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Erez T, Fathia Osabutey A, Hamdo S, Bonda E, Otmy A, Chejanovsky N, Soroker V. Ontogeny of immunity and natural viral infection in Apis mellifera drones and workers. J Invertebr Pathol 2024:108124. [PMID: 38729295 DOI: 10.1016/j.jip.2024.108124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/21/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024]
Abstract
The most common viral diseases affecting honey bees (Apis mellifera) in Israel include deformed wing viruses (DWV A and DWV-B) and acute paralysis viruses (ABPV and IAPV). These viruses are transmitted within and between colonies, both horizontally and vertically. All members of the colony contribute to this transmission, on the other hand individual and social immunity, particularly hygienic behaviour, may affect the outcome of the process. In this study, we evaluated the ontogeny of natural infections of DWV-A, DWV-B, ABPV and IAPV, their prevalence and loads, in workers and drones from high (H) and low (L) hygienic colonies. In parallel, we evaluated the expression of two immune genes: peptidoglycan recognition protein S2(PGRP-S2) and hymenoptaecin. The prevalence of DWV-B and IAPV increased with age and was higher in workers than in drones. ABPV was not detected in drones. The expression of both immune genes was significantly affected by age and sex. Drones from H colonies had higher expression of these genes. The increased expression of immune genes with drones' age, particularly in hygienic colonies, suggest additional value of honey bee breeding for hygienic behaviour for sustainable beekeeping.
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Affiliation(s)
- Tal Erez
- Department of Entomology, Agricultural Research Organization, The Volcani Institute, Israel; Department of Entomology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University in Jerusalem, Israel
| | | | - Sharif Hamdo
- Department of Entomology, Agricultural Research Organization, The Volcani Institute, Israel
| | - Elad Bonda
- Department of Entomology, Agricultural Research Organization, The Volcani Institute, Israel
| | - Assaf Otmy
- Department of Entomology, Agricultural Research Organization, The Volcani Institute, Israel
| | - Nor Chejanovsky
- Department of Entomology, Agricultural Research Organization, The Volcani Institute, Israel
| | - Victoria Soroker
- Department of Entomology, Agricultural Research Organization, The Volcani Institute, Israel.
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Kadlečková D, Saláková M, Erban T, Tachezy R. Discovery and characterization of novel DNA viruses in Apis mellifera: expanding the honey bee virome through metagenomic analysis. mSystems 2024; 9:e0008824. [PMID: 38441971 PMCID: PMC11019937 DOI: 10.1128/msystems.00088-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
To date, many viruses have been discovered to infect honey bees. In this study, we used high-throughput sequencing to expand the known virome of the honey bee, Apis mellifera, by identifying several novel DNA viruses. While the majority of previously identified bee viruses are RNA, our study reveals nine new genomes from the Parvoviridae family, tentatively named Bee densoviruses 1 to 9. In addition, we characterized a large DNA virus, Apis mellifera filamentous-like virus (AmFLV), which shares limited protein identities with the known Apis mellifera filamentous virus. The complete sequence of AmFLV, obtained by a combination of laboratory techniques and bioinformatics, spans 152,678 bp. Linear dsDNA genome encodes for 112 proteins, of which 49 are annotated. Another large virus we discovered is Apis mellifera nudivirus, which belongs to a group of Alphanudivirus. The virus has a length of 129,467 bp and a circular dsDNA genome, and has 106 protein encoding genes. The virus contains most of the core genes of the family Nudiviridae. This research demonstrates the effectiveness of viral binning in identifying viruses in honey bee virology, showcasing its initial application in this field.IMPORTANCEHoney bees contribute significantly to food security by providing pollination services. Understanding the virome of honey bees is crucial for the health and conservation of bee populations and also for the stability of the ecosystems and economies for which they are indispensable. This study unveils previously unknown DNA viruses in the honey bee virome, expanding our knowledge of potential threats to bee health. The use of the viral binning approach we employed in this study offers a promising method to uncovering and understanding the vast viral diversity in these essential pollinators.
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Affiliation(s)
- Dominika Kadlečková
- Department of Genetics and Microbiology, Faculty of Science BIOCEV, Charles University, Vestec, Průmyslová, Czechia
| | - Martina Saláková
- Department of Genetics and Microbiology, Faculty of Science BIOCEV, Charles University, Vestec, Průmyslová, Czechia
| | - Tomáš Erban
- Crop Research Institute, Drnovská, Prague, Czechia
| | - Ruth Tachezy
- Department of Genetics and Microbiology, Faculty of Science BIOCEV, Charles University, Vestec, Průmyslová, Czechia
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Papp M, Tóth AG, Békési L, Farkas R, Makrai L, Maróti G, Solymosi N. Apis mellifera filamentous virus from a honey bee gut microbiome survey in Hungary. Sci Rep 2024; 14:5803. [PMID: 38461199 PMCID: PMC10924886 DOI: 10.1038/s41598-024-56320-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/05/2024] [Indexed: 03/11/2024] Open
Abstract
In Hungary, as part of a nationwide, climatically balanced survey for a next-generation sequencing-based study of the honey bee (Apis mellifera) gut microbiome, repeated sampling was carried out during the honey production season (March and May 2019). Among other findings, the presence of Apis mellifera filamentous virus (AmFV) was detected in all samples, some at very high levels. AmFV-derived reads were more abundant in the March samples than in the May samples. In March, a higher abundance of AmFV-originated reads was identified in samples collected from warmer areas compared to those collected from cooler areas. A lower proportion of AmFV-derived reads were identified in samples collected in March from the wetter areas than those collected from the drier areas. AmFV-read abundance in samples collected in May showed no significant differences between groups based on either environmental temperature or precipitation. The AmFV abundance correlated negatively with Bartonella apihabitans, Bartonella choladocola, and positively with Frischella perrara, Gilliamella apicola, Gilliamella sp. ESL0443, Lactobacillus apis, Lactobacillus kullabergensis, Lactobacillus sp. IBH004. De novo metagenome assembly of four samples resulted in almost the complete AmFV genome. According to phylogenetic analysis based on DNA polymerase, the Hungarian strains are closest to the strain CH-05 isolated in Switzerland.
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Affiliation(s)
- Márton Papp
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, Budapest, 1078, Hungary
| | - Adrienn Gréta Tóth
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, Budapest, 1078, Hungary
| | - László Békési
- Department of Parasitology and Zoology, University of Veterinary Medicine Budapest, Budapest, 1078, Hungary
| | - Róbert Farkas
- Department of Parasitology and Zoology, University of Veterinary Medicine Budapest, Budapest, 1078, Hungary
| | | | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, HUN-REN, Szeged, 6726, Hungary
- Faculty of Water Sciences, University of Public Service, Baja, 6500, Hungary
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, Budapest, 1078, Hungary.
- Department of Phyisics of Complex Systems, Eötvös Loránd University, Budapest, 1117, Hungary.
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Guinet B, Leobold M, Herniou EA, Bloin P, Burlet N, Bredlau J, Navratil V, Ravallec M, Uzbekov R, Kester K, Gundersen Rindal D, Drezen JM, Varaldi J, Bézier A. A novel and diverse family of filamentous DNA viruses associated with parasitic wasps. Virus Evol 2024; 10:veae022. [PMID: 38617843 PMCID: PMC11013392 DOI: 10.1093/ve/veae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/20/2023] [Accepted: 02/23/2024] [Indexed: 04/16/2024] Open
Abstract
Large dsDNA viruses from the Naldaviricetes class are currently composed of four viral families infecting insects and/or crustaceans. Since the 1970s, particles described as filamentous viruses (FVs) have been observed by electronic microscopy in several species of Hymenoptera parasitoids but until recently, no genomic data was available. This study provides the first comparative morphological and genomic analysis of these FVs. We analyzed the genomes of seven FVs, six of which were newly obtained, to gain a better understanding of their evolutionary history. We show that these FVs share all genomic features of the Naldaviricetes while encoding five specific core genes that distinguish them from their closest relatives, the Hytrosaviruses. By mining public databases, we show that FVs preferentially infect Hymenoptera with parasitoid lifestyle and that these viruses have been repeatedly integrated into the genome of many insects, particularly Hymenoptera parasitoids, overall suggesting a long-standing specialization of these viruses to parasitic wasps. Finally, we propose a taxonomical revision of the class Naldaviricetes in which FVs related to the Leptopilina boulardi FV constitute a fifth family. We propose to name this new family, Filamentoviridae.
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Affiliation(s)
- Benjamin Guinet
- LBBE, UMR CNRS 5558, Universite Claude Bernard Lyon 1, 43 bd du 11 novembre 1918, Villeurbanne CEDEX F-69622, France
| | - Matthieu Leobold
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
| | - Pierrick Bloin
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
| | - Nelly Burlet
- LBBE, UMR CNRS 5558, Universite Claude Bernard Lyon 1, 43 bd du 11 novembre 1918, Villeurbanne CEDEX F-69622, France
| | - Justin Bredlau
- Department of Biology, Virginia Commonwealth University, 1000 W. Cary Street, Room 126, Richmond, VA 23284-9067, USA
| | - Vincent Navratil
- PRABI, Rhône-Alpes Bioinformatics Center, Université Lyon 1, 43 bd du 11 novembre 1918, Villeurbanne CEDEX 69622, France
- UMS 3601, Institut Français de Bioinformatique, IFB-Core, 2 rue Gaston Crémieu, Évry CEDEX 91057, France
- European Virus Bioinformatics Center, Leutragraben 1, Jena 07743, Germany
| | - Marc Ravallec
- Diversité, génomes et interactions microorganismes insectes (DGIMI), UMR 1333 INRA, Université de Montpellier 2, 2 Place Eugène Bataillon cc101, Montpellier CEDEX 5 34095, France
| | - Rustem Uzbekov
- Laboratory of Cell Biology and Electron Microscopy, Faculty of Medicine, Université de Tours, 10 bd Tonnelle, BP 3223, Tours CEDEX 37032, France
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Leninskye Gory 73, Moscow 119992, Russia
| | - Karen Kester
- Department of Biology, Virginia Commonwealth University, 1000 W. Cary Street, Room 126, Richmond, VA 23284-9067, USA
| | - Dawn Gundersen Rindal
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD 20705, USA
| | - Jean-Michel Drezen
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
| | - Julien Varaldi
- LBBE, UMR CNRS 5558, Universite Claude Bernard Lyon 1, 43 bd du 11 novembre 1918, Villeurbanne CEDEX F-69622, France
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261 CNRS-Université de Tours, 20 Avenue Monge, Parc de Grandmont, Tours 37200, France
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Kawato S, Nozaki R, Kondo H, Hirono I. Integrase-associated niche differentiation of endogenous large DNA viruses in crustaceans. Microbiol Spectr 2024; 12:e0055923. [PMID: 38063384 PMCID: PMC10871703 DOI: 10.1128/spectrum.00559-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Crustacean genomes harbor sequences originating from a family of large DNA viruses called nimaviruses, but it is unclear why they are present. We show that endogenous nimaviruses selectively insert into repetitive sequences within the host genome, and this insertion specificity was correlated with different types of integrases, which are DNA recombination enzymes encoded by the nimaviruses themselves. This suggests that endogenous nimaviruses have colonized various genomic niches through the acquisition of integrases with different insertion specificities. Our results point to a novel survival strategy of endogenous large DNA viruses colonizing the host genomes. These findings may clarify the evolution and spread of nimaviruses in crustaceans and lead to measures to control and prevent the spread of pathogenic nimaviruses in aquaculture settings.
