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Eroglu GB, Inan C, Nalcacioglu R, Demirbag Z. Genome sequence analysis of a Helicoverpa armigera single nucleopolyhedrovirus (HearNPV-TR) isolated from Heliothis peltigera in Turkey. PLoS One 2020; 15:e0234635. [PMID: 32530959 PMCID: PMC7292396 DOI: 10.1371/journal.pone.0234635] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/29/2020] [Indexed: 12/03/2022] Open
Abstract
The entire genome of Helicoverpa armigera single nucleopolyhedrovirus (HearNPV-TR) was sequenced, and compared to genomes of other existing isolates. HearNPV-TR genome is 130.691 base pairs with a 38.9% G+C content and has 137 open reading frames (ORFs) of ≥ 150 nucleotides. Five homologous repeated sequences (hrs) and two baculovirus repeated ORFs (bro-a and bro-b) were identified. Phylogenetic analysis showed that HearNPV-TR is closer to HaSNPV-C1, HaSNPV-G4, HaSNPV-AU and HasNPV. However, there are significant differences in hr3, hr5 regions and in bro-a gene. Pairwise Kimura-2 parameter analysis of 38 core genes sequences of HearNPV-TR and other Helicoverpa NPVs showed that the genetic distances for these sequences were below 0.015 substitutions/site. Genomic differences as revealed by restriction profiles indicated that hr3, hr5 regions and bro-a gene may play a role in the virulence of HearNPV-TR.
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Affiliation(s)
- Gozde Busra Eroglu
- Department of Biology, Faculty of Science, Karadeniz Technical University, Trabzon, Turkey
| | - Cihan Inan
- Department of Molecular Biology and Genetics, Faculty of Science, Karadeniz Technical University, Trabzon, Turkey
| | - Remziye Nalcacioglu
- Department of Biology, Faculty of Science, Karadeniz Technical University, Trabzon, Turkey
| | - Zihni Demirbag
- Department of Biology, Faculty of Science, Karadeniz Technical University, Trabzon, Turkey
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Huang YF, Chen TH, Chang ZT, Wang TC, Lee SJ, Kim JC, Kim JS, Chiu KP, Nai YS. Genomic sequencing of Troides aeacus nucleopolyhedrovirus (TraeNPV) from golden birdwing larvae (Troides aeacus formosanus) to reveal defective Autographa californica NPV genomic features. BMC Genomics 2019; 20:419. [PMID: 31133070 PMCID: PMC6537400 DOI: 10.1186/s12864-019-5713-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 04/17/2019] [Indexed: 11/25/2022] Open
Abstract
Background The golden birdwing butterfly (Troides aeacus formosanus) is a rarely observed species in Taiwan. Recently, a typical symptom of nuclear polyhedrosis was found in reared T. aeacus larvae. From the previous Kimura-2 parameter (K-2-P) analysis based on the nucleotide sequence of three genes in this isolate, polh, lef-8 and lef-9, the underlying virus did not belong to any known nucleopolyhedrovirus (NPV) species. Therefore, this NPV was provisionally named “TraeNPV”. To understand this NPV, the nucleotide sequence of the whole TraeNPV genome was determined using next-generation sequencing (NGS) technology. Results The genome of TraeNPV is 125,477 bp in length with 144 putative open reading frames (ORFs) and its GC content is 40.45%. A phylogenetic analysis based on the 37 baculoviral core genes suggested that TraeNPV is a Group I NPV that is closely related to Autographa californica nucleopolyhedrovirus (AcMNPV). A genome-wide analysis showed that TraeNPV has some different features in its genome compared with other NPVs. Two novel ORFs (Ta75 and Ta139), three truncated ORFs (pcna, he65 and bro) and one duplicated ORF (38.7 K) were found in the TraeNPV genome; moreover, there are fewer homologous regions (hrs) than there are in AcMNPV, which shares eight hrs within the TraeNPV genome. TraeNPV shares similar genomic features with AcMNPV, including the gene content, gene arrangement and gene/genome identity, but TraeNPV lacks 15 homologous ORFs from AcMNPV in its genome, such as ctx, host cell-specific factor 1 (hcf-1), PNK/PNL, vp15, and apsup, which are involved in the auxiliary functions of alphabaculoviruses. Conclusions Based on these data, TraeNPV would be clarified as a new NPV species with defective AcMNPV genomic features. The precise relationship between TraeNPV and other closely related NPV species were further investigated. This report could provide comprehensive information on TraeNPV for evolutionary insights into butterfly-infected NPV. Electronic supplementary material The online version of this article (10.1186/s12864-019-5713-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu-Feng Huang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Tzu-Han Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Zih-Ting Chang
- Department of Biotechnology and Animal Science, National Ilan University, Yilan, Taiwan
| | - Tai-Chuan Wang
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - Se Jin Lee
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju, South Korea
| | - Jong Cheol Kim
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju, South Korea
| | - Jae Su Kim
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju, South Korea
| | - Kuo-Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Shin Nai
- Department of Entomology, National Chung Hsing University, Taichung, Taiwan.
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van der Merwe M, Jukes MD, Rabalski L, Knox C, Opoku-Debrah JK, Moore SD, Krejmer-Rabalska M, Szewczyk B, Hill MP. Genome Analysis and Genetic Stability of the Cryptophlebia leucotreta Granulovirus (CrleGV-SA) after 15 Years of Commercial Use as a Biopesticide. Int J Mol Sci 2017; 18:E2327. [PMID: 29099796 PMCID: PMC5713296 DOI: 10.3390/ijms18112327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 12/23/2022] Open
Abstract
Thaumatotibia leucotreta Meyrick (Lepidoptera: Tortricidae) is an indigenous pest in southern Africa which attacks citrus fruits and other crops. To control T. leucotreta in South Africa, an integrated pest management (IPM) programme incorporating the baculovirus Cryptophlebialeucotreta granulovirus (CrleGV-SA) as a biopesticide has been implemented. This study investigated the genetic stability of a commercially produced CrleGV-SA product that has been applied in the field since 2000. Seven representative full-genome sequences of the CrleGV-SA isolate spanning a 15-year period were generated and compared with one another. Several open reading frames (ORFs) were identified to have acquired single nucleotide polymorphisms (SNPs) during the 15-year period, with three patterns observed and referred to as "stable", "reversion", and "unstable switching". Three insertion events were also identified, two of which occurred within ORFs. Pairwise multiple alignments of these sequences showed an identity ranging from 99.98% to 99.99%. Concentration-response bioassays comparing samples of CrleGV-SA from 2000 and 2015 showed an increase in virulence toward neonate T. leucotreta larvae. The CrleGV-SA genome sequence generated from the 2015 sample was compared to the Cape Verde reference genome, CrleGV-CV3. Several fusion events were identified between ORFs within these genomes. These sequences shared 96.7% pairwise identity, confirming that CrleGV-SA is a genetically distinct isolate. The results of this study indicate that the genome of CrleGV-SA has remained stable over many years, with implications for its continued use as a biopesticide in the field. Furthermore, the study describes the first complete baculovirus genome to be sequenced with the MinION (Oxford Nanopore, Oxford, UK) platform and the first complete genome sequence of the South African CrleGV isolate.
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Affiliation(s)
- Marcel van der Merwe
- Department of Biochemistry and Microbiology, P.O. Box 94, Rhodes University, Grahamstown 6140, South Africa.
| | - Michael D Jukes
- Department of Biochemistry and Microbiology, P.O. Box 94, Rhodes University, Grahamstown 6140, South Africa.
| | - Lukasz Rabalski
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, 80-210 Gdansk, Poland.
| | - Caroline Knox
- Department of Biochemistry and Microbiology, P.O. Box 94, Rhodes University, Grahamstown 6140, South Africa.
| | - John K Opoku-Debrah
- River Bioscience, P.O. Box 20388, Humewood, Port Elizabeth 6013, South Africa.
| | - Sean D Moore
- Citrus Research International, P.O. Box 20285, Humewood, Port Elizabeth 6013, South Africa.
