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Nigg JC, Castelló-Sanjuán M, Blanc H, Frangeul L, Mongelli V, Godron X, Bardin AJ, Saleh MC. Viral infection disrupts intestinal homeostasis via Sting-dependent NF-κB signaling in Drosophila. Curr Biol 2024; 34:2785-2800.e7. [PMID: 38823381 DOI: 10.1016/j.cub.2024.05.009] [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: 12/13/2023] [Revised: 04/11/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Host-microbe interactions influence intestinal stem cell (ISC) activity to modulate epithelial turnover and composition. Here, we investigated the functional impacts of viral infection on intestinal homeostasis and the mechanisms by which viral infection alters ISC activity. We report that Drosophila A virus (DAV) infection disrupts intestinal homeostasis in Drosophila by inducing sustained ISC proliferation, resulting in intestinal dysplasia, loss of gut barrier function, and reduced lifespan. We found that additional viruses common in laboratory-reared Drosophila also promote ISC proliferation. The mechanism of DAV-induced ISC proliferation involves progenitor-autonomous epidermal growth factor receptor (EGFR) signaling, c-Jun N-terminal kinase (JNK) activity in enterocytes, and requires Sting-dependent nuclear factor κB (NF-κB) (Relish) activity. We further demonstrate that activating Sting-Relish signaling is sufficient to induce ISC proliferation, promote intestinal dysplasia, and reduce lifespan in the absence of infection. Our results reveal that viral infection can significantly disrupt intestinal physiology, highlight a novel role for Sting-Relish signaling, and support a role for viral infection in aging.
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Affiliation(s)
- Jared C Nigg
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Mauro Castelló-Sanjuán
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Hervé Blanc
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Lionel Frangeul
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Vanesa Mongelli
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
| | - Xavier Godron
- DNA Script SAS, 67 Avenue de Fontainebleau, 94270 Le Kremlin-Bicêtre, France
| | - Allison J Bardin
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, INSERM U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Maria-Carla Saleh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France.
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2
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Ning C, Ye ZX, Xu ZT, Li T, Zhang CX, Chen JP, Li JM, Mao Q. Complete genome sequence and genetic characterization of a novel segmented RNA virus infecting Nilaparvata lugens. Arch Virol 2024; 169:141. [PMID: 38850364 DOI: 10.1007/s00705-024-06066-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/03/2024] [Indexed: 06/10/2024]
Abstract
The brown planthopper (BPH), Nilaparvata lugens, is a significant agricultural pest capable of long-distance migration and transmission of viruses that cause severe disease in rice. In this study, we identified a novel segmented RNA virus in a BPH, and this virus exhibited a close relationship to members of a recently discovered virus lineage known as "quenyaviruses" within the viral kingdom Orthornavirae. This newly identified virus was named "Nilaparvata lugens quenyavirus 1" (NLQV1). NLQV1 consists of five positive-sense, single-stranded RNAs, with each segment containing a single open reading frame (ORF). The genomic characteristics and phylogenetic analysis support the classification of NLQV1 as a novel quenyavirus. Notably, all of the genome segments of NLRV contained the 5'-terminal sequence AUCUG. The characteristic virus-derived small interfering RNA (vsiRNA) profile of NLQV1 suggests that the antiviral RNAi pathway of the host BPH was activated in response to virus infection. These findings represent the first documented report of quenyaviruses in planthoppers, contributing to our understanding of quenyaviruses and expanding our knowledge of insect-specific viruses in planthoppers.
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Affiliation(s)
- Chao Ning
- 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
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhong-Tian Xu
- 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
| | - Ting 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
| | - 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
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, 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
| | - Qianzhuo Mao
- 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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3
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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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Obonyo D, Ouma G, Ikawa R, Odeny DA. Meta-transcriptomic identification of groundnut RNA viruses in western Kenya and the novel detection of groundnut as a host for Cauliflower mosaic virus. Virology 2024; 593:110011. [PMID: 38367474 DOI: 10.1016/j.virol.2024.110011] [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: 10/16/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND Groundnut (Arachis hypogaea L.) is the 13th most important global crop grown throughout the tropical and subtropical regions of the world. One of the major constraints to groundnut production is viruses, which are also the most economically important and most abundant pathogens among cultivated legumes. Only a few studies have reported the characterization of RNA viruses in cultivated groundnuts in western Kenya, most of which deployed classical methods of detecting known viruses. METHODS We sampled twenty-one symptomatic and three asymptomatic groundnut leaf samples from farmers' fields in western Kenya. Total RNA was extracted from the samples followed by First-strand cDNA synthesis and sequencing on the Illumina HiSeq 2500 platform. After removing host and rRNA sequences, high-quality viral RNA sequences were de novo assembled and viral genomes annotated using the publicly available NCBI virus database. Multiple sequence alignment and phylogenetic analysis were done using MEGA X. RESULTS Bioinformatics analyses using as low as ∼3.5 million reads yielded complete and partial genomes for Cauliflower mosaic virus (CaMV), Cowpea polerovirus 2 (CPPV2), Groundnut rosette assistor virus (GRAV), Groundnut rosette virus (GRV), Groundnut rosette virus satellite RNA (satRNA) and Peanut mottle virus (PeMoV) falling within the species demarcation criteria. This is the first report of CaMV and the second report of CPPV2 on groundnut hosts in the world. Confirmation of the detected viruses was further verified through phylogenetic analyses alongside reported publicly available highly similar viruses. PeMoV was the only seed-borne virus reported. CONCLUSION Our findings demonstrate the power of Next Generation Sequencing in the discovery and identification of novel viruses in groundnuts. The detection of the new viruses indicates the complexity of virus diseases in groundnuts and would require more focus in future studies to establish the effect of the viruses as sole or mixed infections on the crop. The detection of PeMoV with potential origin from Malawi indicates the importance of seed certification and cross-boundary seed health testing.
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Affiliation(s)
- Dennis Obonyo
- Department of Biotechnology, University of Eldoret, Kenya, P.O Box 1125-30100, Eldoret, Kenya; Centre for Biotechnology and Bioinformatics, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - George Ouma
- Institute for Climate Change and Adaptation, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - Rachel Ikawa
- Centre for Biotechnology and Bioinformatics, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Eastern and Southern Africa, P.O Box 39063-00623, Nairobi, Kenya.
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5
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Wallace MA, Obbard DJ. Naturally occurring viruses of Drosophila reduce offspring number and lifespan. Proc Biol Sci 2024; 291:20240518. [PMID: 38747703 DOI: 10.1098/rspb.2024.0518] [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: 03/02/2024] [Accepted: 04/23/2024] [Indexed: 07/31/2024] Open
Abstract
Drosophila remains a pre-eminent insect model system for host-virus interaction, but the host range and fitness consequences of the drosophilid virome are poorly understood. Metagenomic studies have reported approximately 200 viruses associated with Drosophilidae, but few isolates are available to characterize the Drosophila immune response, and most characterization has relied on injection and systemic infection. Here, we use a more natural infection route to characterize the fitness effects of infection and to study a wider range of viruses. We exposed laboratory Drosophila melanogaster to 23 naturally occurring viruses from wild-collected drosophilids. We recorded transmission rates along with two components of female fitness: survival and the lifetime number of adult offspring produced. Nine different viruses transmitted during contact with laboratory D. melanogaster, although for the majority, rates of transmission were less than 20%. Five virus infections led to a significant decrease in lifespan (D. melanogaster Nora virus, D. immigrans Nora virus, Muthill virus, galbut virus and Prestney Burn virus), and three led to a reduction in the total number of offspring. Our findings demonstrate the utility of the Drosophila model for community-level studies of host-virus interactions, and suggest that viral infection could be a substantial fitness burden on wild flies.
