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Xu L, Bie M, Li J, Zhou H, Hu T, Carr MJ, Lu L, Shi W. Isolation and characterization of a novel rodent hepevirus in long-tailed dwarf hamsters ( Cricetulus longicaudatus) in China. J Gen Virol 2024; 105. [PMID: 38767609 DOI: 10.1099/jgv.0.001989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
Hepeviruses have been identified in a broad range of animal hosts, including mammals, birds, and fish. In this study, rodents (n=91) from seven different species and ten pikas (Ochotona curzoniae) were collected in Qinghai Province, China. Using transcriptomic sequencing and confirmatory molecular testing, hepeviruses were detected in 27 of 45 (60 %) long-tailed dwarf hamsters (Cricetulus longicaudatus) and were undetected in other rodents and pika. The complete genome sequences from 14 representative strains were subsequently obtained, and phylogenetic analyses suggested that they represent a novel species within the genus Rocahepevirus, which we tentatively designated as Cl-2018QH. The virus was successfully isolated in human hepatoma (Huh-7) and murine fibroblast (17 Cl-1) cell lines, though both exhibited limited replication as assayed by detection of negative-sense RNA intermediates. A129 immunodeficient mice were inoculated with Cl-2018QH and the virus was consistently detected in multiple organs, despite relatively low viral loads. In summary, this study has described a novel rodent hepevirus, which enhances our knowledge of the genetic diversity of rodent hepeviruses and highlights its potential for cross-species transmission.
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Affiliation(s)
- Lin Xu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan 250117, PR China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, PR China
| | - Mengyu Bie
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan 250117, PR China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, PR China
| | - Juan Li
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, PR China
| | - Hong Zhou
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, PR China
| | - Tao Hu
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, PR China
| | - Michael J Carr
- National Virus Reference Laboratory, School of Medicine, University College Dublin, Dublin, D04 E1W1, Ireland
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
| | - Liang Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Weifeng Shi
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
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Yuan Z, Yang X, Hu Z, Gao Y, Yan P, Zheng F, Hong K, Cen K, Mai Y, Bai Y, Guo Y, Zhou J. Investigating the impact of inflammatory response-related genes on renal fibrosis diagnosis: a machine learning-based study with experimental validation. J Biomol Struct Dyn 2024:1-13. [PMID: 38381715 DOI: 10.1080/07391102.2024.2317992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
Renal fibrosis plays a crucial role in the progression of renal diseases, yet the lack of effective diagnostic markers poses challenges in scientific and clinical practices. In this study, we employed machine learning techniques to identify potential biomarkers for renal fibrosis. Utilizing two datasets from the GEO database, we applied LASSO, SVM-RFE and RF algorithms to screen for differentially expressed genes related to inflammatory responses between the renal fibrosis group and the control group. As a result, we identified four genes (CCL5, IFITM1, RIPK2, and TNFAIP6) as promising diagnostic indicators for renal fibrosis. These genes were further validated through in vivo experiments and immunohistochemistry, demonstrating their utility as reliable markers for assessing renal fibrosis. Additionally, we conducted a comprehensive analysis to explore the relationship between these candidate biomarkers, immunity, and drug sensitivity. Integrating these findings, we developed a nomogram with a high discriminative ability, achieving a concordance index of 0.933, enabling the prediction of disease risk in patients with renal fibrosis. Overall, our study presents a predictive model for renal fibrosis and highlights the significance of four potential biomarkers, facilitating clinical diagnosis and personalized treatment. This finding presents valuable insights for advancing precision medicine approaches in the management of renal fibrosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ziwei Yuan
- Department of Endocrinology, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Xuejia Yang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zujian Hu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuanyuan Gao
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Penghua Yan
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fan Zheng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kai Hong
- Department of General Surgery, Ningbo First Hospital, Ningbo, China
| | - Kenan Cen
- Department of General Surgery, Ningbo First Hospital, Ningbo, China
| | - Yifeng Mai
- Department of General Surgery, Ningbo First Hospital, Ningbo, China
| | - Yongheng Bai
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yangyang Guo
- Department of General Surgery, Ningbo First Hospital, Ningbo, China
| | - Jingzong Zhou
- Department of Endocrinology, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou, Zhejiang, China
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Wang H, Chao S, Yan Q, Zhang S, Chen G, Mao C, Hu Y, Yu F, Wang S, Lv L, Yang B, He J, Zhang S, Zhang L, Simmonds P, Feng G. Genetic diversity of RNA viruses infecting invertebrate pests of rice. SCIENCE CHINA. LIFE SCIENCES 2024; 67:175-187. [PMID: 37946067 DOI: 10.1007/s11427-023-2398-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/26/2023] [Indexed: 11/12/2023]
Abstract
Invertebrate species are a natural reservoir of viral genetic diversity, and invertebrate pests are widely distributed in crop fields. However, information on viruses infecting invertebrate pests of crops is limited. In this report, we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice fields. We identified 296 new RNA viruses and 13 known RNA viruses. These viruses clustered within 31 families, with many highly divergent viruses constituting potentially new families and genera. Of the identified viruses, 13 RNA viruses clustered within the Fiersviridae family of bacteriophages, and 48 RNA viruses clustered within families and genera of mycoviruses. We detected known rice viruses in novel invertebrate hosts at high abundances. Furthermore, some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus species. Forty-five potential insect pathogenic RNA viruses were detected in invertebrate species. Our analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral diversity. Cross-species transmission of RNA viruses was detected between invertebrate hosts. Newly identified viral genomes showed extensive variation for invertebrate viral families or genera. Together, the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species, the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.