- Department of Zoology and Entomology, P.O. Box 94, Rhodes University, Grahamstown 6140, South Africa.
| | - Martyna Krejmer-Rabalska
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, 80-210 Gdansk, Poland.
| | - Boguslaw Szewczyk
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, 80-210 Gdansk, Poland.
| | - Martin P Hill
- Department of Zoology and Entomology, P.O. Box 94, Rhodes University, Grahamstown 6140, South Africa.
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Genetic and phenotypic comparisons of viral genotypes from two nucleopolyhedroviruses interacting with a common host species, Spodoptera litura (Lepidoptera: Noctuidae). J Invertebr Pathol 2016; 139:42-49. [DOI: 10.1016/j.jip.2016.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 07/15/2016] [Accepted: 07/19/2016] [Indexed: 11/20/2022]
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Brito AFD, Braconi CT, Weidmann M, Dilcher M, Alves JMP, Gruber A, Zanotto PMDA. The Pangenome of the Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV). Genome Biol Evol 2015; 8:94-108. [PMID: 26615220 PMCID: PMC4758234 DOI: 10.1093/gbe/evv231] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The alphabaculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is the world's most successful viral bioinsecticide. Through the 1980s and 1990s, this virus was extensively used for biological control of populations of Anticarsia gemmatalis (Velvetbean caterpillar) in soybean crops. During this period, genetic studies identified several variable loci in the AgMNPV; however, most of them were not characterized at the sequence level. In this study we report a full genome comparison among 17 wild-type isolates of AgMNPV. We found the pangenome of this virus to contain at least 167 hypothetical genes, 151 of which are shared by all genomes. The gene bro-a that might be involved in host specificity and carrying transporter is absent in some genomes, and new hypothetical genes were observed. Among these genes there is a unique rnf12-like gene, probably implicated in ubiquitination. Events of gene fission and fusion are common, as four genes have been observed as single or split open reading frames. Gains and losses of genomic fragments (from 20 to 900 bp) are observed within tandem repeats, such as in eight direct repeats and four homologous regions. Most AgMNPV genes present low nucleotide diversity, and variable genes are mainly located in a locus known to evolve through homologous recombination. The evolution of AgMNPV is mainly driven by small indels, substitutions, gain and loss of nucleotide stretches or entire coding sequences. These variations may cause relevant phenotypic alterations, which probably affect the infectivity of AgMNPV. This work provides novel information on genomic evolution of the AgMNPV in particular and of baculoviruses in general.
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Affiliation(s)
- Anderson Fernandes de Brito
- Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Carla Torres Braconi
- Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Manfred Weidmann
- Department of Virology, University Medical Center, Göttingen, Germany
| | - Meik Dilcher
- Department of Virology, University Medical Center, Göttingen, Germany
| | - João Marcelo Pereira Alves
- Department of Parasitology, Institute of Biomedical Sciences-ICB II, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Arthur Gruber
- Department of Parasitology, Institute of Biomedical Sciences-ICB II, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Paolo Marinho de Andrade Zanotto
- Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil
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Xue JL, Cheng XW. Comparative analysis of a highly variable region within the genomes of Spodoptera frugiperda ascovirus 1d (SfAV-1d) and SfAV-1a. J Gen Virol 2011; 92:2797-2802. [DOI: 10.1099/vir.0.035733-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recently discovered ascoviruses have a worldwide distribution. Here we report a new member of the family Ascoviridae, Spodoptera frugiperda ascovirus 1d (SfAV-1d) with a variable region in the genome. Restriction fragment length polymorphism, Southern hybridization and genome sequencing analyses confirmed that SfAV-1d and the earlier reported SfAV-1a are closely related but are not identical. The genome size of SfAV-1d is approximately 100 kbp, which is about 57 kbp smaller than SfAV-1a. The SfAV-1d genome has a major deletion of 14 kbp that corresponds to one of the inverted repeat (IR) regions of SfAV-1a. Cloning and sequencing revealed that the region flanking the deletion within the SfAV-1d genome is highly variable. In all the variants of this region, the whole IR region is missing, with 88.2 % of the variants missing part of or the whole adjacent SfAV-1a ORF71, 94.1 % missing part of or the whole of adjacent ORF72 and 64.6 % missing part of or the whole of ORF73.
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Affiliation(s)
- Jian-Li Xue
- Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, OH 45056, USA
| | - Xiao-Wen Cheng
- Department of Microbiology, 32 Pearson Hall, Miami University, Oxford, OH 45056, USA
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Liang Z, Zhang X, Yin X, Cao S, Xu F. Genomic sequencing and analysis of Clostera anachoreta granulovirus. Arch Virol 2011; 156:1185-98. [DOI: 10.1007/s00705-011-0977-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2010] [Accepted: 02/24/2011] [Indexed: 11/28/2022]
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Dieu BTM, Zwart MP, Vlak JM. Can VNTRs be used to study genetic variation within white spot syndrome virus isolates? JOURNAL OF FISH DISEASES 2010; 33:689-693. [PMID: 20487140 DOI: 10.1111/j.1365-2761.2010.01163.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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9
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Takatsuka J, Okuno S, Ishii T, Nakai M, Kunimi Y. Fitness-related traits of entomopoxviruses isolated from Adoxophyes honmai (Lepidoptera: Tortricidae) at three localities in Japan. J Invertebr Pathol 2010; 105:121-31. [PMID: 20447402 DOI: 10.1016/j.jip.2010.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 04/21/2010] [Accepted: 04/27/2010] [Indexed: 10/19/2022]
Abstract
Three entomopoxviruses (EPVs) isolated from diseased Adoxophyes honmai larvae at different localities (Tsukuba, Itsukaichi, and Miyazaki) in Japan were compared for biochemical identity and key parameters of virus fitness, fatal infection, speed of kill, and virus yield. When the structural peptides of occlusion bodies (OBs) and occlusion-derived viral particles were compared using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, no difference in banding patterns was observed. However, DNA restriction endonuclease analysis showed that the three isolates were genotypically different, but many commonly sized DNA fragments were observed. Five tortricid species, A. honmai, Adoxophyes orana, Adoxophyesdubia, Homona magnanima, and Archips insulanus were susceptible to all isolates. No significant differences in the key viral fitness parameters were detected among the isolates in A. orana. However, the Miyazaki isolate had a different effect on H. magnanima; it allowed infected insects to survive longer and develop to a larger size, but had a lower yield of OBs per larva at any given time to death. OB yields per unit cadaver weight for the Miyazaki isolate, which indicate the conversion rate of the insect to virus, were lower over time compared to the other two isolates. The implications for selecting a candidate isolate to control tortricid pests are discussed.
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Affiliation(s)
- Jun Takatsuka
- Department of Bioregulation and Biointeraction, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwai, Fuchu, Tokyo 183-8509, Japan.
