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Kumar Pradhan S, Morrow JL, Sharpe SR, Karuppannasamy A, Ramasamy E, Bynakal S, Maligeppagol M, Ramasamy A, Riegler M. RNA virus diversity and prevalence in field and laboratory populations of melon fly throughout its distribution. J Invertebr Pathol 2024; 204:108117. [PMID: 38679365 DOI: 10.1016/j.jip.2024.108117] [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: 12/19/2023] [Revised: 04/17/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Insects have a rich diversity of RNA viruses that can either cause acute infections or persist in host populations without visible symptoms. The melon fly, Zeugodacus cucurbitae (Tephritidae) causes substantial economic losses through infestation of diverse cucurbit and other crops. Of Indomalayan origin, it is now established in many tropical regions of the world. The virome diversity of Z. cucurbitae is largely unknown across large parts of its distribution, including the Indian subcontinent. We have analysed three transcriptomes each of one field-collected and one laboratory-reared Z. cucurbitae population from Bangalore (India) and discovered genomes of ten putative RNA viruses: two sigmaviruses, one chimbavirus, one cripavirus, one noda-like virus, one nora virus, one orbivirus, one partiti-like virus, one sobemovirus and one toti-like virus. Analysis of the only available host genome of a Hawaiian Z. cucurbitae population did not detect host genome integration of the detected viruses. While all ten viruses were found in the Bangalore field population only seven were detected in the laboratory population, indicating that these seven may cause persistent covert infections. Using virus-specific RNA-dependent RNA polymerase gene primers, we detected nine of the RNA viruses with an overall low variant diversity in some but not all individual flies from four out of five Indian regions. We then screened 39 transcriptomes of Z. cucurbitae laboratory populations from eastern Asia (Guangdong, Hainan, Taiwan) and the Pacific region (Hawaii), and detected seven of the ten virus genomes. We found additional genomes of a picorna-like virus and a negev-like virus. Hawaii as the only tested population from the fly's invasive range only had one virus. Our study provides evidence of new and high RNA virus diversity in Indian populations within the original range of Z. cucurbitae, as well as the presence of persistent covert infections in laboratory populations. It builds the basis for future research of tephritid-associated RNA viruses, including their host effects, epidemiology and application potential in biological control.
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Affiliation(s)
- Sanjay Kumar Pradhan
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia; ICAR- Indian Institute of Horticultural Research, Hesaraghatta Lake, Bengaluru 560089, Karnataka, India; Department of Agricultural Entomology, University of Agricultural Sciences, Bengaluru 560065, Karnataka, India.
| | - Jennifer L Morrow
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Stephen R Sharpe
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Ashok Karuppannasamy
- ICAR- Indian Institute of Horticultural Research, Hesaraghatta Lake, Bengaluru 560089, Karnataka, India; Tamil Nadu Agricultural University, Coimbatore 641003, Tamil Nadu, India; Tata Institute for Genetics and Society, Bengaluru 560065, Karnataka, India.
| | - Ellango Ramasamy
- Computational and Mathematical Biology Centre (CMBC), THSTI- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India.
| | - Shivanna Bynakal
- Department of Agricultural Entomology, University of Agricultural Sciences, Bengaluru 560065, Karnataka, India.
| | - Manamohan Maligeppagol
- ICAR- Indian Institute of Horticultural Research, Hesaraghatta Lake, Bengaluru 560089, Karnataka, India.
| | - Asokan Ramasamy
- ICAR- Indian Institute of Horticultural Research, Hesaraghatta Lake, Bengaluru 560089, Karnataka, India.
| | - Markus Riegler
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
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2
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Sun K, Fu K, Hu T, Shentu X, Yu X. Leveraging insect viruses and genetic manipulation for sustainable agricultural pest control. PEST MANAGEMENT SCIENCE 2024; 80:2515-2527. [PMID: 37948321 DOI: 10.1002/ps.7878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/16/2023] [Accepted: 11/11/2023] [Indexed: 11/12/2023]
Abstract
The potential of insect viruses in the biological control of agricultural pests is well-recognized, yet their practical application faces obstacles such as host specificity, variable virulence, and resource scarcity. High-throughput sequencing (HTS) technologies have significantly advanced our capabilities in discovering and identifying new insect viruses, thereby enriching the arsenal for pest management. Concurrently, progress in reverse genetics has facilitated the development of versatile viral expression vectors. These vectors have enhanced the specificity and effectiveness of insect viruses in targeting specific pests, offering a more precise approach to pest control. This review provides a comprehensive examination of the methodologies employed in the identification of insect viruses using HTS. Additionally, it explores the domain of genetically modified insect viruses and their associated challenges in pest management. The adoption of these cutting-edge approaches holds great promise for developing environmentally sustainable and effective pest control solutions. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Kai Sun
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Kang Fu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Tao Hu
- Zhejinag Seed Industry Group Xinchuang Bio-breeding Co., Ltd., Hangzhou, China
| | - Xuping Shentu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
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Nikulin SL, Hesketh-Best PJ, Mckeown DA, Spivak M, Schroeder DC. A semi-automated and high-throughput approach for the detection of honey bee viruses in bee samples. PLoS One 2024; 19:e0297623. [PMID: 38483922 PMCID: PMC10939240 DOI: 10.1371/journal.pone.0297623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/10/2024] [Indexed: 03/17/2024] Open
Abstract
Deformed wing virus (DWV) was first detected in dead honey bees in 1982 but has been in honey bees for at least 300 years. Due to its high prevalence and virulence, they have been linked with the ongoing decline in honey bee populations worldwide. A rapid, simple, semi-automated, high-throughput, and cost-effective method of screening colonies for viruses would benefit bee research and the beekeeping industry. Here we describe a semi-automated approach that combines an RNA-grade liquid homogenizer followed by magnetic bead capture for total virus nucleic acid extraction. We compare it to the more commonly applied nucleic acid column-based purification method and use qPCR plus Oxford Nanopore Technologies sequencing to evaluate the accuracy of analytical results for both methods. Our results showed high reproducibility and accuracy for both approaches. The semi-automated method described here allows for faster screening of viral loads in units of 96 samples at a time. We developed this method to monitor viral loads in honey bee colonies, but it could be easily applied for any PCR or genomic-based screening assays.
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Affiliation(s)
- Sofia Levin Nikulin
- Department of Entomology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Poppy J. Hesketh-Best
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Dean A. Mckeown
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Marla Spivak
- Department of Entomology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Declan C. Schroeder
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
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4
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An X, Gu Q, Wang J, Chang T, Zhang W, Wang JJ, Niu J. Insect-specific RNA virus affects the stylet penetration activity of brown citrus aphid (Aphis citricidus) to facilitate its transmission. INSECT SCIENCE 2024; 31:255-270. [PMID: 37358052 DOI: 10.1111/1744-7917.13242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 06/27/2023]
Abstract
Sap-sucking insects often transmit plant viruses but also carry insect viruses, which infect insects but not plants. The impact of such insect viruses on insect host biology and ecology is largely unknown. Here, we identified a novel insect-specific virus carried by brown citrus aphid (Aphis citricidus), which we tentatively named Aphis citricidus picornavirus (AcPV). Phylogenetic analysis discovered a monophyletic cluster with AcPV and other unassigned viruses, suggesting that these viruses represent a new family in order Picornavirales. Systemic infection with AcPV triggered aphid antiviral immunity mediated by RNA interference, resulting in asymptomatic tolerance. Importantly, we found that AcPV was transmitted horizontally by secretion of the salivary gland into the feeding sites of plants. AcPV influenced aphid stylet behavior during feeding and increased the time required for intercellular penetration, thus promoting its transmission among aphids with plants as an intermediate site. The gene expression results suggested that this mechanism was linked with transcription of salivary protein genes and plant defense hormone signaling. Together, our results show that the horizontal transmission of AcPV in brown citrus aphids evolved in a manner similar to that of the circulative transmission of plant viruses by insect vectors, thus providing a new ecological perspective on the activity of insect-specific viruses found in aphids and improving the understanding of insect virus ecology.
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Affiliation(s)
- Xin An
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Qiaoying Gu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Jing Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Tengyu Chang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Wei Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Science, Southwest University, Chongqing, China
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Poimala A, Vainio E. Discovery and Identification of Viruses Infecting Oomycetes. Methods Mol Biol 2024; 2732:45-65. [PMID: 38060117 DOI: 10.1007/978-1-0716-3515-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
This chapter describes protocols suitable for the detection and identification of RNA viruses infecting oomycetes (so-called water molds of Kingdom Heterokonta, Stramenopila), focusing on species of Phytophthora and exemplified by P. fragariae. The protocol includes laboratory procedures for oomycete cultivation and total RNA extraction from harvested mycelia, followed by instructions on suitable parameters given for sequencing companies on ribosomal RNA depletion, cDNA library preparation, and total RNA-sequencing (RNA-Seq). We also describe the bioinformatics steps needed for de novo assembly of raw reads into contigs, removal of host-associated contigs, and virus identification by database searches, as well as host validation by RT-PCR. All steps are described using an exemplar RNA-Seq library containing a yet undescribed fusagravirus hosted by a P. fragariae isolate.
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Affiliation(s)
- Anna Poimala
- Natural Resources Institute Finland (Luke), Helsinki, Finland.
| | - Eeva Vainio
- Natural Resources Institute Finland (Luke), Helsinki, Finland
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6
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Damayo JE, McKee RC, Buchmann G, Norton AM, Ashe A, Remnant EJ. Virus replication in the honey bee parasite, Varroa destructor. J Virol 2023; 97:e0114923. [PMID: 37966226 PMCID: PMC10746231 DOI: 10.1128/jvi.01149-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/06/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE The parasitic mite Varroa destructor is a significant driver of worldwide colony losses of our most important commercial pollinator, the Western honey bee Apis mellifera. Declines in honey bee health are frequently attributed to the viruses that mites vector to honey bees, yet whether mites passively transmit viruses as a mechanical vector or actively participate in viral amplification and facilitate replication of honey bee viruses is debated. Our work investigating the antiviral RNA interference response in V. destructor demonstrates that key viruses associated with honey bee declines actively replicate in mites, indicating that they are biological vectors, and the host range of bee-associated viruses extends to their parasites, which could impact virus evolution, pathogenicity, and spread.