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Affiliation(s)
- Satoshi Kawato
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Reiko Nozaki
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
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Damayo JE, McKee RC, Buchmann G, Norton AM, Ashe A, Remnant EJ. Virus replication in the honey bee parasite, Varroa destructor. J Virol 2023; 97:e0114923. [PMID: 37966226 PMCID: PMC10746231 DOI: 10.1128/jvi.01149-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/06/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE The parasitic mite Varroa destructor is a significant driver of worldwide colony losses of our most important commercial pollinator, the Western honey bee Apis mellifera. Declines in honey bee health are frequently attributed to the viruses that mites vector to honey bees, yet whether mites passively transmit viruses as a mechanical vector or actively participate in viral amplification and facilitate replication of honey bee viruses is debated. Our work investigating the antiviral RNA interference response in V. destructor demonstrates that key viruses associated with honey bee declines actively replicate in mites, indicating that they are biological vectors, and the host range of bee-associated viruses extends to their parasites, which could impact virus evolution, pathogenicity, and spread.
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Affiliation(s)
- James E. Damayo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Rebecca C. McKee
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Gabriele Buchmann
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- Institute of Plant Genetics, Heinrich-Heine University, Duesseldorf, Germany
| | - Amanda M. Norton
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- Academic Support Unit, Research and Advanced Instrumentation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Emily J. Remnant
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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Cornman RS. Data mining reveals tissue-specific expression and host lineage-associated forms of Apis mellifera filamentous virus. PeerJ 2023; 11:e16455. [PMID: 38025724 PMCID: PMC10655722 DOI: 10.7717/peerj.16455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Background Apis mellifera filamentous virus (AmFV) is a large double-stranded DNA virus of uncertain phylogenetic position that infects honey bees (Apis mellifera). Little is known about AmFV evolution or molecular aspects of infection. Accurate annotation of open-reading frames (ORFs) is challenged by weak homology to other known viruses. This study was undertaken to evaluate ORFs (including coding-frame conservation, codon bias, and purifying selection), quantify genetic variation within AmFV, identify host characteristics that covary with infection rate, and examine viral expression patterns in different tissues. Methods Short-read data were accessed from the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI). Sequence reads were downloaded from accessions meeting search criteria and scanned for kmers representative of AmFV genomic sequence. Samples with kmer counts above specified thresholds were downloaded in full for mapping to reference sequences and de novo assembly. Results At least three distinct evolutionary lineages of AmFV exist. Clade 1 predominates in Europe but in the Americas and Africa it is replaced by the other clades as infection level increases in hosts. Only clade 3 was found at high relative abundance in hosts with African ancestry, whereas all clades achieved high relative abundance in bees of non-African ancestry. In Europe and Africa, clade 2 was generally detected only in low-level infections but was locally dominant in some North American samples. The geographic distribution of clade 3 was consistent with an introduction to the Americas with 'Africanized' honey bees in the 1950s. Localized genomic regions of very high nucleotide divergence in individual isolates suggest recombination with additional, as-yet unidentified AmFV lineages. A set of 155 high-confidence ORFs was annotated based on evolutionary conservation in six AmFV genome sequences representative of the three clades. Pairwise protein-level identity averaged 94.6% across ORFs (range 77.1-100%), which generally exhibited low evolutionary rates and moderate to strong codon bias. However, no robust example of positive diversifying selection on coding sequence was found in these alignments. Most of the genome was detected in RNA short-read alignments. Transcriptome assembly often yielded contigs in excess of 50 kb and containing ORFs in both orientations, and the termini of long transcripts were associated with tandem repeats. Lower levels of AmFV RNA were detected in brain tissue compared to abdominal tissue, and a distinct set of ORFs had minimal to no detectable expression in brain tissue. A scan of DNA accessions from the parasitic mite Varroa destructor was inconclusive with respect to replication in that species. Discussion Collectively, these results expand our understanding of this enigmatic virus, revealing transcriptional complexity and co-evolutionary associations with host lineage.
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van Oers MM, Herniou EA, Jehle JA, Krell PJ, Abd-Alla AMM, Ribeiro BM, Theilmann DA, Hu Z, Harrison RL. Developments in the classification and nomenclature of arthropod-infecting large DNA viruses that contain pif genes. Arch Virol 2023; 168:182. [PMID: 37322175 PMCID: PMC10271883 DOI: 10.1007/s00705-023-05793-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Viruses of four families of arthropod-specific, large dsDNA viruses (the nuclear arthropod large DNA viruses, or NALDVs) possess homologs of genes encoding conserved components involved in the baculovirus primary infection mechanism. The presence of such homologs encoding per os infectivity factors (pif genes), along with their absence from other viruses and the occurrence of other shared characteristics, suggests a common origin for the viruses of these families. Therefore, the class Naldaviricetes was recently established, accommodating these four families. In addition, within this class, the ICTV approved the creation of the order Lefavirales for three of these families, whose members carry homologs of the baculovirus genes that code for components of the viral RNA polymerase, which is responsible for late gene expression. We further established a system for the binomial naming of all virus species in the order Lefavirales, in accordance with a decision by the ICTV in 2019 to move towards a standardized nomenclature for all virus species. The binomial species names for members of the order Lefavirales consist of the name of the genus to which the species belongs (e.g., Alphabaculovirus), followed by a single epithet that refers to the host species from which the virus was originally isolated. The common names of viruses and the abbreviations thereof will not change, as the format of virus names lies outside the remit of the ICTV.
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Affiliation(s)
- Monique M van Oers
- Laboratory of Virology, Wageningen University and Research, Wageningen, the Netherlands.
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS - University of Tours, 37200, Tours, France
| | - Johannes A Jehle
- Institute for Biological Control, Julius Kühn-Institut, 69221, Dossenheim, Germany
| | - Peter J Krell
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1, Canada
| | - Adly M M Abd-Alla
- Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, Vienna International Centre, Vienna, Austria
| | - Bergmann M Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasília, Brasília, Brazil
| | - David A Theilmann
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, 4200 Highway 97, Box 5000, Summerland, BC, V0H1Z0, Canada
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Robert L Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, USDA-ARS, 10300 Baltimore Avenue, Bldg 007 Barc‑West, Beltsville, MD, 20705, USA
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Kwon M, Jung C, Kil EJ. Metagenomic analysis of viromes in honey bee colonies ( Apis mellifera; Hymenoptera: Apidae) after mass disappearance in Korea. Front Cell Infect Microbiol 2023; 13:1124596. [PMID: 36761901 PMCID: PMC9905416 DOI: 10.3389/fcimb.2023.1124596] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
After the nationwide, massive winter losses of honey bees in Korea during the winter of 2021, samplings were conducted from live honey bees in colonies and dead honey bees nearby colonies in the same bee-farms in six regions in Korea. Each sample was subjected to virome analysis using high-throughput sequencing technology. The number of viral reads was the lowest in the live honey bee group sample with 370,503 reads and the highest in the dead honey bee group sample with 42,659,622 reads. Viral contigs were matched with the viral genomes of the black queen cell virus, deformed wing virus, Israeli acute paralysis virus, and sacbrood virus, all of which have been previously reported in Korea. However, Apis rhabdovirus 5, bee macula-like virus, Varroa orthomyxovirus-1, Hubei partiti-like virus 34, Lake Sinai virus 2, 3, and 4, and the Ditton virus, were also discovered in this study, which are the first records in Korea. Plant viral sequences resembling those of Arabidopsis latent virus 1, and a novel viral sequence was also discovered. In the present study 55 complete viral genome sequences were identified. This study is the first virome analysis of domestic honey bees and provides the latest information on the diversity of honey bee viruses in Korea.
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Affiliation(s)
- Minhyeok Kwon
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
- Agriculture Science and Technology Research Institute, Andong National University, Andong, Republic of Korea
| | - Chuleui Jung
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
- Agriculture Science and Technology Research Institute, Andong National University, Andong, Republic of Korea
| | - Eui-Joon Kil
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
- Agriculture Science and Technology Research Institute, Andong National University, Andong, Republic of Korea
- *Correspondence: Eui-Joon Kil,
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Rodríguez-Flores MS, Mazzei M, Felicioli A, Diéguez-Antón A, Seijo MC. Emerging Risk of Cross-Species Transmission of Honey Bee Viruses in the Presence of Invasive Vespid Species. Insects 2022; 14:6. [PMID: 36661935 PMCID: PMC9866884 DOI: 10.3390/insects14010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/05/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
The increase in invasive alien species is a concern for the environment. The establishment of some of these species may be changing the balance between pathogenicity and host factors, which could alter the defense strategies of native host species. Vespid species are among the most successful invasive animals, such as the genera Vespa, Vespula and Polistes. Bee viruses have been extensively studied as an important cause of honey bee population losses. However, knowledge about the transmission of honey bee viruses in Vespids is a relevant and under-researched aspect. The role of some mites such as Varroa in the transmission of honey bee viruses is clearer than in the case of Vespidae. This type of transmission by vectors has not yet been clarified in Vespidae, with interspecific relationships being the main hypotheses accepted for the transmission of bee viruses. A majority of studies describe the presence of viruses or their replicability, but aspects such as the symptomatology in Vespids or the ability to infect other hosts from Vespids are scarcely discussed. Highlighting the case of Vespa velutina as an invader, which is causing huge losses in European beekeeping, is of special interest. The pressure caused by V. velutina leads to weakened hives that become susceptible to pathogens. Gathering this information is necessary to promote further research on the spread of bee viruses in ecosystems invaded by invasive species of Vespids, as well as to prevent the decline of bee populations due to bee viruses.
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Affiliation(s)
| | - Maurizio Mazzei
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
| | - Antonio Felicioli
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
| | - Ana Diéguez-Antón
- Department of Plant Biology and Soil Sciences, University of Vigo, Campus As Lagoas, 32004 Ourense, Spain
| | - María Carmen Seijo
- Department of Plant Biology and Soil Sciences, University of Vigo, Campus As Lagoas, 32004 Ourense, Spain
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Wang X, Chen C, Zhang N, Chen Q, Zhang F, Liu X, Li F, Shi ZL, Vlak JM, Wang M, Hu Z. Functional Peroral Infectivity Complex of White Spot Syndrome Virus of Shrimp. J Virol 2022; 96:e0117322. [PMID: 36448798 DOI: 10.1128/jvi.01173-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
White spot syndrome virus (WSSV) is a major cause of disease in shrimp cultures worldwide. The infection process of this large circular double-stranded DNA virus has been well studied, but its entry mechanism remains controversial. The major virion envelope protein VP28 has been implicated in oral and systemic viral infection in shrimp. However, genetic analysis of viral DNA has shown the presence of a few genes related to proteins of per os infectivity factor (PIF) complex in baculoviruses. This complex is essential for the entry of baculoviruses, large terrestrial circular DNA viruses, into the midgut epithelial cells of insect larvae. In this study, we aimed to determine whether a PIF complex exists in WSSV, the components of this complex, whether it functions as an oral infectivity complex in shrimp, and the biochemical properties that contribute to its function in a marine environment. The results revealed a WSSV PIF complex (~720 kDa) comprising at least eight proteins, four of which were not identified as PIF homologs: WSV134, VP124 (WSV216), WSSV021, and WSV136. WSV134 is suggested to be a PIF4 homolog due to predicted structural similarity and amino acid sequence identity. The WSSV PIF complex is resistant to alkali, proteolysis, and high salt, properties that are important for maintaining infectivity in aquatic environments. Oral infection can be neutralized by PIF-specific antibodies but not by VP28-specific antibodies. These results indicate that the WSSV PIF complex is critical for WSSV entry into shrimp; the complex's evolutionary significance is also discussed. IMPORTANCE White spot disease, caused by the white spot syndrome virus (WSSV), is a major scourge in cultured shrimp production facilities worldwide. This disease is only effectively controlled by sanitation. Intervention strategies are urgently needed but are limited by a lack of appropriate targets. Our identification of a per os infectivity factor (PIF) complex, which is pivotal for the entry of WSSV into shrimp, could provide new targets for antibody- or dsRNA-based intervention strategies. In addition, the presence of a PIF complex with at least eight components in WSSV, which is ancestrally related to the PIF complex of invertebrate baculoviruses, suggests that this complex is structurally and functionally conserved in disparate virus taxa.
