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Yang S, Amberger M, Wennmann JT, Jehle JA. Transcriptome analysis of CpGV in midguts of type II resistant codling moth larvae and identification of contaminant infections by SNP mapping of RNA-Seq data. J Virol 2024; 98:e0053724. [PMID: 38934597 PMCID: PMC11265400 DOI: 10.1128/jvi.00537-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Various isolates of the Cydia pomonella granulovirus (CpGV) are used as insect pest control agents against codling moth (CM, Cydia pomonella L.), a predominant pest in apple orchards. Three different types (I-III) of dominantly inherited field resistance of CM larvae to CpGV have been recently identified. In this study, transcription of virus genes in midgut cells of type II-resistant CM larvae infected with different CpGV isolates, i.e., CpGV-M and CpGV-S (both prone to type II resistance) as well as CpGV-E2 (breaking type II resistance) was determined by strand-specific RNA sequencing (RNA-Seq) at an early infection stage (72 h post infection). Based on principal component analysis of read counts and the quantitative distribution of single nucleotide polymorphisms (SNPs) in the RNA-Seq data, a bioinformatics analysis pipeline was developed for an a posteriori identification of the infective agents. We report that (i) identification of infective agent is crucial, especially in in vivo infection experiments, when activation of covert virus infections is a possibility, (ii) no substantial difference between CpGV-M and CpGV-S transcription was found in type II-resistant CM larvae despite a different resistance mechanism, (iii) the transcription level of CpGV-M and CpGV-S was much lower than that of CpGV-E2, and (iv) orf59 (sod), orf89 (pif-6), orf92 (p18), and orf137 (lef-10) were identified as significantly downregulated genes in resistance-prone isolates CpGV-M and CpGV-S. For type II resistance of CM larvae, we conclude that CpGV-M and CpGV-S are both able to enter midgut cells, but viral transcription is significantly impaired at an early stage of infection compared to the resistance-breaking isolate CpGV-E2. IMPORTANCE CpGV is a highly virulent pathogen of codling moth, and it has been developed into one of the most successful commercial baculovirus biocontrol agents for pome fruit production worldwide. The emergence of field resistance in codling moth to commercial CpGV products is a threat toward the sustainable use of CpGV. In recent years, different types of resistance (type I-III) were identified. For type II resistance, very little is known regarding the infection process. By studying the virus gene expression patterns of different CpGV isolates in midguts of type II-resistant codling moth larvae, we found that the type II resistance mechanism is most likely based on intracellular factors rather than a receptor component. By applying SNP mapping of the RNA-Seq data, we further emphasize the importance of identifying the infective agents in in vivo experiments when activation of a covert infection cannot be excluded.
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Affiliation(s)
- Shili Yang
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Biological Control, Dossenheim, Germany
| | - Maximilian Amberger
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Biological Control, Dossenheim, Germany
| | - Jörg T. Wennmann
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Biological Control, Dossenheim, Germany
| | - Johannes A. Jehle
- Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Biological Control, Dossenheim, Germany
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Krejmer-Rabalska M, Rabalski L, Kosinski M, Skrzecz I, Ziemnicka J, Szewczyk B. Leucoma salicis nucleopolyhedrovirus (LesaNPV) genome sequence shed new light on the origin of the Alphabaculovirus orpseudotsugatae species. Virus Genes 2024; 60:275-286. [PMID: 38594489 PMCID: PMC11139710 DOI: 10.1007/s11262-024-02062-x] [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] [Received: 11/12/2023] [Accepted: 02/25/2024] [Indexed: 04/11/2024]
Abstract