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Affiliation(s)
- Megan A Wallace
- Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Darren J Obbard
- Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
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6
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Sharpe SR, Morrow JL, Cook JM, Papanicolaou A, Riegler M. Transmission mode predicts coinfection patterns of insect-specific viruses in field populations of the Queensland fruit fly. Mol Ecol 2024; 33:e17226. [PMID: 38018898 DOI: 10.1111/mec.17226] [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: 05/03/2023] [Revised: 10/05/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023]
Abstract
Insect-specific viruses (ISVs) can affect insect health and fitness, but can also interact with other insect-associated microorganisms. Despite this, ISVs are often studied in isolation from each other, in laboratory populations. Consequently, their diversity, prevalence and associations with other viruses in field populations are less known, yet these parameters are important to understanding virus epidemiology. To help address this knowledge gap, we assessed the diversity, prevalence and coinfections of three ISVs (horizontally transmitted cripavirus, biparentally transmitted sigmavirus and maternally transmitted iflavirus) in 29 field populations of Queensland fruit fly, Australia's most significant horticultural pest, in the context of their different transmission modes. We detected new virus variant diversity. In contrast to the very high virus prevalence in laboratory populations, 46.8% of 293 field flies carried one virus and 4.8% had two viruses. Cripavirus and sigmavirus occurred in all regions, while iflavirus was restricted to subtropical and tropical regions. Cripavirus was most prevalent (37.5%), followed by sigmavirus (13.7%) and iflavirus (4.4%). Cripavirus coinfected some flies with either one of the two vertically transmitted viruses. However, sigmavirus did not coinfect individuals with iflavirus. Three different modelling approaches detected negative association patterns between sigmavirus and iflavirus, consistent with the absence of such coinfections in laboratory populations. This may be linked with their maternal transmission and the ineffective paternal transmission of sigmavirus. Furthermore, we found that, unlike sigmavirus and iflavirus, cripavirus load was higher in laboratory than field flies. Laboratory and mass-rearing conditions may increase ISV prevalence and load due to increased transmission opportunities. We conclude that a combination of field and laboratory studies is needed to uncover ISV interactions and further our understanding of ISV epidemiology.
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Affiliation(s)
- Stephen R Sharpe
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Jennifer L Morrow
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - James M Cook
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Markus Riegler
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
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7
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Chrostek E. Procedures for the Detection of Wolbachia-Conferred Antiviral Protection in Drosophila melanogaster. Methods Mol Biol 2024; 2739:219-237. [PMID: 38006555 DOI: 10.1007/978-1-0716-3553-7_14] [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: 11/27/2023]
Abstract
Spread of Wolbachia infections in host populations may be enhanced by Wolbachia-conferred protection from viral pathogens. Wolbachia-infected Drosophila melanogaster survive the pathogenic effects of positive-sense single-stranded RNA virus infections at a higher rate than the flies without Wolbachia. The protection can occur with or without detectable reduction in virus titer. For the comparisons to be meaningful, Wolbachia-harboring and Wolbachia-free insects need to be genetically matched, and original populations of gut microbiota need to be restored after the removal of Wolbachia using antibiotics. Here, I describe the procedures needed to detect Wolbachia-conferred antiviral protection against Drosophila C virus measured as the difference in survival and viral titer between flies with and without Wolbachia.
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Affiliation(s)
- Ewa Chrostek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland.
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK.
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8
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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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9
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Lin Y, Pascall DJ. Characterisation of putative novel tick viruses and zoonotic risk prediction. Ecol Evol 2024; 14:e10814. [PMID: 38259958 PMCID: PMC10800298 DOI: 10.1002/ece3.10814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/02/2023] [Accepted: 11/24/2023] [Indexed: 01/24/2024] Open
Abstract
Tick-associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta-genomic and -transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta-genomic and -transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick-associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick-associated viruses using a genome composition-based machine learning model. We found five high-risk tick-associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick-associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick-associated diseases.
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Affiliation(s)
- Yuting Lin
- MRC Biostatistics UnitUniversity of CambridgeCambridgeUK
- Royal Veterinary CollegeUniversity of LondonLondonUK
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10
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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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11
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Dudas G, Batson J. Accumulated metagenomic studies reveal recent migration, whole genome evolution, and undiscovered diversity of orthomyxoviruses. J Virol 2023; 97:e0105623. [PMID: 37830816 PMCID: PMC10653993 DOI: 10.1128/jvi.01056-23] [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: 07/17/2023] [Accepted: 08/29/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE The number of known virus species has increased dramatically through metagenomic studies, which search genetic material sampled from a host for non-host genes. Here, we focus on an important viral family that includes influenza viruses, the Orthomyxoviridae, with over 100 recently discovered viruses infecting hosts from humans to fish. We find that one virus called Wǔhàn mosquito virus 6, discovered in mosquitoes in China, has spread across the globe very recently. Surface proteins used to enter cells show signs of rapid evolution in Wǔhàn mosquito virus 6 and its relatives which suggests an ability to infect vertebrate animals. We compute the rate at which new orthomyxovirus species discovered add evolutionary history to the tree of life, predict that many viruses remain to be discovered, and discuss what appropriately designed future studies can teach us about how diseases cross between continents and species.
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Affiliation(s)
- Gytis Dudas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Joshua Batson
- Chan Zuckerberg Biohub, San Francisco, California, USA
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12
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Abel SM, Hong Z, Williams D, Ireri S, Brown MQ, Su T, Hung KY, Henke JA, Barton JP, Le Roch KG. Small RNA sequencing of field Culex mosquitoes identifies patterns of viral infection and the mosquito immune response. Sci Rep 2023; 13:10598. [PMID: 37391513 PMCID: PMC10313667 DOI: 10.1038/s41598-023-37571-6] [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: 02/08/2023] [Accepted: 06/23/2023] [Indexed: 07/02/2023] Open
Abstract
Mosquito-borne disease remains a significant burden on global health. In the United States, the major threat posed by mosquitoes is transmission of arboviruses, including West Nile virus by mosquitoes of the Culex genus. Virus metagenomic analysis of mosquito small RNA using deep sequencing and advanced bioinformatic tools enables the rapid detection of viruses and other infecting organisms, both pathogenic and non-pathogenic to humans, without any precedent knowledge. In this study, we sequenced small RNA samples from over 60 pools of Culex mosquitoes from two major areas of Southern California from 2017 to 2019 to elucidate the virome and immune responses of Culex. Our results demonstrated that small RNAs not only allowed the detection of viruses but also revealed distinct patterns of viral infection based on location, Culex species, and time. We also identified miRNAs that are most likely involved in Culex immune responses to viruses and Wolbachia bacteria, and show the utility of using small RNA to detect antiviral immune pathways including piRNAs against some pathogens. Collectively, these findings show that deep sequencing of small RNA can be used for virus discovery and surveillance. One could also conceive that such work could be accomplished in various locations across the world and over time to better understand patterns of mosquito infection and immune response to many vector-borne diseases in field samples.
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Affiliation(s)
- Steven M Abel
- Department of Molecular, Cell and Systems Biology, Center for Infection Disease and Vector Research, University of California, Riverside, CA, 92521, USA
| | - Zhenchen Hong
- Department of Physics and Astronomy, University of California, Riverside, CA, 92521, USA
| | - Desiree Williams
- Department of Molecular, Cell and Systems Biology, Center for Infection Disease and Vector Research, University of California, Riverside, CA, 92521, USA
| | - Sally Ireri
- Department of Molecular, Cell and Systems Biology, Center for Infection Disease and Vector Research, University of California, Riverside, CA, 92521, USA
| | - Michelle Q Brown
- West Valley Mosquito & Vector Control District, Ontario, CA, 91761, USA
| | - Tianyun Su
- West Valley Mosquito & Vector Control District, Ontario, CA, 91761, USA
| | - Kim Y Hung
- Coachella Valley Mosquito & Vector Control District, Indio, CA, 92201, USA
| | - Jennifer A Henke
- Coachella Valley Mosquito & Vector Control District, Indio, CA, 92201, USA
| | - John P Barton
- Department of Physics and Astronomy, University of California, Riverside, CA, 92521, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, Center for Infection Disease and Vector Research, University of California, Riverside, CA, 92521, USA.