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12
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Wirta HK, Bahram M, Miller K, Roslin T, Vesterinen E. Reconstructing the ecosystem context of a species: Honey-borne DNA reveals the roles of the honeybee. PLoS One 2022; 17:e0268250. [PMID: 35830374 PMCID: PMC9278776 DOI: 10.1371/journal.pone.0268250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/26/2022] [Indexed: 11/18/2022] Open
Abstract
To assess a species’ impact on its environment–and the environment’s impact upon a species–we need to pinpoint its links to surrounding taxa. The honeybee (Apis mellifera) provides a promising model system for such an exercise. While pollination is an important ecosystem service, recent studies suggest that honeybees can also provide disservices. Developing a comprehensive understanding of the full suite of services and disservices that honeybees provide is a key priority for such a ubiquitous species. In this perspective paper, we propose that the DNA contents of honey can be used to establish the honeybee’s functional niche, as reflected by ecosystem services and disservices. Drawing upon previously published genomic data, we analysed the DNA found within 43 honey samples from Northern Europe. Based on metagenomic analysis, we find that the taxonomic composition of DNA is dominated by a low pathogenicity bee virus with 40.2% of the reads, followed by bacteria (16.7%), plants (9.4%) and only 1.1% from fungi. In terms of ecological roles of taxa associated with the bees or taxa in their environment, bee gut microbes dominate the honey DNA, with plants as the second most abundant group. A range of pathogens associated with plants, bees and other animals occur frequently, but with lower relative read abundance, across the samples. The associations found here reflect a versatile the honeybee’s role in the North-European ecosystem. Feeding on nectar and pollen, the honeybee interacts with plants–in particular with cultivated crops. In doing so, the honeybee appears to disperse common pathogens of plants, pollinators and other animals, but also microbes potentially protective of these pathogens. Thus, honey-borne DNA helps us define the honeybee’s functional niche, offering directions to expound the benefits and drawbacks of the associations to the honeybee itself and its interacting organisms.
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Affiliation(s)
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kirsten Miller
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tomas Roslin
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Lester PJ, Felden A, Baty JW, Bulgarella M, Haywood J, Mortensen AN, Remnant EJ, Smeele ZE. Viral communities in the parasite Varroa destructor and in colonies of their honey bee host (Apis mellifera) in New Zealand. Sci Rep 2022; 12:8809. [PMID: 35614309 PMCID: PMC9133037 DOI: 10.1038/s41598-022-12888-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/11/2022] [Indexed: 11/11/2022] Open
Abstract
The parasitic mite Varroa destructor is a leading cause of mortality for Western honey bee (Apis mellifera) colonies around the globe. We sought to confirm the presence and likely introduction of only one V. destructor haplotype in New Zealand, and describe the viral community within both V. destructor mites and the bees that they parasitise. A 1232 bp fragment from mitochondrial gene regions suggests the likely introduction of only one V. destructor haplotype to New Zealand. Seventeen viruses were found in bees. The most prevalent and abundant was the Deformed wing virus A (DWV-A) strain, which explained 95.0% of the variation in the viral community of bees. Black queen cell virus, Sacbrood virus, and Varroa destructor virus 2 (VDV-2) played secondary roles. DWV-B and the Israeli acute paralysis virus appeared absent from New Zealand. Ten viruses were observed in V. destructor, with > 99.9% of viral reads from DWV-A and VDV-2. Substantially more variation in viral loads was observed in bees compared to mites. Where high levels of VDV-2 occurred in mites, reduced DWV-A occurred in both the mites and the bees co-occurring within the same hive. Where there were high loads of DWV-A in mites, there were typically high viral loads in bees.
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Affiliation(s)
- Philip J Lester
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6012, New Zealand.
| | - Antoine Felden
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6012, New Zealand
| | - James W Baty
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6012, New Zealand
| | - Mariana Bulgarella
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6012, New Zealand
| | - John Haywood
- School of Mathematics and Statistics, Victoria University of Wellington, PO Box 600, Wellington, 6012, New Zealand
| | - Ashley N Mortensen
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 3230, Waikato Mail Centre, Hamilton, 3240, New Zealand
| | - Emily J Remnant
- Behaviour, Ecology and Evolution Laboratory, School of Life and Environmental Sciences, University of Sydney, Science Road, Sydney, NSW, 2006, Australia
| | - Zoe E Smeele
- Centre for Biodiversity and Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6012, New Zealand
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Yang D, Wang J, Wang X, Deng F, Diao Q, Wang M, Hu Z, Hou C. Genomics and Proteomics of Apis mellifera Filamentous Virus Isolated from Honeybees in China. Virol Sin 2022; 37:483-490. [PMID: 35527222 PMCID: PMC9437511 DOI: 10.1016/j.virs.2022.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/21/2022] [Indexed: 11/15/2022] Open
Abstract
Apis mellifera filamentous virus (AmFV) is a large DNA virus that is endemic in honeybee colonies. The genome sequence of the AmFV Swiss isolate (AmFV CH–C05) has been reported, but so far very few molecular studies have been conducted on this virus. In this study, we isolated and purified AmFV (AmFV CN) from Chinese honeybee (Apis mellifera) colonies and elucidated its genomics and proteomics. Electron microscopy showed ovoid purified virions with dimensions of 300–500 × 210–285 nm, wrapping a 3165 × 40 nm filamentous nucleocapsid in three figure-eight loops. Unlike AmFV CH–C05, which was reported to have a circular genome, our data suggest that AmFV CN has a linear genome of approximately 493 kb. A total of 197 ORFs were identified, among which 36 putative genes including 18 baculoviral homologs were annotated. The overall nucleotide similarity between the CN and CH–C05 isolates was 96.9%. Several ORFs were newly annotated in AmFV CN, including homologs of per os infectivity factor 4 (PIF4) and a putative integrase. Phylogenomic analysis placed AmFVs on a separate branch within the newly proposed virus class Naldaviricetes. Proteomic analysis revealed 47 AmFV virion-associated proteins, of which 14 had over 50% sequence coverage, suggesting that they are likely to be main structural proteins. In addition, all six of the annotated PIFs (PIF-0–5) were identified by proteomics, suggesting that they may function as entry factors in AmFV infection. This study provides fundamental information regarding the molecular biology of AmFV. The AmFV CN contains a 493 kb linear genome encoding 197 ORFs. Proteomics revealed 14 putative major structural proteins. AmFV belongs to the class Naldaviricetes but not the order Lefavirales.
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Affiliation(s)
- Dahe Yang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, China; State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jun Wang
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xi Wang
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Fei Deng
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Qingyun Diao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, China
| | - Manli Wang
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhihong Hu
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Chunsheng Hou
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
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Drew GC, Budge GE, Frost CL, Neumann P, Siozios S, Yañez O, Hurst GDD. Transitions in symbiosis: evidence for environmental acquisition and social transmission within a clade of heritable symbionts. ISME J 2021; 15:2956-2968. [PMID: 33941888 PMCID: PMC8443716 DOI: 10.1038/s41396-021-00977-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/17/2021] [Accepted: 04/06/2021] [Indexed: 02/03/2023]
Abstract
A dynamic continuum exists from free-living environmental microbes to strict host-associated symbionts that are vertically inherited. However, knowledge of the forces that drive transitions in symbiotic lifestyle and transmission mode is lacking. Arsenophonus is a diverse clade of bacterial symbionts, comprising reproductive parasites to coevolving obligate mutualists, in which the predominant mode of transmission is vertical. We describe a symbiosis between a member of the genus Arsenophonus and the Western honey bee. The symbiont shares common genomic and predicted metabolic properties with the male-killing symbiont Arsenophonus nasoniae, however we present multiple lines of evidence that the bee Arsenophonus deviates from a heritable model of transmission. Field sampling uncovered spatial and seasonal dynamics in symbiont prevalence, and rapid infection loss events were observed in field colonies and laboratory individuals. Fluorescent in situ hybridisation showed Arsenophonus localised in the gut, and detection was rare in screens of early honey bee life stages. We directly show horizontal transmission of Arsenophonus between bees under varying social conditions. We conclude that honey bees acquire Arsenophonus through a combination of environmental exposure and social contacts. These findings uncover a key link in the Arsenophonus clades trajectory from free-living ancestral life to obligate mutualism, and provide a foundation for studying transitions in symbiotic lifestyle.
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Affiliation(s)
- Georgia C Drew
- Department of Zoology, University of Oxford, Oxford, UK.
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
| | - Giles E Budge
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Crystal L Frost
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Stefanos Siozios
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Orlando Yañez
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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16
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Abstract
Honey bees, and pollinators in general, play a major role in the health of ecosystems. There is a consensus about the steady decrease in pollinator populations, which raises global ecological concern. Several drivers are implicated in this threat. Among them, honey bee pathogens are transmitted to other arthropods populations, including wild and managed pollinators. The western honey bee, Apis mellifera, is quasi-globally spread. This successful species acted as and, in some cases, became a maintenance host for pathogens. This systematic review collects and summarizes spillover cases having in common Apis mellifera as the mainteinance host and some of its pathogens. The reports are grouped by final host species and condition, year, and geographic area of detection and the co-occurrence in the same host. A total of eighty-one articles in the time frame 1960-2021 were included. The reported spillover cases cover a wide range of hymenopteran host species, generally living in close contact with or sharing the same environmental resources as the honey bees. They also involve non-hymenopteran arthropods, like spiders and roaches, which are either likely or unlikely to live in close proximity to honey bees. Specific studies should consider host-dependent pathogen modifications and effects on involved host species. Both the plasticity of bee pathogens and the ecological consequences of spillover suggest a holistic approach to bee health and the implementation of a One Health approach.
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Affiliation(s)
| | - Laura Bortolotti
- Council for Agricultural Research and Agricultural Economics Analysis, Centre for Agriculture and Environment Research (CREA-AA), Via di Saliceto 80, 40128 Bologna, Italy; (A.N.); (G.C.)
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17
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Yuan C, Jiang X, Liu M, Yang S, Deng S, Hou C. An Investigation of Honey Bee Viruses Prevalence in Managed Honey Bees (Apis mellifera and Apis cerana) Undergone Colony Decline. Open Microbiol J 2021. [DOI: 10.2174/1874285802115010058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Objective:
In the absence of known clinical symptoms, viruses were considered to be the most probable key pathogens of honey bee. Therefore, the aim of this study was to investigate the prevalence and distribution of honey bee viruses in managed Apis mellifera and Apis cerana in China.
Methods:
We conducted a screening of 8 honey bee viruses on A. mellifera and A. cerana samples collected from 54 apiaries from 13 provinces in China using RT-PCR.
