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Wennmann JT, Lim FS, Senger S, Gani M, Jehle JA, Keilwagen J. Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants. J Gen Virol 2024; 105. [PMID: 38767624 DOI: 10.1099/jgv.0.001983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
Naturally occurring isolates of baculoviruses, such as the Bombyx mori nucleopolyhedrovirus (BmNPV), usually consist of numerous genetically different haplotypes. Deciphering the different haplotypes of such isolates is hampered by the large size of the dsDNA genome, as well as the short read length of next generation sequencing (NGS) techniques that are widely applied for baculovirus isolate characterization. In this study, we addressed this challenge by combining the accuracy of NGS to determine single nucleotide variants (SNVs) as genetic markers with the long read length of Nanopore sequencing technique. This hybrid approach allowed the comprehensive analysis of genetically homogeneous and heterogeneous isolates of BmNPV. Specifically, this allowed the identification of two putative major haplotypes in the heterogeneous isolate BmNPV-Ja by SNV position linkage. SNV positions, which were determined based on NGS data, were linked by the long Nanopore reads in a Position Weight Matrix. Using a modified Expectation-Maximization algorithm, the Nanopore reads were assigned according to the occurrence of variable SNV positions by machine learning. The cohorts of reads were de novo assembled, which led to the identification of BmNPV haplotypes. The method demonstrated the strength of the combined approach of short- and long-read sequencing techniques to decipher the genetic diversity of baculovirus isolates.
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Affiliation(s)
- Jörg T Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Fang-Shiang Lim
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Sergei Senger
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Mudasir Gani
- Division of Entomology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences & Technology, Kashmir 193 201, J&K, India
| | - Johannes A Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Schwabenheimer Str. 101, 69221 Dossenheim, Germany
| | - Jens Keilwagen
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Ernst-Baur-Str. 27, 06484 Quedlinburg, Germany
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Moore S, Jukes M. The History of Baculovirology in Africa. Viruses 2023; 15:1519. [PMID: 37515205 PMCID: PMC10383191 DOI: 10.3390/v15071519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Baculovirology has been studied on the African continent for the development of insect virus-based biopesticides and, to a much lesser extent, vaccine production and delivery, since the 1960s. In this review, we focus only on baculoviruses as biopesticides for agricultural pests in Africa. At least 11 species of baculovirus have been discovered or studied on the African continent, some with several distinct isolates, with the objective in most cases being the development of a biopesticide. These include the nucleopolyhedroviruses of Helicoverpa armigera, Cryptophlebia peltastica, Spodoptera exempta, Spodoptera frugiperda, Spodoptera littoralis, and Maruca vitrata, as well as the granuloviruses of Cydia pomonella, Plutella xylostella, Thaumatotibia (Cryptophlebia) leucotreta, Choristoneura occidentalis, and Phthorimaea operculella. Eleven different baculovirus-based biopesticides are recorded as being registered and commercially available on the African continent. Baculoviruses are recorded to have been isolated, researched, utilised in field trials, and/or commercially deployed as biopesticides in at least 13 different African countries. Baculovirus research is ongoing in Africa, and researchers are confident that further novel species and isolates will be discovered, to the benefit of environmentally responsible agricultural pest management, not only in Africa but also elsewhere.
