the mite transmits. DWV currently exists as two main genotypes: the formerly widespread DWV-A and the more recently described and rapidly expanding DWV-B. It is an excellent system to understand viral evolution and the replacement of one viral variant by another. Here we synthesise published results on the distribution and prevalence of DWV-A and -B over the period 2008-2021 and present novel data for Germany, Italy and the UK to suggest that (i) DWV-B has rapidly expanded worldwide since its first description in 2004 and (ii) that it is potentially replacing DWV-A. Both genotypes are also found in wild bee species. Based on a simple mathematical model, we suggest that interference between viral genotypes when co-infecting the same host is key to understanding their epidemiology. We finally discuss the consequences of genotype replacement for beekeeping and for wild pollinator species.
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Affiliation(s)
- Robert J. Paxton
- General Zoology, 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, Puschstrasse 4, 04103, Leipzig, Germany
| | - Marc O. Schäfer
- Institute of Infectology Medicine, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Francesco Nazzi
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università degli Studi di Udine, Via delle Scienze 206, 33100, Udine, Italy
| | - Virginia Zanni
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università degli Studi di Udine, Via delle Scienze 206, 33100, Udine, Italy
| | - Desiderato Annoscia
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università degli Studi di Udine, Via delle Scienze 206, 33100, Udine, Italy
| | - Fabio Marroni
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università degli Studi di Udine, Via delle Scienze 206, 33100, Udine, Italy
| | - Diane Bigot
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Eoin R. Laws-Quinn
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Delphine Panziera
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Christina Jenkins
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Hassan Shafiey
- General Zoology, 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, Puschstrasse 4, 04103, Leipzig, Germany
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7
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Mongelli V, Lequime S, Kousathanas A, Gausson V, Blanc H, Nigg J, Quintana-Murci L, Elena SF, Saleh MC. Innate immune pathways act synergistically to constrain RNA virus evolution in Drosophila melanogaster. Nat Ecol Evol 2022; 6:565-578. [PMID: 35273366 PMCID: PMC7612704 DOI: 10.1038/s41559-022-01697-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/14/2021] [Indexed: 02/05/2023]
Abstract
Host-pathogen interactions impose recurrent selective pressures that lead to constant adaptation and counter-adaptation in both competing species. Here, we sought to study this evolutionary arms-race and assessed the impact of the innate immune system on viral population diversity and evolution, using Drosophila melanogaster as model host and its natural pathogen Drosophila C virus (DCV). We isogenized eight fly genotypes generating animals defective for RNAi, Imd and Toll innate immune pathways as well as pathogen-sensing and gut renewal pathways. Wild-type or mutant flies were then orally infected with DCV and the virus was serially passaged ten times via reinfection in naive flies. Viral population diversity was studied after each viral passage by high-throughput sequencing and infection phenotypes were assessed at the beginning and at the end of the evolution experiment. We found that the absence of any of the various immune pathways studied increased viral genetic diversity while attenuating virulence. Strikingly, these effects were observed in a range of host factors described as having mainly antiviral or antibacterial functions. Together, our results indicate that the innate immune system as a whole and not specific antiviral defence pathways in isolation, generally constrains viral diversity and evolution.
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Affiliation(s)
- Vanesa Mongelli
- Viruses and RNA Interference Unit, Institut Pasteur, CNRS, Paris, France
| | - Sebastian Lequime
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | | | - Valérie Gausson
- Viruses and RNA Interference Unit, Institut Pasteur, CNRS, Paris, France
| | - Hervé Blanc
- Viruses and RNA Interference Unit, Institut Pasteur, CNRS, Paris, France
| | - Jared Nigg
- Viruses and RNA Interference Unit, Institut Pasteur, CNRS, Paris, France
| | - Lluis Quintana-Murci
- Human Evolutionary Genetic Unit, Institut Pasteur, CNRS, Paris, France
- Human Genomics and Evolution, Collège de France, Paris, France
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), València, Spain.
- The Santa Fe Institute, Santa Fe, NM, USA.
| | - Maria-Carla Saleh
- Viruses and RNA Interference Unit, Institut Pasteur, CNRS, Paris, France.
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8
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Tiwari T, Zayed A. Practical Applications of Genomics in Managing Honey bee Health. Vet Clin North Am Food Anim Pract 2021; 37:535-543. [PMID: 34689919 DOI: 10.1016/j.cvfa.2021.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The honey bee Apis mellifera is a model organism for sociogenomics and one of the most important managed pollinators. High mortalities experienced by honey bee colonies over the past several decades are expected to have a substantive effect on crop pollination and global food security. These threats and the availability of a growing number of genomic resources for the honey bee have motivated research on how genetics and genomics can be practically applied to manage bee health. The authors review 3 such applications: (1) Certification of bee lineages using single-polymorphism markers; (2) breeding bees using marker-assisted selection; (3) diagnosing honey bee stressors using biomarkers.
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Affiliation(s)
- Tanushree Tiwari
- Department of Biology, York University, 208 Lumbers Building, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Amro Zayed
- Department of Biology, York University, 208 Lumbers Building, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.