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Genomic sequencing and analyses of Lymantria xylina multiple nucleopolyhedrovirus. BMC Genomics 2010; 11:116. [PMID: 20167051 PMCID: PMC2830988 DOI: 10.1186/1471-2164-11-116] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Accepted: 02/18/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Outbreaks of the casuarina moth, Lymantria xylina Swinehoe (Lepidoptera: Lymantriidae), which is a very important forest pest in Taiwan, have occurred every five to 10 years. This moth has expanded its range of host plants to include more than 65 species of broadleaf trees. LyxyMNPV (L. xylina multiple nucleopolyhedrovirus) is highly virulent to the casuarina moth and has been investigated as a possible biopesticide for controlling this moth. LdMNPV-like virus has also been isolated from Lymantria xylina larvae but LyxyMNPV was more virulent than LdMNPV-like virus both in NTU-LY and IPLB-LD-652Y cell lines. To better understand LyxyMNPV, the nucleotide sequence of the LyxyMNPV DNA genome was determined and analysed. RESULTS The genome of LyxyMNPV consists of 156,344 bases, has a G+C content of 53.4% and contains 157 putative open reading frames (ORFs). The gene content and gene order of LyxyMNPV were similar to those of LdMNPV, with 151 ORFs identified as homologous to those reported in the LdMNPV genome. Two genes (Lyxy49 and Lyxy123) were homologous to other baculoviruses, and four unique LyxyMNPV ORFs (Lyxy11, Lyxy19, Lyxy130 and Lyxy131) were identified in the LyxyMNPV genome, including a gag-like gene that was not reported in baculoviruses. LdMNPV contains 23 ORFs that are absent in LyxyMNPV. Readily identifiable homologues of the gene host range factor-1 (hrf-1), which appears to be involved in the susceptibility of L. dispar to NPV infection, were not present in LyxyMNPV. Additionally, two putative odv-e27 homologues were identified in LyxyMNPV. The LyxyMNPV genome encoded 14 bro genes compared with 16 in LdMNPV, which occupied more than 8% of the LyxyMNPV genome. Thirteen homologous regions (hrs) were identified containing 48 repeated sequences composed of 30-bp imperfect palindromes. However, they differed in the relative positions, number of repeats and orientation in the genome compared to LdMNPV. CONCLUSION The gene parity plot analysis, percent identity of the gene homologues and a phylogenetic analysis suggested that LyxyMNPV is a Group II NPV that is most closely related to LdMNPV but with a highly distinct genomic organisation.
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Luo L, Zeng L. A new rod-shaped virus from parasitic wasp Diachasmimorpha longicaudata (Hymenoptera: Braconidae). J Invertebr Pathol 2009; 103:165-9. [PMID: 19682456 DOI: 10.1016/j.jip.2009.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Revised: 07/28/2009] [Accepted: 08/07/2009] [Indexed: 11/27/2022]
Abstract
A new rod-shaped nucleocapsids (NCs) was found inadvertently in Diachasmimorpha longicaudata accessory gland filaments (AGFs). The NCs were 30 nm in diameter and nearly 900 nm in length. They replicated in a small cell type of the AGFs in D. longicaudata, and following oviposition, invaded and proliferated in the hemocytes of a parasitized host Bactrocera dorsalis Hendel. This finding of a completely new virus in the AGF indicate that different geographical populations (subspecies) of D. longicaudata may carry different sybionts. This is the first report showing that the same wasp species, but from a different geographical populations, can carry an entirely different virus.
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Affiliation(s)
- Li Luo
- Laboratory of Insect Ecology, South China Agricultural University, Wushan Road, Tianhe District, Guangzhou, China
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12
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Chen YR, Wu CY, Lee ST, Wu YJ, Lo CF, Tsai MF, Wang CH. Genomic and host range studies of Maruca vitrata nucleopolyhedrovirus. J Gen Virol 2008; 89:2315-2330. [PMID: 18753242 DOI: 10.1099/vir.0.2008/001412-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The complete genome of the Maruca vitrata nucleopolyhedrovirus (MaviNPV) isolated from the legume pod borer, Maruca vitrata (Lepidoptera: Pyralidae), was sequenced. It was found to be 111 953 bp in length, with an overall 39 % G+C content, and contained 126 open reading frames (ORFs) encoding predicted proteins of over 50 aa. The gene content and gene order of MaviNPV have the highest similarity to those of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) and their shared homologous genes are 100 % collinear. In fact, MaviNPV seems to be a mini-AcMNPV that is native to Taiwan and possesses a smaller genome with fewer auxiliary genes than the AcMNPV type species. Except for one ORF (Mv74), all of the MaviNPV ORFs have homologues in the AcMNPV genome. MaviNPV is the first lepidopteran-specific baculovirus to lack homologues of vfgf and odv-e66. In addition, MaviNPV lacks the baculovirus repeat ORF (bro) gene that corresponds to AcMNPV ORF2. Five homologous regions (hrs) were located within the MaviNPV genome, and these contained a total of 44 imperfect palindromes. Phylogenetic analysis of the whole genome revealed that MaviNPV was separated from the common ancestor of AcMNPV and Bombyx mori nucleopolyhedrovirus before these two viral species diverged from each other. Moreover, replication of MaviNPV in several cell lines and an egfp-MaviNPV infection assay revealed that IPLB-LD-652Y cells are only partially permissive to MaviNPV, which supports our conclusion that MaviNPV is a distinct species of the group I lepidopteran NPVs.
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Affiliation(s)
- Yun-Ru Chen
- Department of Entomology, National Taiwan University, Taipei, Taiwan, ROC
| | - Chih-Yu Wu
- Department of Entomology, National Taiwan University, Taipei, Taiwan, ROC
| | - Song-Tay Lee
- Department of Biotechnology, Southern Taiwan University of Technology, No. 1 Nantai Street, Yung-Kang City, Tainan 710, Taiwan, ROC
| | - Yan-Jheng Wu
- Department of Biotechnology, Southern Taiwan University of Technology, No. 1 Nantai Street, Yung-Kang City, Tainan 710, Taiwan, ROC
| | - Chu-Fang Lo
- Department of Zoology, National Taiwan University, Taipei, Taiwan, ROC
| | - Meng-Feng Tsai
- Department of Molecular Biotechnology, Dayeh University, No. 112 Shanjiao Road, Dacun, Changhua, Taiwan, ROC
| | - Chung-Hsiung Wang
- Department of Entomology, National Taiwan University, Taipei, Taiwan, ROC
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Garcia-Maruniak A, Maruniak JE, Farmerie W, Boucias DG. Sequence analysis of a non-classified, non-occluded DNA virus that causes salivary gland hypertrophy of Musca domestica, MdSGHV. Virology 2008; 377:184-96. [PMID: 18495197 DOI: 10.1016/j.virol.2008.04.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Revised: 03/25/2008] [Accepted: 04/14/2008] [Indexed: 11/30/2022]
Abstract
The genome of the virus that causes salivary gland hypertrophy in Musca domestica (MdSGHV) was sequenced. This non-classified, enveloped, double stranded, circular DNA virus had a 124,279bp genome. The G + C content was 43.5% with 108 putative methionine-initiated open reading frames (ORFs). Thirty ORFs had homology to database proteins: eleven to proteins coded by both baculoviruses and nudiviruses (p74, pif-1, pif-2, pif-3, odv-e66, rr1, rr2, iap, dUTPase, MMP, and Ac81-like), seven to nudiviruses (mcp, dhfr, ts, tk and three unknown proteins), one to baculovirus (Ac150-like), one to herpesvirus (dna pol), and ten to cellular proteins. Mass spectrum analysis of the viral particles' protein components identified 29 structural ORFs, with only p74 and odv-e66 previously characterized as baculovirus structural proteins. Although most of the homology observed was to nudiviruses, phylogenetic analysis showed that MdSGHV was not closely related to them or to the baculoviruses.
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Affiliation(s)
- Alejandra Garcia-Maruniak
- Department of Entomology and Nematology, PO Box 110620, University of Florida, Gainesville, Florida 32611-0620, USA.