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Affiliation(s)
- Sean Moore
- Citrus Research International, P.O. Box 5095, Walmer, Gqeberha 6065, South Africa
- Centre for Biological Control, Department of Zoology and Entomology, Rhodes University, P.O. Box 94, Makhanda 6140, South Africa
| | - Michael Jukes
- Centre for Biological Control, Department of Zoology and Entomology, Rhodes University, P.O. Box 94, Makhanda 6140, South Africa
- Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Makhanda 6140, South Africa
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Biological, morphological, and molecular characterization of the baculovirus PlxyMNPV_LBIV-11, and its virulence towards Plutella xylostella, Trichoplusia ni, and Spodoptera frugiperda larvae. Arch Microbiol 2022; 204:598. [PMID: 36056996 DOI: 10.1007/s00203-022-03222-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/19/2022] [Accepted: 08/25/2022] [Indexed: 11/02/2022]
Abstract
PlxyMNPV_LBIV-11 is an alphabaculovirus strain, isolated from Plutella xylostella larvae. This work characterized this strain at a biological, morphological, and molecular level to evaluate its similarity with other baculoviruses. Its ultrastructure showed a multiple arrangement of nucleocapsids within enveloped virions, all occluded within large cubical polyhedra. PlxyMNPV_LBIV-11 showed infectivity on the Hi5 and Sf9 cell lines, despite these being from heterologous origin. This in vitro infectivity was observed using either BVs or by transfection with genomic DNA. Restriction fragment patterns of PlxyMNPV_LBIV-11, using the enzymes EcoRI, BamHI and HindIII, showed a high relationship with those patterns shown by AcMNPV, except for one or two differential bands with each enzyme. Sequences of core genes lef-8 and lef-9 and the conserved polh gene showed identities ranging from 98 to 100% when compared with those of AcMNPV. Somewhat lower was the sequence identity of the gp64 gene (94%) as compared with those of AcMNPV and PlxyMNPV_CL3, which might be related to the difference in virulence. Besides, the presence of this gene in PlxyMNPV_LBIV-11 indicates that it belongs to group 1 of alphabaculoviruses. A phylogram was estimated with the core and conserved gene sequences, corroborating its high relationship with AcMNPV and PlxyMNPV_CL3. Bioassays were performed with P. xylostella larvae reared on a meridic diet, whose LC50 values indicated lower virulence than AcMNPV when tested against P. xylostella, Spodoptera frugiperda, and Trichoplusia ni larvae. Its virulence against S. frugiperda was only seven times lower than AcMNPV. Its potential as a biological control agent is discussed.
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Liu L, Zhang Z, Liu C, Qu L, Wang D. Genome Analysis of an Alphabaculovirus Isolated from the Larch Looper, Erannis ankeraria. Viruses 2021; 14:v14010034. [PMID: 35062240 PMCID: PMC8779214 DOI: 10.3390/v14010034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 11/22/2022] Open
Abstract
The larch looper, Erannis ankeraria Staudinger (Lepidoptera: Geometridae), is one of the major insect pests of larch forests, widely distributed from southeastern Europe to East Asia. A naturally occurring baculovirus, Erannis ankeraria nucleopolyhedrovirus (EranNPV), was isolated from E. ankeraria larvae. This virus was characterized by electron microscopy and by sequencing the whole viral genome. The occlusion bodies (OBs) of EranNPV exhibited irregular polyhedral shapes containing multiple enveloped rod-shaped virions with a single nucleocapsid per virion. The EranNPV genome was 125,247 bp in length with a nucleotide distribution of 34.9% G+C. A total of 131 hypothetical open reading frames (ORFs) were identified, including the 38 baculovirus core genes and five multi-copy genes. Five homologous regions (hrs) were found in the EranNPV genome. Phylogeny and pairwise kimura 2-parameter analysis indicated that EranNPV was a novel group II alphabaculovirus and was most closely related to Apocheima cinerarium NPV (ApciNPV). Field trials showed that EranNPV was effective in controlling E. ankeraria in larch forests. The above results will be relevant to the functional research on EranNPV and promote the use of this virus as a biocontrol agent.
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Affiliation(s)
- Long Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, China;
| | - Zhilin Zhang
- Forest Protection Station, Ulanqab 012000, China;
| | - Chenglin Liu
- Institute of Forest Ecology, Environment and Nature Conservation, Chinese Academy of Forestry, Beijing 100091, China;
| | - Liangjian Qu
- Institute of Forest Ecology, Environment and Nature Conservation, Chinese Academy of Forestry, Beijing 100091, China;
- Correspondence: (L.Q.); (D.W.); Tel.: +86-29-8709-1511 (D.W.)
| | - Dun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, China;
- Correspondence: (L.Q.); (D.W.); Tel.: +86-29-8709-1511 (D.W.)