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13
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Huang L, Liu S, Chen L, Wang F, Ye P, Xia L, Jiang B, Tang H, Zhang Q, Ruan X, Chen W, Jiang J. Identification of novel Jingmen tick virus from parasitic ticks fed on a giant panda and goats in Sichuan Province, southwestern China. Front Microbiol 2023; 14:1179173. [PMID: 37389347 PMCID: PMC10305807 DOI: 10.3389/fmicb.2023.1179173] [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: 03/03/2023] [Accepted: 05/12/2023] [Indexed: 07/01/2023] Open
Abstract
Introduction Tick-borne viruses (TBVs) pose a significant risk to the health of humans and other vertebrates. A class of multisegmented flavi-like viruses, Jingmen tick virus (JMTV) was first discovered in Rhipicephalus microplus ticks collected from Jingmen of Hubei Province, China in 2010. JMTV has been confirmed to have a relatively wide distribution in vectors and hosts and is associated with human diseases. Methods Parasitic and host-seeking ticks were collected in Wolong Nature Reserve, Sichuan Province. Total RNA was extracted and then enriched the viral RNA. The DNA library was constructed and then were sequenced with MGI High-throughput Sequencing Set (PE150). After the adaptor sequences,low-quality bases and host genome were removed, resulting reads classified as a virus were subsequently de novo assembled into contigs, which were then compared to the NT database. Those annotated under the kingdom virus were initially identified as potential virus-associated sequences. Phylogenetic and Reassortment analysis of sequences were performed using MEGA and SimPlot software, respectively. Results and discussion Two host-seeking ticks and 17 ticks that fed on giant pandas and goats were collected. Through high-throughput sequencing, whole virus genomes were attained from four tick samples (PC-13, PC-16, PC-18, and PC-19) that shared 88.7-96.3% similarity with known JMTV. Phylogenetic tree showed that it was a novel JMTV-like virus, referred to as Sichuan tick virus, which also had the signals of reassortment with other JMTV strains, suggesting a cross-species transmission and co-infection of segmented flavi-like viruses among multiple tick hosts. Conclusion We discovered and confirmed one new Jingmen tick virus, Sichuan tick virus. Further investigation is required to determine the pathogenicity of Sichuan tick virus to humans and animals, as well as its epidemiological characteristics in nature.
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Affiliation(s)
- Lin Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shunshuai Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lu Chen
- Beijing Macro & Micro-test Bio-Tech Co., Ltd., Beijing, China
| | - Fei Wang
- Sichuan Forestry and Grassland Pest Control and Quarantine Station, Chengdu, China
| | - Ping Ye
- Wolong National Natural Reserve Administration Bureau, Wenchuan, China
| | - Luoyuan Xia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Baogui Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hao Tang
- Wolong National Natural Reserve Administration Bureau, Wenchuan, China
| | - Qingyu Zhang
- Wolong National Natural Reserve Administration Bureau, Wenchuan, China
| | - Xiangdong Ruan
- Academy of Inventory and Planning, National Forestry and Grassland Administration, Beijing, China
| | - Weijun Chen
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiafu Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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14
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Guinet B, Lepetit D, Charlat S, Buhl PN, Notton DG, Cruaud A, Rasplus JY, Stigenberg J, de Vienne DM, Boussau B, Varaldi J. Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses. eLife 2023; 12:85993. [PMID: 37278068 DOI: 10.7554/elife.85993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/12/2023] [Indexed: 06/07/2023] Open
Abstract
The accidental endogenization of viral elements within eukaryotic genomes can occasionally provide significant evolutionary benefits, giving rise to their long-term retention, that is, to viral domestication. For instance, in some endoparasitoid wasps (whose immature stages develop inside their hosts), the membrane-fusion property of double-stranded DNA viruses have been repeatedly domesticated following ancestral endogenizations. The endogenized genes provide female wasps with a delivery tool to inject virulence factors that are essential to the developmental success of their offspring. Because all known cases of viral domestication involve endoparasitic wasps, we hypothesized that this lifestyle, relying on a close interaction between individuals, may have promoted the endogenization and domestication of viruses. By analyzing the composition of 124 Hymenoptera genomes, spread over the diversity of this clade and including free-living, ecto, and endoparasitoid species, we tested this hypothesis. Our analysis first revealed that double-stranded DNA viruses, in comparison with other viral genomic structures (ssDNA, dsRNA, ssRNA), are more often endogenized and domesticated (that is, retained by selection) than expected from their estimated abundance in insect viral communities. Second, our analysis indicates that the rate at which dsDNA viruses are endogenized is higher in endoparasitoids than in ectoparasitoids or free-living hymenopterans, which also translates into more frequent events of domestication. Hence, these results are consistent with the hypothesis that the endoparasitoid lifestyle has facilitated the endogenization of dsDNA viruses, in turn, increasing the opportunities of domestications that now play a central role in the biology of many endoparasitoid lineages.
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Affiliation(s)
- Benjamin Guinet
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - David Lepetit
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Sylvain Charlat
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Peter N Buhl
- Zoological Museum, Department of Entomology, University of Copenhagen, Universitetsparken, Copenhagen, Denmark
| | - David G Notton
- Natural Sciences Department, National Museums Collection Centre, Edinburgh, United Kingdom
| | - Astrid Cruaud
- INRAE, UMR 1062 CBGP, 755 avenue 11 du campus Agropolis CS 30016, 34988, Montferrier-sur-Lez, France
| | - Jean-Yves Rasplus
- INRAE, UMR 1062 CBGP, 755 avenue 11 du campus Agropolis CS 30016, 34988, Montferrier-sur-Lez, France
| | - Julia Stigenberg
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Damien M de Vienne
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Bastien Boussau
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
| | - Julien Varaldi
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622, Villeurbanne, France
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15
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Chang T, Hunt BPV, Hirai J, Suttle CA. Divergent RNA viruses infecting sea lice, major ectoparasites of fish. PLoS Pathog 2023; 19:e1011386. [PMID: 37347729 DOI: 10.1371/journal.ppat.1011386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/25/2023] [Indexed: 06/24/2023] Open
Abstract
Sea lice, the major ectoparasites of fish, have significant economic impacts on wild and farmed finfish, and have been implicated in the decline of wild salmon populations. As blood-feeding arthropods, sea lice may also be reservoirs for viruses infecting fish. However, except for two groups of negative-strand RNA viruses within the order Mononegavirales, nothing is known about viruses of sea lice. Here, we used transcriptomic data from three key species of sea lice (Lepeophtheirus salmonis, Caligus clemensi, and Caligus rogercresseyi) to identify 32 previously unknown RNA viruses. The viruses encompassed all the existing phyla of RNA viruses, with many placed in deeply branching lineages that likely represent new families and genera. Importantly, the presence of canonical virus-derived small interfering RNAs (viRNAs) indicates that most of these viruses infect sea lice, even though in some cases their closest classified relatives are only known to infect plants or fungi. We also identified both viRNAs and PIWI-interacting RNAs (piRNAs) from sequences of a bunya-like and two qin-like viruses in C. rogercresseyi. Our analyses showed that most of the viruses found in C. rogercresseyi occurred in multiple life stages, spanning from planktonic to parasitic stages. Phylogenetic analysis revealed that many of the viruses infecting sea lice were closely related to those that infect a wide array of eukaryotes with which arthropods associate, including fungi and parasitic tapeworms, implying that over evolutionary time there has been cross-phylum and cross-kingdom switching of viruses between arthropods and other eukaryotes. Overall, this study greatly expands our view of virus diversity in crustaceans, identifies viruses that infect and replicate in sea lice, and provides evidence that over evolutionary time, viruses have switched between arthropods and eukaryotic hosts in other phyla and kingdoms.
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Affiliation(s)
- Tianyi Chang
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Brian P V Hunt
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, Canada
- Hakai Institute, Campbell River, Canada
| | - Junya Hirai
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, Canada
- Hakai Institute, Campbell River, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
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16
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Bruner-Montero G, Jiggins FM. Wolbachia protects Drosophila melanogaster against two naturally occurring and virulent viral pathogens. Sci Rep 2023; 13:8518. [PMID: 37231093 PMCID: PMC10212958 DOI: 10.1038/s41598-023-35726-z] [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: 02/09/2023] [Accepted: 05/23/2023] [Indexed: 05/27/2023] Open
Abstract
Wolbachia is a common endosymbiont that can protect insects against viral pathogens. However, whether the antiviral effects of Wolbachia have a significant effect on fitness remains unclear. We have investigated the interaction between Drosophila melanogaster, Wolbachia and two viruses that we recently isolated from wild flies, La Jolla virus (LJV; Iflaviridae) and Newfield virus (NFV; Permutotetraviridae). Flies infected with these viruses have increased mortality rates, and NFV partially sterilizes females. These effects on fitness were reduced in Wolbachia-infected flies, and this was associated with reduced viral titres. However, Wolbachia alone also reduces survival, and under our experimental conditions these costs of the symbiont can outweigh the benefits of antiviral protection. In contrast, protection against the sterilizing effect of NFV leads to a net benefit of Wolbachia infection after exposure to the virus. These results support the hypothesis that Wolbachia is an important defense against the natural pathogens of D. melanogaster. Furthermore, by reducing the cost of Wolbachia infection, the antiviral effects of Wolbachia may aid its invasion into populations and help explain why it is so common in nature.