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Affiliation(s)
- James E. Damayo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Rebecca C. McKee
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Gabriele Buchmann
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- Institute of Plant Genetics, Heinrich-Heine University, Duesseldorf, Germany
| | - Amanda M. Norton
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- Academic Support Unit, Research and Advanced Instrumentation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Emily J. Remnant
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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Potter-Birriel JM, Pollio AR, Knott BD, Chunashvili T, Fung CK, Conte MA, Reinbold-Wasson DD, Hang J. Metagenomics analysis reveals presence of the Merida-like virus in Georgia. Front Microbiol 2023; 14:1258810. [PMID: 37901812 PMCID: PMC10602647 DOI: 10.3389/fmicb.2023.1258810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/27/2023] [Indexed: 10/31/2023] Open
Abstract
Arbovirus surveillance is fundamental for the discovery of novel viruses and prevention of febrile vector-borne illnesses. Vector-borne pathogens can rapidly expand and adapt in new geographic and environmental conditions. In this study, metagenomic surveillance was conducted to identify novel viruses in the Country of Georgia. A total of 521 mosquitoes were captured near a military training facility and pooled from species Culex pipiens (Linnaeus) (87%) and Aedes albopictus (Skuse) (13%). We decided to further analyze the Culex pipiens mosquitoes, due to the more extensive number of samples collected. Our approach was to utilize an unbiased total RNA-seq for pathogen discovery in order to explore the mosquito virome. The viral reads from this analysis were mostly aligned to Insect-specific viruses from two main families, the Iflaviridae; a positive-stranded RNA virus and the Rhabdoviridae; a negative- and single-stranded RNA virus. Our pathogen discovery analysis revealed viral reads aligning to the Merida-like virus Turkey (MERDLVT) strain among the Rhabdoviridae. To further validate this result, we conducted a BLAST sequence comparison analysis of our samples with the MERDLVT strain. Our positive samples aligned to the MERDLVT strain with 96-100% sequence identity and 99.7-100% sequence coverage. A bootstrapped maximum-likelihood phylogenetic tree was used to evaluate the evolutionary relationships among these positive pooled specimens with the (MERDLVT) strain. The Georgia samples clustered most closely with two strains from Turkey, the Merida-like virus KE-2017a isolate 139-1-21 and the Merida-like virus Turkey isolate P431. Collectively, these results show the presence of the MERDLVT strain in Georgia.
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Affiliation(s)
| | - Adam R. Pollio
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Brian D. Knott
- U.S. Army Medical Research Directorate – Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Tamar Chunashvili
- U.S. Army Medical Research Directorate – Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Christian K. Fung
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Matthew A. Conte
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Drew D. Reinbold-Wasson
- U.S. Army Medical Research Directorate – Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Jun Hang
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
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8
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Qi YH, Ye ZX, Zhang CX, Chen JP, Li JM. Diversity of RNA viruses in agricultural insects. Comput Struct Biotechnol J 2023; 21:4312-4321. [PMID: 37711182 PMCID: PMC10497914 DOI: 10.1016/j.csbj.2023.08.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023] Open
Abstract
Recent advancements in next-generation sequencing (NGS) technology and bioinformatics tools have revealed a vast array of viral diversity in insects, particularly RNA viruses. However, our current understanding of insect RNA viruses has primarily focused on hematophagous insects due to their medical importance, while research on the viromes of agriculturally relevant insects remains limited. This comprehensive review aims to address the gap by providing an overview of the diversity of RNA viruses in agricultural pests and beneficial insects within the agricultural ecosystem. Based on the NCBI Virus Database, over eight hundred RNA viruses belonging to 39 viral families have been reported in more than three hundred agricultural insect species. These viruses are predominantly found in the insect orders of Hymenoptera, Hemiptera, Thysanoptera, Lepidoptera, Diptera, Coleoptera, and Orthoptera. These findings have significantly enriched our understanding of RNA viral diversity in agricultural insects. While further virome investigations are necessary to expand our knowledge to more insect species, it is crucial to explore the biological roles of these identified RNA viruses within insects in future studies. This review also highlights the limitations and challenges for the effective virus discovery through NGS and their potential solutions, which might facilitate for the development of innovative bioinformatic tools in the future.
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Affiliation(s)
- Yu-Hua Qi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zhuang-Xin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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9
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Xiao J, Zhu K, Ma R, Zhang C, Lv K, Ge D, Liu R. Full genome sequence of a novel iflavirus from the aster leafhopper Macrosteles fascifrons. Virus Genes 2023; 59:338-342. [PMID: 36508145 DOI: 10.1007/s11262-022-01962-0] [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: 11/01/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022]
Abstract
The aster leafhopper Macrosteles fascifrons is a common insect pest that feeds on rice and other plants and may serve as a vector to transmit various viruses. Here, we discovered a novel virus from M. fascifrons using metagenomic sequencing. We obtained its complete genome sequence by contig assembly and rapid amplification of cDNA ends, and verified the genome sequence by Sanger sequencing of overlapping segments. Based on homology search and phylogenetic analysis, the new virus belongs to the family Iflaviridae and it is tentatively named "Macrosteles fascifrons iflavirus 1" (MfIV1). Excluding the poly(A) tail, the MfIV1 genome is 10,581 nucleotides in length and it is predicted to encode a polyprotein of 3119 amino acids long, which is likely further processed to several polypeptides with conserved domains, including two rhinovirus like (rhv-like) capsid domains, a cricket paralysis virus (CRPV) capsid domain, a helicase domain, and an RNA-dependent RNA polymerase (RdRp) domain. BLAST searches show that the highest amino acid sequence identity between the capsid proteins of MfIV1 and those of other reported iflaviruses is 60.22%, indicating that MfIV1 is a new member in the family Iflaviridae.
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Affiliation(s)
- Jiajing Xiao
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kai Zhu
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rui Ma
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chunmin Zhang
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Keliang Lv
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Danfeng Ge
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Renyi Liu
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Valles SM, Zhao C, Rivers AR, Iwata RL, Oi DH, Cha DH, Collignon RM, Cox NA, Morton GJ, Calcaterra LA. RNA virus discoveries in the electric ant, Wasmannia auropunctata. Virus Genes 2023; 59:276-289. [PMID: 36729322 PMCID: PMC10025213 DOI: 10.1007/s11262-023-01969-1] [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: 11/08/2022] [Accepted: 01/13/2023] [Indexed: 02/03/2023]
Abstract
Despite being one of the most destructive invasive species of ants, only two natural enemies are known currently for Wasmannia auropunctata, commonly known as the electric ant or little fire ant. Because viruses can be effective biological control agents against many insect pests, including ants, a metagenomics/next-generation sequencing approach was used to facilitate discovery of virus sequences from the transcriptomes of W. auropunctata. Five new and complete positive sense, single-stranded RNA virus genomes, and one new negative sense, single-stranded RNA virus genome were identified, sequenced, and characterized from W. auropunctata collected in Argentina by this approach, including a dicistrovirus (Electric ant dicistrovirus), two polycipiviruses (Electric ant polycipivirus 1; Electric ant polycipivirus 2), a solinvivirus (Electric ant solinvivirus), a divergent genome with similarity to an unclassified group in the Picornavirales (Electric ant virus 1), and a rhabdovirus (Electric ant rhabdovirus). An additional virus genome was detected that is likely Solenopsis invicta virus 10 (MH727527). The virus genome sequences were absent from the transcriptomes of W. auropunctata collected in the USA (Hawaii and Florida). Additional limited field surveys corroborated the absence of these viruses in regions where the electric ant is invasive (the USA and Australia). The replicative genome strand of four of the viruses (Electric ant polycipivirus 2, Electric ant solinvivirus, Electric ant virus 1, and Solenopsis invicta virus 10 (in the electric ant) was detected in Argentinean-collected W. auropunctata indicating that the ant is a host for these viruses. These are the first virus discoveries to be made from W. auropunctata.
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Affiliation(s)
- Steven M Valles
- Center for Medical, Agricultural and Veterinary Entomology, USDA-ARS, 1600 SW 23rd Drive, Gainesville, FL, USA.
| | - Chaoyang Zhao
- Center for Medical, Agricultural and Veterinary Entomology, USDA-ARS, 1600 SW 23rd Drive, Gainesville, FL, USA
| | - Adam R Rivers
- Genomics and Bioinformatics Research Unit, USDA-ARS, 1600 SW 23rd Drive, Gainesville, FL, USA
| | - Ryo L Iwata
- Genomics and Bioinformatics Research Unit, USDA-ARS, 1600 SW 23rd Drive, Gainesville, FL, USA
| | - David H Oi
- Center for Medical, Agricultural and Veterinary Entomology, USDA-ARS, 1600 SW 23rd Drive, Gainesville, FL, USA
| | - Dong H Cha
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, USDA-ARS, 64 Nowelo St, Hilo, HI, USA
| | - R Max Collignon
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, USDA-ARS, 64 Nowelo St, Hilo, HI, USA
| | - Nastassja A Cox
- National Electric Ant Eradication Program, Department of Agriculture and Fisheries, Biosecurity Queensland, 21-23 Redden Street, Cairns, QLD, 4870, Australia
| | - Gary J Morton
- National Electric Ant Eradication Program, Department of Agriculture and Fisheries, Biosecurity Queensland, 21-23 Redden Street, Cairns, QLD, 4870, Australia
| | - Luis A Calcaterra
- Fundación para el Estudio de Especies Invasivas, Bolívar 1559, B1686EFA, Hurlingham, Buenos Aires, Argentina
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11
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Kwon M, Jung C, Kil EJ. Metagenomic analysis of viromes in honey bee colonies ( Apis mellifera; Hymenoptera: Apidae) after mass disappearance in Korea. Front Cell Infect Microbiol 2023; 13:1124596. [PMID: 36761901 PMCID: PMC9905416 DOI: 10.3389/fcimb.2023.1124596] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
After the nationwide, massive winter losses of honey bees in Korea during the winter of 2021, samplings were conducted from live honey bees in colonies and dead honey bees nearby colonies in the same bee-farms in six regions in Korea. Each sample was subjected to virome analysis using high-throughput sequencing technology. The number of viral reads was the lowest in the live honey bee group sample with 370,503 reads and the highest in the dead honey bee group sample with 42,659,622 reads. Viral contigs were matched with the viral genomes of the black queen cell virus, deformed wing virus, Israeli acute paralysis virus, and sacbrood virus, all of which have been previously reported in Korea. However, Apis rhabdovirus 5, bee macula-like virus, Varroa orthomyxovirus-1, Hubei partiti-like virus 34, Lake Sinai virus 2, 3, and 4, and the Ditton virus, were also discovered in this study, which are the first records in Korea. Plant viral sequences resembling those of Arabidopsis latent virus 1, and a novel viral sequence was also discovered. In the present study 55 complete viral genome sequences were identified. This study is the first virome analysis of domestic honey bees and provides the latest information on the diversity of honey bee viruses in Korea.
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Affiliation(s)
- Minhyeok Kwon
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
- Agriculture Science and Technology Research Institute, Andong National University, Andong, Republic of Korea
| | - Chuleui Jung
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
- Agriculture Science and Technology Research Institute, Andong National University, Andong, Republic of Korea
| | - Eui-Joon Kil
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
- Agriculture Science and Technology Research Institute, Andong National University, Andong, Republic of Korea
- *Correspondence: Eui-Joon Kil,
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12
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Rodríguez-Flores MS, Mazzei M, Felicioli A, Diéguez-Antón A, Seijo MC. Emerging Risk of Cross-Species Transmission of Honey Bee Viruses in the Presence of Invasive Vespid Species. INSECTS 2022; 14:6. [PMID: 36661935 PMCID: PMC9866884 DOI: 10.3390/insects14010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/05/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
The increase in invasive alien species is a concern for the environment. The establishment of some of these species may be changing the balance between pathogenicity and host factors, which could alter the defense strategies of native host species. Vespid species are among the most successful invasive animals, such as the genera Vespa, Vespula and Polistes. Bee viruses have been extensively studied as an important cause of honey bee population losses. However, knowledge about the transmission of honey bee viruses in Vespids is a relevant and under-researched aspect. The role of some mites such as Varroa in the transmission of honey bee viruses is clearer than in the case of Vespidae. This type of transmission by vectors has not yet been clarified in Vespidae, with interspecific relationships being the main hypotheses accepted for the transmission of bee viruses. A majority of studies describe the presence of viruses or their replicability, but aspects such as the symptomatology in Vespids or the ability to infect other hosts from Vespids are scarcely discussed. Highlighting the case of Vespa velutina as an invader, which is causing huge losses in European beekeeping, is of special interest. The pressure caused by V. velutina leads to weakened hives that become susceptible to pathogens. Gathering this information is necessary to promote further research on the spread of bee viruses in ecosystems invaded by invasive species of Vespids, as well as to prevent the decline of bee populations due to bee viruses.