Results:
We found that the types and numbers of viral species significantly differed between A. mellifera and A. cerana. Black Queen Cell Virus (BQCV), Chronic Bee Paralysis Virus (CBPV), Apis mellifera filamentous virus (AmFV), and Kakugo virus (DWV-A/KV) were the primary viruses found in A. mellifera colonies, whereas Chinese Sacbrood Bee Virus (CSBV) and Sacbrood Bee Virus (SBV) were the primary viruses found in A. cerana. The percentage infection of BQCV and CSBV were 84.6% and 61.6% in all detected samples. We first detected the occurrences of Varroa destructor virus-1 (VDV-1 or DWV-B) and DWV-A/KV in China but not ABPV in both A. mellifera and A. cerana.
Conclusion:
This study showed that BQCV and CSBV are the major threat to investigated A. mellifera and A. cerana colonies.
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18
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de Landa GF, Porrini MP, Revainera P, Porrini DP, Farina J, Correa-Benítez A, Maggi MD, Eguaras MJ, Quintana S. Pathogens Detection in the Small Hive Beetle (Aethina tumida (Coleoptera: Nitidulidae)). Neotrop Entomol 2021; 50:312-316. [PMID: 32845459 DOI: 10.1007/s13744-020-00812-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
Aethina tumida Murray is currently a worldwide emergent pest of Apis mellifera L. hives. Although the damaging effect on the colony stores and brood is well known, the possible role of these beetles as a disease carrier is not clear. This is the first report of DNA presence of the trypanosome honeybee parasite Lotmaria passim and Crithidia bombi, and the Apis mellifera filamentous virus (AmFV) in A. tumida. Further studies will be needed to determine if A. tumida is indeed a mechanical or biological vector of these pathogens.
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Affiliation(s)
- G Fernandez de Landa
- Centro de Investigación en Abejas Sociales (CIAS), Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM-CONICET-CIC), Facultad de Ciencias Exactas y Naturales, Univ Nacional de Mar del Plata, Buenos Aires, Argentina.
| | - M P Porrini
- Centro de Investigación en Abejas Sociales (CIAS), Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM-CONICET-CIC), Facultad de Ciencias Exactas y Naturales, Univ Nacional de Mar del Plata, Buenos Aires, Argentina
| | - P Revainera
- Centro de Investigación en Abejas Sociales (CIAS), Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM-CONICET-CIC), Facultad de Ciencias Exactas y Naturales, Univ Nacional de Mar del Plata, Buenos Aires, Argentina
| | - D P Porrini
- GENEBSO, INBIOTEC, UNMdP, CONICET, Mar del Plata, Argentina
| | - J Farina
- Museo Municipal de Ciencias Naturales de Mar del Plata (Lorenzo Scaglia), Buenos Aires, Argentina
| | - A Correa-Benítez
- Depto de Medicina y Zootecnia de Abejas, Conejos y Organismos Acuáticos (DMZA:CyOA), Facultad de Medicina Veterinaria y Zootecnia (FMVZ), Univ Nacional Autónoma de Mexico (UNAM), Ciudad de Mexico, Mexico
| | - M D Maggi
- Centro de Investigación en Abejas Sociales (CIAS), Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM-CONICET-CIC), Facultad de Ciencias Exactas y Naturales, Univ Nacional de Mar del Plata, Buenos Aires, Argentina
| | - M J Eguaras
- Centro de Investigación en Abejas Sociales (CIAS), Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM-CONICET-CIC), Facultad de Ciencias Exactas y Naturales, Univ Nacional de Mar del Plata, Buenos Aires, Argentina
| | - S Quintana
- Centro de Investigación en Abejas Sociales (CIAS), Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM-CONICET-CIC), Facultad de Ciencias Exactas y Naturales, Univ Nacional de Mar del Plata, Buenos Aires, Argentina
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Salina MD, Garcia MLG, Bais B, Bravi ME, Brasesco C, Maggi M, Pecoraro M, Larsen A, Sguazza HG, Reynaldi FJ. Viruses that affect Argentinian honey bees (Apis mellifera). Arch Virol 2021; 166:1533-45. [PMID: 33683476 DOI: 10.1007/s00705-021-05000-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/28/2020] [Indexed: 10/22/2022]
Abstract
Beekeeping is a widespread activity in Argentina, mainly producing honey that has gained both national and international recognition. There are more than 3,000,000 hives in the country, mainly concentrated in Buenos Aires Province (approximately 1,000,000 hives). In recent decades, worrying rates of hive loss have been observed in many countries around the world. In Latin America, the estimated loss of hives is between 13% (Peru and Ecuador) and 53% (Chile). Argentina had annual losses of 34% for the period of October 1, 2016 to October 1, 2017. The causes of these losses are not clear but probably involve multiple stressors that can act simultaneously. One of the main causes of loss of bee colonies worldwide is infestation by the ectoparasitic mite Varroa destructor in combination with viral infections. To date, 10 viruses have been detected that affect honey bees (Apis mellifera) in Argentina. Of these, deformed wing virus, sacbrood virus, acute bee paralysis virus, chronic bee paralysis virus, and Israeli acute bee paralysis can be transmitted by mites. Deformed wing virus and the AIK complex are the viruses most often associated with loss of hives worldwide. Considering that bee viruses have been detected in Argentina in several hymenopteran and non-hymenopteran insects, these hosts could act as important natural reservoirs for viruses and play an important role in their dispersal in the environment. Further studies to investigate the different mechanisms by which viruses spread in the environment will enable us to develop various strategies for the control of infected colonies and the spread of viruses in the habitat where they are found.
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Daughenbaugh KF, Kahnonitch I, Carey CC, McMenamin AJ, Wiegand T, Erez T, Arkin N, Ross B, Wiedenheft B, Sadeh A, Chejanovsky N, Mandelik Y, Flenniken ML. Metatranscriptome Analysis of Sympatric Bee Species Identifies Bee Virus Variants and a New Virus, Andrena-Associated Bee Virus-1. Viruses 2021; 13:291. [PMID: 33673324 PMCID: PMC7917660 DOI: 10.3390/v13020291] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/22/2021] [Accepted: 02/03/2021] [Indexed: 12/11/2022] Open
Abstract
Bees are important plant pollinators in agricultural and natural ecosystems. High average annual losses of honey bee (Apis mellifera) colonies in some parts of the world, and regional population declines of some mining bee species (Andrena spp.), are attributed to multiple factors including habitat loss, lack of quality forage, insecticide exposure, and pathogens, including viruses. While research has primarily focused on viruses in honey bees, many of these viruses have a broad host range. It is therefore important to apply a community level approach in studying the epidemiology of bee viruses. We utilized high-throughput sequencing to evaluate viral diversity and viral sharing in sympatric, co-foraging bees in the context of habitat type. Variants of four common viruses (i.e., black queen cell virus, deformed wing virus, Lake Sinai virus 2, and Lake Sinai virus NE) were identified in honey bee and mining bee samples, and the high degree of nucleotide identity in the virus consensus sequences obtained from both taxa indicates virus sharing. We discovered a unique bipartite + ssRNA Tombo-like virus, Andrena-associated bee virus-1 (AnBV-1). AnBV-1 infects mining bees, honey bees, and primary honey bee pupal cells maintained in culture. AnBV-1 prevalence and abundance was greater in mining bees than in honey bees. Statistical modeling that examined the roles of ecological factors, including floral diversity and abundance, indicated that AnBV-1 infection prevalence in honey bees was greater in habitats with low floral diversity and abundance, and that interspecific virus transmission is strongly modulated by the floral community in the habitat. These results suggest that land management strategies that aim to enhance floral diversity and abundance may reduce AnBV-1 spread between co-foraging bees.
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Affiliation(s)
- Katie F. Daughenbaugh
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (K.F.D.); (B.R.)
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA; (C.C.C.); (A.J.M.); (T.W.)
| | - Idan Kahnonitch
- The Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 5290002, Israel; (I.K.); (Y.M.)
- Agroecology Lab, Newe Ya’ar Research Center, ARO, Ramat Yishay 30095, Israel; (N.A.); (A.S.)
| | - Charles C. Carey
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA; (C.C.C.); (A.J.M.); (T.W.)
| | - Alexander J. McMenamin
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA; (C.C.C.); (A.J.M.); (T.W.)
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA;
| | - Tanner Wiegand
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA; (C.C.C.); (A.J.M.); (T.W.)
| | - Tal Erez
- Entomology Department, ARO, The Volcani Center, Rishon Lezion 7528809, Israel; (T.E.); (N.C.)
| | - Naama Arkin
- Agroecology Lab, Newe Ya’ar Research Center, ARO, Ramat Yishay 30095, Israel; (N.A.); (A.S.)
- The Mina & Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Brian Ross
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (K.F.D.); (B.R.)
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA; (C.C.C.); (A.J.M.); (T.W.)
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA;
| | - Asaf Sadeh
- Agroecology Lab, Newe Ya’ar Research Center, ARO, Ramat Yishay 30095, Israel; (N.A.); (A.S.)
| | - Nor Chejanovsky
- Entomology Department, ARO, The Volcani Center, Rishon Lezion 7528809, Israel; (T.E.); (N.C.)
| | - Yael Mandelik
- The Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 5290002, Israel; (I.K.); (Y.M.)
| | - Michelle L. Flenniken
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; (K.F.D.); (B.R.)
- Pollinator Health Center, Montana State University, Bozeman, MT 59717, USA; (C.C.C.); (A.J.M.); (T.W.)
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA;
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Bovo S, Utzeri VJ, Ribani A, Cabbri R, Fontanesi L. Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity. Sci Rep 2020; 10:9279. [PMID: 32518251 DOI: 10.1038/s41598-020-66127-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 05/15/2020] [Indexed: 11/09/2022] Open
Abstract
Honey bees are large-scale monitoring tools due to their extensive environmental exploration. In their activities and from the hive ecosystem complex, they get in close contact with many organisms whose traces can be transferred into the honey, which can represent an interesting reservoir of environmental DNA (eDNA) signatures and information useful to analyse the honey bee hologenome complexity. In this study, we tested a deep shotgun sequencing approach of honey DNA coupled with a specifically adapted bioinformatic pipeline. This methodology was applied to a few honey samples pointing out DNA sequences from 191 organisms spanning different kingdoms or phyla (viruses, bacteria, plants, fungi, protozoans, arthropods, mammals). Bacteria included the largest number of species. These multi-kingdom signatures listed common hive and honey bee gut microorganisms, honey bee pathogens, parasites and pests, which resembled a complex interplay that might provide a general picture of the honey bee pathosphere. Based on the Apis mellifera filamentous virus genome diversity (the most abundant detected DNA source) we obtained information that could define the origin of the honey at the apiary level. Mining Apis mellifera sequences made it possible to identify the honey bee subspecies both at the mitochondrial and nuclear genome levels.