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9
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Hasegawa N, Techer M, Mikheyev AS. A toolkit for studying Varroa genomics and transcriptomics: preservation, extraction, and sequencing library preparation. BMC Genomics 2021; 22:54. [PMID: 33446105 PMCID: PMC7809802 DOI: 10.1186/s12864-020-07363-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/30/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The honey bee parasite, Varroa destructor, is a leading cause of honey bee population declines. In addition to being an obligate ectoparasitic mite, Varroa carries several viruses that infect honey bees and act as the proximal cause of colony collapses. Nevertheless, until recently, studies of Varroa have been limited by the paucity of genomic tools. Lab- and field-based methods exploiting such methods are still nascent. This study developed a set of methods for preserving Varroa DNA and RNA from the field to the lab and processing them into sequencing libraries. We performed preservation experiments in which Varroa mites were immersed in TRIzol, RNAlater, and absolute ethanol for preservation periods up to 21 days post-treatment to assess DNA and RNA integrity. RESULTS For both DNA and RNA, mites preserved in TRIzol and RNAlater at room temperature degraded within 10 days post-treatment. Mites preserved in ethanol at room temperature and 4 °C remained intact through 21 days. Varroa mite DNA and RNA libraries were created and sequenced for ethanol preserved samples, 15 and 21 days post-treatment. All DNA sequences mapped to the V. destructor genome at above 95% on average, while RNA sequences mapped to V. destructor, but also sometimes to high levels of the deformed-wing virus and to various organisms. CONCLUSIONS Ethanolic preservation of field-collected mites is inexpensive and simple, and allows them to be shipped and processed successfully in the lab for a wide variety of sequencing applications. It appears to preserve RNA from both Varroa and at least some of the viruses it vectors.
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Affiliation(s)
- Nonno Hasegawa
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, 904-0495, Okinawa, Japan.
| | - Maeva Techer
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, 904-0495, Okinawa, Japan
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, 904-0495, Okinawa, Japan.
- Australian National University, 2600, Canberra, ACT, Australia.
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10
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Velazquez-Salinas L, Zarate S, Eberl S, Gladue DP, Novella I, Borca MV. Positive Selection of ORF1ab, ORF3a, and ORF8 Genes Drives the Early Evolutionary Trends of SARS-CoV-2 During the 2020 COVID-19 Pandemic. Front Microbiol 2020; 11:550674. [PMID: 33193132 PMCID: PMC7644918 DOI: 10.3389/fmicb.2020.550674] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/28/2020] [Indexed: 11/13/2022] Open
Abstract
In this study, we analyzed full-length SARS-CoV-2 genomes from multiple countries to determine early trends in the evolutionary dynamics of the novel COVID-19 pandemic. Results indicated SARS-CoV-2 evolved early into at least three phylogenetic groups, characterized by positive selection at specific residues of the accessory proteins ORF3a and ORF8. Also, we are reporting potential relevant sites under positive selection at specific sites of non-structural proteins nsp6 and helicase. Our analysis of co-evolution showed evidence of epistatic interactions among sites in the genome that may be important in the generation of variants adapted to humans. These observations might impact not only public health but also suggest that more studies are needed to understand the genetic mechanisms that may affect the development of therapeutic and preventive tools, like antivirals and vaccines. Collectively, our results highlight the identification of ongoing selection even in a scenario of conserved sequences collected over the first 3 months of this pandemic.
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Affiliation(s)
- Lauro Velazquez-Salinas
- Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Greenport, NY, United States.,College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Selene Zarate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de Mexico, Mexico City, Mexico
| | - Samantha Eberl
- Department of Psychological Science, Central Connecticut State University, New Britain, CT, United States
| | - Douglas P Gladue
- Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Greenport, NY, United States
| | | | - Manuel V Borca
- Foreign Animal Disease Research Unit, USDA/ARS Plum Island Animal Disease Center, Greenport, NY, United States
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11
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Li-Byarlay H, Boncristiani H, Howell G, Herman J, Clark L, Strand MK, Tarpy D, Rueppell O. Transcriptomic and Epigenomic Dynamics of Honey Bees in Response to Lethal Viral Infection. Front Genet 2020; 11:566320. [PMID: 33101388 PMCID: PMC7546774 DOI: 10.3389/fgene.2020.566320] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/17/2020] [Indexed: 12/28/2022] Open
Abstract
Honey bees (Apis mellifera L.) suffer from many brood pathogens, including viruses. Despite considerable research, the molecular responses and dynamics of honey bee pupae to viral pathogens remain poorly understood. Israeli Acute Paralysis Virus (IAPV) is emerging as a model virus since its association with severe colony losses. Using worker pupae, we studied the transcriptomic and methylomic consequences of IAPV infection over three distinct time points after inoculation. Contrasts of gene expression and 5 mC DNA methylation profiles between IAPV-infected and control individuals at these time points - corresponding to the pre-replicative (5 h), replicative (20 h), and terminal (48 h) phase of infection - indicate that profound immune responses and distinct manipulation of host molecular processes accompany the lethal progression of this virus. We identify the temporal dynamics of the transcriptomic response to with more genes differentially expressed in the replicative and terminal phases than in the pre-replicative phase. However, the number of differentially methylated regions decreased dramatically from the pre-replicative to the replicative and terminal phase. Several cellular pathways experienced hyper- and hypo-methylation in the pre-replicative phase and later dramatically increased in gene expression at the terminal phase, including the MAPK, Jak-STAT, Hippo, mTOR, TGF-beta signaling pathways, ubiquitin mediated proteolysis, and spliceosome. These affected biological functions suggest that adaptive host responses to combat the virus are mixed with viral manipulations of the host to increase its own reproduction, all of which are involved in anti-viral immune response, cell growth, and proliferation. Comparative genomic analyses with other studies of viral infections of honey bees and fruit flies indicated that similar immune pathways are shared. Our results further suggest that dynamic DNA methylation responds to viral infections quickly, regulating subsequent gene activities. Our study provides new insights of molecular mechanisms involved in epigenetic that can serve as foundation for the long-term goal to develop anti-viral strategies for honey bees, the most important commercial pollinator.
