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Barth S, Affeldt S, Blaurock C, Lobedank I, Netsch A, Seitz K, Rümenapf T, Lamp B. Characterization of a Molecular Clone of Deformed Wing Virus B. Viruses 2024; 16:980. [PMID: 38932270 PMCID: PMC11209315 DOI: 10.3390/v16060980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 06/06/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
Honey bees (Apis mellifera) play a crucial role in agriculture through their pollination activities. However, they have faced significant health challenges over the past decades that can limit colony performance and even lead to collapse. A primary culprit is the parasitic mite Varroa destructor, known for transmitting harmful bee viruses. Among these viruses is deformed wing virus (DWV), which impacts bee pupae during their development, resulting in either pupal demise or in the emergence of crippled adult bees. In this study, we focused on DWV master variant B. DWV-B prevalence has risen sharply in recent decades and appears to be outcompeting variant A of DWV. We generated a molecular clone of a typical DWV-B strain to compare it with our established DWV-A clone, examining RNA replication, protein expression, and virulence. Initially, we analyzed the genome using RACE-PCR and RT-PCR techniques. Subsequently, we conducted full-genome RT-PCR and inserted the complete viral cDNA into a bacterial plasmid backbone. Phylogenetic comparisons with available full-length sequences were performed, followed by functional analyses using a live bee pupae model. Upon the transfection of in vitro-transcribed RNA, bee pupae exhibited symptoms of DWV infection, with detectable viral protein expression and stable RNA replication observed in subsequent virus passages. The DWV-B clone displayed a lower virulence compared to the DWV-A clone after the transfection of synthetic RNA, as evidenced by a reduced pupal mortality rate of only 20% compared to 80% in the case of DWV-A and a lack of malformations in 50% of the emerging bees. Comparable results were observed in experiments with low infection doses of the passaged virus clones. In these tests, 90% of bees infected with DWV-B showed no clinical symptoms, while 100% of pupae infected with DWV-A died. However, at high infection doses, both DWV-A and DWV-B caused mortality rates exceeding 90%. Taken together, we have generated an authentic virus clone of DWV-B and characterized it in animal experiments.
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Affiliation(s)
- Sandra Barth
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (S.B.); (S.A.); (C.B.); (I.L.); (A.N.)
| | - Sebastian Affeldt
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (S.B.); (S.A.); (C.B.); (I.L.); (A.N.)
| | - Claudia Blaurock
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (S.B.); (S.A.); (C.B.); (I.L.); (A.N.)
| | - Irmin Lobedank
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (S.B.); (S.A.); (C.B.); (I.L.); (A.N.)
| | - Anette Netsch
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (S.B.); (S.A.); (C.B.); (I.L.); (A.N.)
| | - Kerstin Seitz
- Institute of Virology, Department for Pathobiology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria; (K.S.); (T.R.)
| | - Till Rümenapf
- Institute of Virology, Department for Pathobiology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria; (K.S.); (T.R.)
| | - Benjamin Lamp
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (S.B.); (S.A.); (C.B.); (I.L.); (A.N.)
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Aziz RK, Ackermann HW, Petty NK, Kropinski AM. Essential Steps in Characterizing Bacteriophages: Biology, Taxonomy, and Genome Analysis. Methods Mol Biol 2018; 1681:197-215. [PMID: 29134597 DOI: 10.1007/978-1-4939-7343-9_15] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Because of the rise in antimicrobial resistance there has been a significant increase in interest in phages for therapeutic use. Furthermore, the cost of sequencing phage genomes has decreased to the point where it is being used as a teaching tool for genomics. Unfortunately, the quality of the descriptions of the phage and its annotation frequently are substandard. The following chapter is designed to help people working on phages, particularly those new to the field, to accurately describe their newly isolated viruses.
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Affiliation(s)
- Ramy Karam Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Qasr El-Ainy, 11562, Cairo, Egypt.
| | - Hans-Wolfgang Ackermann
- Department of Microbiology, Immunology, and Infectiology, Faculty of Medicine, Université Laval, Quebec, QC, Canada, G1X 4C6
| | - Nicola K Petty
- The ithree Institute, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Andrew M Kropinski
- Departments of Food Science, Molecular and Cellular Biology, and Pathobiology, University of Guelph, Guelph, ON, Canada, N1G 2W1
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Scholl D, Rogers S, Adhya S, Merril CR. Bacteriophage K1-5 encodes two different tail fiber proteins, allowing it to infect and replicate on both K1 and K5 strains of Escherichia coli. J Virol 2001; 75:2509-15. [PMID: 11222673 PMCID: PMC115872 DOI: 10.1128/jvi.75.6.2509-2515.2001] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2000] [Accepted: 12/11/2000] [Indexed: 11/20/2022] Open
Abstract
A virulent double-stranded DNA bacteriophage, Phi K1-5, has been isolated and found to be capable of infecting Escherichia coli strains that possess either the K1 or the K5 polysaccharide capsule. Electron micrographs show that the virion consists of a small icosohedral head with short tail spikes, similar to members of the Podoviridae family. DNA sequence analysis of the region encoding the tail fiber protein showed two open reading frames encoding previously characterized hydrolytic phage tail fiber proteins. The first is the K5 lyase protein gene of Phi K5, which allows this phage to specifically infect K5 E. coli strains. A second open reading frame encodes a protein almost identical in amino acid sequence to the N-acetylneuraminidase (endosialidase) protein of Phi K1E, which allows this phage to specifically infect K1 strains of E. coli. We provide experimental evidence that mature phage particles contain both tail fiber proteins, and mutational analysis indicates that each protein can be independently inactivated. A comparison of the tail gene regions of Phi K5, Phi K1E, and Phi K1-5 shows that the genes are arranged in a modular or cassette configuration and suggests that this family of phages can broaden host range by horizontal gene transfer.
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Affiliation(s)
- D Scholl
- National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland 20892, USA
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Ermolaeva MD, Khalak HG, White O, Smith HO, Salzberg SL. Prediction of transcription terminators in bacterial genomes. J Mol Biol 2000; 301:27-33. [PMID: 10926490 DOI: 10.1006/jmbi.2000.3836] [Citation(s) in RCA: 202] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This study describes an algorithm that finds rho-independent transcription terminators in bacterial genomes and evaluates the accuracy of its predictions. The algorithm identifies terminators by searching for a common mRNA motif: a hairpin structure followed by a short uracil-rich region. For each terminator, an energy-scoring function that reflects hairpin stability, and a tail-scoring function based on the number of U nucleotides and their proximity to the stem, are computed. A confidence value can be assigned to each terminator by analyzing candidate terminators found both within and between genes, and taking into account the energy and tail scores. The confidence is an empirical estimate of the probability that the sequence is a true terminator. The algorithm was used to conduct a comprehensive analysis of 12 bacterial genomes to identify likely candidates for rho-independent transcription terminators. Four of these genomes (Deinococcus radiodurans, Escherichia coli, Haemophilus influenzae and Vibrio cholerae) were found to have large numbers of rho-independent terminators. Among the other genomes, most appear to have no transcription terminators of this type, with the exception of Thermotoga maritima. A set of 131 experimentally determined E. coli terminators was used to evaluate the sensitivity of the method, which ranges from 89 % to 98 %, with corresponding false positive rates of 2 % and 18 %.
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Affiliation(s)
- M D Ermolaeva
- The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA.
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