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Jukes MD. Reads in a haystack: extracting complete mitogenome sequences hidden in baculovirus datasets. INSECT MOLECULAR BIOLOGY 2021; 30:541-551. [PMID: 34251705 DOI: 10.1111/imb.12724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/26/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Thaumatotibia leucotreta (Lepidoptera, Tortricidae) is one of many economically important insect pests for which no complete mitogenome sequence is available. The complete mitochondrial sequences for this species and other key pests could assist in the development of novel molecular techniques, such as enabling the identification of population-specific markers which could assist in improved monitoring of populations. The objective of this study was to determine whether NGS datasets generated for entomopathogenic viruses contain reads originating from host mitochondrial DNA. A total of 28 NGS datasets generated for the baculovirus Cryptophlebia leucotreta granulovirus (CrleGV) were analysed in this study. Three datasets contained sufficient reads providing adequate coverage for the assembly of complete mitogenomes. All 13 protein-coding genes, 22 tRNAs and both rRNAs present in the mitogenomes of other species within the Grapholitini tribe, were identified. Phylogenetic analysis of the mitogenomes at both an intrafamilial and interspecies level grouped the sequences within the Olethreutinae and T. leucotreta clades, respectively. Analysis of single nucleotide variations (SNVs) between each T. leucotreta sequence indicated up to 75 differences across the mitogenome. The methodology used in this study could be expanded to other baculovirus NGS datasets enabling the generation of novel lepidopteran mitogenome sequences.
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Affiliation(s)
- M D Jukes
- Centre for Biological Control, Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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CpGV-M Replication in Type I Resistant Insects: Helper Virus and Order of Ingestion Are Important. Viruses 2021; 13:v13091695. [PMID: 34578277 PMCID: PMC8473414 DOI: 10.3390/v13091695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
The genetic diversity of baculoviruses provides a sustainable agronomic solution when resistance to biopesticides seems to be on the rise. This genetic diversity promotes insect infection by several genotypes (i.e., multiple infections) that are more likely to kill the host. However, the mechanism and regulation of these virus interactions are still poorly understood. In this article, we focused on baculoviruses infecting the codling moth, Cydia pomonella: two Cydia pomonella granulovirus genotypes, CpGV-M and CpGV-R5, and Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV). The influence of the order of ingestion of the virus genotypes, the existence of an ingestion delay between the genotypes and the specificity of each genotype involved in the success of multiple infection were studied in the case of Cydia pomonella resistance. To obtain a multiple infection in resistant insects, the order of ingestion is a key factor, but the delay for ingestion of the second virus is not. CrpeNPV cannot substitute CpGV-R5 to allow replication of CpGV-M.
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Moore SD. Biological Control of a Phytosanitary Pest ( Thaumatotibia leucotreta): A Case Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18031198. [PMID: 33572807 PMCID: PMC7908599 DOI: 10.3390/ijerph18031198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/20/2021] [Accepted: 01/23/2021] [Indexed: 11/16/2022]
Abstract
Thaumatotibia leucotreta, known as the false codling moth, is a pest of citrus and other crops in sub-Saharan Africa. As it is endemic to this region and as South Africa exports most of its citrus around the world, T. leucotreta has phytosanitary status for most markets. This means that there is zero tolerance for any infestation with live larvae in the market. Consequently, control measures prior to exporting must be exemplary. Certain markets require a standalone postharvest disinfestation treatment for T. leucotreta. However, the European Union accepts a systems approach, consisting of three measures and numerous components within these measures. Although effective preharvest control measures are important under all circumstances, they are most critical where a standalone postharvest disinfestation treatment is not applied, such as within a systems approach. Conventional wisdom may lead a belief that effective chemical control tools are imperative to achieve this end. However, we demonstrate that it is possible to effectively control T. leucotreta to a level acceptable for a phytosanitary market, using only biological control tools. This includes parasitoids, predators, microbial control, semiochemicals, and sterile insects. Simultaneously, on-farm and environmental safety is improved and compliance with the increasing stringency of chemical residue requirements imposed by markets is achieved.