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Affiliation(s)
- Hongmei Li-Byarlay
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Humberto Boncristiani
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, United States
| | - Gary Howell
- High Performance Cluster, Office of Information Technology, North Carolina State University, Raleigh, NC, United States
| | - Jake Herman
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, United States
| | - Lindsay Clark
- High Performance Computing in Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Micheline K. Strand
- Army Research Office, Army Research Laboratory, Research Triangle Park, NC, United States
| | - David Tarpy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
- W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, United States
| | - Olav Rueppell
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, United States
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12
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Fan J, Wennmann JT, Wang D, Jehle JA. Single nucleotide polymorphism (SNP) frequencies and distribution reveal complex genetic composition of seven novel natural isolates of Cydia pomonella granulovirus. Virology 2019; 541:32-40. [PMID: 31826844 DOI: 10.1016/j.virol.2019.11.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/24/2022]
Abstract
The co-evolution between baculoviruses and their insect hosts results in selection of virus populations. To explore this phenomenon at the molecular level, seven natural isolates of Cydia pomonella granulovirus (CpGV) collected from orchards in northwest China were studied using Illumina next generation sequencing (NGS). A total of 540 genome positions with single nucleotide polymorphisms (SNPs) were detected in comparison with known CpGV isolates. New members of previously defined phylogenetic genome groups A, D and E of CpGV, as well as two novel phylogenetic lines, termed genome group F and G, were identified. Combining SNP frequency distribution with the prevalence of genome group-specific SNPs, revealed that six isolates of CpGV were mixtures of different ratios of at least two genotypes, whereas only one isolate, CpGV-WW, was genetically highly homogeneous. This study significantly extends our current understanding of the genetic diversity of CpGV and opens new lines of application of this virus.
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Affiliation(s)
- Jiangbin Fan
- Institute for Biological Control, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Heinrichstraße 243, 64287, Darmstadt, Germany; State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Jörg T Wennmann
- Institute for Biological Control, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Heinrichstraße 243, 64287, Darmstadt, Germany
| | - Dun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Johannes A Jehle
- Institute for Biological Control, Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Heinrichstraße 243, 64287, Darmstadt, Germany.
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13
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Abstract
Bees-including solitary, social, wild, and managed species-are key pollinators of flowering plant species, including nearly three-quarters of global food crops. Their ecological importance, coupled with increased annual losses of managed honey bees and declines in populations of key wild species, has focused attention on the factors that adversely affect bee health, including viral pathogens. Genomic approaches have dramatically expanded understanding of the diversity of viruses that infect bees, the complexity of their transmission routes-including intergenus transmission-and the diversity of strategies bees have evolved to combat virus infections, with RNA-mediated responses playing a prominent role. Moreover, the impacts of viruses on their hosts are exacerbated by the other major stressors bee populations face, including parasites, poor nutrition, and exposure to chemicals. Unraveling the complex relationships between viruses and their bee hosts will lead to improved understanding of viral ecology and management strategies that support better bee health.
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Affiliation(s)
- Christina M Grozinger
- Department of Entomology, Center for Pollinator Research, Center for Infectious Disease Dynamics, and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;
| | - Michelle L Flenniken
- Department of Plant Sciences and Plant Pathology and Pollinator Health Center, Montana State University, Bozeman, Montana 59717, USA;
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14
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A real-time PCR method for quantification of the total and major variant strains of the deformed wing virus. PLoS One 2017; 12:e0190017. [PMID: 29261772 PMCID: PMC5736226 DOI: 10.1371/journal.pone.0190017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/06/2017] [Indexed: 11/19/2022] Open
Abstract
European honey bees (Apis mellifera) are critically important to global food production by virtue of their pollination services but are severely threatened by deformed wing virus (DWV) especially in the presence of the external parasite Varroa destructor. DWV exists as many viral strains with the two major variants (DWV-A and DWV-B) varying in virulence. A single plasmid standard was constructed containing three sections for the specific determination of DWV-A (VP2 capsid region), DWV-B (IRES) and a conserved region suitable for total DWV (helicase region). The assays were confirmed as specific and discriminatory with limits of detections of 25, 25 and 50 genome equivalents for DWV-A, DWV-B and total-DWV, respectively. The methods were successfully tested on Apis mellifera and V. destructor samples with varying DWV profiles. The new method determined a more accurate total DWV titre in samples with substantial DWV-B than the method currently described in the COLOSS Beebook. The proposed assays could be utilized for the screening of large quantities of bee material for both a total DWV load overview along with more detailed investigations into DWV-A and DWV-B profiles.