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22
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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: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Manley R, Temperton B, Boots M, Wilfert L. Contrasting impacts of a novel specialist vector on multihost viral pathogen epidemiology in wild and managed bees. Mol Ecol 2020; 29:380-393. [PMID: 31834965 PMCID: PMC7003859 DOI: 10.1111/mec.15333] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/27/2019] [Accepted: 12/03/2019] [Indexed: 01/27/2023]
Abstract
Typically, pathogens infect multiple host species. Such multihost pathogens can show considerable variation in their degree of infection and transmission specificity, which has important implications for potential disease emergence. Transmission of multihost pathogens can be driven by key host species and changes in such transmission networks can lead to disease emergence. We study two viruses that show contrasting patterns of prevalence and specificity in managed honeybees and wild bumblebees, black queen cell virus (BQCV) and slow bee paralysis virus (SBPV), in the context of the novel transmission route provided by the virus‐vectoring Varroa destructor. Our key result is that viral communities and RNA virus genetic variation are structured by location, not host species or V. destructor presence. Interspecific transmission is pervasive with the same viral variants circulating between pollinator hosts in each location; yet, we found virus‐specific host differences in prevalence and viral load. Importantly, V. destructor presence increases the prevalence in honeybees and, indirectly, in wild bumblebees, but in contrast to its impact on deformed wing virus (DWV), BQCV and SBPV viral loads are not increased by Varroa presence, and do not show genetic evidence of recent emergence. Effective control of Varroa in managed honeybee colonies is necessary to mitigate further disease emergence, and alleviate disease pressure on our vital wild bee populations. More generally, our results highlight the over‐riding importance of geographical location to the epidemiological outcome despite the complexity of multihost‐parasite interactions.
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Affiliation(s)
- Robyn Manley
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK.,Department of Biosciences, University of Exeter, Exeter, UK
| | - Ben Temperton
- Department of Biosciences, University of Exeter, Exeter, UK
| | - Mike Boots
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Lena Wilfert
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK.,Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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24
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Yang S, Gayral P, Zhao H, Wu Y, Jiang X, Wu Y, Bigot D, Wang X, Yang D, Herniou EA, Deng S, Li F, Diao Q, Darrouzet E, Hou C. Occurrence and Molecular Phylogeny of Honey Bee Viruses in Vespids. Viruses 2019; 12:v12010006. [PMID: 31861567 PMCID: PMC7019919 DOI: 10.3390/v12010006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 11/26/2022] Open
Abstract
Since the discovery that honey bee viruses play a role in colony decline, researchers have made major breakthroughs in understanding viral pathology and infection processes in honey bees. Work on virus transmission patterns and virus vectors, such as the mite Varroa destructor, has prompted intense efforts to manage honey bee health. However, little is known about the occurrence of honey bee viruses in bee predators, such as vespids. In this study, we characterized the occurrence of 11 honey bee viruses in five vespid species and one wasp from four provinces in China and two vespid species from four locations in France. The results showed that all the species from China carried certain honey bee viruses, notably Apis mellifera filamentous virus (AmFV), Deformed wing virus (DWV), and Israeli acute paralysis virus (IAPV); furthermore, in some vespid colonies, more than three different viruses were identified. In France, DWV was the most common virus; Sacbrood virus (SBV) and Black queen cell virus (BQCV) were observed in one and two samples, respectively. Phylogenetic analyses of IAPV and BQCV sequences indicated that most of the IAPV sequences belonged to a single group, while the BQCV sequences belonged to several groups. Additionally, our study is the first to detect Lake Sinai virus (LSV) in a hornet from China. Our findings can guide further research into the origin and transmission of honey bee viruses in Vespidae, a taxon of ecological, and potentially epidemiological, relevance.
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Affiliation(s)
- Sa Yang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China; (S.Y.); (Y.W.); (X.W.); (D.Y.); (S.D.); (Q.D.)
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, China
| | - Philippe Gayral
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS—Université de Tours, F-37200 Tours, France; (P.G.); (D.B.); (E.A.H.)
| | - Hongxia Zhao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou 510260, China;
| | - Yaojun Wu
- Institute of Forestry Protection, Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning 530002, China
| | - Xuejian Jiang
- Institute of Forestry Protection, Guangxi Zhuang Autonomous Region Forestry Research Institute, Nanning 530002, China
| | - Yanyan Wu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China; (S.Y.); (Y.W.); (X.W.); (D.Y.); (S.D.); (Q.D.)
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, China
| | - Diane Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS—Université de Tours, F-37200 Tours, France; (P.G.); (D.B.); (E.A.H.)
| | - Xinling Wang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China; (S.Y.); (Y.W.); (X.W.); (D.Y.); (S.D.); (Q.D.)
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, China
| | - Dahe Yang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China; (S.Y.); (Y.W.); (X.W.); (D.Y.); (S.D.); (Q.D.)
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, China
| | - Elisabeth A. Herniou
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS—Université de Tours, F-37200 Tours, France; (P.G.); (D.B.); (E.A.H.)
| | - Shuai Deng
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China; (S.Y.); (Y.W.); (X.W.); (D.Y.); (S.D.); (Q.D.)
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, China
| | - Fei Li
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China; (S.Y.); (Y.W.); (X.W.); (D.Y.); (S.D.); (Q.D.)
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, China
| | - Qingyun Diao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China; (S.Y.); (Y.W.); (X.W.); (D.Y.); (S.D.); (Q.D.)
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, China
| | - Eric Darrouzet
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS—Université de Tours, F-37200 Tours, France; (P.G.); (D.B.); (E.A.H.)
- Correspondence: (E.D.); (C.H.); Tel.: +33-(0)2-47-36-71-60 (E.D.); +86-1062597285 (C.H.)
| | - Chunsheng Hou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China; (S.Y.); (Y.W.); (X.W.); (D.Y.); (S.D.); (Q.D.)
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, China
- Correspondence: (E.D.); (C.H.); Tel.: +33-(0)2-47-36-71-60 (E.D.); +86-1062597285 (C.H.)
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Maggi M, Quintana S, Revainera PD, Porrini LP, Meroi Arcerito FR, Fernández de Landa G, Brasesco C, Di Gerónimo V, Ruffinengo SR, Eguaras MJ. Biotic Stressors Affecting Key Apiaries in Argentina. ACTA ACUST UNITED AC 2019. [DOI: 10.1080/0005772x.2019.1699007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Matías Maggi
- Centro de Investigación en Abejas Sociales (CIAS), Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC). Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Buenos Aires, Argentine
| | - Silvina Quintana
- Centro de Investigación en Abejas Sociales (CIAS), Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC). Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Buenos Aires, Argentine Laboratorio de Biología Molecular, Instituto de Análisis Fares Taie, Mar Del Plata, Argentine
| | - Pablo D. Revainera
- Centro de Investigación en Abejas Sociales (CIAS), Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC). Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Buenos Aires, Argentine Laboratorio de Biología Molecular, Instituto de Análisis Fares Taie, Mar Del Plata, Argentine
| | - Leonardo Pablo Porrini
- Centro de Investigación en Abejas Sociales (CIAS), Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC). Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Buenos Aires, Argentine
| | - Facundo René Meroi Arcerito
- Centro de Investigación en Abejas Sociales (CIAS), Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC). Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Buenos Aires, Argentine
| | - G. Fernández de Landa
- Centro de Investigación en Abejas Sociales (CIAS), Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC). Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Buenos Aires, Argentine Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), Buenos Aires, Argentine
| | - Constanza Brasesco
- Centro de Investigación en Abejas Sociales (CIAS), Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC). Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Buenos Aires, Argentine
| | - V. Di Gerónimo
- Laboratorio de Biología Molecular, Instituto de Análisis Fares Taie, Mar Del Plata, Argentine
| | - Sergio Roberto Ruffinengo
- Centro de Investigación en Abejas Sociales (CIAS), Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC). Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Buenos Aires, Argentine
| | - Martín Javier Eguaras
- Centro de Investigación en Abejas Sociales (CIAS), Instituto de Investigaciones en Producción Sanidad y Ambiente (IIPROSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC). Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Buenos Aires, Argentine
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26
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Abstract
Endogenous viral elements (EVEs) can play a significant role in the evolution of their hosts and have been identified in animals, plants, and fungi. Additionally, EVEs potentially provide an important snapshot of the evolutionary frequency of viral infection. The purpose of this study is to take a comparative host-centered approach to EVE discovery in ant genomes to better understand the relationship of EVEs to their ant hosts. Using a comprehensive bioinformatic pipeline, we screened all nineteen published ant genomes for EVEs. Once the EVEs were identified, we assessed their phylogenetic relationships to other closely related exogenous viruses. A diverse group of EVEs were discovered in all screened ant host genomes and in many cases are similar to previously identified exogenous viruses. EVEs similar to ssRNA viral proteins are the most common viral lineage throughout the ant hosts, which is potentially due to more chronic infection or more effective endogenization of certain ssRNA viruses in ants. In addition, both EVEs similar to viral glycoproteins and retrovirus-derived proteins are also abundant throughout ant genomes, suggesting their tendency to endogenize. Several of these newly discovered EVEs are found to be potentially functional within the genome. The discovery and analysis of EVEs is essential in beginning to understand viral–ant interactions over evolutionary time.
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Affiliation(s)
- Peter J Flynn
- Committee on Evolutionary Biology, The University of Chicago, Chicago, IL, United States.,Department of Science and Education, Integrative Research Center, Field Museum of Natural History, Chicago, IL, United States
| | - Corrie S Moreau
- Department of Science and Education, Integrative Research Center, Field Museum of Natural History, Chicago, IL, United States.,Departments of Entomology and Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States
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27
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Prodělalová J, Moutelíková R, Titěra D. Multiple Virus Infections in Western Honeybee ( Apis mellifera L.) Ejaculate Used for Instrumental Insemination. Viruses 2019; 11:E306. [PMID: 30934858 DOI: 10.3390/v11040306] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 01/18/2023] Open
Abstract
Instrumental insemination of Apis mellifera L. queens is a widely employed technique used in honeybee breeding that enables the effective control of mating. However, drone semen represents a potential source of honeybee viruses. In this study, 43 semen doses collected from apparently healthy drones, and consequently used in instrumental insemination, were analysed using PCR or RT-PCR to detect the presence of viral genome of 11 honeybee viruses. In 91% of samples, viral infection was detected. The survey revealed genomes of five viruses, namely Deformed wing virus (DWV), Acute bee paralysis virus (ABPV), Black queen cell virus (BQCV), Sacbrood virus (SBV), and A. mellifera filamentous virus (AmFV) in 84%, 19%, 14%, 2%, and 67% of samples, respectively. Single infection (30% of samples) as well as multiple infection (61% of samples) of two, three or four pathogens were also evaluated. To the best of our knowledge, this is the first study describing the presence of the BQCV and SBV genome sequence in drone ejaculate. Phylogenetic analysis of BQCV partial helicase gene sequence revealed the high similarity of nucleotide sequence of described Czech strains, which varied from 91.4% to 99.6%. The findings of our study indicate the possibility of venereal transmission of BQCV and SBV.
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28
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Kraberger S, Cook CN, Schmidlin K, Fontenele RS, Bautista J, Smith B, Varsani A. Diverse single-stranded DNA viruses associated with honey bees (Apis mellifera). Infect Genet Evol 2019; 71:179-188. [PMID: 30928605 DOI: 10.1016/j.meegid.2019.03.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/28/2019] [Accepted: 03/25/2019] [Indexed: 11/26/2022]
Abstract
Honey bees (Apis mellifera) research has increased in light of their progressive global decline over the last decade and the important role they play in pollination. One expanding area of honey bee research is analysis of their microbial community including viruses. Several RNA viruses have been characterized but little is known about DNA viruses associated with bees. Here, using a metagenomics based approach, we reveal the presence of a broad range of novel single-stranded DNA viruses from the hemolymph and brain of nurse and forager (worker divisions of labour) bees belonging to two honey bees subspecies, Italian (Apis mellifera linguistica) and New World Carniolan (Apis mellifera carnica). Genomes of 100 diverse viruses were identified, designated into three groupings; genomoviruses (family Genomoviridae) (n = 4), unclassified replication associated protein encoding single-stranded DNA viruses (n = 28), and microviruses (family Microviridae; subfamily Gokushovirinae) (n = 70). Amongst the viruses identified, it appears that nurses harbour a higher diversity of these viruses comparative to the foragers. Between subspecies, the most striking outcome was the extremely high number of diverse microviruses identified in the Italian bees comparative to the New World Carniolan, likely indicating an association to the diversity of the bacterial community associated with these subspecies.