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Affiliation(s)
| | - Maurizio Mazzei
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
| | - Antonio Felicioli
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
| | - Ana Diéguez-Antón
- Department of Plant Biology and Soil Sciences, University of Vigo, Campus As Lagoas, 32004 Ourense, Spain
| | - María Carmen Seijo
- Department of Plant Biology and Soil Sciences, University of Vigo, Campus As Lagoas, 32004 Ourense, Spain
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13
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Mendes Dos Santos MA, Dias LS, Ramirez Pavon JA, Viniski AE, Campos Souza CL, Pepato MA, Correa de Azevedo V, Teixeira Nunes MR, Slhessarenko RD. Regional mutations in CHIKV-ECSA genomes and detection of other viruses in the serum of acute febrile patients by a metagenomic approach in Mato Grosso, Central-Western Brazil, 2018. Virology 2022; 576:18-29. [PMID: 36126430 DOI: 10.1016/j.virol.2022.08.013] [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: 04/29/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022]
Abstract
Mato Grosso (MT) State is part of central western Brazil and has a tropical permissive environment that favors arbovirus outbreaks. A metagenomic approach was used to identify viral genomes in seven pools of serum from patients (n=65) with acute febrile disease. Seven chikungunya virus (CHIKV) genomes were determined, showing four amino acid changes found only in CHIKV genomes obtained in MT since 2018: nsP2:T31I, nsP3: A388V, E3:T201I and E3:H57R, in addition to other mutations in E1, nsP2 and nsP4. Six parvovirus B19 (B19V) genotype I genomes (4771-5131 nt) showed four aa alterations (NS1:N473D, R579Q; VP1:I716T; and 11 kDa:V44A) compared to most similar B19V from the USA. Coinfection between CHIKV and B19V was evidenced in 22/65 (33.8%) patients by RT‒PCR and PCR, respectively. Other viruses found in these pools include human pegivirus C, torque teno virus 3, an unclassified TTV and torque teno mini virus. Metagenomics represents a useful approach to detect viruses in the serum of acute febrile patients suspected of arbovirus disease.
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Affiliation(s)
- Marcelo Adriano Mendes Dos Santos
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil; Faculdade de Medicina, Universidade do Estado de Mato Grosso, Cáceres, MT, Brazil
| | - Lucas Silva Dias
- Curso de Graduação em Medicina, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Janeth Aracely Ramirez Pavon
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Ana Elisa Viniski
- Laboratório Central do Estado de Mato Grosso, Secretaria Estadoual de Saúde, Cuiabá, MT, Brazil
| | | | - Marco Andrey Pepato
- Laboratório Central do Estado de Mato Grosso, Secretaria Estadoual de Saúde, Cuiabá, MT, Brazil; Hospital Universitário Júlio Muller, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | | | | | - Renata Dezengrini Slhessarenko
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil.
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14
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Martinez-Mercado MA, de Jesús JLD, Galindo-Sánchez CE, Saavedra-Flores A, Carrillo-Tripp J. Novel viral RNA genomes of the vine mealybug Planococcus ficus. J Gen Virol 2022; 103. [PMID: 35259086 DOI: 10.1099/jgv.0.001717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The vine mealybug, Planococcus ficus (Signoret, 1875), is the most important insect pest in growing areas of the grapevine Vitis vinifera L. in several countries, including Mexico. In Mexico, Baja California (B.C.) is the region with the highest production of V. vinifera L. grapes for industrial purposes. Recently, the diversity of viruses infecting insects only (insect-specific viruses) has been broadly explored to elucidate further ecological viral-host interactions in many insect species, which in some cases has resulted in the application of virus-based biological control agents for insect pests. However, a survey of the Pl. ficus virome has not been done yet. In the present study, we pooled Pl. ficus individuals collected through different vineyards of Ensenada, B.C., Mexico and analysed them by meta-transcriptomics. Novel nearly complete genomes of five RNA viruses were retrieved. These viruses were related to the Iflaviridae and Reoviridae families, and to the Picornavirales and Tolivirales orders. A new isolate belonging to the Dicistroviridae family was also found. Phylogenetic analyses showed that these putative viral genomes group with viruses having hemipteran (including a mealybug species) or other insect hosts, or with viruses associated with insects. Our results suggest that the identified novel RNA viruses could be insect-specific viruses of Pl. ficus. This work is the first insight into the Pl. ficus virome; it guarantees further studies aimed to characterize those viruses with potential for application in biological control of this economically important insect.
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Affiliation(s)
- Miguel A Martinez-Mercado
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Baja California 22860, Mexico
| | - José Luis Duarte de Jesús
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Baja California 22860, Mexico
| | - Clara E Galindo-Sánchez
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Baja California 22860, Mexico
| | - Anaid Saavedra-Flores
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Baja California 22860, Mexico
| | - Jimena Carrillo-Tripp
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Baja California 22860, Mexico
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15
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Liu S, Zhang SM, Buddenborg SK, Loker ES, Bonning BC. Virus-derived sequences from the transcriptomes of two snail vectors of schistosomiasis, Biomphalaria pfeifferi and Bulinus globosus from Kenya. PeerJ 2021; 9:e12290. [PMID: 34820163 PMCID: PMC8601052 DOI: 10.7717/peerj.12290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/21/2021] [Indexed: 11/20/2022] Open
Abstract
Schistosomiasis, which infects more than 230 million people, is vectored by freshwater snails. We identified viral sequences in the transcriptomes of Biomphalaria pfeifferi (BP) and Bulinus globosus (BuG), two of the world's most important schistosomiasis vectors in Africa. Sequences from 26 snails generated using Illumina Hi-Seq or 454 sequencing were assembled using Trinity and CAP3 and putative virus sequences were identified using a bioinformatics pipeline. Phylogenetic analyses were performed using viral RNA-dependent RNA polymerase and coat protein sequences to establish relatedness between virus sequences identified and those of known viruses. Viral sequences were identified from the entire snail holobiont, including symbionts, ingested material and organisms passively associated with the snails. Sequences derived from more than 17 different viruses were found including five near full-length genomes, most of which were small RNA viruses with positive sense RNA genomes (i.e., picorna-like viruses) and some of which are likely derived from adherent or ingested diatoms. Based on phylogenetic analysis, five of these viruses (including BPV2 and BuGV2) along with four Biomphalaria glabrata viruses reported previously, cluster with known invertebrate viruses and are putative viruses of snails. The presence of RNA sequences derived from four of these novel viruses in samples was confirmed. Identification of the genome sequences of candidate snail viruses provides a first step toward characterization of additional gastropod viruses, including from species of biomedical significance.
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Affiliation(s)
- Sijun Liu
- Department of Entomology, Iowa State University, Ames, Iowa, United States
| | - Si-Ming Zhang
- Center for Evolutionary and Theoretical Immunology, Parasite Division Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States
| | - Sarah K. Buddenborg
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States
| | - Eric S. Loker
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States
| | - Bryony C. Bonning
- Entomology & Nematology Department, University of Florida, Gainesville, Florida, United States
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16
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Cheng RL, Li XF, Zhang CX. Novel Dicistroviruses in an Unexpected Wide Range of Invertebrates. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:423-431. [PMID: 33837925 DOI: 10.1007/s12560-021-09472-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
Dicistroviruses are members of a rapidly growing family of small RNA viruses. Related sequences have been discovered in many environmental samples, indicating that our knowledge about dicistrovirus diversity and host range is still limited. In this study, we performed a systematic search against the publicly available transcriptome database, and identified large numbers of dicistrovirus-like sequences in a wide variety of eukaryotic species. The origins of these sequences were 108 invertebrates (including 77 insect species belonging to 18 orders) and 11 plants, revealing new associations between dicistroviruses and hosts. Finally, 83 transcripts corresponding to nearly-complete viral genomes were retrieved from the RNA-seq data, of which most sequences showed limited similarity to known dicistroviruses and might present previously unreported virus species. Phylogenetic analysis suggested that horizontal virus transfer has occurred between diverse hosts and has important implications for dicistrovirus evolution. The results will provide new insight into the hidden diversity of the Dicistroviridae, and help us to better understand the viral evolution, host range and the possible way of transmission.
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Affiliation(s)
- Ruo-Lin Cheng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Xiao-Feng Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Chuan-Xi Zhang
- Institute of Plant Virology, Ningbo University, Ningbo, China.
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17
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Novel RNA Viruses from the Transcriptome of Pheromone Glands in the Pink Bollworm Moth, Pectinophora gossypiella. INSECTS 2021; 12:insects12060556. [PMID: 34203764 PMCID: PMC8232680 DOI: 10.3390/insects12060556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/29/2022]
Abstract
Simple Summary The pink bollworm, Pectinophora gossypiella (Lepidoptera: Gelechiidae), is a major pest of cotton. In this study, we analyzed the mRNA from pheromone glands of two populations in Israel. We found several virus sequences that were the same in these populations. We identified these viruses based on high-throughput sequencing data and analysis of the assembled transcripts. Through analysis of the sequences, we identified several unique viral sequences representing possible novel viral species. Two of the viral sequences were found in relatively high abundance in pheromone glands. One of the virus sequences was also found through analysis of previous transcriptome sequencing data from the midgut of pink bollworm larvae. This is the first report of these unique viral sequences found in the pink bollworm, and these viruses could be developed to help control this pest around the world, but more research is needed to determine their utility as biological control agents. Abstract In this study, we analyzed the transcriptome obtained from the pheromone gland isolated from two Israeli populations of the pink bollworm Pectinophora gossypiella to identify viral sequences. The lab population and the field samples carried the same viral sequences. We discovered four novel viruses: two positive-sense single-stranded RNA viruses, Pectinophora gossypiella virus 1 (PecgV1, a virus of Iflaviridae) and Pectinophora gossypiella virus 4 (PecgV4, unclassified), and two negative-sense single-stranded RNA viruses, Pectinophora gossypiella virus 2 (PecgV2, a virus of Phasmaviridae) and Pectinophora gossypiella virus 3 (PecgV3, a virus of Phenuiviridae). In addition, sequences derived from two negative-sense single-stranded RNA viruses that belong to Mononegavirales were found in the data. Analysis of previous transcriptome sequencing data derived from the midgut of pink bollworm larvae of a USA population only identified PecgV1, but no other viruses. High viral sequence coverages of PecgV1 and PecgV4 were observed in both field and lab populations. This is the first report of viral sequences discovered from the pink bollworm. Results from this investigation suggest that the pink bollworm harbors multiple viruses. Further investigation of the viral pathogens may help to develop novel pest management strategies for control of the pink bollworm.