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Affiliation(s)
- Haoran Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shufen Chao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Qing Yan
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Shu Zhang
- Institute of Plant Protection & Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Guoqing Chen
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Chonghui Mao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Yang Hu
- Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, 550000, China
| | - Fengquan Yu
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China
| | - Shuo Wang
- Sanya Agricultural Technology Extension and Service Centre, Sanya, 572000, China
| | - Liang Lv
- Institute of Plant Protection & Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Baojun Yang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Jiachun He
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Songbai Zhang
- College of Agriculture, Yangtze University, Jingzhou, 434000, China
| | - Liangsheng Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310012, China
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK
| | - Guozhong Feng
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China.
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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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Zhang W, Li R, Li S, Li SY, Niu J, Wang JJ. RNA virus diversity in three parasitoid wasps of tephritid flies: insights from novel and known species. Microbiol Spectr 2023; 11:e0313923. [PMID: 37930041 PMCID: PMC10714968 DOI: 10.1128/spectrum.03139-23] [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: 08/20/2023] [Accepted: 09/29/2023] [Indexed: 11/07/2023] Open
Abstract
IMPORTANCE Parasitoid wasp populations have developed persistent beneficial symbiotic relationships with several viruses through repeated evolution. However, there have been limited reports on RNA viruses in parasitoid wasps of tephritid flies, a significant pest group affecting fruits and vegetables. This study explores the diversity of RNA viruses in three parasitoid wasps of tephritid flies and highlights the potential biological significance of specific viruses in Diachasmimorpha longicaudata. These findings have important implications for the development of sustainable pest management strategies and the enhancement of artificial rearing techniques for parasitoid wasps.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Rong Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Shuai Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Shao-Yang Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), International Joint Laboratory of China-Belgium on 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
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
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Cornman RS. Data mining reveals tissue-specific expression and host lineage-associated forms of Apis mellifera filamentous virus. PeerJ 2023; 11:e16455. [PMID: 38025724 PMCID: PMC10655722 DOI: 10.7717/peerj.16455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Background Apis mellifera filamentous virus (AmFV) is a large double-stranded DNA virus of uncertain phylogenetic position that infects honey bees (Apis mellifera). Little is known about AmFV evolution or molecular aspects of infection. Accurate annotation of open-reading frames (ORFs) is challenged by weak homology to other known viruses. This study was undertaken to evaluate ORFs (including coding-frame conservation, codon bias, and purifying selection), quantify genetic variation within AmFV, identify host characteristics that covary with infection rate, and examine viral expression patterns in different tissues. Methods Short-read data were accessed from the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI). Sequence reads were downloaded from accessions meeting search criteria and scanned for kmers representative of AmFV genomic sequence. Samples with kmer counts above specified thresholds were downloaded in full for mapping to reference sequences and de novo assembly. Results At least three distinct evolutionary lineages of AmFV exist. Clade 1 predominates in Europe but in the Americas and Africa it is replaced by the other clades as infection level increases in hosts. Only clade 3 was found at high relative abundance in hosts with African ancestry, whereas all clades achieved high relative abundance in bees of non-African ancestry. In Europe and Africa, clade 2 was generally detected only in low-level infections but was locally dominant in some North American samples. The geographic distribution of clade 3 was consistent with an introduction to the Americas with 'Africanized' honey bees in the 1950s. Localized genomic regions of very high nucleotide divergence in individual isolates suggest recombination with additional, as-yet unidentified AmFV lineages. A set of 155 high-confidence ORFs was annotated based on evolutionary conservation in six AmFV genome sequences representative of the three clades. Pairwise protein-level identity averaged 94.6% across ORFs (range 77.1-100%), which generally exhibited low evolutionary rates and moderate to strong codon bias. However, no robust example of positive diversifying selection on coding sequence was found in these alignments. Most of the genome was detected in RNA short-read alignments. Transcriptome assembly often yielded contigs in excess of 50 kb and containing ORFs in both orientations, and the termini of long transcripts were associated with tandem repeats. Lower levels of AmFV RNA were detected in brain tissue compared to abdominal tissue, and a distinct set of ORFs had minimal to no detectable expression in brain tissue. A scan of DNA accessions from the parasitic mite Varroa destructor was inconclusive with respect to replication in that species. Discussion Collectively, these results expand our understanding of this enigmatic virus, revealing transcriptional complexity and co-evolutionary associations with host lineage.