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Affiliation(s)
- Sean D. Moore
- Citrus Research International, P.O. Box 5095, Walmer, Port Elizabeth 6065, South Africa;
- Centre for Biological Control, Department of Zoology and Entomology, Rhodes University, P.O. Box 94, Makhanda 6140, South Africa
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Wennmann JT, Fan J, Jehle JA. Bacsnp: Using Single Nucleotide Polymorphism (SNP) Specificities and Frequencies to Identify Genotype Composition in Baculoviruses. Viruses 2020; 12:v12060625. [PMID: 32526997 PMCID: PMC7354547 DOI: 10.3390/v12060625] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/26/2020] [Accepted: 06/05/2020] [Indexed: 11/16/2022] Open
Abstract
Natural isolates of baculoviruses (as well as other dsDNA viruses) generally consist of homogenous or heterogenous populations of genotypes. The number and positions of single nucleotide polymorphisms (SNPs) from sequencing data are often used as suitable markers to study their genotypic composition. Identifying and assigning the specificities and frequencies of SNPs from high-throughput genome sequencing data can be very challenging, especially when comparing between several sequenced isolates or samples. In this study, the new tool “bacsnp”, written in R programming langue, was developed as a downstream process, enabling the detection of SNP specificities across several virus isolates. The basis of this analysis is the use of a common, closely related reference to which the sequencing reads of an isolate are mapped. Thereby, the specificities of SNPs are linked and their frequencies can be used to analyze the genetic composition across the sequenced isolate. Here, the downstream process and analysis of detected SNP positions is demonstrated on the example of three baculovirus isolates showing the fast and reliable detection of a mixed sequenced sample.
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Wennmann JT, Eigenbrod M, Marsberg T, Moore SD, Knox CM, Hill MP, Jehle JA. Cryptophlebia peltastica Nucleopolyhedrovirus Is Highly Infectious to Codling Moth Larvae and Cells. Appl Environ Microbiol 2019; 85:e00795-19. [PMID: 31227557 PMCID: PMC6696965 DOI: 10.1128/aem.00795-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/19/2019] [Indexed: 11/20/2022] Open
Abstract
Cydia pomonella granulovirus (CpGV) is a cornerstone of codling moth (Cydia pomonella) control in integrated and organic pome fruit production, though different types of resistance to CpGV products have been recorded in codling moth field populations in Europe for several years. Recently, a novel baculovirus named Cryptophlebia peltastica nucleopolyhedrovirus (CrpeNPV) was isolated from a laboratory culture of the litchi moth, Cryptophlebia peltastica, in South Africa. Along with CpGV, it is the third known baculovirus that is infectious to codling moth. In the present study, parameters of infectiveness of CrpeNPV, such as the median lethal concentration and median survival time, were determined for codling moth larvae susceptible or resistant to CpGV. In addition, the permissiveness of a codling moth cell line with respect to infection by CrpeNPV budded virus was demonstrated by infection and gene expression studies designed to investigate the complete replication cycle. Investigations of the high degree of virulence of CrpeNPV for codling moth larvae and cells are of high significant scientific and economic value and may offer new strategies for the biological control of susceptible and resistant populations of codling moth.IMPORTANCE The emergence of codling moth populations resistant to commercially applied isolates of CpGV is posing an imminent threat to organic pome fruit production. Very few CpGV isolates are left that are able to overcome the reported types of resistance, emphasizing the demand for new and highly virulent baculoviruses. Here we report the recently discovered CrpeNPV as highly infectious to all types of resistant codling moth populations with a high speed of killing, making it a promising candidate baculovirus in fighting the spread of resistant codling moth populations.
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Affiliation(s)
- Jörg T Wennmann
- Federal Research Centre for Cultivated Plants, Institute for Biological Control, Julius Kühn Institute, Darmstadt, Germany
| | - Marina Eigenbrod
- Federal Research Centre for Cultivated Plants, Institute for Biological Control, Julius Kühn Institute, Darmstadt, Germany
| | - Tamryn Marsberg
- Centre for Biological Control, Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Sean D Moore
- Centre for Biological Control, Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
- Citrus Research International (CRI), Walmer, Port Elizabeth, South Africa
| | - Caroline M Knox
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Martin P Hill
- Centre for Biological Control, Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Johannes A Jehle
- Federal Research Centre for Cultivated Plants, Institute for Biological Control, Julius Kühn Institute, Darmstadt, Germany
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