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Oliveira JVDC, Wolff JLC, Garcia-Maruniak A, Ribeiro BM, de Castro MEB, de Souza ML, Moscardi F, Maruniak JE, Zanotto PMDA. Genome of the most widely used viral biopesticide: Anticarsia gemmatalis multiple nucleopolyhedrovirus. J Gen Virol 2006; 87:3233-3250. [PMID: 17030857 DOI: 10.1099/vir.0.82161-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genome of Anticarsia gemmatalis multiple nucleopolyhedrovirus isolate 2D (AgMNPV-2D), which is the most extensively used virus pesticide in the world, was completely sequenced and shown to have 132 239 bp (G+C content 44.5 mol%) and to be capable of encoding 152 non-overlapping open reading frames (ORFs). Three ORFs were unique to AgMNPV-2D, one of which (ag31) had similarity to eukaryotic poly(ADP-ribose) polymerases. The lack of chiA and v-cath may explain some of the success and growth of the AgMNPV biological control programme, as it may explain the high recovery of polyhedra sequestered inside dead larvae in the field, which are collected and used for further application as biological pesticides in soybean fields. The genome organization was similar to that of the Choristoneura fumiferana defective MNPV (CfDefNPV). Most of the variation between the two genomes took place near highly repetitive regions, which were also closely associated with bro-coding regions. The separation of the NPVs into groups I and II was supported by: (i) a phenogram of the complete genomes of 28 baculovirus and Heliothis zea virus 1, (ii) the most parsimonious reconstruction of gene content along the phenograms and (iii) comparisons of genomic features. Moreover, these data also reinforced the notion that group I of the NPVs can be split further into the AgMNPV lineage (AgMNPV, CfDefNPV, Epiphyas postvittana NPV, Orgyia pseudotsugata MNPV and C. fumiferana MNPV), sharing eight defining genes, and the Autographa californica MNPV (AcMNPV) lineage (AcMNPV, Rachiplusia ou NPV and Bombyx mori NPV), sharing nine defining genes.
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Affiliation(s)
- Juliana Velasco de Castro Oliveira
- Laboratório de Evolução Molecular e Bionformática, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, SP, Brazil
| | - José Luiz Caldas Wolff
- Laboratório de Virologia Molecular, Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes, Mogi das Cruzes, SP, Brazil
| | - Alejandra Garcia-Maruniak
- Entomology and Nematology Department, PO Box 110620, University of Florida, Gainesville, FL 32611-0620, USA
| | | | | | - Marlinda Lobo de Souza
- Embrapa Recursos Genéticos e Biotecnologia-Núcleo Temático de Controle Biológico (NTCB), Brasília, DF, Brazil
| | | | - James Edward Maruniak
- Entomology and Nematology Department, PO Box 110620, University of Florida, Gainesville, FL 32611-0620, USA
| | - Paolo Marinho de Andrade Zanotto
- Laboratório de Evolução Molecular e Bionformática, Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, SP, Brazil
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15
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Belaich MN, Rodríguez VA, Bilen MF, Pilloff MG, Romanowski V, Sciocco-Cap A, Ghiringhelli PD. Sequencing and characterisation of p74 gene in two isolates of Anticarsia gemmatalis MNPV. Virus Genes 2006; 32:59-70. [PMID: 16525736 DOI: 10.1007/s11262-005-5846-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2005] [Accepted: 06/26/2005] [Indexed: 10/24/2022]
Abstract
P74 is a protein encoded in the genome of baculoviruses, associated with the envelopes of occluded virus. Its presence proved to be essential for per os infection. In first place, in this work we designed two universal primers to amplify a sequence region of the p74 ORF in baculoviruses from different classification groups. Then, by the use of these amplicons we obtained the complete sequence of the p74 locus from two isolates of AgMNPV, 2D (Brazil) and SF (Argentina). In the flanking regions we determined the complete sequence of p10 gene and a portion of p26 gene. Comparing both p74 sequence data (ORFs of 1935 bp) we found fifteen nucleotide changes that result in six amino acid changes. Comparisons of AgMNPV p74s with other baculovirus homologous genes indicate a close relationship with other group I Nucleopolyhedrovirus, in particular CfDEFNPV. These results were based on ORF sequence, amino acid sequence and gene order. The predictive studies about secondary structure and hydrophobic index point at six regions potentially associated to its function or native conformation. Finally, the detection of p74 mRNA after virus DNA replication confirms a late expression pattern.
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Affiliation(s)
- Mariano Nicolás Belaich
- LIGBCM (Laboratorio de Ingeniería Genética y Biología Celular y Molecular), Departamento Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Saenz Peña 180, Bernal (1876), Argentina
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16
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Murillo R, Muñoz D, Williams T, Mugeta N, Caballero P. Application of the PCR-RFLP method for the rapid differentiation of Spodoptera exigua nucleopolyhedrovirus genotypes. J Virol Methods 2006; 135:1-8. [PMID: 16494953 DOI: 10.1016/j.jviromet.2006.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2005] [Revised: 01/12/2006] [Accepted: 01/17/2006] [Indexed: 10/25/2022]
Abstract
Quality control during mass production of Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV), and studies on environmental fate following the use of this virus as a biological pesticide, would be facilitated by a rapid method for the detection and identification of isolates. A molecular biology tool was developed that combined the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) to differentiate SeMNPV isolates. Oligonucleotide primers were designed to amplify five variable SeMNPV genomic regions (V01, V02, V03, V04, V05). Four wild-type SeMNPV strains isolated from the United States (US2) and Spain (SP1, SP2, and SP3), and a laboratory cloned genotype (US1A), were analyzed with 36 different primer-endonuclease combinations. BglII digestion of the variable region 1 (V01) amplicon was the only combination that differentiated each of the five virus isolates tested, although genetic heterogeneity limited the discriminatory power of the technique. Six novel SeMNPV isolates originating from greenhouse soils in southern Spain were successfully identified using this method. As judged by sequence analysis, the V01 region, which comprises the homologous region 1 (hr1), is the most variable genomic region among the genotypes present in the Spanish isolates. This method constitutes a useful tool for processing large number of environmental samples and could be used to address environmental biosafety concerns.
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Affiliation(s)
- Rosa Murillo
- Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona 31006, Spain
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17
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Toprak U, Bayram S, Gürkan OM. Comparative biological activities of a plaque-purified variant and a Turkish native isolate of SpliNPV-B against Spodoptera littoralis (Lepidoptera: Noctuidae). PEST MANAGEMENT SCIENCE 2006; 62:57-63. [PMID: 16235266 DOI: 10.1002/ps.1128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The noctuid moth Spodoptera littoralis (Boisduval) is an important pest of many cultivated plants worldwide and five different geographical Nucleopolyhedrovirus (NPV) strains of this pest have been isolated to date. Two of these, a plaque-purified variant of the S. littoralis NPV from Morocco (SpliNPV-M2) and a SpliNPV isolated from field-infected S. littoralis larvae found in Turkey (SpliNPV-TR1), were compared biologically in terms of infectiveness (median lethal dose, LD50) for third instars and in terms of virulence (median lethal time, LT50) for neonates and third-instar S. littoralis larvae. The LD50 values of SpliNPV-TR1 and SpliNPV-M2 were 20.73 and 185.21 occlusion bodies (OBs)/larva, respectively, with non-overlapping confidence limits indicating they were significantly different. Thus, SpliNPV-M2 was found to be significantly less infective (about nine times higher LD50) than SpliNPV-TR1. The LT50 values of neonates for SpliNPV-M2 and SpliNPV-TR1 were 37 and 43.9 h at a concentration of 10(6) OBs ml(-1), respectively. For these same isolates, the LT50 values at a concentration of 3 x 10(6) OBs ml(-1) were calculated as 35.6 and 41.7 h, respectively. The LT(50) values of third instars for SpliNPV-M2 and SpliNPV-TR1 were 147.4 and 160.5 h, respectively, at a dose of 3000 OBs/larva and 145.4 and 152.4 h, respectively, for the same isolates at a dose of 20,000 OBs/larva. On the other hand, Helicoverpa armigera (Hübner) and Agrotis ipsilon (Hufnagel) revealed a lack of lethality of the SpliNPV-TR1 isolate.