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Affiliation(s)
- Gaspar Bruner-Montero
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
- Coiba Scientific Station, City of Knowledge, 0843-03081, Clayton, Panama.
| | - Francis M Jiggins
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
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17
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Ant TH, Mancini MV, McNamara CJ, Rainey SM, Sinkins SP. Wolbachia-Virus interactions and arbovirus control through population replacement in mosquitoes. Pathog Glob Health 2023; 117:245-258. [PMID: 36205550 PMCID: PMC10081064 DOI: 10.1080/20477724.2022.2117939] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022] Open
Abstract
Following transfer into the primary arbovirus vector Aedes aegypti, several strains of the intracellular bacterium Wolbachia have been shown to inhibit the transmission of dengue, Zika, and chikungunya viruses, important human pathogens that cause significant morbidity and mortality worldwide. In addition to pathogen inhibition, many Wolbachia strains manipulate host reproduction, resulting in an invasive capacity of the bacterium in insect populations. This has led to the deployment of Wolbachia as a dengue control tool, and trials have reported significant reductions in transmission in release areas. Here, we discuss the possible mechanisms of Wolbachia-virus inhibition and the implications for long-term success of dengue control. We also consider the evidence presented in several reports that Wolbachia may cause an enhancement of replication of certain viruses under particular conditions, and conclude that these should not cause any concerns with respect to the application of Wolbachia to arbovirus control.
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Affiliation(s)
- Thomas H Ant
- Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Maria Vittoria Mancini
- Centre for Virus Research, University of Glasgow, Glasgow, UK
- Polo d’Innovazione di Genomica, Genetica e Biologia, Terni, Italy
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18
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Bruner-Montero G, Luque CM, Cesar CS, Ding SD, Day JP, Jiggins FM. Hunting Drosophila viruses from wild populations: A novel isolation approach and characterisation of viruses. PLoS Pathog 2023; 19:e1010883. [PMID: 36996192 PMCID: PMC10109509 DOI: 10.1371/journal.ppat.1010883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 04/17/2023] [Accepted: 03/08/2023] [Indexed: 04/01/2023] Open
Abstract
Metagenomic studies have demonstrated that viruses are extremely diverse and abundant in insects, but the difficulty of isolating them means little is known about the biology of these newly discovered viruses. To overcome this challenge in Drosophila, we created a cell line that was more permissive to infection and detected novel viruses by the presence of double-stranded RNA. We demonstrate the utility of these tools by isolating La Jolla virus (LJV) and Newfield virus (NFV) from several wild Drosophila populations. These viruses have different potential host ranges, with distinct abilities to replicate in five Drosophila species. Similarly, in some species they cause high mortality and in others they are comparatively benign. In three species, NFV but not LJV caused large declines in female fecundity. This sterilization effect was associated with differences in tissue tropism, as NFV but not LJV was able to infect Drosophila melanogaster ovaries. We saw a similar effect in the invasive pest of fruit crops Drosophila suzukii, where oral infection with NFV caused reductions in the fecundity, suggesting it has potential as a biocontrol agent. In conclusion, a simple protocol allowed us to isolate new viruses and demonstrate that viruses identified by metagenomics have a large effect on the fitness of the model organism D. melanogaster and related species.
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Affiliation(s)
- Gaspar Bruner-Montero
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Coiba Scientific Station, City of Knowledge, Clayton, Panama
| | - Carlos M Luque
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Cássia Siqueira Cesar
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Ecology Department, Universidade de São Paulo, São Paulo, Brazil
| | | | - Jonathan P Day
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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19
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Viljakainen L, Fürst MA, Grasse AV, Jurvansuu J, Oh J, Tolonen L, Eder T, Rattei T, Cremer S. Antiviral immune response reveals host-specific virus infections in natural ant populations. Front Microbiol 2023; 14:1119002. [PMID: 37007485 PMCID: PMC10060816 DOI: 10.3389/fmicb.2023.1119002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management.
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Affiliation(s)
- Lumi Viljakainen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
- *Correspondence: Lumi Viljakainen,
| | - Matthias A. Fürst
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Anna V. Grasse
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Jaana Jurvansuu
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Jinook Oh
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Lassi Tolonen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Thomas Eder
- Centre for Microbiology and Environmental Systems Science, Division of Computational System Biology, University of Vienna, Vienna, Austria
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, Division of Computational System Biology, University of Vienna, Vienna, Austria
| | - Sylvia Cremer
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
- Sylvia Cremer,
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20
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Kageyama D, Harumoto T, Nagamine K, Fujiwara A, Sugimoto TN, Jouraku A, Tamura M, Katoh TK, Watada M. A male-killing gene encoded by a symbiotic virus of Drosophila. Nat Commun 2023; 14:1357. [PMID: 36914655 PMCID: PMC10011393 DOI: 10.1038/s41467-023-37145-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 03/03/2023] [Indexed: 03/16/2023] Open
Abstract
In most eukaryotes, biparentally inherited nuclear genomes and maternally inherited cytoplasmic genomes have different evolutionary interests. Strongly female-biased sex ratios that are repeatedly observed in various arthropods often result from the male-specific lethality (male-killing) induced by maternally inherited symbiotic bacteria such as Spiroplasma and Wolbachia. However, despite some plausible case reports wherein viruses are raised as male-killers, it is not well understood how viruses, having much smaller genomes than bacteria, are capable of inducing male-killing. Here we show that a maternally inherited double-stranded RNA (dsRNA) virus belonging to the family Partitiviridae (designated DbMKPV1) induces male-killing in Drosophila. DbMKPV1 localizes in the cytoplasm and possesses only four genes, i.e., one gene in each of the four genomic segments (dsRNA1-dsRNA4), in contrast to ca. 1000 or more genes possessed by Spiroplasma or Wolbachia. We also show that a protein (designated PVMKp1; 330 amino acids in size), encoded by a gene on the dsRNA4 segment, is necessary and sufficient for inducing male-killing. Our results imply that male-killing genes can be easily acquired by symbiotic viruses through reassortment and that symbiotic viruses are hidden players in arthropod evolution. We anticipate that host-manipulating genes possessed by symbiotic viruses can be utilized for controlling arthropods.
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Affiliation(s)
- Daisuke Kageyama
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-0851, Japan.
| | - Toshiyuki Harumoto
- Hakubi Center for Advanced Research, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto, 606-8501, Japan
- Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Keisuke Nagamine
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-0851, Japan
| | - Akiko Fujiwara
- Center for Food Science and Wellness, Gunma University, 4-2 Aramaki, Maebashi, Gunma, 371-8510, Japan
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan
| | - Takafumi N Sugimoto
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-0851, Japan
| | - Akiya Jouraku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-0851, Japan
| | - Masaru Tamura
- Division of Food Safety Information, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takehiro K Katoh
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, 780-8857, Japan
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 192-0397, Japan
| | - Masayoshi Watada
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, 780-8857, Japan.
- Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo, 192-0397, Japan.
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21
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Morrow JL, Sharpe SR, Tilden G, Wyatt P, Oczkowicz S, Riegler M. Transmission modes and efficiency of iflavirus and cripavirus in Queensland fruit fly, Bactrocera tryoni. J Invertebr Pathol 2023; 197:107874. [PMID: 36574813 DOI: 10.1016/j.jip.2022.107874] [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: 10/08/2022] [Revised: 12/13/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
Infections of insects with insect-specific RNA viruses are common and can affect host fitness and health. Previously, persistent RNA virus infections were detected in tephritid fruit flies, including the Queensland fruit fly (Bactrocera tryoni), Australia's most significant horticultural pest. Their transmission modes and efficiency are unclear yet may influence virus epidemiology in field and laboratory populations. Using standard RT-PCR and RT-qPCR we detected iflavirus, cripavirus and sigmavirus in five laboratory populations recently established with field-collected B.tryoni. Virus absence in some individuals suggested that virus transmission is incomplete. Random virus segregation in an isofemale experiment resulted in the establishment of isofemale lines with and without iflavirus and cripavirus. In infected lines, viral loads normalised against host gene transcripts were variable, but did not differ between pupae and adults. Iflavirus and cripavirus were transmitted horizontally, with viruses detected (including at low viral loads) in many previously uninfected individuals after four days, and in most after 12 days cohabitation with infected flies. Iflavirus, but not cripavirus, was transmitted vertically, and surface-sterilised embryos contained high loads. Furthermore, high iflavirus loads in individual females resulted in high loads in their offspring. We demonstrated that viruses are highly prevalent in laboratory populations and that it is possible to establish and maintain uninfected fly lines for the assessment of virus transmission and host effects. This is important for pest management strategies such as the sterile insect technique which requires the mass-rearing of flies, as their fitness and performance may be affected by covert virus infections.