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Affiliation(s)
- Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA.
| | - Chelsea N Cook
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joshua Bautista
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA
| | - Brian Smith
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, 7925 Cape Town, South Africa.
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29
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Abstract
Lake Sinai Viruses (Sinaivirus) are commonly detected in honey bees (Apis mellifera) but no disease phenotypes or fitness consequences have yet been demonstrated. This viral group is genetically diverse, lacks obvious geographic structure, and multiple lineages can co-infect individual bees. While phylogenetic analyses have been performed, the molecular evolution of LSV has not been studied extensively. Here, I use LSV isolates from GenBank as well as contigs assembled from honey bee Sequence Read Archive (SRA) accessions to better understand the evolutionary history of these viruses. For each ORF, substitution rate variation, codon usage, and tests of positive selection were evaluated. Outlier regions of high or low diversity were sought with sliding window analysis and the role of recombination in creating LSV diversity was explored. Phylogenetic analysis consistently identified two large clusters of sequences that correspond to the current LSV1 and LSV2 nomenclature, however lineages sister to LSV1 were the most frequently detected in honey bee SRA accessions. Different expression levels among ORFs suggested the occurrence of subgenomic transcripts. ORF1 and RNA-dependent RNA polymerase had higher evolutionary rates than the capsid and ORF4. A hypervariable region of the ORF1 protein-coding sequence was identified that had reduced selective constraint, but a site-based model of positive selection was not significantly more likely than a neutral model for any ORF. The only significant recombination signals detected between LSV1 and LSV2 initiated within this hypervariable region, but assumptions of the test (single-frame coding and independence of substitution rate by site) were violated. LSV codon usage differed strikingly from that of honey bees and other common honey-bee viruses, suggesting LSV is not strongly co-evolved with that host. LSV codon usage was significantly correlated with that of Varroa destructor, however, despite the relatively weak codon bias exhibited by the latter. While codon usage between the LSV1 and LSV2 clusters was similar for three ORFs, ORF4 codon usage was uncorrelated between these clades, implying rapid divergence of codon use for this ORF only. Phylogenetic placement and relative abundance of LSV isolates reconstructed from SRA accessions suggest that detection biases may be over-representing LSV1 and LSV2 in public databases relative to their sister lineages.
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Affiliation(s)
- Robert S. Cornman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
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30
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Wang X, Shang Y, Chen C, Liu S, Chang M, Zhang N, Hu H, Zhang F, Zhang T, Wang Z, Liu X, Lin Z, Deng F, Wang H, Zou Z, Vlak JM, Wang M, Hu Z. Baculovirus Per Os Infectivity Factor Complex: Components and Assembly. J Virol 2019; 93:e02053-18. [PMID: 30602603 DOI: 10.1128/JVI.02053-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 12/17/2018] [Indexed: 12/17/2022] Open
Abstract
Baculovirus entry into insect midgut cells is dependent on a multiprotein complex of per os infectivity factors (PIFs) on the envelopes of occlusion-derived virions (ODVs). The structure and assembly of the PIF complex are largely unknown. To reveal the complete members of the complex, a combination of blue native polyacrylamide gel electrophoresis, liquid chromatography-tandem mass spectrometry, and Western blotting was conducted on three different baculoviruses. The results showed that the PIF complex has a molecular mass of ∼500 kDa and consists of nine PIFs, including a newly discovered member (PIF9). To decipher the assembly process, each pif gene was knocked out from the Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) genome individually by use of synthetic baculovirus technology, and the impact on PIF complex formation was investigated. Deletion of pif8 resulted in the formation of an ∼400-kDa subcomplex. Deletion of pif0, -4, -6, -7, or -9 resulted in a subcomplex of ∼230 kDa, but deletion of pif1, -2, or -3 abolished formation of any complex. Taken together, our data identified a core complex of ∼230 kDa, consisting of PIF1, -2, and -3. This revised the previous knowledge that the core complex was about 170 kDa and contained PIF1 to -4. Analysis of the PIF complex in cellular fractions suggested that it is assembled in the cytoplasm before being transported to the nucleus and subsequently incorporated into the envelopes of ODVs. Only the full complex, not the subcomplex, is resistant to proteolytic attack, indicating the essentiality of correct complex assembly for oral infection.IMPORTANCE Entry of baculovirus into host insects is mediated by a per os infectivity factor (PIF) complex on the envelopes of occlusion-derived viruses (ODVs). Knowledge of the composition and structure of the PIF complex is fundamental to understanding its mode of action. By using multiple approaches, we determined the complete list of proteins (nine) in the PIF complex. In contrast to previous knowledge in the field, the core complex is revised to ∼230 kDa and consists of PIF1 to -3 but not PIF4. Interestingly, our results suggest that the PIF complex is formed in the cytoplasm prior to its transport to the nucleus and subsequent incorporation into ODVs. Only the full complex is resistant to proteolytic degradation in the insect midgut, implying the critical role of the entire complex. These findings provide the baseline for future studies on the ODV entry mechanism mediated by the multiprotein complex.
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31
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Zana B, Geiger L, Kepner A, Földes F, Urbán P, Herczeg R, Kemenesi G, Jakab F. First molecular detection of Apis mellifera filamentous virus in honey bees (Apis mellifera) in Hungary. Acta Vet Hung 2019; 67:151-157. [PMID: 30922090 DOI: 10.1556/004.2019.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Western honey bees (Apis mellifera) are important pollinators in the ecosystem and also play a crucial economic role in the honey industry. During the last decades, a continuous decay was registered in honey bee populations worldwide, including Hungary. In our study, we used metagenomic approaches and conventional PCR screening on healthy and winter mortality affected colonies from multiple sites in Hungary. The major goal was to discover presumed bee pathogens with viral metagenomic experiments and gain prevalence and distribution data by targeted PCR screening. We examined 664 honey bee samples that had been collected during winter mortality from three seemingly healthy colonies and from one colony infested heavily by the parasitic mite Varroa destructor in 2016 and 2017. The subsequent PCR screening of honey bee samples revealed the abundant presence of Apis mellifera filamentous virus (AmFV) for the first time in Central Europe. Based on phylogeny reconstruction, the newly-detected virus was found to be most closely related to a Chinese AmFV strain. More sequence data from multiple countries would be needed for studying the detailed phylogeographical patterns and worldwide spreading process of AmFV. Here we report the prevalent presence of this virus in Hungarian honey bee colonies.
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Affiliation(s)
- Brigitta Zana
- 1 Virological Research Group, Szentágothai Research Centre, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
- 2 Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Lili Geiger
- 1 Virological Research Group, Szentágothai Research Centre, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
- 2 Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | | | - Fanni Földes
- 1 Virological Research Group, Szentágothai Research Centre, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
- 2 Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Péter Urbán
- 2 Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
- 4 Microbial Biotechnology Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Róbert Herczeg
- 1 Virological Research Group, Szentágothai Research Centre, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
| | - Gábor Kemenesi
- 1 Virological Research Group, Szentágothai Research Centre, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
- 2 Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Ferenc Jakab
- 1 Virological Research Group, Szentágothai Research Centre, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
- 2 Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
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Levin S, Sela N, Erez T, Nestel D, Pettis J, Neumann P, Chejanovsky N. New Viruses from the Ectoparasite Mite Varroa destructor Infesting Apis mellifera and Apis cerana. Viruses 2019; 11:E94. [PMID: 30678330 DOI: 10.3390/v11020094] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 11/16/2022] Open
Abstract
Varroa destructor is an ectoparasitic mite of Asian or Eastern honeybees Apis cerana(A. cerana) which has become a serious threat to European subspecies of Western honeybees Apis mellifera (A. mellifera) within the last century. V.destructor and its vectored honeybee viruses became serious threats for colony survival. This is a short period for pathogen- and host-populations to adapt. To look for possible variation in the composition of viral populations we performed RNA metagenomic analysis of the Western honeybee subspecies A. m. ligustica, A. m.syriaca, A. m. intermissa, and A. cerana and their respective V. destructor mites. The analysis revealed two novel viruses: Varroa orthomyxovirus-1 (VOV-1) in A. mellifera and V. destructor and a Hubei like-virga virus-14 homolog in V. destructor. VOV-1 was more prevalent in V. destructor than in A. mellifera and we found evidence for viral replication in both hosts. Interestingly, we found differences in viral loads of A. cerana and their V. destructor, A. m. intermissa, and its V. destructor showed partial similarity, while A. m.ligustica and A. m.syriaca and their varroa where very similar. Deformed wing virus exhibited 82.20%, 99.20%, 97.90%, and 0.76% of total viral reads in A. m. ligustica, A. m. syriaca, A. m. intermissa, and A. cerana, respectively. This is the first report of a complete segmented-single-stranded negative-sense RNA virus genome in honeybees and V. destructor mites.
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Kawato S, Shitara A, Wang Y, Nozaki R, Kondo H, Hirono I. Crustacean Genome Exploration Reveals the Evolutionary Origin of White Spot Syndrome Virus. J Virol 2019; 93:e01144-18. [PMID: 30404800 DOI: 10.1128/JVI.01144-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/23/2018] [Indexed: 01/25/2023] Open
Abstract
White spot syndrome virus (WSSV) is a crustacean-infecting, double-stranded DNA virus and is the most serious viral pathogen in the global shrimp industry. WSSV is the sole recognized member of the family Nimaviridae, and the lack of genomic data on other nimaviruses has obscured the evolutionary history of WSSV. Here, we investigated the evolutionary history of WSSV by characterizing WSSV relatives hidden in host genomic data. We surveyed 14 host crustacean genomes and identified five novel nimaviral genomes. Comparative genomic analysis of Nimaviridae identified 28 "core genes" that are ubiquitously conserved in Nimaviridae; unexpected conservation of 13 uncharacterized proteins highlighted yet-unknown essential functions underlying the nimavirus replication cycle. The ancestral Nimaviridae gene set contained five baculoviral per os infectivity factor homologs and a sulfhydryl oxidase homolog, suggesting a shared phylogenetic origin of Nimaviridae and insect-associated double-stranded DNA viruses. Moreover, we show that novel gene acquisition and subsequent amplification reinforced the unique accessory gene repertoire of WSSV. Expansion of unique envelope protein and nonstructural virulence-associated genes may have been the key genomic event that made WSSV such a deadly pathogen.IMPORTANCE WSSV is the deadliest viral pathogen threatening global shrimp aquaculture. The evolutionary history of WSSV has remained a mystery, because few WSSV relatives, or nimaviruses, had been reported. Our aim was to trace the history of WSSV using the genomes of novel nimaviruses hidden in host genome data. We demonstrate that WSSV emerged from a diverse family of crustacean-infecting large DNA viruses. By comparing the genomes of WSSV and its relatives, we show that WSSV possesses an expanded set of unique host-virus interaction-related genes. This extensive gene gain may have been the key genomic event that made WSSV such a deadly pathogen. Moreover, conservation of insect-infecting virus protein homologs suggests a common phylogenetic origin of crustacean-infecting Nimaviridae and other insect-infecting DNA viruses. Our work redefines the previously poorly characterized crustacean virus family and reveals the ancient genomic events that preordained the emergence of a devastating shrimp pathogen.