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Affiliation(s)
- Umut Toprak
- University of Ankara, Faculty of Agriculture, Department of Plant Protection, 06110 Dişkapi, Ankara, Turkey.
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18
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Cory JS, Green BM, Paul RK, Hunter-Fujita F. Genotypic and phenotypic diversity of a baculovirus population within an individual insect host. J Invertebr Pathol 2005; 89:101-11. [PMID: 15876438 DOI: 10.1016/j.jip.2005.03.008] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2004] [Revised: 03/07/2005] [Accepted: 03/25/2005] [Indexed: 10/25/2022]
Abstract
It is becoming increasingly apparent that many pathogen populations, including those of insects, show high levels of genotypic variation. Baculoviruses are known to be highly variable, with isolates collected from the same species in different geographical locations frequently showing genetic variation and differences in their biology. More recent studies at smaller scales have also shown that virus DNA profiles from individual larvae can show polymorphisms within and between populations of the same species. Here, we investigate the genotypic and phenotypic variation of an insect baculovirus infection within a single insect host. Twenty four genotypically distinct nucleopolyhedrovirus (NPV) variants were isolated from an individual pine beauty moth, Panolis flammea, caterpillar by in vivo cloning techniques. No variant appeared to be dominant in the population. The PaflNPV variants have been mapped using three restriction endonucleases and shown to contain three hypervariable regions containing insertions of 70-750 bp. Comparison of seven of these variants in an alternative host, Mamestra brassicae, demonstrated that the variants differed significantly in both pathogenicity and speed of kill. The generation and maintenance of pathogen heterogeneity are discussed.
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Affiliation(s)
- Jenny S Cory
- Molecular Ecology and Biocontrol Group, NERC Centre for Ecology and Hydrology, Mansfield Road, Oxford OX1 3SR, UK.
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19
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Lauzon HAM, Jamieson PB, Krell PJ, Arif BM. Gene organization and sequencing of the Choristoneura fumiferana defective nucleopolyhedrovirus genome. J Gen Virol 2005; 86:945-961. [PMID: 15784888 DOI: 10.1099/vir.0.80489-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Two distinct nucleopolyhedrovirus species of the eastern spruce budworm, Choristoneura fumiferana, exist in a symbiont-like relationship. C. fumiferana defective nucleopolyhedrovirus (CfDEFNPV) only infects C. fumiferana larvae per os in the presence of C. fumiferana nucleopolyhedrovirus Ireland strain (CfMNPV), but is infective when injected into the haemolymph. CfDEFNPV synergizes CfMNPV in per os infections and CfMNPV is always the predominant progeny. This study was undertaken to report the genomic makeup and organization of CfDEFNPV in an attempt to identify its defect and understand its synergistic role. The genome was mapped, sequenced, characterized and compared to other baculoviruses. The CfDEFNPV genome was 131 160 nt long with 149 putative open reading frames (ORFs) and a G+C content of 45·8 mol%. Homologues of all 62 conserved lepidopteran baculovirus genes were found including those implicated in per os infectivity, p74, per os infectivity factor (pif) and pif-2. Although no obvious deletions were observed to explain the defect, two ORFs, Cfdef79 and Cfdef99 (inhibitor of apoptosis-4), contained potential deletions. Cfdef50 (late expression factor-10)/Cfdef51 (vp1054) and Cfdef76/Cfdef77 (telokin-like protein) had large overlaps and a potential homologue to ac105/he65 was split. Four baculovirus repeat ORFs were present, as were two unique genes, but no enhancins were identified. CfDEFNPV contained 13 homologous regions, each with one to five palindromes. Comparison with fully sequenced baculovirus genomes identified CfDEFNPV as a group I NPV with the closest average amino acid identity to Epiphyas postvittana NPV, followed by Orgyia pseudotsugata MNPV and CfMNPV, with its closest matches being to individual Anticarsia gemmatalis MNPV gene sequences.
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Affiliation(s)
- Hilary A M Lauzon
- Canadian Forest Service, Great Lakes Forestry Centre, 1219 Queen Street East, Sault Ste Marie, Ontario, Canada, P6A 2E5
| | - Peter B Jamieson
- Canadian Forest Service, Great Lakes Forestry Centre, 1219 Queen Street East, Sault Ste Marie, Ontario, Canada, P6A 2E5
| | - Peter J Krell
- Department of Microbiology, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Basil M Arif
- Canadian Forest Service, Great Lakes Forestry Centre, 1219 Queen Street East, Sault Ste Marie, Ontario, Canada, P6A 2E5
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20
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Li L, Li Q, Willis LG, Erlandson M, Theilmann DA, Donly C. Complete comparative genomic analysis of two field isolates of Mamestra configurata nucleopolyhedrovirus-A. J Gen Virol 2005; 86:91-105. [PMID: 15604435 DOI: 10.1099/vir.0.80488-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A second genotype of Mamestra configurata nucleopolyhedrovirus-A (MacoNPV-A), variant 90/4 (v90/4), was identified due to its altered restriction endonuclease profile and reduced virulence for the host insect, M. configurata, relative to the archetypal genotype, MacoNPV-A variant 90/2 (v90/2). To investigate the genetic differences between these two variants, the genome of v90/4 was sequenced completely. The MacoNPV-A v90/4 genome is 153 656 bp in size, 1404 bp smaller than the v90/2 genome. Sequence alignment showed that there was 99·5 % nucleotide sequence identity between the genomes of v90/4 and v90/2. However, the v90/4 genome has 521 point mutations and numerous deletions and insertions when compared to the genome of v90/2. Gene content and organization in the genome of v90/4 is identical to that in v90/2, except for an additional bro gene that is found in the v90/2 genome. The region between hr1 and orf31 shows the greatest divergence between the two genomes. This region contains three bro genes, which are among the most variable baculovirus genes. These results, together with other published data, suggest that bro genes may influence baculovirus genome diversity and may be involved in recombination between baculovirus genomes. Many ambiguous residues found in the v90/4 sequence also reveal the presence of 214 sequence polymorphisms. Sequence analysis of cloned HindIII fragments of the original MacoNPV field isolate that the 90/4 variant was derived from indicates that v90/4 is an authentic variant and may represent approximately 25 % of the genotypes in the field isolate. These results provide evidence of extensive sequence variation among the individual genomes comprising a natural baculovirus outbreak in a continuous host population.