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15
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Cornman RS. Relative abundance of deformed wing virus, Varroa destructor virus 1, and their recombinants in honey bees (Apis mellifera) assessed by kmer analysis of public RNA-Seq data. J Invertebr Pathol 2017; 149:44-50. [PMID: 28743669 DOI: 10.1016/j.jip.2017.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 07/06/2017] [Accepted: 07/20/2017] [Indexed: 11/17/2022]
Abstract
Deformed wing virus (DWV) is a major pathogen of concern to apiculture, and recent reports have indicated the local predominance and potential virulence of recombinants between DWV and a related virus, Varroa destructor virus 1 (VDV). However, little is known about the frequency and titer of VDV and recombinants relative to DWV generally. In this study, I assessed the relative occurrence and titer of DWV and VDV in public RNA-seq accessions of honey bee using a rapid, kmer-based approach. Three recombinant types were detectable graphically and corroborated by de novo assembly. Recombination breakpoints did not disrupt the capsid-encoding region, consistent with previous reports, and both VDV- and DWV-derived capsids were observed in recombinant backgrounds. High abundance of VDV kmers was largely restricted to recombinant forms. Non-metric multidimensional scaling identified genotypic clusters among DWV isolates, which was corroborated by read mapping and consensus generation. The recently described DWV-C lineage was not detected in the searched accessions. The data further highlight the utility of high-throughput sequencing to monitor viral polymorphisms and statistically test biological predictors of titer, and point to the need for consistent methodologies and sampling schemes.
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16
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Natsopoulou ME, McMahon DP, Doublet V, Frey E, Rosenkranz P, Paxton RJ. The virulent, emerging genotype B of Deformed wing virus is closely linked to overwinter honeybee worker loss. Sci Rep 2017; 7:5242. [PMID: 28701778 PMCID: PMC5507926 DOI: 10.1038/s41598-017-05596-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/31/2017] [Indexed: 12/31/2022] Open
Abstract
Bees are considered to be threatened globally, with severe overwinter losses of the most important commercial pollinator, the Western honeybee, a major concern in the Northern Hemisphere. Emerging infectious diseases have risen to prominence due to their temporal correlation with colony losses. Among these is Deformed wing virus (DWV), which has been frequently linked to colony mortality. We now provide evidence of a strong statistical association between overwintering colony decline in the field and the presence of DWV genotype-B (DWV-B), a genetic variant of DWV that has recently been shown to be more virulent than the original DWV genotype-A. We link the prevalence of DWV-B directly to a quantitative measure of overwinter decline (workforce mortality) of honeybee colonies in the field. We demonstrate that increased prevalence of virus infection in individual bees is associated with higher overwinter mortality. We also observed a substantial reduction of infected colonies in the spring, suggesting that virus-infected individuals had died during the winter. Our findings demonstrate that DWV-B, plus possible A/B recombinants exhibiting DWV-B at PCR primer binding sites, may be a major cause of elevated overwinter honeybee loss. Its potential emergence in naïve populations of bees may have far-reaching ecological and economic impacts.
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Affiliation(s)
- Myrsini E Natsopoulou
- Institute for Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany. .,Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg, Denmark.
| | - Dino P McMahon
- School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, UK.,Institute of Biology, Free University Berlin, Schwendenerstr. 1, 14195, Berlin, Germany.,Department for Materials and Environment, BAM Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205, Berlin, Germany
| | - Vincent Doublet
- Institute for Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig (iDiv), Deutscher Platz 5e, 04103, Leipzig, Germany.,Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Eva Frey
- Apicultural State Institute, University of Hohenheim, 70599, Stuttgart, Germany
| | - Peter Rosenkranz
- Apicultural State Institute, University of Hohenheim, 70599, Stuttgart, Germany
| | - Robert J Paxton
- Institute for Biology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany.,School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, UK.,German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig (iDiv), Deutscher Platz 5e, 04103, Leipzig, Germany
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17
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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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18
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Dalmon A, Desbiez C, Coulon M, Thomasson M, Le Conte Y, Alaux C, Vallon J, Moury B. Evidence for positive selection and recombination hotspots in Deformed wing virus (DWV). Sci Rep 2017; 7:41045. [PMID: 28120868 PMCID: PMC5264398 DOI: 10.1038/srep41045] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 12/15/2016] [Indexed: 01/05/2023] Open
Abstract
Deformed wing virus (DWV) is considered one of the most damaging pests in honey bees since the spread of its vector, Varroa destructor. In this study, we sequenced the whole genomes of two virus isolates and studied the evolutionary forces that act on DWV genomes. The isolate from a Varroa-tolerant bee colony was characterized by three recombination breakpoints between DWV and the closely related Varroa destructor virus-1 (VDV-1), whereas the variant from the colony using conventional Varroa management was similar to the originally described DWV. From the complete sequence dataset, nine independent DWV-VDV-1 recombination breakpoints were detected, and recombination hotspots were found in the 5′ untranslated region (5′ UTR) and the conserved region encoding the helicase. Partial sequencing of the 5′ UTR and helicase-encoding region in 41 virus isolates suggested that most of the French isolates were recombinants. By applying different methods based on the ratio between non-synonymous (dN) and synonymous (dS) substitution rates, we identified four positions that showed evidence of positive selection. Three of these positions were in the putative leader protein (Lp), and one was in the polymerase. These findings raise the question of the putative role of the Lp in viral evolution.