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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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Parmentier A, Billiet A, Smagghe G, Vandamme P, Deforce D, Van Nieuwerburgh F, Meeus I. A prokaryotic-eukaryotic relation in the fat body of Bombus terrestris. Environ Microbiol Rep 2018; 10:644-650. [PMID: 30066470 DOI: 10.1111/1758-2229.12673] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 05/23/2023]
Abstract
The interaction between the insect host and its microbiota plays a central role in insect health and is mostly studied in relation to the digestive system. Nonetheless, there are numerous microorganisms occupying multiple habitats in and on insects. We studied microbial communities in the gut and fat body of bumblebees (Bombus terrestris) using the V4 region of the 16S rRNA gene on the Illumina MiSeq platform. In one of the two study locations, the fat body microbial composition was marked by the dominant presence of Arsenophonus sp. and Phyllobacterium sp. Bumblebees infected with Apicystis bombi, a eukaryotic parasite multiplying in the fat body, had a significant higher relative abundance of Arsenophonus sp. compared with the non-infected individuals. In general, the infection of A. bombi correlated with a more interlinked microbial association network, as we observed an increase of significant associations between the relative abundance of bacteria present in the gut and fat body of infected bumblebees. The causality within this potential prokaryotic-eukaryotic relation is important when assessing the health impact on bees.
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Affiliation(s)
- Anneleen Parmentier
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Annelies Billiet
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Ivan Meeus
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
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Regan T, Barnett MW, Laetsch DR, Bush SJ, Wragg D, Budge GE, Highet F, Dainat B, de Miranda JR, Watson M, Blaxter M, Freeman TC. Characterisation of the British honey bee metagenome. Nat Commun 2018; 9:4995. [PMID: 30478343 PMCID: PMC6255801 DOI: 10.1038/s41467-018-07426-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 10/29/2018] [Indexed: 12/30/2022] Open
Abstract
The European honey bee (Apis mellifera) plays a major role in pollination and food production. Honey bee health is a complex product of the environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of these factors will help manage modern challenges to bee health. Here we used DNA sequencing to characterise the genomes and metagenomes of 19 honey bee colonies from across Britain. Low heterozygosity was observed in many Scottish colonies which had high similarity to the native dark bee. Colonies exhibited high diversity in composition and relative abundance of individual microbiome taxa. Most non-bee sequences were derived from known honey bee commensal bacteria or pathogens. However, DNA was also detected from additional fungal, protozoan and metazoan species. To classify cobionts lacking genomic information, we developed a novel network analysis approach for clustering orphan DNA contigs. Our analyses shed light on microbial communities associated with honey bees and demonstrate the power of high-throughput, directed metagenomics for identifying novel biological threats in agroecosystems.
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Affiliation(s)
- Tim Regan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK.
| | - Mark W Barnett
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK
| | - Dominik R Laetsch
- The Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3JG, UK
| | - Stephen J Bush
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK
| | - David Wragg
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK
| | - Giles E Budge
- Fera, The National Agrifood Innovation Campus, Sand Hutton, YO41 1LZ, York, UK
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Fiona Highet
- Science and Advice for Scottish Agriculture, 1 Roddinglaw Road, Edinburgh, EH12 9FJ, UK
| | - Benjamin Dainat
- Agroscope, Swiss Bee Research Centre, Schwarzenburgstrasse 161, CH-3003, Bern, Switzerland
| | - Joachim R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Mick Watson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK
| | - Mark Blaxter
- The Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3JG, UK.
| | - Tom C Freeman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK.
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37
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Bovo S, Ribani A, Utzeri VJ, Schiavo G, Bertolini F, Fontanesi L. Shotgun metagenomics of honey DNA: Evaluation of a methodological approach to describe a multi-kingdom honey bee derived environmental DNA signature. PLoS One 2018; 13:e0205575. [PMID: 30379893 PMCID: PMC6209200 DOI: 10.1371/journal.pone.0205575] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/27/2018] [Indexed: 12/27/2022] Open
Abstract
Honey bees are considered large-scale monitoring tools due to their environmental exploration and foraging activities. Traces of these activities can be recovered in the honey that also may reflect the hive ecological micro-conditions in which it has been produced. This study applied a next generation sequencing platform (Ion Torrent) for shotgun metagenomic analysis of honey environmental DNA (eDNA). The study tested a methodological framework to interpret DNA sequence information useful to describe the complex ecosystems of the honey bee colony superorganism, its pathosphere and the heterogeneity of the agroecological environments and environmental sources that left DNA marks in the honey. Analysis of two honeys reported sequence reads from five main organism groups (kingdoms or phyla): arthropods (that mainly included reads from Apis mellifera, several other members of the Hymenotpera, in addition to members of the Diptera, Coleoptera and Lepidoptera, as well as aphids and mites), plants (that clearly confirmed the botanical origin of the two honeys, i.e. orange tree blossom and eucalyptus tree blossom honeys), fungi and bacteria (including common hive and honey bee gut microorganisms, honey bee pathogens and plant pathogens), and viruses (which accounted for the largest number of reads in both honeys, mainly assigned to Apis mellifera filamentous virus). The shotgun metagenomic approach that was used in this study can be applied in large scale experiments that might have multiple objectives according to the multi-kingdom derived eDNA that is contained in the honey.
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Affiliation(s)
- Samuele Bovo
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Valerio Joe Utzeri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Francesca Bertolini
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
- * E-mail:
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Sadeghi M, Altan E, Deng X, Barker CM, Fang Y, Coffey LL, Delwart E. Virome of > 12 thousand Culex mosquitoes from throughout California. Virology 2018; 523:74-88. [DOI: 10.1016/j.virol.2018.07.029] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 12/25/2022]
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39
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McMenamin AJ, Daughenbaugh KF, Parekh F, Pizzorno MC, Flenniken ML. Honey Bee and Bumble Bee Antiviral Defense. Viruses 2018; 10:E395. [PMID: 30060518 PMCID: PMC6115922 DOI: 10.3390/v10080395] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/24/2018] [Accepted: 07/26/2018] [Indexed: 12/12/2022] Open
Abstract
Bees are important plant pollinators in both natural and agricultural ecosystems. Managed and wild bees have experienced high average annual colony losses, population declines, and local extinctions in many geographic regions. Multiple factors, including virus infections, impact bee health and longevity. The majority of bee-infecting viruses are positive-sense single-stranded RNA viruses. Bee-infecting viruses often cause asymptomatic infections but may also cause paralysis, deformity or death. The severity of infection is governed by bee host immune responses and influenced by additional biotic and abiotic factors. Herein, we highlight studies that have contributed to the current understanding of antiviral defense in bees, including the Western honey bee (Apis mellifera), the Eastern honey bee (Apis cerana) and bumble bee species (Bombus spp.). Bee antiviral defense mechanisms include RNA interference (RNAi), endocytosis, melanization, encapsulation, autophagy and conserved immune pathways including Jak/STAT (Janus kinase/signal transducer and activator of transcription), JNK (c-Jun N-terminal kinase), MAPK (mitogen-activated protein kinases) and the NF-κB mediated Toll and Imd (immune deficiency) pathways. Studies in Dipteran insects, including the model organism Drosophila melanogaster and pathogen-transmitting mosquitos, provide the framework for understanding bee antiviral defense. However, there are notable differences such as the more prominent role of a non-sequence specific, dsRNA-triggered, virus limiting response in honey bees and bumble bees. This virus-limiting response in bees is akin to pathways in a range of organisms including other invertebrates (i.e., oysters, shrimp and sand flies), as well as the mammalian interferon response. Current and future research aimed at elucidating bee antiviral defense mechanisms may lead to development of strategies that mitigate bee losses, while expanding our understanding of insect antiviral defense and the potential evolutionary relationship between sociality and immune function.
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Affiliation(s)
- Alexander J McMenamin
- Department of Plant Sciences and Plant Pathology, Bozeman, MT 59717, USA.
- Department of Microbiology and Immunology, Bozeman, MT 59717, USA.
- Center for Pollinator Health, Montana State University, Bozeman, MT 59717, USA.
| | - Katie F Daughenbaugh
- Department of Plant Sciences and Plant Pathology, Bozeman, MT 59717, USA.
- Center for Pollinator Health, Montana State University, Bozeman, MT 59717, USA.
| | - Fenali Parekh
- Department of Plant Sciences and Plant Pathology, Bozeman, MT 59717, USA.
- Department of Microbiology and Immunology, Bozeman, MT 59717, USA.
- Center for Pollinator Health, Montana State University, Bozeman, MT 59717, USA.
| | - Marie C Pizzorno
- Biology Department, Bucknell University, Lewisburg, PA 17837, USA.
| | - Michelle L Flenniken
- Department of Plant Sciences and Plant Pathology, Bozeman, MT 59717, USA.
- Department of Microbiology and Immunology, Bozeman, MT 59717, USA.
- Center for Pollinator Health, Montana State University, Bozeman, MT 59717, USA.
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40
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Galbraith DA, Fuller ZL, Ray AM, Brockmann A, Frazier M, Gikungu MW, Martinez JFI, Kapheim KM, Kerby JT, Kocher SD, Losyev O, Muli E, Patch HM, Rosa C, Sakamoto JM, Stanley S, Vaudo AD, Grozinger CM. Investigating the viral ecology of global bee communities with high-throughput metagenomics. Sci Rep 2018; 8:8879. [PMID: 29891995 PMCID: PMC5995813 DOI: 10.1038/s41598-018-27164-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/29/2018] [Indexed: 01/25/2023] Open
Abstract
Bee viral ecology is a fascinating emerging area of research: viruses exert a range of effects on their hosts, exacerbate impacts of other environmental stressors, and, importantly, are readily shared across multiple bee species in a community. However, our understanding of bee viral communities is limited, as it is primarily derived from studies of North American and European Apis mellifera populations. Here, we examined viruses in populations of A. mellifera and 11 other bee species from 9 countries, across 4 continents and Oceania. We developed a novel pipeline to rapidly and inexpensively screen for bee viruses. This pipeline includes purification of encapsulated RNA/DNA viruses, sequence-independent amplification, high throughput sequencing, integrated assembly of contigs, and filtering to identify contigs specifically corresponding to viral sequences. We identified sequences for (+)ssRNA, (−)ssRNA, dsRNA, and ssDNA viruses. Overall, we found 127 contigs corresponding to novel viruses (i.e. previously not observed in bees), with 27 represented by >0.1% of the reads in a given sample, and 7 contained an RdRp or replicase sequence which could be used for robust phylogenetic analysis. This study provides a sequence-independent pipeline for viral metagenomics analysis, and greatly expands our understanding of the diversity of viruses found in bee communities.