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Affiliation(s)
- 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
| | - Geraldine Tilden
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Pauline Wyatt
- Department of Agriculture and Fisheries Queensland, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Sybilla Oczkowicz
- Department of Agriculture and Fisheries Queensland, Redden Street Research Facility, 21-23 Redden Street, Portsmith, QLD 4870, Australia
| | - Markus Riegler
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
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22
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Kutzer MAM, Gupta V, Neophytou K, Doublet V, Monteith KM, Vale PF. Intraspecific genetic variation in host vigour, viral load and disease tolerance during Drosophila C virus infection. Open Biol 2023; 13:230025. [PMID: 36854375 PMCID: PMC9974301 DOI: 10.1098/rsob.230025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Genetic variation for resistance and disease tolerance has been described in a range of species. In Drosophila melanogaster, genetic variation in mortality following systemic Drosophila C virus (DCV) infection is driven by large-effect polymorphisms in the restriction factor pastrel (pst). However, it is unclear if pst contributes to disease tolerance. We investigated systemic DCV challenges spanning nine orders of magnitude, in males and females of 10 Drosophila Genetic Reference Panel lines carrying either a susceptible (S) or resistant (R) pst allele. We find among-line variation in fly survival, viral load and disease tolerance measured both as the ability to maintain survival (mortality tolerance) and reproduction (fecundity tolerance). We further uncover novel effects of pst on host vigour, as flies carrying the R allele exhibited higher survival and fecundity even in the absence of infection. Finally, we found significant genetic variation in the expression of the JAK-STAT ligand upd3 and the epigenetic regulator of JAK-STAT G9a. However, while G9a has been previously shown to mediate tolerance of DCV infection, we found no correlation between the expression of either upd3 or G9a on fly tolerance or resistance. Our work highlights the importance of both resistance and tolerance in viral defence.
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Affiliation(s)
- Megan A. M. Kutzer
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, UK
| | - Vanika Gupta
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, UK
| | - Kyriaki Neophytou
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, UK
| | - Vincent Doublet
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, UK
| | - Katy M. Monteith
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, UK
| | - Pedro F. Vale
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, UK
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23
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Moonen JP, Schinkel M, van der Most T, Miesen P, van Rij RP. Composition and global distribution of the mosquito virome - A comprehensive database of insect-specific viruses. One Health 2023; 16:100490. [PMID: 36817977 PMCID: PMC9929601 DOI: 10.1016/j.onehlt.2023.100490] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Mosquitoes are vectors for emerging and re-emerging infectious viral diseases of humans, livestock and other animals. In addition to these arthropod-borne (arbo)viruses, mosquitoes are host to an array of insect-specific viruses, collectively referred to as the mosquito virome. Mapping the mosquito virome and understanding if and how its composition modulates arbovirus transmission is critical to understand arboviral disease emergence and outbreak dynamics. In recent years, next-generation sequencing as well as PCR and culture-based methods have been extensively used to identify mosquito-associated viruses, providing insights into virus ecology and evolution. Until now, the large amount of mosquito virome data, specifically those acquired by metagenomic sequencing, has not been comprehensively integrated. We have constructed a searchable database of insect-specific viruses associated with vector mosquitoes from 175 studies, published between October 2000 and February 2022. We identify the most frequently detected and widespread viruses of the Culex, Aedes and Anopheles mosquito genera and report their global distribution. In addition, we highlight the challenges of extracting and integrating published virome data and we propose that a standardized reporting format will facilitate data interpretation and re-use by other scientists. We expect our comprehensive database, summarizing mosquito virome data collected over 20 years, to be a useful resource for future studies.
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24
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Li N, Li C, Hu T, Li J, Zhou H, Ji J, Wu J, Kang W, Holmes EC, Shi W, Xu S. Nationwide genomic surveillance reveals the prevalence and evolution of honeybee viruses in China. MICROBIOME 2023; 11:6. [PMID: 36631833 PMCID: PMC9832778 DOI: 10.1186/s40168-022-01446-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/08/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND The economic and environmental value of honeybees has been severely challenged in recent years by the collapse of their colonies worldwide, often caused by outbreaks of infectious diseases. However, our understanding of the diversity, prevalence, and transmission of honeybee viruses is largely obscure due to a lack of large-scale and longitudinal genomic surveillance on a global scale. RESULTS We report the meta-transcriptomic sequencing of nearly 2000 samples of the two most important economic and widely maintained honeybee species, as well as an associated ectoparasite mite, collected across China during 2016-2019. We document the natural diversity and evolution of honeybee viruses in China, providing evidence that multiple viruses commonly co-circulate within individual bee colonies. We also expanded the genomic data for 12 important honeybee viruses and revealed novel genetic variants and lineages associated with China. We identified more than 23 novel viruses from the honeybee and mite viromes, with some exhibiting ongoing replication in their respective hosts. Together, these data provide additional support to the idea that mites are an important reservoir and spill-over host for honeybee viruses. CONCLUSIONS Our data show that honeybee viruses are more widespread, prevalent, and genetically diverse than previously realized. The information provided is important in mitigating viral infectious diseases in honeybees, in turn helping to maintain sustainable productive agriculture on a global scale. Video Abstract.
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Affiliation(s)
- Nannan Li
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Cixiu Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Tao Hu
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Juan Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Hong Zhou
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Jingkai Ji
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China
| | - Jiangli Wu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Weipeng Kang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Edward C Holmes
- Sydeny Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Weifeng Shi
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China.
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China.
| | - Shufa Xu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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25
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Wu Z, Chen J, Zhang L, Zhang Y, Liu L, Niu G. Molecular evidence for potential transovarial transmission of Jingmen tick virus in Haemaphysalis longicornis fed on cattle from Yunnan Province, China. J Med Virol 2023; 95:e28357. [PMID: 36443647 DOI: 10.1002/jmv.28357] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022]
Abstract
Jingmen tick virus (JMTV) is a novel tick-borne virus first identified from Jingmen city, Hubei Province of China in 2010. It has been proved that JMTV can cause human diseases and is widely distributed both inside and outside of China. However, the survival mode and transmission characteristics of JMTV still need further research, particularly in terms of transovarial transmission. In this study, an investigation was conducted to explore the presence of JMTV from engorged female ticks to their offspring. All engorged female adult ticks were collected from domestic cattle and allowed to lay eggs in appropriate humidity and temperature conditions. Maternal ticks, eggs and larvae were screened for JMTV RNA through real-time polymerase chain reaction (RT-PCR) and nested PCR methods. The results revealed the positive rate of 10.53% (10/95) in engorged ticks, 9.09% (2/22) in eggs and 8% (4/50) in larvae pools, respectively. Phylogenetic analysis confirmed that sequences from eggs and larvae had closer relationship with those isolates from maternal engorged ticks with more than 99.7% homology and JMTV manifested with evolutional conservatism. Our study has identified for the first time that JMTV could be transmitted from mother generation to offspring of Haemaphysalis Longicornis. Nonetheless, the efficiency of transovarial transmission in JMTV and the significance of ticks as amplification hosts still need to be further illustrated.
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Affiliation(s)
- Zhen Wu
- School of Public Health, WeiFang Medical University, Weifang, China
| | - Junhao Chen
- School of Public Health, WeiFang Medical University, Weifang, China
| | | | - Yuli Zhang
- School of Public Health, WeiFang Medical University, Weifang, China
| | - Lin Liu
- Immune-Path Biotechnology (Suzhou) Co., Ltd, Suzhou, China
| | - Guoyu Niu
- School of Public Health, WeiFang Medical University, Weifang, China
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26
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Palatini U, Alfano N, Carballar RL, Chen XG, Delatte H, Bonizzoni M. Virome and nrEVEome diversity of Aedes albopictus mosquitoes from La Reunion Island and China. Virol J 2022; 19:190. [DOI: 10.1186/s12985-022-01918-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022] Open
Abstract
Abstract
Background
Aedes albopictus is a public health threat for its worldwide spread and ability to transmit arboviruses. Understanding mechanisms of mosquito immunity can provide new tools to control arbovirus spread. The genomes of Aedes mosquitoes contain hundreds of nonretroviral endogenous viral elements (nrEVEs), which are enriched in piRNA clusters and produce piRNAs, with the potential to target cognate viruses. Recently, one nrEVE was shown to limit cognate viral infection through nrEVE-derived piRNAs. These findings suggest that nrEVEs constitute an archive of past viral infection and that the landscape of viral integrations may be variable across populations depending on their viral exposure.