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Affiliation(s)
- Lulin Li
- Pacific Agri-Food Research Centre, AAFC, Summerland, BC, Canada
| | - Qianjun Li
- Saskatoon Research Centre, AAFC-Saskatoon, SK, Canada
| | - Leslie G Willis
- Pacific Agri-Food Research Centre, AAFC, Summerland, BC, Canada
| | | | | | - Cam Donly
- Southern Crop Protection and Food Research Centre, AAFC, London, ON, Canada
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21
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Dieu BTM, Marks H, Siebenga JJ, Goldbach RW, Zuidema D, Duong TP, Vlak JM. Molecular epidemiology of white spot syndrome virus within Vietnam. J Gen Virol 2004; 85:3607-3618. [PMID: 15557233 DOI: 10.1099/vir.0.80344-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
White spot syndrome virus (WSSV), the sole member of the virus family Nimaviridae, is a large double-stranded DNA virus that infects shrimp and other crustaceans. By alignment of three completely sequenced isolates originating from Taiwan (WSSV-TW), China (WSSV-CN) and Thailand (WSSV-TH), the variable loci in the genome were mapped. The variation suggests the spread of WSSV from a common ancestor originating from either side of the Taiwan Strait to Thailand, but support for this hypothesis through analysis of geographical intermediates is sought. RFLP analysis of eight Vietnamese WSSV isolates, of which six were collected along the central coast (VN-central) and two along the south coast (VN-south), showed apparent sequence variation in the variable loci identified previously. These loci were characterized in detail by PCR amplification, cloning and sequencing. Relative to WSSV-TW, all VN-central isolates showed a approximately 8.5 kb deletion in the major variable region ORF23/24, whereas the VN-south isolates contain a deletion of approximately 11.5 or approximately 12.2 kb, compared to a approximately 1.2 or approximately 13.2 kb deletion in WSSV-CN and WSSV-TH, respectively. The minor variable region ORF14/15 showed deletions of various sizes compared with WSSV-TH for all eight VN isolates. The data suggest that the VN isolates and WSSV-TH have a common lineage, which branched off from WSSV-TW and WSSV-CN early on, and that WSSV entered Vietnam by multiple introductions. A model is presented for the spread of WSSV from either side of the Taiwan Strait into Vietnam based on the gradually increasing deletions of both 'variable regions'. The number and order of repeat units within ORF75 and ORF125 appeared to be suitable markers to study regional spread of WSSV.
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Affiliation(s)
- Bui Thi Minh Dieu
- Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands
- Biotechnological Research and Development Institute, Can Tho University, 3/2 Street Nr 1, 008471 Can Tho City, Vietnam
| | - Hendrik Marks
- Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands
| | - J Joukje Siebenga
- Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands
| | - Rob W Goldbach
- Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands
| | - Douwe Zuidema
- Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands
| | - Tran Phuoc Duong
- Biotechnological Research and Development Institute, Can Tho University, 3/2 Street Nr 1, 008471 Can Tho City, Vietnam
| | - Just M Vlak
- Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands
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22
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Simón O, Williams T, López-Ferber M, Caballero P. Genetic structure of a Spodoptera frugiperda nucleopolyhedrovirus population: high prevalence of deletion genotypes. Appl Environ Microbiol 2004; 70:5579-88. [PMID: 15345446 PMCID: PMC520846 DOI: 10.1128/aem.70.9.5579-5588.2004] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A Nicaraguan field isolate (SfNIC) of Spodoptera frugiperda nucleopolyhedrovirus was purified by plaque assay on Sf9 cells. Nine distinct genotypes, A to I, were identified by their restriction endonuclease profiles. Variant SfNIC-B was selected as the standard because its restriction profile corresponded to that of the wild-type isolate. Physical maps were generated for each of the variants. The differences between variants and the SfNIC-B standard were confined to the region between map units 9 and 32.5. This region included PstI-G, PstI-F, PstI-L, PstI-K and EcoRI-L fragments. Eight genotypes presented a deletion in their genome compared with SfNIC-B. Occlusion body-derived virions of SfNIC-C, -D and -G accounted for 41% of plaque-purified clones. These variants were not infectious per os but retained infectivity by injection into S. frugiperda larvae. Median 50% lethal concentration values for the other cloned genotypes were significantly higher than that of the wild type. The variants also differed in their speed of kill. Noninfectious variants SfNIC-C and -D lacked the pif and pif-2 genes. Infectivity was restored to these variants by plasmid rescue with a plasmid comprising both pif and pif-2. Transcription of an SfNIC-G gene was detected by reverse transcription-PCR in insects, but no fatal disease developed. Transcription was not detected in SfNIC-C or -D-inoculated larvae. We conclude that the SfNIC population presents high levels of genetic diversity, localized to a 17-kb region containing pif and pif-2, and that interactions among complete and deleted genotypic variants will likely influence the capacity of this virus to control insect pests.
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Affiliation(s)
- Oihane Simón
- Departamento de Producción Agraria, Universidad Pública de Navarra, 31006 Pamplona, Spain.
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23
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Slack JM, Ribeiro BM, de Souza ML. The gp64 locus of Anticarsia gemmatalis multicapsid nucleopolyhedrovirus contains a 3′ repair exonuclease homologue and lacks v-cath and ChiA genes. J Gen Virol 2004; 85:211-219. [PMID: 14718636 DOI: 10.1099/vir.0.19617-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Anticarsia gemmatalis multicapsid nucleopolyhedrovirus (AgMNPV) is one of the most successful biological insecticides. In this study, we cloned and sequenced a 12.5 kbp BamHI-D restriction endonuclease fragment of the AgMNPV isolate 2D genome that includes the gp64 gene. We compared this highly conserved region with that of other baculoviruses. AgMNPV contained two genes, p22.2 and v-trex, in common with Choristoneura fumiferana MNPV (CfMNPV) that were not present in other baculoviruses. The v-trex gene has homology to a eukaryotic 3' repair exonuclease and appears to have been acquired from an invertebrate host. The v-trex gene product has the potential to be involved in virus recombination or UV-light tolerance. Multigene phylogenetic analysis suggested that AgMNPV is most closely related to Orgyia pseudotsugata MNPV (OpMNPV). AgMNPV differed from other group I NPVs in that ChiA and v-cath gene homologues were missing from the region downstream of the gp64 gene. Proteinase assays and genetic probes suggest the v-cath gene is absent from AgMNPV.
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Affiliation(s)
- Jeffrey M Slack
- Insect Biocontrol Laboratory, USDA, Beltsville, MD 20852, USA
| | - Bergmann M Ribeiro
- Departamento de Biologia Cellular, Universidade de Brasília, CEP 70910-900 Brasília DF, Brazil
| | - Marlinda Lobo de Souza
- Embrapa Recursos Genéticos e Biotecnologia Parque Estação Biológica, CEP 70770-900 Brasília-DF, Brazil
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24
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Cory JS, Myers JH. The Ecology and Evolution of Insect Baculoviruses. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2003. [DOI: 10.1146/annurev.ecolsys.34.011802.132402] [Citation(s) in RCA: 228] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jenny S. Cory
- Molecular Ecology and Biocontrol Group, NERC Center for Ecology and Hydrology, Mansfield Road, Oxford, United Kingdom, OX1 3SR;
- Center for Biodiversity Research, Departments of Zoology and Agricultural Science, University of British Columbia, Vancouver, Canada, V6T 1Z4;
| | - Judith H. Myers
- Molecular Ecology and Biocontrol Group, NERC Center for Ecology and Hydrology, Mansfield Road, Oxford, United Kingdom, OX1 3SR;
- Center for Biodiversity Research, Departments of Zoology and Agricultural Science, University of British Columbia, Vancouver, Canada, V6T 1Z4;
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25
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Jehle JA. The expansion of a hypervariable, non-hr ori-like region in the genome of Cryptophlebia leucotreta granulovirus provides in vivo evidence for the utilization of baculovirus non-hr oris during replication. J Gen Virol 2002; 83:2025-2034. [PMID: 12124467 DOI: 10.1099/0022-1317-83-8-2025] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this report a naturally occurring hypervariable region within the genome of different Cryptophlebia leucotreta granulovirus genotypes is characterized. The region consists of a stretch of direct repeats, short palindromes and an unusual AT-rich region. Although the organization of these repeat sequences is unique to baculoviruses, it has the structural features of a 'non-hr' origin of DNA replication (ori). Restriction analysis and Southern hybridization revealed that this region is expanded during virus replication. Sequence comparison of different isolated genotypes indicated that the expansion is caused by concatenation of short repeats within the region or by concatenation of the complete region. These findings indicate that the expansion of non-hr origin-like regions is not restricted to defective-interfering particles, as was found previously for baculoviruses propagated in cell culture. Moreover, it appears that non-hr complexity contributes to the natural heterogeneity and genetic plasticity of baculovirus genomes. Also, circumstantial evidence is discussed that hr oris might have developed from internal rearrangement and multiplication of a non-hr ori during baculovirus evolution.