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Affiliation(s)
- David A Galbraith
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences Pennsylvania State University, University Park, PA, USA.
| | - Zachary L Fuller
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences Pennsylvania State University, University Park, PA, USA.,Department of Biology, Pennsylvania State University, University Park, PA, USA.,Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Allyson M Ray
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences Pennsylvania State University, University Park, PA, USA
| | - Axel Brockmann
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Maryann Frazier
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences Pennsylvania State University, University Park, PA, USA
| | - Mary W Gikungu
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | | | - Karen M Kapheim
- Department of Biology, Utah State University, Logan, UT, USA.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Jeffrey T Kerby
- Neukom Institute for Computational Science, Dartmouth College, Hanover, NH, USA
| | - Sarah D Kocher
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Oleksiy Losyev
- Department of Beekeeping, The National University of Life and Environmental Sciences of Ukraine, Kyiv, Ukraine
| | - Elliud Muli
- The International Center of Insect Physiology and Ecology, Nairobi, Kenya
| | - Harland M Patch
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences Pennsylvania State University, University Park, PA, USA
| | - Cristina Rosa
- Department of Plant Pathology, Pennsylvania State University, University Park, PA, USA
| | - Joyce M Sakamoto
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences Pennsylvania State University, University Park, PA, USA
| | - Scott Stanley
- Division of Pediatric Hematology and Oncology, Pennsylvania State University Children's Hospital, Hershey, PA, USA
| | - Anthony D Vaudo
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences Pennsylvania State University, University Park, PA, USA
| | - Christina M Grozinger
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences Pennsylvania State University, University Park, PA, USA
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41
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McMenamin AJ, Flenniken ML. Recently identified bee viruses and their impact on bee pollinators. Curr Opin Insect Sci 2018; 26:120-129. [PMID: 29764651 DOI: 10.1016/j.cois.2018.02.009] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/22/2017] [Accepted: 02/02/2018] [Indexed: 06/08/2023]
Abstract
Bees are agriculturally and ecologically important plant pollinators. Recent high annual losses of honey bee colonies, and reduced populations of native and wild bees in some geographic locations, may impact the availability of affordable food crops and the diversity and abundance of native and wild plant species. Multiple factors including viral infections affect pollinator health. The majority of well-characterized bee viruses are picorna-like RNA viruses, which may be maintained as covert infections or cause symptomatic infections or death. Next generation sequencing technologies have been utilized to identify additional bee-infecting viruses including the Lake Sinai viruses and Rhabdoviruses. In addition, sequence data is instrumental for defining specific viral strains and characterizing associated pathogenicity, such as the recent characterization of Deformed wing virus master variants (DWV-A, DWV-B, and DWV-C) and their impact on bee health.
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Affiliation(s)
- Alexander J McMenamin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA; Pollinator Health Center, Montana State University, Bozeman, MT, USA; Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Michelle L Flenniken
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA; Pollinator Health Center, Montana State University, Bozeman, MT, USA.
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42
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Lepetit D, Gillet B, Hughes S, Kraaijeveld K, Varaldi J. Genome Sequencing of the Behavior Manipulating Virus LbFV Reveals a Possible New Virus Family. Genome Biol Evol 2018; 8:3718-3739. [PMID: 28173110 PMCID: PMC5381508 DOI: 10.1093/gbe/evw277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 12/26/2022] Open
Abstract
Parasites are sometimes able to manipulate the behavior of their hosts. However, the molecular cues underlying this phenomenon are poorly documented. We previously reported that the parasitoid wasp Leptopilina boulardi which develops from Drosophila larvae is often infected by an inherited DNA virus. In addition to being maternally transmitted, the virus benefits from horizontal transmission in superparasitized larvae (Drosophila that have been parasitized several times). Interestingly, the virus forces infected females to lay eggs in already parasitized larvae, thus increasing the chance of being horizontally transmitted. In a first step towards the identification of virus genes responsible for the behavioral manipulation, we present here the genome sequence of the virus, called LbFV. The sequencing revealed that its genome contains an homologous repeat sequence (hrs) found in eight regions in the genome. The presence of this hrs may explain the genomic plasticity that we observed for this genome. The genome of LbFV encodes 108 ORFs, most of them having no homologs in public databases. The virus is however related to Hytrosaviridae, although distantly. LbFV may thus represent a member of a new virus family. Several genes of LbFV were captured from eukaryotes, including two anti-apoptotic genes. More surprisingly, we found that LbFV captured from an ancestral wasp a protein with a Jumonji domain. This gene was afterwards duplicated in the virus genome. We hypothesized that this gene may be involved in manipulating the expression of wasp genes, and possibly in manipulating its behavior.
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Affiliation(s)
- David Lepetit
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, France
| | - Benjamin Gillet
- Université de Lyon, CNRS, Ecole Normale Supérieure de Lyon, Université Lyon 1, Institut de Génomique Fonctionnelle de Lyon UMR 5242, France
| | - Sandrine Hughes
- Université de Lyon, CNRS, Ecole Normale Supérieure de Lyon, Université Lyon 1, Institut de Génomique Fonctionnelle de Lyon UMR 5242, France
| | - Ken Kraaijeveld
- Department of Ecological Science, Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Julien Varaldi
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, France
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Bigot D, Dalmon A, Roy B, Hou C, Germain M, Romary M, Deng S, Diao Q, Weinert LA, Cook JM, Herniou EA, Gayral P. The discovery of Halictivirus resolves the Sinaivirus phylogeny. J Gen Virol 2017; 98:2864-2875. [DOI: 10.1099/jgv.0.000957] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Diane Bigot
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Anne Dalmon
- INRA UR 406 Abeilles et environnement, Centre de recherche Provence-Alpes-Côte d'Azur, Site Agroparc, Domaine St Paul 228, Route de l'aérodrome CS40509 84914 Avignon, France
| | - Bronwen Roy
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Chunsheng Hou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, PR China
| | - Michèle Germain
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Manon Romary
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Shuai Deng
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, PR China
| | - Qingyun Diao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, PR China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Beijing 100093, PR China
| | - Lucy A. Weinert
- Institut des Sciences de l'Evolution UMR5554, Université Montpellier–CNRS–IRD–EPHE, Montpellier, France
- Present address: Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - James M. Cook
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Elisabeth A. Herniou
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
| | - Philippe Gayral
- Institut de Recherche sur la Biologie de l’Insecte, UMR 7261, CNRS, Université de Tours, 37200 Tours, France
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Remnant EJ, Shi M, Buchmann G, Blacquière T, Holmes EC, Beekman M, Ashe A. A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations. J Virol 2017; 91:e00158-17. [PMID: 28515299 PMCID: PMC5533899 DOI: 10.1128/jvi.00158-17] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/26/2017] [Indexed: 01/16/2023] Open
Abstract
Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees (Apis mellifera) has changed dramatically since the emergence of the parasitic mite Varroa destructor, which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity. To capture the viral diversity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa This analysis revealed seven novel viruses isolated from honey bees sampled globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically diverse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral diversity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management.IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been described in honey bees, with most belonging to the order Picornavirales Collapsing Varroa-infected colonies are often overwhelmed with high levels of picornaviruses. To examine the underlying viral diversity in honey bees, we employed viral metatranscriptomics analyses on three geographically diverse Varroa-resistant populations from Europe, Africa, and the Pacific. We describe seven novel viruses from a range of diverse viral families, including two viruses that are present in all three locations. In honey bees, small RNA sequences indicate that these viruses are processed by Dicer and the RNA interference pathway, whereas Varroa mites produce strikingly novel small RNA patterns. This work increases the number and diversity of known honey bee viruses and will ultimately contribute to improved disease management in our most important agricultural pollinator.
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Affiliation(s)
- Emily J Remnant
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Mang Shi
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Gabriele Buchmann
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | | | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
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Wang X, Liu X, Makalliwa GA, Li J, Wang H, Hu Z, Wang M. Per os infectivity factors: a complicated and evolutionarily conserved entry machinery of baculovirus. Sci China Life Sci 2017; 60:806-15. [PMID: 28755302 DOI: 10.1007/s11427-017-9127-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/06/2017] [Indexed: 01/12/2023]
Abstract
Baculoviruses are a family of arthropod-specific large DNA viruses that infect insect species belonging to the orders Lepidoptera, Hymenoptera and Diptera. In nature, occlusion-derived viruses (ODVs) initiate baculovirus primary infection in the midgut epithelium of insect hosts, and this process is largely dependent on a number of ODV envelope proteins designated as per os infectivity factors (PIFs). Interestingly, PIF homologs are also present in other invertebrate large DNA viruses, which is indicative that per os infection is an ancient and phylogenetically conserved entry mechanism shared by these viruses. Here, we review the advances in the knowledge of the functions of individual PIFs and recent discoveries about the PIF complex, and discuss the evolutionary implications of PIF homologs in invertebrate DNA viruses. Furthermore, future research highlights on the per os infection mechanism are also prospected.
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Gisder S, Genersch E. Viruses of commercialized insect pollinators. J Invertebr Pathol 2017; 147:51-59. [DOI: 10.1016/j.jip.2016.07.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/18/2016] [Accepted: 07/20/2016] [Indexed: 02/05/2023]
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47
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Williams T, Bergoin M, van Oers MM. Diversity of large DNA viruses of invertebrates. J Invertebr Pathol 2017; 147:4-22. [DOI: 10.1016/j.jip.2016.08.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 11/17/2022]
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van Aerle R, Santos EM. Advances in the application of high-throughput sequencing in invertebrate virology. J Invertebr Pathol 2017; 147:145-156. [PMID: 28249815 DOI: 10.1016/j.jip.2017.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 10/20/2022]
Abstract
Over the last decade, advances in high-throughput sequencing technologies have revolutionised biological research, making it possible for DNA/RNA sequencing of any organism of interest to be undertaken. Sequencing approaches are now routinely used in the detection and characterisation of (novel) viruses, investigation of host-pathogen interactions, and effective development of disease treatment strategies. For the sequencing and identification of viruses of interest, metagenomics approaches using infected host tissue are frequently used, as it is not always possible to culture and isolate these pathogens. High-throughput sequencing can also be used to investigate host-pathogen interactions by investigating (temporal) transcriptomic responses of both the host and virus, potentially leading to the discovery of novel opportunities for treatment and drug targets. In addition, viruses in environmental samples (e.g. water or soil samples) can be identified using eDNA/metagenomics approaches. The promise that recent developments in sequencing brings to the field of invertebrate virology are not devoid of technical challenges, including the need for better laboratory and bioinformatics strategies to sequence and assemble virus genomes within complex tissue or environmental samples, and the difficulties associated with the annotation of the large number of novel viruses being discovered.
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Affiliation(s)
- R van Aerle
- Centre for Environment, Fisheries, and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK.
| | - E M Santos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
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Bézier A, Harichaux G, Musset K, Labas V, Herniou EA. Qualitative proteomic analysis of Tipula oleracea nudivirus occlusion bodies. J Gen Virol 2017; 98:284-295. [DOI: 10.1099/jgv.0.000661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Annie Bézier
- Institut de Recherche sur la Biologie de l’Insecte (IRBI), UMR 7261 CNRS Université François-Rabelais, Tours 37200, France
| | - Grégoire Harichaux
- INRA, PRC UMR85-CNRS 7247-UFR-IFCE, Laboratoire de Spectrométrie de masse, Plateforme d’Analyse Intégrative des Biomolécules et de Phénomique des Animaux d’Intérêt Bio-agronomique (PAIB2), Nouzilly 37380, France
| | - Karine Musset
- Institut de Recherche sur la Biologie de l’Insecte (IRBI), UMR 7261 CNRS Université François-Rabelais, Tours 37200, France
| | - Valérie Labas
- INRA, PRC UMR85-CNRS 7247-UFR-IFCE, Laboratoire de Spectrométrie de masse, Plateforme d’Analyse Intégrative des Biomolécules et de Phénomique des Animaux d’Intérêt Bio-agronomique (PAIB2), Nouzilly 37380, France
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l’Insecte (IRBI), UMR 7261 CNRS Université François-Rabelais, Tours 37200, France
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50
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Affiliation(s)
- Laura M. Brutscher
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, United States of America
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, United States of America
| | - Alexander J. McMenamin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, United States of America
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, United States of America
| | - Michelle L. Flenniken
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, United States of America
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, United States of America
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