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18
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Zhang W, Gu Q, Niu J, Wang JJ. The RNA Virome and Its Dynamics in an Invasive Fruit Fly, Bactrocera dorsalis, Imply Interactions Between Host and Viruses. MICROBIAL ECOLOGY 2020; 80:423-434. [PMID: 32300830 DOI: 10.1007/s00248-020-01506-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/17/2020] [Indexed: 06/11/2023]
Abstract
The oriental fruit fly, Bactrocera dorsalis (Hendel), is an important invasive agricultural insect pest with a wide host range, and has spread around the world over the last century. This evolutionary trait may have arisen primarily from interactions between B. dorsalis and other invertebrates that share the same ecological niches. The invasive behavior of B. dorsalis also frequently exposes them to diverse species of viruses. Thereby, RNA viromes may be useful microbial markers to understand the ecological evolution of B. dorsalis as well as to investigate virus-host interactions. Here, we reported eight novel RNA viruses in B. dorsalis of a lab colony, including four positive-strand RNA viruses, two negative-strand RNA viruses, and two double-stranded RNA viruses using high-throughput sequencing technology. Analysis of the virus-derived small RNAs suggested that most of these viruses may be active and trigger the host antiviral RNAi responses. The viruses were also detected in various geographical populations of B. dorsalis, implying that there is a strong association between the viromes and host. In addition, these viruses infected specific fly tissues, predominately the central nervous system and gut. Furthermore, we explored the dynamics of the viruses when hosts were exposed to short- or long-term stressors, which showed that titers of some viruses were responsively altered in the stressed B. dorsalis. The discovery of these viruses may enrich our understanding of the species diversity of RNA viruses and also provide information on viruses in association with host adaptation in insects.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Qiaoying Gu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
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19
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Sosa-Gómez DR, Morgado FS, Corrêa RFT, Silva LA, Ardisson-Araújo DMP, Rodrigues BMP, Oliveira EE, Aguiar RWS, Ribeiro BM. Entomopathogenic Viruses in the Neotropics: Current Status and Recently Discovered Species. NEOTROPICAL ENTOMOLOGY 2020; 49:315-331. [PMID: 32358711 DOI: 10.1007/s13744-020-00770-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/03/2020] [Indexed: 06/11/2023]
Abstract
The market for biological control of insect pests in the world and in Brazil has grown in recent years due to the unwanted ecological and human health impacts of chemical insecticides. Therefore, research on biological control agents for pest management has also increased. For instance, insect viruses have been used to protect crops and forests around the world for decades. Among insect viruses, the baculoviruses are the most studied and used viral biocontrol agent. More than 700 species of insects have been found to be naturally infected by baculoviruses, with 90% isolated from lepidopteran insects. In this review, some basic aspects of baculovirus infection in vivo and in vitro infection, gene content, viral replication will be discussed. Furthermore, we provide examples of the use of insect viruses for biological pest control and recently characterized baculoviruses in Brazil.
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Affiliation(s)
- D R Sosa-Gómez
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Soja, Londrina, PR, Brasil
| | - F S Morgado
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - R F T Corrêa
- Depto de Biotecnologia, Univ Federal de Tocantins, Gurupi, TO, Brasil
| | - L A Silva
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - D M P Ardisson-Araújo
- Depto de Bioquímica e Biologia Molecular, Univ Federal de Santa Maria, Santa Maria, RS, Brasil
| | - B M P Rodrigues
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - E E Oliveira
- Depto de Entomologia, Univ Federal de Viçosa, Viçosa, MG, Brasil
| | - R W S Aguiar
- Depto de Biotecnologia, Univ Federal de Tocantins, Gurupi, TO, Brasil
| | - B M Ribeiro
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil.
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20
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López-Ferber M. Special Issue "Insect Viruses and Pest Management". Viruses 2020; 12:v12040431. [PMID: 32290253 PMCID: PMC7232507 DOI: 10.3390/v12040431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 11/16/2022] Open
Abstract
Most revues consider the work on Lymantria monarcha in central Europe [...].
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21
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Bubici G, Prigigallo MI, Garganese F, Nugnes F, Jansen M, Porcelli F. First Report of Aleurocanthus spiniferus on Ailanthus altissima: Profiling of the Insect Microbiome and MicroRNAs. INSECTS 2020; 11:E161. [PMID: 32138145 PMCID: PMC7142546 DOI: 10.3390/insects11030161] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/20/2020] [Accepted: 02/27/2020] [Indexed: 12/19/2022]
Abstract
We report the first occurrence of the orange spiny whitefly (Aleurocanthus spiniferus; OSW) on the tree of heaven (Ailanthus altissima) in Bari, Apulia region, Italy. After our first observation in 2016, the infestation recurred regularly during the following years and expanded to the neighboring trees. Since then, we have also found the insect on numerous patches of the tree of heaven and other plant species in the Bari province. Nevertheless, the tree of heaven was not particularly threatened by the insect, so that a possible contribution by OSW for the control of such an invasive plant cannot be hypothesized hitherto. This work was also aimed at profiling the microbiome of OSW feeding on A. altissima. For this purpose, we used the denaturing gradient gel electrophoresis (DGGE) and the deep sequencing of small RNAs (sRNAs). Both techniques unveiled the presence of "Candidatus Portiera" (primary endosymbiont), Wolbachia sp. and Rickettsia sp., endosymbionts already reported for other Aleyrodidae. Deep sequencing data were analyzed by four computational pipelines in order to understand the reliability of the detection of fungi, bacteria, and viruses: Kraken, Kaiju, Velvet, and VelvetOptimiser. Some contigs assembled by Velvet or VelvetOptimiser were associated with insects, but not necessarily in the Aleurocanthus genus or Aleyrodidae family, suggesting the non-specificity of sRNAs or possible traces of parasitoids in the sample (e.g., Eretmocerus sp.). Finally, deep sequencing data were used to describe the microtranscriptome of OSW: 56 canonical and at least four high-confidence novel microRNAs (miRNAs) were identified. The overall miRNA abundance in OSW was in agreement with previous works on Bemisia tabaci, and bantam-3p, miR-276a-3p, miR-317-3p, miR-750-3p, and mir-8-3p were the most represented miRNAs.
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Affiliation(s)
- Giovanni Bubici
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, via Amendola 165/A, 70126 Bari, Italy;
| | - Maria Isabella Prigigallo
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, via Amendola 165/A, 70126 Bari, Italy;
| | - Francesca Garganese
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, via Amendola 165/A, 70126 Bari, Italy; (F.G.); (F.P.)
| | - Francesco Nugnes
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, via Università 133, 80055 Portici, Italy;
| | - Maurice Jansen
- Ministry of Agriculture, Nature and Food Quality, Laboratories Division, Netherlands Food and Consumer Product Safety Authority (NVWA), Geertjesweg 15, 6706 EA Wageningen, The Netherlands;
| | - Francesco Porcelli
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, via Amendola 165/A, 70126 Bari, Italy; (F.G.); (F.P.)
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22
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Lüthi MN, Vorburger C, Dennis AB. A Novel RNA Virus in the Parasitoid Wasp Lysiphlebus fabarum: Genomic Structure, Prevalence, and Transmission. Viruses 2020; 12:E59. [PMID: 31947801 PMCID: PMC7019493 DOI: 10.3390/v12010059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/19/2019] [Accepted: 12/31/2019] [Indexed: 12/30/2022] Open
Abstract
We report on a novel RNA virus infecting the wasp Lysiphlebus fabarum, a parasitoid of aphids. This virus, tentatively named "Lysiphlebus fabarum virus" (LysV), was discovered in transcriptome sequences of wasps from an experimental evolution study in which the parasitoids were allowed to adapt to aphid hosts (Aphis fabae) with or without resistance-conferring endosymbionts. Based on phylogenetic analyses of the viral RNA-dependent RNA polymerase (RdRp), LysV belongs to the Iflaviridae family in the order of the Picornavirales, with the closest known relatives all being parasitoid wasp-infecting viruses. We developed an endpoint PCR and a more sensitive qPCR assay to screen for LysV in field samples and laboratory lines. These screens verified the occurrence of LysV in wild parasitoids and identified the likely wild-source population for lab infections in Western Switzerland. Three viral haplotypes could be distinguished in wild populations, of which two were found in the laboratory. Both vertical and horizontal transmission of LysV were demonstrated experimentally, and repeated sampling of laboratory populations suggests that the virus can form persistent infections without obvious symptoms in infected wasps.
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Affiliation(s)
- Martina N. Lüthi
- Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland; (C.V.); (A.B.D.)
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Christoph Vorburger
- Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland; (C.V.); (A.B.D.)
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Alice B. Dennis
- Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland; (C.V.); (A.B.D.)
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
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23
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Comparison Between the Microbial Diversity in Carpenter Ant (Camponotus) Gut and Weaver Ant (Oecophylla) Gut. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.4.58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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24
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Batovska J, Mee PT, Lynch SE, Sawbridge TI, Rodoni BC. Sensitivity and specificity of metatranscriptomics as an arbovirus surveillance tool. Sci Rep 2019; 9:19398. [PMID: 31852942 PMCID: PMC6920425 DOI: 10.1038/s41598-019-55741-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/29/2019] [Indexed: 01/30/2023] Open
Abstract
The ability to identify all the viruses within a sample makes metatranscriptomic sequencing an attractive tool to screen mosquitoes for arboviruses. Practical application of this technique, however, requires a clear understanding of its analytical sensitivity and specificity. To assess this, five dilutions (1:1, 1:20, 1:400, 1:8,000 and 1:160,000) of Ross River virus (RRV) and Umatilla virus (UMAV) isolates were spiked into subsamples of a pool of 100 Culex australicus mosquitoes. The 1:1 dilution represented the viral load of one RRV-infected mosquito in a pool of 100 mosquitoes. The subsamples underwent nucleic acid extraction, mosquito-specific ribosomal RNA depletion, and Illumina HiSeq sequencing. The viral load of the subsamples was also measured using reverse transcription droplet digital PCR (RT-ddPCR) and quantitative PCR (RT-qPCR). Metatranscriptomic sequencing detected both RRV and UMAV in the 1:1, 1:20 and 1:400 subsamples. A high specificity was achieved, with 100% of RRV and 99.6% of UMAV assembled contigs correctly identified. Metatranscriptomic sequencing was not as sensitive as RT-qPCR or RT-ddPCR; however, it recovered whole genome information and detected 19 other viruses, including four first detections for Australia. These findings will assist arbovirus surveillance programs in utilising metatranscriptomics in routine surveillance activities to enhance arbovirus detection.
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Affiliation(s)
- Jana Batovska
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia.