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Affiliation(s)
- A Dalmon
- INRA, Unité Abeilles et Environnement, F-84000 Avignon, France.,UMT PRADE, F-84000 Avignon, France
| | - C Desbiez
- INRA, Unité Pathologie végétale, F-84000 Avignon, France
| | - M Coulon
- INRA, Unité Abeilles et Environnement, F-84000 Avignon, France.,ANSES, laboratoire de Sophia Antipolis, F-06902 Sophia Antipolis
| | - M Thomasson
- INRA, Unité Abeilles et Environnement, F-84000 Avignon, France
| | - Y Le Conte
- INRA, Unité Abeilles et Environnement, F-84000 Avignon, France.,UMT PRADE, F-84000 Avignon, France
| | - C Alaux
- INRA, Unité Abeilles et Environnement, F-84000 Avignon, France.,UMT PRADE, F-84000 Avignon, France
| | - J Vallon
- UMT PRADE, F-84000 Avignon, France
| | - B Moury
- INRA, Unité Pathologie végétale, F-84000 Avignon, France
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19
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20
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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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21
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Lequime S, Fontaine A, Ar Gouilh M, Moltini-Conclois I, Lambrechts L. Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes. PLoS Genet 2016; 12:e1006111. [PMID: 27304978 PMCID: PMC4909269 DOI: 10.1371/journal.pgen.1006111] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 05/17/2016] [Indexed: 01/15/2023] Open
Abstract
Due to their error-prone replication, RNA viruses typically exist as a diverse population of closely related genomes, which is considered critical for their fitness and adaptive potential. Intra-host demographic fluctuations that stochastically reduce the effective size of viral populations are a challenge to maintaining genetic diversity during systemic host infection. Arthropod-borne viruses (arboviruses) traverse several anatomical barriers during infection of their arthropod vectors that are believed to impose population bottlenecks. These anatomical barriers have been associated with both maintenance of arboviral genetic diversity and alteration of the variant repertoire. Whether these patterns result from stochastic sampling (genetic drift) rather than natural selection, and/or from the influence of vector genetic heterogeneity has not been elucidated. Here, we used deep sequencing of full-length viral genomes to monitor the intra-host evolution of a wild-type dengue virus isolate during infection of several mosquito genetic backgrounds. We estimated a bottleneck size ranging from 5 to 42 founding viral genomes at initial midgut infection, irrespective of mosquito genotype, resulting in stochastic reshuffling of the variant repertoire. The observed level of genetic diversity increased following initial midgut infection but significantly differed between mosquito genetic backgrounds despite a similar initial bottleneck size. Natural selection was predominantly negative (purifying) during viral population expansion. Taken together, our results indicate that dengue virus intra-host genetic diversity in the mosquito vector is shaped by genetic drift and purifying selection, and point to a novel role for vector genetic factors in the genetic breadth of virus populations during infection. Identifying the evolutionary forces acting on arboviral populations within their arthropod vector provides novel insights into arbovirus evolution. During infection of their arthropod vectors, arthropod-borne viruses (arboviruses) such as dengue viruses traverse several anatomical barriers that are believed to cause dramatic reductions in population size. Such population bottlenecks challenge the maintenance of viral genetic diversity, which is considered critical for fitness and adaptability of arboviruses. Anatomical barriers in the vector were previously associated with both maintenance of arboviral genetic diversity and alteration of the variant repertoire. However, the relative role of random processes and natural selection, and the influence of vector genetic heterogeneity have not been elucidated. In this study, we used high-throughput sequencing to monitor dengue virus genetic diversity during infection of several genetic backgrounds of their mosquito vector. Our results show that initial infection of the vector is randomly founded by only a few tens of individual virus genomes. The overall level of viral genetic diversity generated during infection was predominantly under purifying selection but differed significantly between mosquito genetic backgrounds. Thus, in addition to random evolutionary forces and the purging of deleterious mutations that shape dengue virus genetic diversity during vector infection, our results also point to a novel role for vector genetic factors in the genetic breadth of virus populations.
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Affiliation(s)
- Sebastian Lequime
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France
- Université Pierre et Marie Curie, Cellule Pasteur UPMC, Paris, France
- * E-mail: (SL); (LL)
| | - Albin Fontaine
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France
- Equipe Résidente de Recherche d’Infectiologie Tropicale, Division Expertise, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
| | - Meriadeg Ar Gouilh
- Unité Environnement et Risques Infectieux, Cellule d’Intervention Biologique d’Urgence, Department of Infection and Epidemiology, Institut Pasteur, Paris, France
- EA4655, Unité Risques Microbiens U2RM, Université de Caen Normandie, Caen, France
| | - Isabelle Moltini-Conclois
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France
| | - Louis Lambrechts
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France
- * E-mail: (SL); (LL)
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22
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Reddy KE, Yoo MS, Kim YH, Kim NH, Ramya M, Jung HN, Thao LTB, Lee HS, Kang SW. Homology differences between complete Sacbrood virus genomes from infected Apis mellifera and Apis cerana honeybees in Korea. Virus Genes 2016; 52:281-9. [PMID: 26810400 DOI: 10.1007/s11262-015-1268-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/01/2015] [Indexed: 11/27/2022]
Abstract
Sacbrood virus (SBV) represents a serious threat to the health of managed honeybees. We determined four complete SBV genomic sequences (AmSBV-Kor1, AmSBV-Kor2, AcSBV-Kor3, and AcSBV-Kor4) isolated from Apis mellifera and Apis cerana in various regions of South Korea. A phylogenetic tree was constructed from the complete genomic sequences of these Korean SBVs (KSBVs) and 21 previously reported SBV sequences from other countries. Three KSBVs (not AmSBV-Kor1) clustered with previously reported Korean genomes, but separately from SBV genomes from other countries. The KSBVs shared 90-98 % identity, and 89-97 % identity with the genomes from other countries. AmSBV-Kor1 was least similar (~90 % identity) to the other KSBVs, and was most similar to previously reported strains AmSBV-Kor21 (97 %) and AmSBV-UK (93 %). Phylogenetic analysis of the partial VP1 region sequences indicated that SBVs clustered by host species and country of origin. The KSBVs were aligned with nine previously reported complete SBV genomes and compared. The KSBVs were most different from the other genomes at the end of the 5' untranslated region and in the entire open reading frame. A SimPlot graph of the VP1 region confirmed its high variability, especially between the SBVs infecting A. mellifera and A. cerana. In this genomic region, SBVs from A. mellifera species contain an extra continuous 51-nucleotide sequence relative to the SBVs from A. cerana. This genomic diversity may reflect the adaptation of SBV to specific hosts, viral cross-infections, and the spatial distances separating the KSBVs from other SBVs.