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Xiao Y, Fei D, Li M, Ma Y, Ma M. Establishment and Application of CRISPR-Cas12a-Based Recombinase Polymerase Amplification and a Lateral Flow Dipstick and Fluorescence for the Detection and Distinction of Deformed Wing Virus Types A and B. Viruses 2023; 15:2041. [PMID: 37896818 PMCID: PMC10612068 DOI: 10.3390/v15102041] [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: 08/04/2023] [Revised: 09/21/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Deformed wing virus (DWV) is one of the important pathogens of the honey bee (Apis mellifera), which consists of three master variants: types A, B, and C. Among them, DWV types A (DWV-A) and B (DWV-B) are the most prevalent variants in honey bee colonies and have been linked to colony decline. DWV-A and DWV-B have different virulence, but it is difficult to distinguish them via traditional methods. In this study, we established a visual detection assay for DWV-A and DWV-B using recombinase polymerase amplification (RPA) and a lateral flow dipstick (LFD) coupled with the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) 12a fluorescence system (RPA-CRISPR-Cas12a-LFD). The limit of detection of this system was ~6.5 × 100 and 6.2 × 101 copies/μL for DWV-A and DWV-B, respectively. The assays were specific and non-cross-reactive against other bee viruses, and the results could be visualized within 1 h. The assays were validated by extracting cDNA from 36 clinical samples of bees that were suspected to be infected with DWV. The findings were consistent with those of traditional reverse transcription-quantitative polymerase chain reaction, and the RPA-CRISPR-Cas12a assay showed the specific, sensitive, simple, and appropriate detection of DWV-A and DWV-B. This method can facilitate the visual and qualitative detection of DWV-A and DWV-B as well as the monitoring of different subtypes, thereby providing potentially better control and preventing current and future DWV outbreaks.
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Affiliation(s)
- Yuting Xiao
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou 121000, China; (Y.X.); (M.L.)
| | - Dongliang Fei
- Experimental Animal Center of Jinzhou Medical University, Jinzhou 121000, China; (D.F.); (Y.M.)
| | - Ming Li
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou 121000, China; (Y.X.); (M.L.)
| | - Yueyu Ma
- Experimental Animal Center of Jinzhou Medical University, Jinzhou 121000, China; (D.F.); (Y.M.)
| | - Mingxiao Ma
- College of Animal Husbandry and Veterinary Medicine, Jinzhou Medical University, Jinzhou 121000, China; (Y.X.); (M.L.)
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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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Chantaphanwattana T, Shafiey H, Phokasem P, Disayathanoowat T, Paxton RJ. The presence of identical deformed wing virus sequence variants in co-occurring Apis species in Northern Thailand may represent a potential epidemiological threat to native honey bees of Southeast Asia. J Invertebr Pathol 2023; 200:107957. [PMID: 37364674 DOI: 10.1016/j.jip.2023.107957] [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: 02/03/2023] [Revised: 06/15/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Widespread native honey bee species in South and East Asia (Apis cerana, Apis dorsata and Apis florea) and the imported western honey bee (Apis mellifera) share habitats and potentially also share pathogens. Chief among the threats facing A. mellifera in Europe and North America is deformed wing virus (DWV), including its two principal genotypes: A and B (DWV-A and DWV-B respectively). Though DWV-A has been recorded in Asia's native Apis species, it is not known if DWV-B, or both DWV-A and DWV-B, are currently widespread in Asia and, if so, whether viral transmission is primarily intraspecific or interspecific. This study aims to fill these knowledge gaps by (i) determining the DWV genotype in four co-occurring Apis host species using qPCR and (ii) inferring viral transmission between them using nucleotide sequences of DWV from Apis host species collected at three independent localities in Northern Thailand. We found DWV-A and -B in all four Apis species, the exotic A. mellifera and the native A. cerana, A. dorsata and A. florea. That DWV-A sequences were identical across Apis species at the same locality, with a similar pattern for DWV-B sequences, suggests that DWV's epidemiology is largely driven by ongoing interspecific transmission (spillover) of DWV across co-occurring native and exotic Apis species. Both genotypes of DWV represent a serious threat to Asia's exotic and native honey bee species.