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia.
| | - Peter T Mee
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Stacey E Lynch
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia.
| | - Tim I Sawbridge
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
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25
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Wang H, Gao B, Chen H, Diao Y, Tang Y. Isolation and characterization of a variant duck orthoreovirus causing spleen necrosis in Peking ducks, China. Transbound Emerg Dis 2019; 66:2033-2044. [PMID: 31131546 DOI: 10.1111/tbed.13252] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/26/2019] [Accepted: 05/04/2019] [Indexed: 01/01/2023]
Abstract
Since December 2017, an infectious disease has caused economic hardship for duck farms and breeding ducks in many regions of China. This disease characterized by spleen necrosis and swelling, is due to a variant strain of duck orthoreovirus (DRV) (Duck/N-DRV-XT18/China/2018), which we isolated from the spleen of diseased ducks. After isolating the virus, we used next-generation sequencing technology to determine the entire genomic of the virus. Our phylogenetic analysis of 10 genomic segments showed that the N-DRV-XT18 strain is closely related to orthoreovirus isolates derived from ducks and geese, with nucleotide sequence identities for 10 genomic fragments ranging between 49.8% and 99.3%. In contract, the nucleotide sequence of N-DRV-XT18 genomic fragments are only 38.6% to 78.8% similar to the chicken orthoreovirus isolate. Therefore, we determined that this pathogen, causing duck spleen necrosis, is a new variant of a duck orthoreovirus that is significantly different from any previously reported waterfowl-derived othoreovirus.
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Affiliation(s)
- Hongzhi Wang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Tai'an, China
| | - Bin Gao
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Tai'an, China
| | - Hao Chen
- College of Life Science, Qufu Normal University, Qufu, China
| | - Youxiang Diao
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Tai'an, China
| | - Yi Tang
- College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Tai'an, China
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26
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Jagdale SS, Joshi RS. Facilitator roles of viruses in enhanced insect resistance to biotic stress. CURRENT OPINION IN INSECT SCIENCE 2019; 33:111-116. [PMID: 31358189 DOI: 10.1016/j.cois.2019.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 06/10/2023]
Abstract
Virus-insect interactions are primarily parasitic, yet diverse mutualistic interactions, some of which are symbiogenic, also occur. These viruses can modify insect physiology and behavior so that hosts can gain resistance against various biotic challenges like pathogen and parasites. In the recent past, many insect mutualistic viruses have been reported. Viruses can show symbiogenic interactions with some insects, which have been explored at the molecular level. However, understanding about molecular mechanisms for many of the mutualistic viruses is still enigmatic. Exploration of these interactions and its mechanism can shed light on phenomenon of virus mediated biotic stress resistance in insects.
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Affiliation(s)
- Shounak S Jagdale
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, Maharashtra, India
| | - Rakesh S Joshi
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, Maharashtra, India; Biochemical Sciences Division, CSIR National Chemical Laboratory, Pune 411008, Maharashtra, India.
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27
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Zhang W, Wu T, Guo M, Chang T, Yang L, Tan Y, Ye C, Niu J, Wang JJ. Characterization of a new bunyavirus and its derived small RNAs in the brown citrus aphid, Aphis citricidus. Virus Genes 2019; 55:557-561. [PMID: 31079289 DOI: 10.1007/s11262-019-01667-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 04/29/2019] [Indexed: 01/15/2023]
Abstract
High-throughput sequencing is widely used for virus discovery, and many RNA viruses have been discovered and identified. A new negative-sense single-stranded RNA virus was identified in the brown citrus aphid and named Aphis citricidus bunyavirus. The genome consists of large (7037 nt), medium (3462 nt), and small (1163 nt) segments. Phylogenetic analysis and amino acid sequences identities of this virus with other bunyaviruses suggest that it is a new species belonging to the family Phenuiviridae. The small interfering RNA pathway could be involved against the infection of this virus in brown citrus aphid as supported by the viral derived small RNAs. The discovery of this virus illustrates the diversity of RNA viruses and contributes to the classification of bunyaviruses.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Tengfei Wu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Mengmeng Guo
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Tengyu Chang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Li Yang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yang Tan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Chao Ye
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China. .,International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
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28
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The First Complete Genome Sequence of a Novel Tetrastichus brontispae RNA Virus-1 (TbRV-1). Viruses 2019; 11:v11030257. [PMID: 30871248 PMCID: PMC6466307 DOI: 10.3390/v11030257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/09/2019] [Accepted: 03/10/2019] [Indexed: 11/17/2022] Open
Abstract
The complete sequence of a novel RNA virus isolated from Tetrastichus brontispae (TbRV-1) was determined to be 12,239 nucleotides in length with five non-overlapping, linearly arranged coding sequences (CDS), potentially encoding nucleoproteins, hypothetical proteins, matrix proteins, glycoproteins, and RNA-dependent RNA polymerases. Sequence analysis indicated that the RNA-dependent RNA polymerase of TbRV-1 shares a 65% nucleotide and 67% amino acid sequence identity with Hubei dimarhabdovirus 2, suggesting that TbRV-1 is a member of the dimarhabdovirus supergroup. This corresponded to the result of the phylogenetic analysis. The affiliation of TbRV-1 with members of the family Rhabdoviridae was further validated by similar transcription termination motifs (GGAACUUUUUUU) to the Drosophila sigmavirus. The prevalence of TbRV-1 in all tissues suggested that the virus was constitutive of, and not specific to, any wasp tissue. To our knowledge, this is the first report on the complete genome sequence of a dimarhabdovirus in parasitoids.
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29
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Valles SM, Rivers AR. Nine new RNA viruses associated with the fire ant Solenopsis invicta from its native range. Virus Genes 2019; 55:368-380. [PMID: 30847760 DOI: 10.1007/s11262-019-01652-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/15/2019] [Indexed: 12/11/2022]
Abstract
The red imported fire ant (Solenopsis invicta) escaped its natural enemies when it was introduced into North America in the 1930s from South America. US efforts have focused on discovery of natural enemies, like viruses, to provide sustainable control of the ant. Nine new virus genomes were sequenced from the invasive fire ant Solenopsis invicta using metagenomic RNA sequencing. The virus genomes were verified by Sanger sequencing and random amplification of cDNA ends reactions. In addition to the nine new virus genomes, the previously described Solenopsis viruses were also detected, including Solenopsis invicta virus 1 (SINV-1), SINV-2, SINV-3, SINV-4, SINV-5, and Solenopsis invicta densovirus. The virus sequences came from S. invicta workers, larvae, pupae, and dead workers taken from midden piles collected from across the ant's native range in Formosa, Argentina. One of the new virus genomes (Solenopsis invicta virus 6) was also detected in populations of North American S. invicta. Phylogenetic analysis of the RNA dependent RNA polymerase, the entire nonstructural polyprotein, and genome characteristics were used to tentatively taxonomically place these new virus genome sequences; these include four new species of Dicistroviridae, one Polycipiviridae, one Iflaviridae, one Totiviridae, and two genome sequences that were too taxonomically divergent to be placed with certainty. The S. invicta virome is the best characterized from any ant species and includes 13 positive-sense, single-stranded RNA viruses (Solenopsis invicta virus 1 to Solenopsis invicta virus 13), one double-stranded RNA virus (Solenopsis midden virus), and one double-stranded DNA virus (Solenopsis invicta densovirus). These new additions to the S. invicta virome offer potentially new classical biological control agents for S. invicta.
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Affiliation(s)
- Steven M Valles
- Center for Medical, Agricultural and Veterinary Entomology, USDA-ARS, Gainesville, FL, USA.
| | - Adam R Rivers
- Genomics and Bioinformatics Research Unit, USDA-ARS, Gainesville, FL, USA
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30
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Cholleti H, Berg M, Hayer J, Blomström AL. Vector-borne viruses and their detection by viral metagenomics. Infect Ecol Epidemiol 2018. [DOI: 10.1080/20008686.2018.1553465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Harindranath Cholleti
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mikael Berg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Juliette Hayer
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anne-Lie Blomström
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
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31
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Charles J, Tangudu CS, Hurt SL, Tumescheit C, Firth AE, Garcia-Rejon JE, Machain-Williams C, Blitvich BJ. Detection of novel and recognized RNA viruses in mosquitoes from the Yucatan Peninsula of Mexico using metagenomics and characterization of their in vitro host ranges. J Gen Virol 2018; 99:1729-1738. [PMID: 30412047 DOI: 10.1099/jgv.0.001165] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
A metagenomics approach was used to detect novel and recognized RNA viruses in mosquitoes from the Yucatan Peninsula of Mexico. A total of 1359 mosquitoes of 7 species and 5 genera (Aedes, Anopheles, Culex, Mansonia and Psorophora) were sorted into 37 pools, homogenized and inoculated onto monolayers of Aedes albopictus (C6/36) cells. A second blind passage was performed and then total RNA was extracted and analysed by RNA-seq. Two novel viruses, designated Uxmal virus and Mayapan virus, were identified. Uxmal virus was isolated from three pools of Aedes (Ochlerotatus) taeniorhynchus and phylogenetic data indicate that it should be classified within the recently proposed taxon Negevirus. Mayapan virus was recovered from two pools of Psorophora ferox and is most closely related to unclassified Nodaviridae-like viruses. Two recognized viruses were also detected: Culex flavivirus (family Flaviviridae) and Houston virus (family Mesoniviridae), with one and two isolates being recovered, respectively. The in vitro host ranges of all four viruses were determined by assessing their replicative abilities in cell lines of avian, human, monkey, hamster, murine, lepidopteran and mosquito (Aedes, Anopheles and Culex) origin, revealing that all viruses possess vertebrate replication-incompetent phenotypes. In conclusion, we report the isolation of both novel and recognized RNA viruses from mosquitoes collected in Mexico, and add to the growing plethora of viruses discovered recently through the use of metagenomics.
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Affiliation(s)
- Jermilia Charles
- 1Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Chandra S Tangudu
- 1Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Stefanie L Hurt
- 1Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | | | - Andrew E Firth
- 2Department of Pathology, University of Cambridge, Cambridge, UK
| | - Julian E Garcia-Rejon
- 3Laboratorio de Arbovirologia, Centro de Investigaciones Regionales 'Dr Hideyo Noguchi', Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Carlos Machain-Williams
- 3Laboratorio de Arbovirologia, Centro de Investigaciones Regionales 'Dr Hideyo Noguchi', Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Bradley J Blitvich
- 1Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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32
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Lambert C, Braxton C, Charlebois RL, Deyati A, Duncan P, La Neve F, Malicki HD, Ribrioux S, Rozelle DK, Michaels B, Sun W, Yang Z, Khan AS. Considerations for Optimization of High-Throughput Sequencing Bioinformatics Pipelines for Virus Detection. Viruses 2018; 10:E528. [PMID: 30262776 PMCID: PMC6213042 DOI: 10.3390/v10100528] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 02/07/2023] Open
Abstract
High-throughput sequencing (HTS) has demonstrated capabilities for broad virus detection based upon discovery of known and novel viruses in a variety of samples, including clinical, environmental, and biological. An important goal for HTS applications in biologics is to establish parameter settings that can afford adequate sensitivity at an acceptable computational cost (computation time, computer memory, storage, expense or/and efficiency), at critical steps in the bioinformatics pipeline, including initial data quality assessment, trimming/cleaning, and assembly (to reduce data volume and increase likelihood of appropriate sequence identification). Additionally, the quality and reliability of the results depend on the availability of a complete and curated viral database for obtaining accurate results; selection of sequence alignment programs and their configuration, that retains specificity for broad virus detection with reduced false-positive signals; removal of host sequences without loss of endogenous viral sequences of interest; and use of a meaningful reporting format, which can retain critical information of the analysis for presentation of readily interpretable data and actionable results. Furthermore, after alignment, both automated and manual evaluation may be needed to verify the results and help assign a potential risk level to residual, unmapped reads. We hope that the collective considerations discussed in this paper aid toward optimization of data analysis pipelines for virus detection by HTS.