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Affiliation(s)
- Kondreddy Eswar Reddy
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea.
- Plant Molecular Biology Lab, Department of Botany, S. K. University, Anantapur, Andhrapradesh, India.
| | - Mi Sun Yoo
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
| | - Young-Ha Kim
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
| | - Nam-Hee Kim
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
| | - Mummadireddy Ramya
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
- Plant Molecular Biology Lab, Department of Botany, S. K. University, Anantapur, Andhrapradesh, India
| | - Ha-Na Jung
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
| | - Le Thi Bich Thao
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Hee-Soo Lee
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
| | - Seung-Won Kang
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea.
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23
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Grozinger CM, Robinson GE. The power and promise of applying genomics to honey bee health. CURRENT OPINION IN INSECT SCIENCE 2015; 10:124-132. [PMID: 26273565 PMCID: PMC4528376 DOI: 10.1016/j.cois.2015.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
New genomic tools and resources are now being used to both understand honey bee health and develop tools to better manage it. Here, we describe the use of genomic approaches to identify and characterize bee parasites and pathogens, examine interactions among these parasites and pathogens, between them and their bee hosts, and to identify genetic markers for improved breeding of more resilient bee stocks. We also discuss several new genomic techniques that can be used to more efficiently study, monitor and improve bee health. In the case of using RNAi-based technologies to mitigate diseases in bee populations, we highlight advantages, disadvantages and strategies to reduce risk. The increased use of genomic analytical tools and manipulative technologies has already led to significant advances, and holds great promise for improvements in the health of honey bees and other critical pollinator species.
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Affiliation(s)
- Christina M. Grozinger
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, University Park, PA 16803
| | - Gene E. Robinson
- Department of Entomology, Neuroscience Program, Institute for Genomic Biology, University of Illinois, Urbana-Champaign, 61801
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24
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de Miranda JR, Cornman RS, Evans JD, Semberg E, Haddad N, Neumann P, Gauthier L. Genome Characterization, Prevalence and Distribution of a Macula-Like Virus from Apis mellifera and Varroa destructor. Viruses 2015; 7:3586-602. [PMID: 26154017 PMCID: PMC4517118 DOI: 10.3390/v7072789] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/29/2015] [Accepted: 07/01/2015] [Indexed: 12/13/2022] Open
Abstract
Around 14 distinct virus species-complexes have been detected in honeybees, each with one or more strains or sub-species. Here we present the initial characterization of an entirely new virus species-complex discovered in honeybee (Apis mellifera L.) and varroa mite (Varroa destructor) samples from Europe and the USA. The virus has a naturally poly-adenylated RNA genome of about 6500 nucleotides with a genome organization and sequence similar to the Tymoviridae (Tymovirales; Tymoviridae), a predominantly plant-infecting virus family. Literature and laboratory analyses indicated that the virus had not previously been described. The virus is very common in French apiaries, mirroring the results from an extensive Belgian survey, but could not be detected in equally-extensive Swedish and Norwegian bee disease surveys. The virus appears to be closely linked to varroa, with the highest prevalence found in varroa samples and a clear seasonal distribution peaking in autumn, coinciding with the natural varroa population development. Sub-genomic RNA analyses show that bees are definite hosts, while varroa is a possible host and likely vector. The tentative name of Bee Macula-like virus (BeeMLV) is therefore proposed. A second, distantly related Tymoviridae-like virus was also discovered in varroa transcriptomes, tentatively named Varroa Tymo-like virus (VTLV).
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Affiliation(s)
- Joachim R de Miranda
- Department of Entomology, Pennsylvania State University, State College, PA 16802, USA.
- School of Biological Sciences, Queen's University Belfast, Belfast BT9 7BL, UK.
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden.
| | - R Scott Cornman
- Bee Research Laboratory, US Department of Agriculture, Beltsville, MD 20705, USA.
| | - Jay D Evans
- Bee Research Laboratory, US Department of Agriculture, Beltsville, MD 20705, USA.
| | - Emilia Semberg
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden.
| | - Nizar Haddad
- Bee Research Department, National Center for Agricultural Research and Extension, Baqa' 19381, Jordan.
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland.
| | - Laurent Gauthier
- Agroscope, Bee Research Center, Schwarzenburgstrasse 161, Bern CH-3003, Switzerland.