LesaNPV (Leucoma salicis nucleopolyhedrovirus) is an alphabaculovirus group Ib. Potentially, it can be an eco-friendly agent to control the white satin moth Leucoma salicis population. In this study, we have established the relationship between LesaNPV and other closely related alphabaculoviruses. Environmental samples of late instar of white satin moth collected in Poland infected with baculovirus have been homogenized, polyhedra were purified and subjected to scanning and transmission electron microscopy. Viral DNA was sequenced using the Illumina platform and the whole-genome sequence was established by de novo assembly of paired reads. Genome annotation and phylogenetic analyses were performed with the use of bioinformatics tools. The genome of LesaNPV is 132 549 bp long with 154 ORFs and 54.9% GC content. Whole-genome sequencing revealed deletion of dUTPase as well as ribonucleoside reductases small and large subunits region in LesaNPV genome compared to Dasychira pudibunda nucleopolyhedrovirus (DapuNPV) and Orgyia pseudotsugata multiple nucleopolyhedrovirus (OpMNPV) where this region is complete. Phylogenetic analysis of Baculoviridae family members showed that LesaNPV is less divergent from a common ancestor than closely related species DapuNPV and OpMNPV. This is interesting because their hosts do not occur in the same area. The baculoviruses described in this manuscript are probably isolates of one species and could be assigned to recently denominated species Alphabaculovirus orpseudotsugatae, historically originating from OpMNPV. This finding could have significant implications for the classification and understanding of the phylogeographical spread of baculoviruses.
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Affiliation(s)
- Martyna Krejmer-Rabalska
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307, Gdansk, Poland.
| | - Lukasz Rabalski
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307, Gdansk, Poland
- Biological Threats Identification and Countermeasure Center, General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, 24-100, Pulawy, Poland
| | - Maciej Kosinski
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307, Gdansk, Poland
| | - Iwona Skrzecz
- Department of Forest Protection, Forest Research Institute, 05-090, Sekocin Stary, Poland
| | - Jadwiga Ziemnicka
- Department of Biological Control and Quarantine, Institute of Plant Protection, 60-318, Poznan, Poland
| | - Boguslaw Szewczyk
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307, Gdansk, Poland
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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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Erlandson M, Baldwin D, Vlak JM, Theilmann D. Genomics of alphabaculovirus isolates infecting Mamestra species from North America and Eurasia. J Invertebr Pathol 2024; 203:108063. [PMID: 38286330 DOI: 10.1016/j.jip.2024.108063] [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] [Received: 11/15/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 01/31/2024]
Abstract
Whole genome sequencing and multiplex PCR analysis were used to characterize previously isolated baculovirus isolates from Mamestra populations in Eurasia. Although these viruses have been previously described as Mamestra brassicae nucleopolyhedrovirus (MbNPV/MabrNPV), we demonstrate here that these isolates represent strains of the baculovirus species Alphabaculovirus maconfiguratae (MacoNPV-A) and Alphabaculovirus altermaconfiguratae (MacoNPV-B). The MabrNPV-Bu and -Uk isolates had 96% nucleotide (nt) identity to the type isolate MacoNPV-A 90/2 at the whole genome level and in addition contained a lef-7 homologue which is found in MacoNPV-A but not MacoNPV-B. MabrNPV-Si, -De and -Nl had 96.6, 96.6 and 98.5% nt identity to the type isolate MacoNPV-B 96/2 at the whole genome level, respectively and contained a helicase-2 homologue. Gene content, synteny and K-2-P lef-8, lef-9 and polh analysis also confirmed the presence of both MacoNPV-A and MacoNPV-B isolates in Eurasia. Thus, both these alphabaculovirus species have wide Holarctic distributions in Mamestra host species. MacoNPV-A and MacoNPV-B have wide host ranges and in addition we showed that MacoNPV-B isolates trended to higher infectivity for T. ni larvae.
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Affiliation(s)
- Martin Erlandson
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan S7N 0X2, Canada.
| | - Doug Baldwin
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan S7N 0X2, Canada
| | - Just M Vlak
- Wageningen UR, Laboratory of Virology, PO Box 16, 6700AA Wageningen, the Netherlands
| | - David Theilmann
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia V0H 1Z0, Canada
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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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