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Affiliation(s)
| | | | - Robert L Charlebois
- Analytical Research and Development, Sanofi Pasteur, Toronto, ON M2R 3T4, Canada.
| | | | - Paul Duncan
- Merck & Co. Inc., West Point, PA 19486, USA.
| | | | | | | | | | - Brandye Michaels
- Analytical Research and Development: Microbiology, Pfizer Inc., Andover, MA 01810, USA.
| | | | - Zhihui Yang
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA.
| | - Arifa S Khan
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA.
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Abstract
Viruses are an important but sequence-diverse and often understudied component of the phytobiome. We succinctly review current information on how plant viruses directly affect plant health and physiology and consequently have the capacity to modulate plant interactions with their biotic and abiotic environments. Virus interactions with other biota in the phytobiome, including arthropods, fungi, and nematodes, may also impact plant health. For example, viruses interact with and modulate the interface between plants and insects. This has been extensively studied for insect-vectored plant viruses, some of which also infect their vectors. Other viruses have been shown to alter the impacts of plant-interacting phytopathogenic and nonpathogenic fungi and bacteria. Viruses that infect nematodes have also recently been discovered, but the impact of these and phage infecting soil bacteria on plant health remain largely unexplored.
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Affiliation(s)
- James E Schoelz
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Lucy R Stewart
- Corn, Soybean and Wheat Quality Research Unit, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Wooster, Ohio 44691, USA;
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34
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Insect-specific viruses: from discovery to potential translational applications. Curr Opin Virol 2018; 33:33-41. [PMID: 30048906 DOI: 10.1016/j.coviro.2018.07.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 06/29/2018] [Accepted: 07/04/2018] [Indexed: 12/17/2022]
Abstract
Over the past decade the scientific community has experienced a new age of virus discovery in arthropods in general, and in insects in particular. Next generation sequencing and advanced bioinformatics tools have provided new insights about insect viromes and viral evolution. In this review, we discuss some high-throughput sequencing technologies used to discover viruses in insects and the challenges raised in data interpretations. Additionally, the discovery of these novel viruses that are considered as insect-specific viruses (ISVs) has gained increasing attention in their potential use as biological agents. As example, we show how the ISV Nhumirim virus was used to reduce West Nile virus transmission when co-infecting the mosquito vector. We also discuss new translational opportunities of using ISVs to limit insect vector competence by using them to interfere with pathogen acquisition, to directly target the insect vector or to confer pathogen resistance by the insect vector.
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35
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Teixeira MA, Sela N, Atamian HS, Bao E, Chaudhary R, MacWilliams J, He J, Mantelin S, Girke T, Kaloshian I. Sequence analysis of the potato aphid Macrosiphum euphorbiae transcriptome identified two new viruses. PLoS One 2018; 13:e0193239. [PMID: 29596449 PMCID: PMC5875755 DOI: 10.1371/journal.pone.0193239] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 02/07/2018] [Indexed: 11/19/2022] Open
Abstract
The potato aphid, Macrosiphum euphorbiae, is an important agricultural pest that causes economic losses to potato and tomato production. To establish the transcriptome for this aphid, RNA-Seq libraries constructed from aphids maintained on tomato plants were used in Illumina sequencing generating 52.6 million 75-105 bp paired-end reads. The reads were assembled using Velvet/Oases software with SEED preprocessing resulting in 22,137 contigs with an N50 value of 2,003bp. After removal of contigs from tomato host origin, 20,254 contigs were annotated using BLASTx searches against the non-redundant protein database from the National Center for Biotechnology Information (NCBI) as well as IntereProScan. This identified matches for 74% of the potato aphid contigs. The highest ranking hits for over 12,700 contigs were against the related pea aphid, Acyrthosiphon pisum. Gene Ontology (GO) was used to classify the identified M. euphorbiae contigs into biological process, cellular component and molecular function. Among the contigs, sequences of microbial origin were identified. Sixty five contigs were from the aphid bacterial obligate endosymbiont Buchnera aphidicola origin and two contigs had amino acid similarities to viruses. The latter two were named Macrosiphum euphorbiae virus 2 (MeV-2) and Macrosiphum euphorbiae virus 3 (MeV-3). The highest sequence identity to MeV-2 had the Dysaphis plantaginea densovirus, while to MeV-3 is the Hubei sobemo-like virus 49. Characterization of MeV-2 and MeV-3 indicated that both are transmitted vertically from adult aphids to nymphs. MeV-2 peptides were detected in the aphid saliva and only MeV-2 and not MeV-3 nucleic acids were detected inside tomato leaves exposed to virus-infected aphids. However, MeV-2 nucleic acids did not persist in tomato leaf tissues, after clearing the plants from aphids, indicating that MeV-2 is likely an aphid virus.
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Affiliation(s)
- Marcella A. Teixeira
- Department of Nematology, University of California, Riverside, California, United States of America
| | - Noa Sela
- Department of Plant Pathology and Weed Research, Volcani Center, Bet Dagan, Israel
| | - Hagop S. Atamian
- Department of Nematology, University of California, Riverside, California, United States of America
| | - Ergude Bao
- Graduate Program in Computer Science and Engineering, University of California, Riverside, California, United States of America
| | - Ritu Chaudhary
- Department of Nematology, University of California, Riverside, California, United States of America
| | - Jacob MacWilliams
- Department of Nematology, University of California, Riverside, California, United States of America
| | - Jiangman He
- Department of Nematology, University of California, Riverside, California, United States of America
| | - Sophie Mantelin
- Department of Nematology, University of California, Riverside, California, United States of America
| | - Thomas Girke
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
- Institute for Integrative Genome Biology, University of California, Riverside, California, United States of America
| | - Isgouhi Kaloshian
- Department of Nematology, University of California, Riverside, California, United States of America
- Institute for Integrative Genome Biology, University of California, Riverside, California, United States of America
- Center for Infectious Disease Vector Research, University of California, Riverside, California, United States of America
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36
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Zhou C, Liu S, Song W, Luo S, Meng G, Yang C, Yang H, Ma J, Wang L, Gao S, Wang J, Yang H, Zhao Y, Wang H, Zhou X. Characterization of viral RNA splicing using whole-transcriptome datasets from host species. Sci Rep 2018; 8:3273. [PMID: 29459752 PMCID: PMC5818608 DOI: 10.1038/s41598-018-21190-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 01/31/2018] [Indexed: 01/16/2023] Open
Abstract
RNA alternative splicing (AS) is an important post-transcriptional mechanism enabling single genes to produce multiple proteins. It has been well demonstrated that viruses deploy host AS machinery for viral protein productions. However, knowledge on viral AS is limited to a few disease-causing viruses in model species. Here we report a novel approach to characterizing viral AS using whole transcriptome dataset from host species. Two insect transcriptomes (Acheta domesticus and Planococcus citri) generated in the 1,000 Insect Transcriptome Evolution (1KITE) project were used as a proof of concept using the new pipeline. Two closely related densoviruses (Acheta domesticus densovirus, AdDNV, and Planococcus citri densovirus, PcDNV, Ambidensovirus, Densovirinae, Parvoviridae) were detected and analyzed for AS patterns. The results suggested that although the two viruses shared major AS features, dramatic AS divergences were observed. Detailed analysis of the splicing junctions showed clusters of AS events occurred in two regions of the virus genome, demonstrating that transcriptome analysis could gain valuable insights into viral splicing. When applied to large-scale transcriptomics projects with diverse taxonomic sampling, our new method is expected to rapidly expand our knowledge on RNA splicing mechanisms for a wide range of viruses.
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Affiliation(s)
- Chengran Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.,BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Shanlin Liu
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Wenhui Song
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Shiqi Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Guanliang Meng
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Chentao Yang
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Hua Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jinmin Ma
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Liang Wang
- CAS Key Laboratory of Biomedical & Diagnostic Technology, CAS/Suzhou Institute of Biomedical Engineering and Technology, Suzhou, 215163, China
| | - Shan Gao
- CAS Key Laboratory of Biomedical & Diagnostic Technology, CAS/Suzhou Institute of Biomedical Engineering and Technology, Suzhou, 215163, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Yun Zhao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Hui Wang
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China. .,The Institute of Biomedical Engineering, University of Oxford, Oxford, OX3 7DQ, UK.
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Plant Protection, China Agricultural University, Beijing, 100193, China. .,National Engineering Research Center for Fruit and Vegetable Processing, China Agricultural University, Beijing, 100193, China.
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37
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Varghese FS, van Rij RP. Insect Virus Discovery by Metagenomic and Cell Culture-Based Approaches. Methods Mol Biol 2018; 1746:197-213. [PMID: 29492897 DOI: 10.1007/978-1-4939-7683-6_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Insects are the most abundant and diverse group of animals on earth, but our knowledge of their viruses is biased toward insect-borne viruses that cause disease in plants, animals, or humans. Recent metagenomic studies and systematic surveys of viruses in wild-caught insects have identified an unanticipated large repertoire of novel viruses and viral sequences. These include new members of existing clades, new clades, and even entirely new virus families. These studies greatly expand the known virosphere in insects, provide opportunities to study virus-host interactions, and generate new insights into virus evolution. In this chapter, we discuss the methods used to identify novel viruses in insects and highlight some notable surprises arising from these studies.
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Affiliation(s)
- Finny S Varghese
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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38
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Krejmer-Rabalska M, Rabalski L, Lobo de Souza M, Moore SD, Szewczyk B. New Method for Differentiation of Granuloviruses (Betabaculoviruses) Based on Multitemperature Single Stranded Conformational Polymorphism. Int J Mol Sci 2017; 19:ijms19010083. [PMID: 29283392 PMCID: PMC5796033 DOI: 10.3390/ijms19010083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/20/2017] [Accepted: 12/23/2017] [Indexed: 12/15/2022] Open
Abstract
Baculoviruses have been used as biopesticides for decades. Recently, due to the excessive use of chemical pesticides there is a need for finding new agents that may be useful in biological protection. Sometimes few isolates or species are discovered in one host. In the past few years, many new baculovirus species have been isolated from environmental samples, thoroughly characterized and thanks to next generation sequencing methods their genomes are being deposited in the GenBank database. Next generation sequencing (NGS) methodology is the most certain way of detection, but it has many disadvantages. During our studies, we have developed a method based on Polymerase chain reaction (PCR) followed by Multitemperature Single Stranded Conformational Polymorphism (MSSCP) which allows for distinguishing new granulovirus isolates in only a few hours and at low-cost. On the basis of phylogenetic analysis of betabaculoviruses, representative species have been chosen. The alignment of highly conserved genes—granulin and late expression factor-9, was performed and the degenerate primers were designed to amplify the most variable, short DNA fragments flanked with the most conserved sequences. Afterwards, products of PCR reaction were analysed by MSSCP technique. In our opinion, the proposed method may be used for screening of new isolates derived from environmental samples.