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25
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Liu S, Chen Y, Bonning BC. RNA virus discovery in insects. CURRENT OPINION IN INSECT SCIENCE 2015; 8:54-61. [PMID: 32846679 DOI: 10.1016/j.cois.2014.12.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 12/05/2014] [Indexed: 06/11/2023]
Abstract
The advent of next generation sequencing (NGS) technology has allowed for significant advances in insect RNA virus discovery, particularly for identification of covert viruses and for identification of previously undescribed virus groups. Recent research has revealed the complexity and diversity both of viral populations within an insect, and of different virus groups infecting insects. While appropriate verification of the ability of a given virus to infect a putative host is essential, this is frequently challenging for newly discovered viruses. In this chapter, we describe recently discovered RNA viruses of insects, optimization of NGS data analysis for virus discovery, and challenges associated with virus nomenclature.
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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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26
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Tozkar CÖ, Kence M, Kence A, Huang Q, Evans JD. Metatranscriptomic analyses of honey bee colonies. Front Genet 2015; 6:100. [PMID: 25852743 PMCID: PMC4365734 DOI: 10.3389/fgene.2015.00100] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 02/25/2015] [Indexed: 01/05/2023] Open
Abstract
Honey bees face numerous biotic threats from viruses to bacteria, fungi, protists, and mites. Here we describe a thorough analysis of microbes harbored by worker honey bees collected from field colonies in geographically distinct regions of Turkey. Turkey is one of the World's most important centers of apiculture, harboring five subspecies of Apis mellifera L., approximately 20% of the honey bee subspecies in the world. We use deep ILLUMINA-based RNA sequencing to capture RNA species for the honey bee and a sampling of all non-endogenous species carried by bees. After trimming and mapping these reads to the honey bee genome, approximately 10% of the sequences (9–10 million reads per library) remained. These were then mapped to a curated set of public sequences containing ca. Sixty megabase-pairs of sequence representing known microbial species associated with honey bees. Levels of key honey bee pathogens were confirmed using quantitative PCR screens. We contrast microbial matches across different sites in Turkey, showing new country recordings of Lake Sinai virus, two Spiroplasma bacterium species, symbionts Candidatus Schmidhempelia bombi, Frischella perrara, Snodgrassella alvi, Gilliamella apicola, Lactobacillus spp.), neogregarines, and a trypanosome species. By using metagenomic analysis, this study also reveals deep molecular evidence for the presence of bacterial pathogens (Melissococcus plutonius, Paenibacillus larvae), Varroa destructor-1 virus, Sacbrood virus, and fungi. Despite this effort we did not detect KBV, SBPV, Tobacco ringspot virus, VdMLV (Varroa Macula like virus), Acarapis spp., Tropilaeleps spp. and Apocephalus (phorid fly). We discuss possible impacts of management practices and honey bee subspecies on microbial retinues. The described workflow and curated microbial database will be generally useful for microbial surveys of healthy and declining honey bees.
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Affiliation(s)
- Cansu Ö Tozkar
- Ecological Genetics Laboratory, Department of Biological Sciences, Middle East Technical University Ankara, Turkey
| | - Meral Kence
- Ecological Genetics Laboratory, Department of Biological Sciences, Middle East Technical University Ankara, Turkey
| | - Aykut Kence
- Ecological Genetics Laboratory, Department of Biological Sciences, Middle East Technical University Ankara, Turkey
| | - Qiang Huang
- Bee Research Laboratory, United States Department of Agriculture-Agricultural Research Service Beltsville, MD, USA
| | - Jay D Evans
- Bee Research Laboratory, United States Department of Agriculture-Agricultural Research Service Beltsville, MD, USA
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27
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Ren J, Cone A, Willmot R, Jones IM. Assembly of recombinant Israeli Acute Paralysis Virus capsids. PLoS One 2014; 9:e105943. [PMID: 25153716 PMCID: PMC4143317 DOI: 10.1371/journal.pone.0105943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 07/31/2014] [Indexed: 01/30/2023] Open
Abstract
The dicistrovirus Israeli Acute Paralysis Virus (IAPV) has been implicated in the worldwide decline of honey bees. Studies of IAPV and many other bee viruses in pure culture are restricted by available isolates and permissive cell culture. Here we show that coupling the IAPV major structural precursor protein ORF2 to its cognate 3C-like processing enzyme results in processing of the precursor to the individual structural proteins in a number of insect cell lines following expression by a recombinant baculovirus. The efficiency of expression is influenced by the level of IAPV 3C protein and moderation of its activity is required for optimal expression. The mature IAPV structural proteins assembled into empty capsids that migrated as particles on sucrose velocity gradients and showed typical dicistrovirus like morphology when examined by electron microscopy. Monoclonal antibodies raised to recombinant capsids were configured into a diagnostic test specific for the presence of IAPV. Recombinant capsids for each of the many bee viruses within the picornavirus family may provide virus specific reagents for the on-going investigation of the causes of honeybee loss.