Methods
We used bioinformatics and molecular approaches to identify known and novel (i.e. absent in the reference genome) viral integrations in the genome of wild collected Aedes albopictus mosquitoes and characterize their virome.
Results
We showed that the landscape of viral integrations is dynamic with seven novel viral integrations being characterized, but does not correlate with the virome, which includes both viral species known and unknown to infect mosquitoes. However, the small RNA coverage profile of nrEVEs and the viral genomic contigs we identified confirmed an interaction among these elements and the piRNA and siRNA pathways in mosquitoes.
Conclusions
Mosquitoes nrEVEs have been recently described as a new form of heritable, sequence-specific mechanism of antiviral immunity. Our results contribute to understanding the dynamic distribution of nrEVEs in the genomes of wild Ae. albopictus and their interaction with mosquito viruses.
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27
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Colmant AMG, Charrel RN, Coutard B. Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses. Front Microbiol 2022; 13:997058. [PMID: 36299728 PMCID: PMC9589506 DOI: 10.3389/fmicb.2022.997058] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/22/2022] [Indexed: 11/21/2022] Open
Abstract
Jingmenviruses are a group of viruses identified recently, in 2014, and currently classified by the International Committee on Taxonomy of Viruses as unclassified Flaviviridae. These viruses closely related to flaviviruses are unique due to the segmented nature of their genome. The prototype jingmenvirus, Jingmen tick virus (JMTV), was discovered in Rhipicephalus microplus ticks collected from China in 2010. Jingmenviruses genomes are composed of four to five segments, encoding for up to seven structural proteins and two non-structural proteins, both of which display strong similarities with flaviviral non-structural proteins (NS2B/NS3 and NS5). Jingmenviruses are currently separated into two phylogenetic clades. One clade includes tick- and vertebrate-associated jingmenviruses, which have been detected in ticks and mosquitoes, as well as in humans, cattle, monkeys, bats, rodents, sheep, and tortoises. In addition to these molecular and serological detections, over a hundred human patients tested positive for jingmenviruses after developing febrile illness and flu-like symptoms in China and Serbia. The second phylogenetic clade includes insect-associated jingmenvirus sequences, which have been detected in a wide range of insect species, as well as in crustaceans, plants, and fungi. In addition to being found in various types of hosts, jingmenviruses are endemic, as they have been detected in a wide range of environments, all over the world. Taken together, all of these elements show that jingmenviruses correspond exactly to the definition of emerging viruses at risk of causing a pandemic, since they are already endemic, have a close association with arthropods, are found in animals in close contact with humans, and have caused sporadic cases of febrile illness in multiple patients. Despite these arguments, the vast majority of published data is from metagenomics studies and many aspects of jingmenvirus replication remain to be elucidated, such as their tropism, cycle of transmission, structure, and mechanisms of replication and restriction or epidemiology. It is therefore crucial to prioritize jingmenvirus research in the years to come, to be prepared for their emergence as human or veterinary pathogens.
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28
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Linscheid Y, Kessel T, Vilcinskas A, Lee KZ. Pathogenicity of La Jolla Virus in Drosophila suzukii following Oral Administration. Viruses 2022; 14:v14102158. [PMID: 36298712 PMCID: PMC9609637 DOI: 10.3390/v14102158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/20/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022] Open
Abstract
Drosophila suzukii (Ds) is an invasive pest insect that causes severe and widespread damage to soft fruit crops. Chemical control based on topical insecticides is inefficient and harmful to consumers and the environment, prompting interest in the development of biological control measures such as insect viruses with narrow host specificity. We previously described a strain of La Jolla virus (LJV) found in moribund Ds specimens in Germany. We demonstrated a pathogenic effect following the intrathoracic injection of LJV into adult Ds flies. However, the development of an effective biocontrol product based on LJV would require the characterization of (1) virulence following oral delivery, particularly in larvae, and (2) stability under different pH and temperature conditions reflecting realistic exposure scenarios. Here we describe the pathogenicity of LJV following oral delivery to Ds adults and larvae. The oral infection of Ds adults with LJV reduced survival in a concentration-dependent manner, whereas the oral infection of Ds larvae caused the arrest of development during pupation. LJV remained stable and infectious following exposure to a broad pH range and different temperatures. We, therefore, demonstrated that LJV is promising as a candidate biological control agent against Ds.
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Affiliation(s)
- Yvonne Linscheid
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Branch of Bioresources, Ohlebergsweg 12, D-35392 Giessen, Germany
| | - Tobias Kessel
- Institute for Insect Biotechnology, Justus Liebig University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Andreas Vilcinskas
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Branch of Bioresources, Ohlebergsweg 12, D-35392 Giessen, Germany
- Institute for Insect Biotechnology, Justus Liebig University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Kwang-Zin Lee
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Branch of Bioresources, Ohlebergsweg 12, D-35392 Giessen, Germany
- Correspondence: ; Tel.: +49-641-97-219150
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29
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Zhang Y, Li Z, Pang Z, Wu Z, Lin Z, Niu G. Identification of Jingmen tick virus (JMTV) in Amblyomma testudinarium from Fujian Province, southeastern China. Parasit Vectors 2022; 15:339. [PMID: 36167570 PMCID: PMC9513871 DOI: 10.1186/s13071-022-05478-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Background Jingmen tick virus (JMTV) is a newly discovered tick-borne virus that can cause disease in humans. This virus has been authenticated as being extremely widespread worldwide and as posing a significant threat to public health and safety. Methods We collected 35 ticks belonging to two tick species from wild boars in Nanping, Fujian Province, China. JMTV-specific genes were amplified by qRT-PCR and nested PCR to confirm the presence of this pathogen. Results More than one third of of all ticks collected (11/35) were positive for JMTV. Viral sequences were obtained from three of the JMTV-positive ticks, including the complete genomic sequence from one tick. This was the first time that JMTV was identified in the hard-bodied tick Amblyomma testudinarium. Phylogenetic analysis revealed that JMTV from Fujian Province shared > 90% identity with other isolates derived from China, but was distinct from those reported in France and Cambodia. Conclusions JMTV is characterized by relatively low mutations and has its own local adaptive characteristics in different regions. Our findings provide molecular evidence of the presence of JMTV in an overlooked tick species from an area not unrecognized as being endemic. They also suggest that JMTV occupies a wider geographical distribution than currently believed and is a potential disease vector. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05478-2.
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Affiliation(s)
- Yuli Zhang
- WeiFang Medical University, Weifang, 261053, China
| | - Zhenfeng Li
- Department of Public Health, Gaomi People's Hospital, Weifang, 261500, China
| | - Zheng Pang
- Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, China
| | - Zhen Wu
- WeiFang Medical University, Weifang, 261053, China
| | - Zhijuan Lin
- WeiFang Medical University, Weifang, 261053, China.
| | - Guoyu Niu
- WeiFang Medical University, Weifang, 261053, China.
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30
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Ortiz-Baez AS, Holmes EC, Charon J, Pettersson JHO, Hesson JC. Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites. Virus Evol 2022; 8:veac090. [PMID: 36320615 PMCID: PMC9604308 DOI: 10.1093/ve/veac090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/29/2022] [Accepted: 09/23/2022] [Indexed: 11/14/2022] Open
Abstract
Arthropods harbor a largely undocumented diversity of RNA viruses. Some arthropods, like mosquitoes, can transmit viruses to vertebrates but are themselves parasitized by other arthropod species, such as mites. Very little is known about the viruses of these ectoparasites and how they move through the host-parasite relationship. To address this, we determined the virome of both mosquitoes and the mites that feed on them. The mosquito Aedes communis is an abundant and widely distributed species in Sweden, in northern Europe. These dipterans are commonly parasitized by water mite larvae (Trombidiformes: Mideopsidae) that are hypothesized to impose negative selection pressures on the mosquito by reducing fitness. In turn, viruses are dual-host agents in the mosquito-mite interaction. We determined the RNA virus diversity of mite-free and mite-detached mosquitoes, as well as their parasitic mites, using meta-transcriptomic sequencing. Our results revealed an extensive RNA virus diversity in both mites and mosquitoes, including thirty-seven putative novel RNA viruses that cover a wide taxonomic range. Notably, a high proportion of viruses (20/37) were shared between mites and mosquitoes, while a limited number of viruses were present in a single host. Comparisons of virus composition and abundance suggest potential virus transfer between mosquitoes and mites during their symbiotic interaction. These findings shed light on virome diversity and ecology in the context of arthropod host-parasite-virus relationships.