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Affiliation(s)
- Martyna Krejmer-Rabalska
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, 80-807 Gdansk, Poland.
| | - Lukasz Rabalski
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, 80-807 Gdansk, Poland.
| | - Marlinda Lobo de Souza
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estacao Biológica, 70770-900 Brasilia, Brazil.
| | - Sean D Moore
- Citrus Research International (CRI), P.O. Box 20285, Humewood 6013, Port Elizabeth, South Africa.
- Department of Zoology and Entomology, Rhodes University, P.O. Box 94, Grahamstown 6140, South Africa.
| | - Boguslaw Szewczyk
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, 80-807 Gdansk, Poland.
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39
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de Lara Pinto AZ, Santos de Carvalho M, de Melo FL, Ribeiro ALM, Morais Ribeiro B, Dezengrini Slhessarenko R. Novel viruses in salivary glands of mosquitoes from sylvatic Cerrado, Midwestern Brazil. PLoS One 2017; 12:e0187429. [PMID: 29117239 PMCID: PMC5678729 DOI: 10.1371/journal.pone.0187429] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 10/19/2017] [Indexed: 12/22/2022] Open
Abstract
Viruses may represent the most diverse microorganisms on Earth. Novel viruses and variants continue to emerge. Mosquitoes are the most dangerous animals to humankind. This study aimed at identifying viral RNA diversity in salivary glands of mosquitoes captured in a sylvatic area of Cerrado at the Chapada dos Guimarães National Park, Mato Grosso, Brazil. In total, 66 Culicinae mosquitoes belonging to 16 species comprised 9 pools, subjected to viral RNA extraction, double-strand cDNA synthesis, random amplification and high-throughput sequencing, revealing the presence of seven insect-specific viruses, six of which represent new species of Rhabdoviridae (Lobeira virus), Chuviridae (Cumbaru and Croada viruses), Totiviridae (Murici virus) and Partitiviridae (Araticum and Angico viruses). In addition, two mosquito pools presented Kaiowa virus sequences that had already been reported in South Pantanal, Brazil. These findings amplify the understanding of viral diversity in wild-type Culicinae. Insect-specific viruses may present a broader diversity than previously imagined and future studies may address their possible role in mosquito vector competence.
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Affiliation(s)
- Andressa Zelenski de Lara Pinto
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Michellen Santos de Carvalho
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Fernando Lucas de Melo
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Ana Lúcia Maria Ribeiro
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Bergmann Morais Ribeiro
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Distrito Federal, Brazil
| | - Renata Dezengrini Slhessarenko
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
- * E-mail:
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40
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Cao X, Jiang H. An analysis of 67 RNA-seq datasets from various tissues at different stages of a model insect, Manduca sexta. BMC Genomics 2017; 18:796. [PMID: 29041902 PMCID: PMC5645894 DOI: 10.1186/s12864-017-4147-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 10/02/2017] [Indexed: 12/16/2022] Open
Abstract
Background Manduca sexta is a large lepidopteran insect widely used as a model to study biochemistry of insect physiological processes. As a part of its genome project, over 50 cDNA libraries have been analyzed to profile gene expression in different tissues and life stages. While the RNA-seq data were used to study genes related to cuticle structure, chitin metabolism and immunity, a vast amount of the information has not yet been mined for understanding the basic molecular biology of this model insect. In fact, the basic features of these data, such as composition of the RNA-seq reads and lists of library-correlated genes, are unclear. From an extended view of all insects, clear-cut tempospatial expression data are rarely seen in the largest group of animals including Drosophila and mosquitoes, mainly due to their small sizes. Results We obtained the transcriptome data, analyzed the raw reads in relation to the assembled genome, and generated heatmaps for clustered genes. Library characteristics (tissues, stages), number of mapped bases, and sequencing methods affected the observed percentages of genome transcription. While up to 40% of the reads were not mapped to the genome in the initial Cufflinks gene modeling, we identified the causes for the mapping failure and reduced the number of non-mappable reads to <8%. Similarities between libraries, measured based on library-correlated genes, clearly identified differences among tissues or life stages. We calculated gene expression levels, analyzed the most abundantly expressed genes in the libraries. Furthermore, we analyzed tissue-specific gene expression and identified 18 groups of genes with distinct expression patterns. Conclusion We performed a thorough analysis of the 67 RNA-seq datasets to characterize new genomic features of M. sexta. Integrated knowledge of gene functions and expression features will facilitate future functional studies in this biochemical model insect. Electronic supplementary material The online version of this article doi: (10.1186/s12864-017-4147-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaolong Cao
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA.,Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Haobo Jiang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA.
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41
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Remnant EJ, Shi M, Buchmann G, Blacquière T, Holmes EC, Beekman M, Ashe A. A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations. J Virol 2017; 91:e00158-17. [PMID: 28515299 PMCID: PMC5533899 DOI: 10.1128/jvi.00158-17] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/26/2017] [Indexed: 01/16/2023] Open
Abstract
Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees (Apis mellifera) has changed dramatically since the emergence of the parasitic mite Varroa destructor, which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity. To capture the viral diversity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa This analysis revealed seven novel viruses isolated from honey bees sampled globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically diverse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral diversity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management.IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been described in honey bees, with most belonging to the order Picornavirales Collapsing Varroa-infected colonies are often overwhelmed with high levels of picornaviruses. To examine the underlying viral diversity in honey bees, we employed viral metatranscriptomics analyses on three geographically diverse Varroa-resistant populations from Europe, Africa, and the Pacific. We describe seven novel viruses from a range of diverse viral families, including two viruses that are present in all three locations. In honey bees, small RNA sequences indicate that these viruses are processed by Dicer and the RNA interference pathway, whereas Varroa mites produce strikingly novel small RNA patterns. This work increases the number and diversity of known honey bee viruses and will ultimately contribute to improved disease management in our most important agricultural pollinator.
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Affiliation(s)
- Emily J Remnant
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Mang Shi
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Gabriele Buchmann
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | | | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
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42
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Williams T, Virto C, Murillo R, Caballero P. Covert Infection of Insects by Baculoviruses. Front Microbiol 2017; 8:1337. [PMID: 28769903 PMCID: PMC5511839 DOI: 10.3389/fmicb.2017.01337] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 07/03/2017] [Indexed: 12/19/2022] Open
Abstract
Baculoviruses (Baculoviridae) are occluded DNA viruses that are lethal pathogens of the larval stages of some lepidopterans, mosquitoes, and sawflies (phytophagous Hymenoptera). These viruses have been developed as biological insecticides for control of insect pests and as expression vectors in biotechnological applications. Natural and laboratory populations frequently harbor covert infections by baculoviruses, often at a prevalence exceeding 50%. Covert infection can comprise either non-productive latency or sublethal infection involving low level production of virus progeny. Latency in cell culture systems involves the expression of a small subset of viral genes. In contrast, covert infection in lepidopterans is associated with differential infection of cell types, modulation of virus gene expression and avoidance of immune system clearance. The molecular basis for covert infection may reside in the regulation of host-virus interactions through the action of microRNAs (miRNA). Initial findings suggest that insect nudiviruses and vertebrate herpesviruses may provide useful analogous models for exploring the mechanisms of covert infection by baculoviruses. These pathogens adopt mixed-mode transmission strategies that depend on the relative fitness gains that accrue through vertical and horizontal transmission. This facilitates virus persistence when opportunities for horizontal transmission are limited and ensures virus dispersal in migratory host species. However, when host survival is threatened by environmental or physiological stressors, latent or persistent infections can be activated to produce lethal disease, followed by horizontal transmission. Covert infection has also been implicated in population level effects on host-pathogen dynamics due to the reduced reproductive capacity of infected females. We conclude that covert infections provide many opportunities to examine the complexity of insect-virus pathosystems at the organismal level and to explore the evolutionary and ecological relationships of these pathogens with major crop and forest pests.
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Affiliation(s)
| | - Cristina Virto
- Bioinsecticidas Microbianos, Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas, Universidad Pública de NavarraMutilva, Spain
- Laboratorio de Entomología Agrícola y Patología de Insectos, Departamento de Producción Agraria, Universidad Pública de NavarraPamplona, Spain
| | - Rosa Murillo
- Bioinsecticidas Microbianos, Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas, Universidad Pública de NavarraMutilva, Spain
- Laboratorio de Entomología Agrícola y Patología de Insectos, Departamento de Producción Agraria, Universidad Pública de NavarraPamplona, Spain
| | - Primitivo Caballero
- Bioinsecticidas Microbianos, Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas, Universidad Pública de NavarraMutilva, Spain
- Laboratorio de Entomología Agrícola y Patología de Insectos, Departamento de Producción Agraria, Universidad Pública de NavarraPamplona, Spain
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43
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Ryabov EV. Invertebrate RNA virus diversity from a taxonomic point of view. J Invertebr Pathol 2017; 147:37-50. [PMID: 27793741 PMCID: PMC7094257 DOI: 10.1016/j.jip.2016.10.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 10/03/2016] [Accepted: 10/14/2016] [Indexed: 02/04/2023]
Abstract
Invertebrates are hosts to diverse RNA viruses that have all possible types of encapsidated genomes (positive, negative and ambisense single stranded RNA genomes, or a double stranded RNA genome). These viruses also differ markedly in virion morphology and genome structure. Invertebrate RNA viruses are present in three out of four currently recognized orders of RNA viruses: Mononegavirales, Nidovirales, and Picornavirales, and 10 out of 37 RNA virus families that have yet to be assigned to an order. This mini-review describes general properties of the taxonomic groups, which include invertebrate RNA viruses on the basis of their current classification by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Eugene V Ryabov
- ER Healthcare Consulting Ltd., Poundgate Lane, Coventry CV4 8HJ, United Kingdom.
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44
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Kolliopoulou A, Taning CNT, Smagghe G, Swevers L. Viral Delivery of dsRNA for Control of Insect Agricultural Pests and Vectors of Human Disease: Prospects and Challenges. Front Physiol 2017; 8:399. [PMID: 28659820 PMCID: PMC5469917 DOI: 10.3389/fphys.2017.00399] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/26/2017] [Indexed: 12/12/2022] Open
Abstract
RNAi is applied as a new and safe method for pest control in agriculture but efficiency and specificity of delivery of dsRNA trigger remains a critical issue. Various agents have been proposed to augment dsRNA delivery, such as engineered micro-organisms and synthetic nanoparticles, but the use of viruses has received relatively little attention. Here we present a critical view of the potential of the use of recombinant viruses for efficient and specific delivery of dsRNA. First of all, it requires the availability of plasmid-based reverse genetics systems for virus production, of which an overview is presented. For RNA viruses, their application seems to be straightforward since dsRNA is produced as an intermediate molecule during viral replication, but DNA viruses also have potential through the production of RNA hairpins after transcription. However, application of recombinant virus for dsRNA delivery may not be straightforward in many cases, since viruses can encode RNAi suppressors, and virus-induced silencing effects can be determined by the properties of the encoded RNAi suppressor. An alternative is virus-like particles that retain the efficiency and specificity determinants of natural virions but have encapsidated non-replicating RNA. Finally, the use of viruses raises important safety issues which need to be addressed before application can proceed.