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Affiliation(s)
- Junyuan Ren
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Abigail Cone
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Rebecca Willmot
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Ian M. Jones
- School of Biological Sciences, University of Reading, Reading, United Kingdom
- * E-mail:
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28
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Chen YP, Pettis JS, Corona M, Chen WP, Li CJ, Spivak M, Visscher PK, DeGrandi-Hoffman G, Boncristiani H, Zhao Y, vanEngelsdorp D, Delaplane K, Solter L, Drummond F, Kramer M, Lipkin WI, Palacios G, Hamilton MC, Smith B, Huang SK, Zheng HQ, Li JL, Zhang X, Zhou AF, Wu LY, Zhou JZ, Lee ML, Teixeira EW, Li ZG, Evans JD. Israeli acute paralysis virus: epidemiology, pathogenesis and implications for honey bee health. PLoS Pathog 2014; 10:e1004261. [PMID: 25079600 PMCID: PMC4117608 DOI: 10.1371/journal.ppat.1004261] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 06/06/2014] [Indexed: 12/22/2022] Open
Abstract
Israeli acute paralysis virus (IAPV) is a widespread RNA virus of honey bees that has been linked with colony losses. Here we describe the transmission, prevalence, and genetic traits of this virus, along with host transcriptional responses to infections. Further, we present RNAi-based strategies for limiting an important mechanism used by IAPV to subvert host defenses. Our study shows that IAPV is established as a persistent infection in honey bee populations, likely enabled by both horizontal and vertical transmission pathways. The phenotypic differences in pathology among different strains of IAPV found globally may be due to high levels of standing genetic variation. Microarray profiles of host responses to IAPV infection revealed that mitochondrial function is the most significantly affected biological process, suggesting that viral infection causes significant disturbance in energy-related host processes. The expression of genes involved in immune pathways in adult bees indicates that IAPV infection triggers active immune responses. The evidence that silencing an IAPV-encoded putative suppressor of RNAi reduces IAPV replication suggests a functional assignment for a particular genomic region of IAPV and closely related viruses from the Family Dicistroviridae, and indicates a novel therapeutic strategy for limiting multiple honey bee viruses simultaneously and reducing colony losses due to viral diseases. We believe that the knowledge and insights gained from this study will provide a new platform for continuing studies of the IAPV–host interactions and have positive implications for disease management that will lead to mitigation of escalating honey bee colony losses worldwide. The mysterious outbreak of honey bee Colony Collapse Disorder (CCD) in the US in 2006–2007 has attracted massive media attention and created great concerns over the effects of various risk factors on bee health. Understanding the factors that are linked to the honey bee colony declines may provide insights for managing similar incidents in the future. We conducted this study to elucidate traits of a key honey bee virus, Israeli acute paralysis virus. We then developed an innovative strategy to control virus levels. The knowledge and insights gained from this study will have positive implications for bee disease management, helping to mitigate worldwide colony losses.
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Affiliation(s)
- Yan Ping Chen
- USDA-ARS Bee Research Laboratory, BARC-East Building, Beltsville, Maryland, United States of America
- * E-mail:
| | - Jeffery S. Pettis
- USDA-ARS Bee Research Laboratory, BARC-East Building, Beltsville, Maryland, United States of America
| | - Miguel Corona
- USDA-ARS Bee Research Laboratory, BARC-East Building, Beltsville, Maryland, United States of America
| | - Wei Ping Chen
- Microarray Core Facility, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cong Jun Li
- USDA-ARS Bovine Functional Genomic Laboratory, BARC-East Building, Beltsville, Maryland, United States of America
| | - Marla Spivak
- Department of Entomology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - P. Kirk Visscher
- Department of Entomology, University of California, Riverside, Riverside, California, United States of America
| | | | - Humberto Boncristiani
- Department of Biology, University of North Carolina, Greensboro, Greensboro, North Carolina, United States of America
| | - Yan Zhao
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
| | - Dennis vanEngelsdorp
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
| | - Keith Delaplane
- Department of Entomology, University of Georgia, Athens, Georgia, United States of America
| | - Leellen Solter
- Illinois Natural History Survey, University of Illinois, Urbana, Illinois, United States of America
| | - Francis Drummond
- School of Biology and Ecology, University of Maine, Orono, Maine, United States of America
| | - Matthew Kramer
- USDA-ARS Biometrical Consulting Services, Beltsville, Maryland, United States of America
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Gustavo Palacios
- National Center for Biodefense and Infectious Disease, George Mason University, Manassas, Virginia, United States of America
| | - Michele C. Hamilton
- USDA-ARS Bee Research Laboratory, BARC-East Building, Beltsville, Maryland, United States of America
| | - Barton Smith
- USDA-ARS Bee Research Laboratory, BARC-East Building, Beltsville, Maryland, United States of America
| | - Shao Kang Huang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, People‚s Republic of China
| | - Huo Qing Zheng
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, People‚s Republic of China
| | - Ji Lian Li
- Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, People‚s Republic of China
| | - Xuan Zhang
- Eastern Bee Research Institute, Yunnan Agricultural University, Kunming, People‚s Republic of China
| | - Ai Fen Zhou
- Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, Oklahoma, United States of America
| | - Li You Wu
- Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, Oklahoma, United States of America
| | - Ji Zhong Zhou
- Institute for Environmental Genomics (IEG), University of Oklahoma, Norman, Oklahoma, United States of America
| | - Myeong-L. Lee
- Sericulture and Apiculture Department, National Academy of Agricultural Science, RDA Suwon, Republic of Korea
| | - Erica W. Teixeira
- Agência Paulista de Tecnologia dos Agronegócios/SAA-SP, Pindamonhangaba, São Paulo, Brazil
| | - Zhi Guo Li
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, People‚s Republic of China
| | - Jay D. Evans
- USDA-ARS Bee Research Laboratory, BARC-East Building, Beltsville, Maryland, United States of America
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