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Affiliation(s)
- Johannes A Jehle
- State Education and Research Center for Agriculture, Viticulture and Horticulture (SLFA), Section Biotechnological Crop Protection, Breitenweg 71, 67435 Neustadt an der Weinstraße, Germany1
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26
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Chen X, Zhang WJ, Wong J, Chun G, Lu A, McCutchen BF, Presnail JK, Herrmann R, Dolan M, Tingey S, Hu ZH, Vlak JM. Comparative analysis of the complete genome sequences of Helicoverpa zea and Helicoverpa armigera single-nucleocapsid nucleopolyhedroviruses. J Gen Virol 2002; 83:673-684. [PMID: 11842262 DOI: 10.1099/0022-1317-83-3-673] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The complete nucleotide sequence of Helicoverpa zea single-nucleocapsid nucleopolyhedrovirus (HzSNPV) has been determined (130869 bp) and compared to the nucleotide sequence of Helicoverpa armigera (Ha) SNPV. These two genomes are very similar in their nucleotide (97% identity) and amino acid (99% identity) sequences. The coding regions are much more conserved than the non-coding regions. In HzSNPV/HaSNPV, the 63 open reading frames (ORFs) present in all baculoviruses sequenced so far are much more conserved than other ORFs. HzSNPV has four additional small ORFs compared with HaSNPV, one of these (Hz42) being in a correct transcriptional context. The major differences between HzSNPV and HaSNPV are found in the sequence and organization of the homologous regions (hrs) and the baculovirus repeat ORFs (bro genes). The sequence identity between the HzSNPV and HaSNPV hrs ranges from 90% (hr1) to almost 100% (hr5) and the hrs differ in the presence/absence of one or more type A and/or B repeats. The three HzSNPV bro genes differ significantly from those in HaSNPV and may have been acquired independently in the ancestral past. The sequence data suggest strongly that HzSNPV and HaSNPV are variants of the same virus species, a conclusion that is supported by the physical and biological data.
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Affiliation(s)
- Xinwen Chen
- Joint Lab of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, People's Republic of China2
- Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands1
| | - W-J Zhang
- Dupont Agricultural Products, Stine-Haskell Research Center, E.I. du Pont de Nemours and Co., PO Box 30, Newark, DE 19714-0030, USA3
| | - J Wong
- Dupont Agricultural Products, Stine-Haskell Research Center, E.I. du Pont de Nemours and Co., PO Box 30, Newark, DE 19714-0030, USA3
| | - G Chun
- Dupont Agricultural Products, Stine-Haskell Research Center, E.I. du Pont de Nemours and Co., PO Box 30, Newark, DE 19714-0030, USA3
| | - A Lu
- Dupont Agricultural Products, Stine-Haskell Research Center, E.I. du Pont de Nemours and Co., PO Box 30, Newark, DE 19714-0030, USA3
| | - B F McCutchen
- Dupont Agricultural Products, Stine-Haskell Research Center, E.I. du Pont de Nemours and Co., PO Box 30, Newark, DE 19714-0030, USA3
| | - J K Presnail
- Dupont Agricultural Products, Stine-Haskell Research Center, E.I. du Pont de Nemours and Co., PO Box 30, Newark, DE 19714-0030, USA3
| | - R Herrmann
- Dupont Agricultural Products, Stine-Haskell Research Center, E.I. du Pont de Nemours and Co., PO Box 30, Newark, DE 19714-0030, USA3
| | - M Dolan
- Dupont Agricultural Products, Stine-Haskell Research Center, E.I. du Pont de Nemours and Co., PO Box 30, Newark, DE 19714-0030, USA3
| | - S Tingey
- Dupont Agricultural Products, Stine-Haskell Research Center, E.I. du Pont de Nemours and Co., PO Box 30, Newark, DE 19714-0030, USA3
| | - Z H Hu
- Joint Lab of Invertebrate Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, People's Republic of China2
| | - Just M Vlak
- Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands1
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Hayakawa T, Ko R, Okano K, Seong SI, Goto C, Maeda S. Sequence analysis of the Xestia c-nigrum granulovirus genome. Virology 1999; 262:277-97. [PMID: 10502508 DOI: 10.1006/viro.1999.9894] [Citation(s) in RCA: 166] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The nucleotide sequence of the Xestia c-nigrum granulovirus (XcGV) genome was determined and found to comprise 178,733 bases with a G+C content of 40.7%. It contained 181 putative genes of 150 nucleotides or greater that showed minimal overlap. Eighty-four of these putative genes, which collectively accounted for 43% of the genome, are homologs of genes previously identified in the Autographa californica multinucleocapsid nucleopolyhedrovirus (AcMNPV) genome. These homologs showed on average 33% amino acid sequence identity to those from AcMNPV. Several genes reported to have major roles in AcMNPV biology including ie-2, gp64, and egt were not found in the XcGV genome. However, open reading frames with homology to DNA ligase, two DNA helicases (one similar to a yeast mitochondrial helicase and the other to a putative AcMNPV helicase), and four enhancins (virus enhancing factors) were found. In addition, several ORFs are repeated; there are 7 genes related to AcMNPV orf2, 4 genes related to AcMNPV orf145/150, and a number of repeated genes unique to XcGV. Eight major repeated sequences (XcGV hrs) that are similar to sequences found in the Trichoplusia ni GV genome (TnGV) were found.
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Affiliation(s)
- T Hayakawa
- Department of Entomology, University of California, Davis, One Shields Avenue, Davis, California, 95616, USA
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Muñoz D, Murillo R, Krell PJ, Vlak JM, Caballero P. Four genotypic variants of a Spodoptera exigua Nucleopolyhedrovirus (Se-SP2) are distinguishable by a hypervariable genomic region. Virus Res 1999; 59:61-74. [PMID: 10854166 DOI: 10.1016/s0168-1702(98)00125-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Four genotypes named SP2A, SP2B, SP2C and SP2D were obtained in vivo by infecting S. exigua larvae with limiting dilutions of the Spanish field isolate Spodoptera exigua Nucleopolyhedrovirus (Se-SP2) of SeMNPV. The cloning of variants SP2A, SP2B and SP2C took 1, 6, and 3 passages, respectively, before the DNA profiles showed all bands in equimolar concentrations, and they remained constant for at least six further passages indicating the stability of their genotypes. The SP2D variant isolation took over ten passages and it was genetically less stable. Physical maps of their genomes were constructed for the restriction enzymes BamHI, BglII, PstI, and XbaI. The region between 8-10 m.u. was highly variable and characteristic of each cloned genotype and, hence, can be used as RFLP markers for all four genotypic variants. This region, included in the PstI-MB fragment, was cloned and sequenced showing that all the Se-SP2 variants contained a homologous region (hr) with a variable number of 98 bp sequences tandemly repeated, which were used to distinguish genotypic variants from each other. The biological activity of the genotypic variants SP2A, SP2B, and SP2C when compared in terms of LD50 and LT50, were not significantly different. However, the SP2D genotypic variant was found to be significantly less infective (higher LD50). The emergence of new genotypes in the Se-SP2 field populations is discussed.