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Affiliation(s)
- Anna Kolliopoulou
- Insect Molecular Genetics and Biotechnology Research Group, Institute of Biosciences and Applications, NCSR “Demokritos,”Aghia Paraskevi, Greece
| | - Clauvis N. T. Taning
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent UniversityGhent, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent UniversityGhent, Belgium
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology Research Group, Institute of Biosciences and Applications, NCSR “Demokritos,”Aghia Paraskevi, Greece
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45
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Lawrence SA, Floge SA, Davy JE, Davy SK, Wilson WH. Exploratory analysis of
Symbiodinium
transcriptomes reveals potential latent infection by large dsDNA viruses. Environ Microbiol 2017; 19:3909-3919. [DOI: 10.1111/1462-2920.13782] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 04/24/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Scott A. Lawrence
- School of Biological SciencesVictoria University of WellingtonWellington6140 New Zealand
| | - Sheri A. Floge
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, PO Box 380East Boothbay Maine USA
| | - Joanne E. Davy
- School of Biological SciencesVictoria University of WellingtonWellington6140 New Zealand
| | - Simon K. Davy
- School of Biological SciencesVictoria University of WellingtonWellington6140 New Zealand
| | - William H. Wilson
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, PO Box 380East Boothbay Maine USA
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46
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Hashimoto Y, Macri D, Srivastava I, McPherson C, Felberbaum R, Post P, Cox M. Complete study demonstrating the absence of rhabdovirus in a distinct Sf9 cell line. PLoS One 2017; 12:e0175633. [PMID: 28423032 PMCID: PMC5397025 DOI: 10.1371/journal.pone.0175633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 03/29/2017] [Indexed: 12/26/2022] Open
Abstract
A putative novel rhabdovirus (SfRV) was previously identified in a Spodoptera frugiperda cell line (Sf9 cells [ATCC CRL-1711 lot 58078522]) by next generation sequencing and extensive bioinformatic analysis. We performed an extensive analysis of our Sf9 cell bank (ATCC CRL-1711 lot 5814 [Sf9L5814]) to determine whether this virus was already present in cells obtained from ATCC in 1987. Inverse PCR of DNA isolated from Sf9 L5814 cellular DNA revealed integration of SfRV sequences in the cellular genome. RT-PCR of total RNA showed a deletion of 320 nucleotides in the SfRV RNA that includes the transcriptional motifs for genes X and L. Concentrated cell culture supernatant was analyzed by sucrose density gradient centrifugation and revealed a single band at a density of 1.14 g/ml. This fraction was further analysed by electron microscopy and showed amorphous and particulate debris that did not resemble a rhabdovirus in morphology or size. SDS-PAGE analysis confirmed that the protein composition did not contain the typical five rhabdovirus structural proteins and LC-MS/MS analysis revealed primarily of exosomal marker proteins, the SfRV N protein, and truncated forms of SfRV N, P, and G proteins. The SfRV L gene fragment RNA sequence was recovered from the supernatant after ultracentrifugation of the 1.14 g/ml fraction treated with diethyl ether suggesting that the SfRV L gene fragment sequence is not associated with a diethyl ether resistant nucleocapsid. Interestingly, the 1.14 g/ml fraction was able to transfer baculovirus DNA into Sf9L5814 cells, consistent with the presence of functional exosomes. Our results demonstrate the absence of viral particles in ATCC CRL-1711 lot 5814 Sf9 cells in contrast to a previous study that suggested the presence of infectious rhabdoviral particles in Sf9 cells from a different lot. This study highlights how cell lines with different lineages may present different virosomes and therefore no general conclusions can be drawn across Sf9 cells from different laboratories.
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Affiliation(s)
- Yoshifumi Hashimoto
- Protein Sciences Corporation, Meriden, Connecticut, Unites States of America
| | - Daniel Macri
- Protein Sciences Corporation, Meriden, Connecticut, Unites States of America
| | - Indresh Srivastava
- Protein Sciences Corporation, Meriden, Connecticut, Unites States of America
| | - Clifton McPherson
- Protein Sciences Corporation, Meriden, Connecticut, Unites States of America
| | - Rachael Felberbaum
- Protein Sciences Corporation, Meriden, Connecticut, Unites States of America
| | - Penny Post
- Protein Sciences Corporation, Meriden, Connecticut, Unites States of America
| | - Manon Cox
- Protein Sciences Corporation, Meriden, Connecticut, Unites States of America
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47
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Yang X, Xu P, Graham RI, Yuan H, Wu K. Protocols for Investigating the Host-tissue Distribution, Transmission-mode, and Effect on the Host Fitness of a Densovirus in the Cotton Bollworm. J Vis Exp 2017:55534. [PMID: 28448051 PMCID: PMC5564690 DOI: 10.3791/55534] [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: 10/31/2022] Open
Abstract
Many novel viruses have been discovered in animal hosts using next-generation sequencing technologies. Previously, we reported a mutualistic virus, Helicoverpa armigera densovirus (HaDV2), in a lepidopteran species, the cotton bollworm, Helicoverpa armigera (Hubner). Here, we describe the protocols that are currently used to study the effect of HaDV2 on its host. First, we establish a HaDV2-free cotton bollworm colony from a single breeding pair. Then, we orally inoculate some neonate larval offspring with HaDV2-containing filtered liquid to produce two colonies with the same genetic background: one HaDV2-infected, the other uninfected. A protocol to compare life table parameters (e.g., larval, pupal, and adult periods and fecundity) between the HaDV2-infected and -uninfected individuals is also presented, as are the protocols for determining the host-tissue distribution and transmission efficiency of HaDV2. These protocols would also be suitable for investigating the effects of other orally transmitted viruses on their insect hosts, lepidopteran hosts in particular.
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Affiliation(s)
- Xianming Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences
| | - Pengjun Xu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences
| | | | - He Yuan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences
| | - Kongming Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences;
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48
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Galinier R, Tetreau G, Portet A, Pinaud S, Duval D, Gourbal B. First characterization of viruses from freshwater snails of the genus Biomphalaria, the intermediate host of the parasite Schistosoma mansoni. Acta Trop 2017; 167:196-203. [PMID: 28012902 DOI: 10.1016/j.actatropica.2016.12.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/16/2016] [Accepted: 12/18/2016] [Indexed: 12/11/2022]
Abstract
We report the genome sequence and organization of five viruses infecting snails of both Biomphalaria glabrata and Biomphalaria pfeifferi, which are vectors of the intestinal schistosomiasis. Four viruses presented a polyadenylated positive single strand RNA genome encoding one or two large open reading frames (ORFs) flanked by untranslated region. Conserved protein motifs typical of the picorna-like virus superfamily were identified in these viruses but they all presented different genome organization. Phylogenetic analysis confirmed their assignment to this superfamily. The partially characterized fifth virus presented sequence similarity for Totiviridae, a family of non-polyadenylated double-strand RNA viruses. Virus distribution and relative abundance between the five strains of Biomphalaria originating from different geographical areas was determined. Our results provide valuable information of new viruses from Biomphalaria and pave the way for future studies dedicated to their impact on snail fitness and Biomphalaria/Schistosoma interactions.
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49
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van Aerle R, Santos EM. Advances in the application of high-throughput sequencing in invertebrate virology. J Invertebr Pathol 2017; 147:145-156. [PMID: 28249815 DOI: 10.1016/j.jip.2017.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 10/20/2022]
Abstract
Over the last decade, advances in high-throughput sequencing technologies have revolutionised biological research, making it possible for DNA/RNA sequencing of any organism of interest to be undertaken. Sequencing approaches are now routinely used in the detection and characterisation of (novel) viruses, investigation of host-pathogen interactions, and effective development of disease treatment strategies. For the sequencing and identification of viruses of interest, metagenomics approaches using infected host tissue are frequently used, as it is not always possible to culture and isolate these pathogens. High-throughput sequencing can also be used to investigate host-pathogen interactions by investigating (temporal) transcriptomic responses of both the host and virus, potentially leading to the discovery of novel opportunities for treatment and drug targets. In addition, viruses in environmental samples (e.g. water or soil samples) can be identified using eDNA/metagenomics approaches. The promise that recent developments in sequencing brings to the field of invertebrate virology are not devoid of technical challenges, including the need for better laboratory and bioinformatics strategies to sequence and assemble virus genomes within complex tissue or environmental samples, and the difficulties associated with the annotation of the large number of novel viruses being discovered.
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Affiliation(s)
- R van Aerle
- Centre for Environment, Fisheries, and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset DT4 8UB, UK.
| | - E M Santos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
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50
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Llopis-Giménez A, Maria González R, Millán-Leiva A, Catalá M, Llacer E, Urbaneja A, Herrero S. Novel RNA viruses producing simultaneous covert infections in Ceratitis capitata. Correlations between viral titers and host fitness, and implications for SIT programs. J Invertebr Pathol 2016; 143:50-60. [PMID: 27914927 DOI: 10.1016/j.jip.2016.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 12/25/2022]
Abstract
The Mediterranean fruit fly (medfly), Ceratitis capitata is a highly polyphagous pest, which infests multiple species of fruits and vegetables worldwide. In addition to the traditional control with chemical insecticides, sterile insect technique (SIT) has been implemented in integrated programs worldwide, and has become an essential measure for the control of this pest. A key issue for SIT is to release sterile males that are sufficiently competitive with males from the wild population. Using sequence information available in public databases, three novel picornaviruses infecting medflies were discovered and named as C. capitata iflavirus 1 and 2 (CcaIV1 and CcaIV2), and C. capitata noravirus (CcaNV). Additional analyses have revealed the presence of CcaIV2 and CcaNV covertly infecting most of the medfly strains used in the different SIT programs around the world, as well as in field captures in the east of Spain. High viral titers of CcaNV were associated with a reduction in the lifespan of males released to the field for the control of this pest, suggesting the possibility that CcaNV may impair the fitness of sterile flies produced by SIT programs.
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Affiliation(s)
- Angel Llopis-Giménez
- Department of Genetics, Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain; Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI-BIOTECMED), Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain
| | - Rosa Maria González
- Department of Genetics, Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain; Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI-BIOTECMED), Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain
| | - Anabel Millán-Leiva
- Department of Genetics, Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain; Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI-BIOTECMED), Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain
| | - Marta Catalá
- Instituto Valenciano de Investigaciones Agrarias, Unidad Asociada de Entomología IVIA-UJI, Centro de Protección Vegetal y Biotecnología, 46113 Moncada, Spain
| | - Elena Llacer
- Instituto Valenciano de Investigaciones Agrarias, Unidad Asociada de Entomología IVIA-UJI, Centro de Protección Vegetal y Biotecnología, 46113 Moncada, Spain
| | - Alberto Urbaneja
- Instituto Valenciano de Investigaciones Agrarias, Unidad Asociada de Entomología IVIA-UJI, Centro de Protección Vegetal y Biotecnología, 46113 Moncada, Spain
| | - Salvador Herrero
- Department of Genetics, Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain; Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI-BIOTECMED), Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain.
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