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Affiliation(s)
- Ayda Susana Ortiz-Baez
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Justine Charon
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - John H-O Pettersson
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Clinical Microbiology and Hospital Hygiene, Uppsala University Hospital, Dag Hammarskjölds väg 38, Uppsala SE-751 85, Sweden
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, University of Uppsala, Husargatan 3, C8:3, Uppsala SE-751 23, Sweden
| | - Jenny C Hesson
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, University of Uppsala, Husargatan 3, C8:3, Uppsala SE-751 23, Sweden
- Biologisk Myggkontroll, Nedre Dalälven Utvecklings AB, Vårdsätravägen 5, Uppsala SE 75646, Sweden
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31
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Santiago-Rodriguez TM, Hollister EB. Unraveling the viral dark matter through viral metagenomics. Front Immunol 2022; 13:1005107. [PMID: 36189246 PMCID: PMC9523745 DOI: 10.3389/fimmu.2022.1005107] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses are part of the microbiome and have essential roles in immunology, evolution, biogeochemical cycles, health, and disease progression. Viruses influence a wide variety of systems and processes, and the continued discovery of novel viruses is anticipated to reveal new mechanisms influencing the biology of diverse environments. While the identity and roles of viruses continue to be discovered and understood through viral metagenomics, most of the sequences in virome datasets cannot be attributed to known viruses or may be only distantly related to species already described in public sequence databases, at best. Such viruses are known as the viral dark matter. Ongoing discoveries from the viral dark matter have provided insights into novel viruses from a variety of environments, as well as their potential in immunological processes, virus evolution, health, disease, therapeutics, and surveillance. Increased understanding of the viral dark matter will continue with a combination of cultivation, microscopy, sequencing, and bioinformatic efforts, which are discussed in the present review.
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32
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Wang J, Gou QY, Luo GY, Hou X, Liang G, Shi M. Total RNA sequencing of Phlebotomus chinensis, a neglected vector in China, simultaneously revealed viral, bacterial, and eukaryotic microbes that are potentially pathogenic to humans. Emerg Microbes Infect 2022; 11:2080-2092. [PMID: 35916448 PMCID: PMC9448391 DOI: 10.1080/22221751.2022.2109516] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Phlebotomus chinensis sandfly is a neglected insect vector in China that is well-known for carrying Leishmania. Recent studies have expanded its pathogen repertoire with two novel arthropod-borne phleboviruses capable of infecting humans and animals. Despite these discoveries, our knowledge of the general pathogen diversity and overall microbiome composition of this vector species is still very limited. Here we carried out a meta-transcriptomics analysis that revealed the actively replicating/transcribing RNA viruses, DNA viruses, bacteria, and eukaryotic microbes, namely, the “total microbiome”, of several sandfly populations in China. Strikingly, “microbiome” made up 1.8% of total non-ribosomal RNA and comprised more than 87 species, among which 70 were novel, including divergent members of the genera Flavivirus and of the family Trypanosomatidae. Importantly, among these microbes we were able to reveal four distinguished types of human and/or mammalian pathogens, including two phleboviruses (hedi and wuxiang viruses), one novel Spotted fever group rickettsia, as well as a member of Leishmania donovani complex, among which hedi virus and Leishmania each had > 50% pool prevalence rate and relatively high abundance levels. Our study also showed the ubiquitous presence of an endosymbiont, namely Wolbachia, although no anti-viral or anti-pathogen effects were detected based on our data. In summary, our results uncovered the much un-explored diversity of microbes harboured by sandflies in China and demonstrated that high pathogen diversity and abundance are currently present in multiple populations, implying disease potential for exposed local human population or domestic animals.
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Affiliation(s)
- Jing Wang
- The Center for Infection & Immunity Study, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Qin-Yu Gou
- The Center for Infection & Immunity Study, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Geng-Yan Luo
- The Center for Infection & Immunity Study, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Xin Hou
- The Center for Infection & Immunity Study, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Guodong Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Mang Shi
- The Center for Infection & Immunity Study, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen 518107, China
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Pang Z, Jin Y, Pan M, Zhang Y, Wu Z, Liu L, Niu G. Geographical distribution and phylogenetic analysis of Jingmen tick virus in China. iScience 2022; 25:105007. [PMID: 36097615 PMCID: PMC9463580 DOI: 10.1016/j.isci.2022.105007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/08/2022] [Accepted: 08/19/2022] [Indexed: 11/26/2022] Open
Abstract
Jingmen tick virus (JMTV) is a novel tick-borne segmented RNA virus that is closely related to un-segmental RNA virus in evolution. It has been confirmed that JMTV could be a causative agent of human disease. In this study, a total of 3658 ticks were sampled from 7 provinces of China and then divided into 545 pools according to the location and species. QRT-PCR and nested PCR were performed to confirm the presence of JMTV. The results showed JMTV was identified in 5 out of 7 provinces with an average infection rate of 1.4% (51/3658). Phylogenetic analysis indicated that all JMTV strains identified in this study were closely related to each other and formed a well-supported sub-lineage. Our results provide molecular evidence of JMTV in different species of ticks from endemic and non-endemic regions and demonstrate that JMTV, as a natural foci pathogen, may be widely distributed all over China. JMTV was first identified in unrecognized endemic regions of China Two complete genomes and 13 partial S1 segments of JMTV were sequenced and analyzed JMTV was relatively conservative in evolution JMTV was widely distributed in China as a potential health threat to humans and animals
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Brosh O, Fabian DK, Cogni R, Tolosana I, Day JP, Olivieri F, Merckx M, Akilli N, Szkuta P, Jiggins FM. A novel transposable element-mediated mechanism causes antiviral resistance in Drosophila through truncating the Veneno protein. Proc Natl Acad Sci U S A 2022; 119:e2122026119. [PMID: 35858337 PMCID: PMC9304006 DOI: 10.1073/pnas.2122026119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/18/2022] [Indexed: 01/13/2023] Open
Abstract
Hosts are continually selected to evolve new defenses against an ever-changing array of pathogens. To understand this process, we examined the genetic basis of resistance to the Drosophila A virus in Drosophila melanogaster. In a natural population, we identified a polymorphic transposable element (TE) insertion that was associated with an ∼19,000-fold reduction in viral titers, allowing flies to largely escape the harmful effects of infection by this virulent pathogen. The insertion occurs in the protein-coding sequence of the gene Veneno, which encodes a Tudor domain protein. By mutating Veneno with CRISPR-Cas9 in flies and expressing it in cultured cells, we show that the ancestral allele of the gene has no effect on viral replication. Instead, the TE insertion is a gain-of-function mutation that creates a gene encoding a novel resistance factor. Viral titers remained reduced when we deleted the TE sequence from the transcript, indicating that resistance results from the TE truncating the Veneno protein. This is a novel mechanism of virus resistance and a new way by which TEs can contribute to adaptation.
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Affiliation(s)
- Osama Brosh
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Daniel K. Fabian
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Rodrigo Cogni
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
- Department of Ecology, University of São Paulo, 05508-220 São Paulo, Brazil
| | - Ignacio Tolosana
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Jonathan P. Day
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Francesca Olivieri
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Manon Merckx
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Nazli Akilli
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Piotr Szkuta
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Francis M. Jiggins
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
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35
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Han S, Dias GB, Basting PJ, Nelson MG, Patel S, Marzo M, Bergman CM. Ongoing transposition in cell culture reveals the phylogeny of diverse Drosophila S2 sublines. Genetics 2022; 221:iyac077. [PMID: 35536183 PMCID: PMC9252272 DOI: 10.1093/genetics/iyac077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Cultured cells are widely used in molecular biology despite poor understanding of how cell line genomes change in vitro over time. Previous work has shown that Drosophila cultured cells have a higher transposable element content than whole flies, but whether this increase in transposable element content resulted from an initial burst of transposition during cell line establishment or ongoing transposition in cell culture remains unclear. Here, we sequenced the genomes of 25 sublines of Drosophila S2 cells and show that transposable element insertions provide abundant markers for the phylogenetic reconstruction of diverse sublines in a model animal cell culture system. DNA copy number evolution across S2 sublines revealed dramatically different patterns of genome organization that support the overall evolutionary history reconstructed using transposable element insertions. Analysis of transposable element insertion site occupancy and ancestral states support a model of ongoing transposition dominated by episodic activity of a small number of retrotransposon families. Our work demonstrates that substantial genome evolution occurs during long-term Drosophila cell culture, which may impact the reproducibility of experiments that do not control for subline identity.