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Affiliation(s)
- D Muñoz
- Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona, Spain
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Moscardi F. Assessment of the application of baculoviruses for control of Lepidoptera. ANNUAL REVIEW OF ENTOMOLOGY 1999; 44:257-289. [PMID: 15012374 DOI: 10.1146/annurev.ento.44.1.257] [Citation(s) in RCA: 274] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Baculoviruses, among other insect viruses, are regarded as safe and selective bioinsecticides, restricted to invertebrates. They have been used worldwide against many insect pests, mainly Lepidoptera. Their application as microbial pesticides, however, has not met their potential to control pests in crops, forests, and pastures, with the exception of the nuclear polyhedrosis virus of the soybean caterpillar (Anticarsia gemmatalis), which is used on approximately 1 million ha annually in Brazil. Problems that have limited expansion of baculovirus use include narrow host range, slow killing speed, technical and economical difficulties for in vitro commercial production, timing of application based on frequent host population monitoring, variability of field efficacy due to climatic conditions, and farmers' attitudes toward pest control, which have been based on application of fast-killing chemical insecticides. Farmer education regarding use of biological insecticides and their characteristics is considered one of the major actions necessary for increased use of baculoviruses. Strategies to counteract some of the limitations of baculoviruses, especially their slow killing activity, have been investigated and are promising. These include the use of chemical or biological substances added to virus formulations and genetic engineering of the viruses themselves to express insect toxins or hormones. Such strategies can enhance viral activity and increase speed of kill as well as reduce larval feeding activity. The use of baculoviruses against Lepidoptera is reviewed, with the utilization of the nuclear polyhedrosis virus of A. gemmatalis in Brazil serving as a case-study.
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Affiliation(s)
- F Moscardi
- Embrapa-National Soybean Research Center, C postal 231, Londrina, PR 86001-970, Brazil.
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Naturally occurring deletion mutants are parasitic genotypes in a wild-type nucleopolyhedrovirus population of spodoptera exigua. Appl Environ Microbiol 1998; 64:4372-7. [PMID: 9797293 PMCID: PMC106655 DOI: 10.1128/aem.64.11.4372-4377.1998] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A wild-type nucleopolyhedrovirus (NPV) isolate from Spodoptera exigua from Florida (Se-US2) is a variant of the SeMNPV type strain since it has a unique DNA profile but is closely related to other known geographical isolates of SeMNPV. It consists of several genotypic variants, of which seven were identified in a Se-US2 virus stock by a modification of the in vivo cloning method developed by Smith and Crook (Virology 166:240-244, 1988). The US2A variant was the most prevalent genotype, and it was designated the prototype Se-US2 variant, while four of the variants (US2B, US2D, US2F, and US2H) were found at low frequency. US2C and US2E were also very abundant, and their diagnostic bands were easily observed in wild-type isolate restriction endonuclease patterns. The analysis of each variant, compared to the prototype US2A, showed that US2B and US2H presented minor differences, while US2D and US2F contained slightly larger insertions or deletions. Variants US2C and US2E contained major deletions of 21.1 and 14 kb, respectively, mapping at the same genomic region (between 14.5 and 30.2 map units [m.u.] and between 12.8 and 23 m.u., respectively). This is the first report of such deletion mutants in a natural baculovirus population. Variants US2A, US2B, US2D, US2F, and US2H were isolated as pure genotypes, but we failed to clone US2C and US2E in vivo. When these two variants appeared without apparent contamination with any other variant, they lost their pathogenicity for Spodoptera exigua larvae. A further biological characterization showed evidence that these two naturally occurring deletion mutants act as parasitic genotypes in the virus population. Bioassay data also demonstrated that pure US2A is significantly more pathogenic against second-instar S. exigua larvae than the wild-type isolate. The need for precise genotypic characterization of a baculovirus prior to its development as a bioinsecticide is discussed.
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Pearson MN, Rohrmann GF. Splicing is required for transactivation by the immediate early gene 1 of the Lymantria dispar multinucleocapsid nuclear polyhedrosis virus. Virology 1997; 235:153-65. [PMID: 9300047 DOI: 10.1006/viro.1997.8687] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A region of the Lymantria disper multinucleocapsid nuclear polyhedrosis virus (LdMNPV) genome containing the homolog of the baculovirus ie-1 gene was identified using a series of overlapping cosmids and individual plasmids in a transient transcriptional expression assay. Sequence analysis of the active region identified two ORFs, one of which is 32% identical to AcMNPV ORF141 (ie-0) and contains a putative splice donor site and the other of which is 29% identical to AcMNPV ie-1 and contains a highly conserved splice acceptor consensus sequences. Plasmids containing the LdMNPV ORF141 and ie-1 regions were able to stimulate expression of a GUS reporter gene, while plasmids containing the ie-1 region alone were inactive, suggesting that only the spliced, IE-0 form of the gene product is an active transactivator. Primer extension analysis confirmed the presence of spliced ie-0 mRNA transcripts starting at 6 hr and continuing throughout the time course of viral infection of the L dispar cell line Ld652Y. Using a plasmid containing the ie-0 spliced form of the gene as a transactivator, hr4, one of the eight homologous regions of LdMNPV, was shown to act as a transcriptional enhancer. In contrast, a reporter plasmid containing the AcMNPV hr5 enhancer did not show increased activity when cotransfected with LdMNPV ie-0, suggesting that these enhancer sequences are viral specific. In a transient replication assay system. LdMNPV ie-0 acted as an essential replication gene, but LdMNPV ie-1 was inactive. These results indicate that splicing is required to obtain an active gene product in LdMNPV in the Ld652Y cell line.
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Affiliation(s)
- M N Pearson
- Department of Microbiology, Oregon State University, Corvallis 97331-7301, USA.
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Abstract
Advances in the use of molecular techniques-particularly for virus identification, the investigation of latency and the infection process, plus the development of a theoretical framework containing a higher degree of biological realism-have pushed baculovirus ecology forward in the past few years. This has created a scenario in which many hitherto intractable questions about the behaviour of natural and genetically modified baculoviruses can now be addressed.
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Affiliation(s)
- J S Cory
- Ecology and Biocontrol Group, National Environmental Research Council, Institute of Virology and Environmental Microbiology, Oxford, UK.
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Ahrens CH, Russell RL, Funk CJ, Evans JT, Harwood SH, Rohrmann GF. The sequence of the Orgyia pseudotsugata multinucleocapsid nuclear polyhedrosis virus genome. Virology 1997; 229:381-99. [PMID: 9126251 DOI: 10.1006/viro.1997.8448] [Citation(s) in RCA: 190] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The nucleotide sequence of the Orgyia pseudotsugata multinucleocapsid nuclear polyhedrosis virus (OpMNPV) genome was completed and analyzed. It is composed of 131,990 bases with a G + C content of 55% and contains 152 putative genes of 150 nucleotides or greater. Major differences in gene content and arrangement between OpMNPV and the Autographa californica MNPV were found. These include the presence in OpMNPV of three complete iap gene homologs, two conotoxin gene homologs, two protein tyrosine phosphatase homologs, and genes encoding homologs of dUTPase and the large and small subunits of ribonucleotide reductase. Seven major intergenic repeated regions were identified. Five of these are homologous regions that are related to similar regions from other baculoviruses.
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Affiliation(s)
- C H Ahrens
- Department of Agricultural Chemistry, Oregon State University, Corvallis 97331-7301, USA
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