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Affiliation(s)
- Thunyarat Chantaphanwattana
- Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Hassan Shafiey
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle, (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
| | - Patcharin Phokasem
- Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Terd Disayathanoowat
- Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; Research Center in Deep Technology Associated with Beekeeping and Bee Products for Sustainable Development Goals, Chiang Mai University, Chiang Mai 50200, Thailand.
| | - Robert J Paxton
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle, (Saale), Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany.
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Lee E, Vansia R, Phelan J, Lofano A, Smith A, Wang A, Bilodeau GJ, Pernal SF, Guarna MM, Rott M, Griffiths JS. Area Wide Monitoring of Plant and Honey Bee ( Apis mellifera) Viruses in Blueberry ( Vaccinium corymbosum) Agroecosystems Facilitated by Honey Bee Pollination. Viruses 2023; 15:v15051209. [PMID: 37243295 DOI: 10.3390/v15051209] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Healthy agroecosystems are dependent on a complex web of factors and inter-species interactions. Flowers are hubs for pathogen transmission, including the horizontal or vertical transmission of plant-viruses and the horizontal transmission of bee-viruses. Pollination by the European honey bee (Apis mellifera) is critical for industrial fruit production, but bees can also vector viruses and other pathogens between individuals. Here, we utilized commercial honey bee pollination services in blueberry (Vaccinium corymbosum) farms for a metagenomics-based bee and plant virus monitoring system. Following RNA sequencing, viruses were identified by mapping reads to a reference sequence database through the bioinformatics portal Virtool. In total, 29 unique plant viral species were found at two blueberry farms in British Columbia (BC). Nine viruses were identified at one site in Ontario (ON), five of which were not identified in BC. Ilarviruses blueberry shock virus (BlShV) and prune dwarf virus (PDV) were the most frequently detected viruses in BC but absent in ON, while nepoviruses tomato ringspot virus and tobacco ringspot virus were common in ON but absent in BC. BlShV coat protein (CP) nucleotide sequences were nearly identical in all samples, while PDV CP sequences were more diverse, suggesting multiple strains of PDV circulating at this site. Ten bee-infecting viruses were identified, with black queen cell virus frequently detected in ON and BC. Area-wide bee-mediated pathogen monitoring can provide new insights into the diversity of viruses present in, and the health of, bee-pollination ecosystems. This approach can be limited by a short sampling season, biased towards pollen-transmitted viruses, and the plant material collected by bees can be very diverse. This can obscure the origin of some viruses, but bee-mediated virus monitoring can be an effective preliminary monitoring approach.
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Affiliation(s)
- Eunseo Lee
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
| | - Raj Vansia
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - James Phelan
- Sidney Laboratory, Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Rd., North Saanich, BC V8L 1H3, Canada
| | - Andrea Lofano
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
| | - Adam Smith
- Sidney Laboratory, Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Rd., North Saanich, BC V8L 1H3, Canada
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
| | - Guillaume J Bilodeau
- Ottawa Plant Laboratory, Canadian Food Inspection Agency, 3851 Fallowfield Rd., Ottawa, ON K2J 4S1, Canada
| | - Stephen F Pernal
- Beaverlodge Research Farm, Agriculture and Agri-Food Canada, P.O. Box 29, Beaverlodge, AB T0H 0C0, Canada
| | - M Marta Guarna
- Beaverlodge Research Farm, Agriculture and Agri-Food Canada, P.O. Box 29, Beaverlodge, AB T0H 0C0, Canada
| | - Michael Rott
- Sidney Laboratory, Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Rd., North Saanich, BC V8L 1H3, Canada
| | - Jonathan S Griffiths
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
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Baril C, LeMoine CMR, Cassone BJ. Black queen cell virus detected in Canadian mosquitoes. JOURNAL OF INSECT SCIENCE (ONLINE) 2023; 23:10. [PMID: 37004145 PMCID: PMC10066845 DOI: 10.1093/jisesa/iead016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/24/2023] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Black queen cell virus (BQCV) is a ubiquitous honeybee virus and a significant pathogen to queen bee (Apis mellifera) larvae. However, many aspects of the virus remain poorly understood, including the transmission dynamics. In this study, we used next-generation sequencing to identify BQCV in Aedes vexans (n = 4,000) collected in 2019 and 2020 from Manitoba, Canada. We assembled de novo the nearly complete (>96%) genome sequence of the virus, which is the first available from North America and the first report of BQCV being harbored by mosquitoes. Phylogenetic tree reconstructions indicated that the genome had 95.5% sequence similarity to a BQCV isolate from Sweden. Sequences of a potential vector (Varroa destructor) and a microsporidian associated with BQCV (Nosema apis) were not identified in the mosquito samples, however, we did detect sequences of plant origin. We, therefore, hypothesize that the virus was indirectly acquired by mosquitoes foraging at the same nectar sources as honeybees.
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Affiliation(s)
- Cole Baril
- Department of Biology, Brandon University, Brandon, Manitoba R7A 6A9, Canada
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