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Affiliation(s)
- Shunhua Han
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Guilherme B Dias
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Preston J Basting
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Michael G Nelson
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Sanjai Patel
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Mar Marzo
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Casey M Bergman
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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36
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de Faria IJS, Aguiar ERGR, Olmo RP, Alves da Silva J, Daeffler L, Carthew RW, Imler JL, Marques JT. Invading viral DNA triggers dsRNA synthesis by RNA polymerase II to activate antiviral RNA interference in Drosophila. Cell Rep 2022; 39:110976. [PMID: 35732126 PMCID: PMC10041815 DOI: 10.1016/j.celrep.2022.110976] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 03/24/2022] [Accepted: 05/26/2022] [Indexed: 11/03/2022] Open
Abstract
dsRNA sensing triggers antiviral responses against RNA and DNA viruses in diverse eukaryotes. In Drosophila, Invertebrate iridescent virus 6 (IIV-6), a large DNA virus, triggers production of small interfering RNAs (siRNAs) by the dsRNA sensor Dicer-2. Here, we show that host RNA polymerase II (RNAPII) bidirectionally transcribes specific AT-rich regions of the IIV-6 DNA genome to generate dsRNA. Both replicative and naked IIV-6 genomes trigger production of dsRNA in Drosophila cells, implying direct sensing of invading DNA. Loquacious-PD, a Dicer-2 co-factor essential for the biogenesis of endogenous siRNAs, is dispensable for processing of IIV-6-derived dsRNAs, which suggests that they are distinct. Consistent with this finding, inhibition of the RNAPII co-factor P-TEFb affects the synthesis of endogenous, but not virus-derived, dsRNA. Altogether, our results suggest that a non-canonical RNAPII complex recognizes invading viral DNA to synthesize virus-derived dsRNA, which activates the antiviral siRNA pathway in Drosophila.
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Affiliation(s)
- Isaque J S de Faria
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil; Université de Strasbourg, CNRS UPR9022, INSERM U1257, 67084 Strasbourg, France
| | - Eric R G R Aguiar
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil; Department of Biological Science (DCB), Center of Biotechnology and Genetics (CBG), Universidade Estadual de Santa Cruz (UESC), 45662-900 Ilhéus, Brazil
| | - Roenick P Olmo
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil; Université de Strasbourg, CNRS UPR9022, INSERM U1257, 67084 Strasbourg, France
| | - Juliana Alves da Silva
- Department of Morphology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil
| | - Laurent Daeffler
- Université de Strasbourg, CNRS UPR9022, INSERM U1257, 67084 Strasbourg, France
| | - Richard W Carthew
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; NSF Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Jean-Luc Imler
- Université de Strasbourg, CNRS UPR9022, INSERM U1257, 67084 Strasbourg, France
| | - João T Marques
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil; Université de Strasbourg, CNRS UPR9022, INSERM U1257, 67084 Strasbourg, France.
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37
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Xu Y, Jiang J, Lin X, Shi W, Cao C. Identification of Diverse Viruses Associated with Grasshoppers Unveils Parallel Relationship Between Host Phylogeny and Virome Composition. Virus Evol 2022; 8:veac057. [PMID: 35821717 PMCID: PMC9271882 DOI: 10.1093/ve/veac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/02/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022] Open
Abstract
Grasshoppers (Orthoptera: Acridoidea) are one of the most dangerous agricultural pests. Environmentally benign microbial pesticides are increasingly desirable for controlling grasshopper outbreaks in fragile ecosystems. However, little is known about natural pathogens infecting this pest. Here we profile the rich viral communities in forty-five grasshopper species and report 302 viruses, including 231 novel species. Most of the identified viruses are related to other insect viruses, and small RNA sequencing indicates that some are targeted by host antiviral RNA interference (RNAi) pathway. Our analysis of relationships between host phylogeny and virus diversity suggests that the composition of viromes is closely allied with host evolution. Overall, this study is a first extensive exploration of viruses in grasshoppers and provides a valuable comparative dataset of both academic and applied interest.
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Affiliation(s)
- Yao Xu
- Department of Entomology, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
| | - Jingyi Jiang
- Department of Entomology, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
| | - Xiaoju Lin
- Department of Entomology, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
| | - Wangpeng Shi
- Department of Entomology, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
| | - Chuan Cao
- Department of Entomology, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
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38
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Stenglein MD. The Case for Studying New Viruses of New Hosts. Annu Rev Virol 2022; 9:157-172. [PMID: 35671564 DOI: 10.1146/annurev-virology-100220-112915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Virology has largely focused on viruses that are pathogenic to humans or to the other species that we care most about. There is no doubt that this has been a worthwhile investment. But many transformative advances have been made through the in-depth study of relatively obscure viruses that do not appear on lists of prioritized pathogens. In this review, I highlight the benefits that can accrue from the study of viruses and hosts off the beaten track. I take stock of viral sequence diversity across host taxa as an estimate of the bias that exists in our understanding of host-virus interactions. I describe the gains that have been made through the metagenomic discovery of thousands of new viruses in previously unsampled hosts as well as the limitations of metagenomic surveys. I conclude by suggesting that the study of viruses that naturally infect existing and emerging model organisms represents an opportunity to push virology forward in useful and hard to predict ways.Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Mark D Stenglein
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA;
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39
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Forgia M, Chiapello M, Daghino S, Pacifico D, Crucitti D, Oliva D, Ayllon M, Turina M, Turina M. Three new clades of putative viral RNA-dependent RNA polymerases with rare or unique catalytic triads discovered in libraries of ORFans from powdery mildews and the yeast of oenological interest Starmerella bacillaris. Virus Evol 2022; 8:veac038. [PMID: 35615103 PMCID: PMC9125799 DOI: 10.1093/ve/veac038] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/14/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
High throughput sequencing allowed the discovery of many new viruses and viral organizations increasing our comprehension of virus origin and evolution. Most RNA viruses are currently characterized through similarity searches of annotated virus databases. This approach limits the possibility to detect completely new virus-encoded proteins with no detectable similarities to existing ones, i.e. ORFan proteins. A strong indication of the ORFan viral origin in a metatranscriptome is the lack of DNA corresponding to an assembled RNA sequence in the biological sample. Furthermore, sequence homology among ORFans and evidence of co-occurrence of these ORFans in specific host individuals provides further indication of a viral origin. Here, we use this theoretical framework to report the finding of three conserved clades of protein-coding RNA segments without a corresponding DNA in fungi. Protein sequence and structural alignment suggest these proteins are distantly related to viral RNA-dependent RNA polymerases (RdRP). In these new putative viral RdRP clades, no GDD catalytic triad is present, but the most common putative catalytic triad is NDD and a clade with GDQ, a triad previously unreported at that site. SDD, HDD, and ADD are also represented. For most members of these three clades, we were able to associate a second genomic segment, coding for a protein of unknown function. We provisionally named this new group of viruses ormycovirus. Interestingly, all the members of one of these sub-clades (gammaormycovirus) accumulate more minus sense RNA than plus sense RNA during infection.
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Affiliation(s)
- Marco Forgia
- Institute for Sustainable Plant Protection (IPSP), CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - M Chiapello
- Institute for Sustainable Plant Protection (IPSP), CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - Stefania Daghino
- Institute for Sustainable Plant Protection (IPSP), CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - D Pacifico
- Institute of Biosciences and Bioresources (IBBR), CNR, Corso Calatafimi 414, Palermo 90129, Italy
| | - D Crucitti
- Institute of Biosciences and Bioresources (IBBR), CNR, Corso Calatafimi 414, Palermo 90129, Italy
- Dipartimento di Scienze Agrarie, Alimentari e Forestali (SAAF), Università degli Studi di Palermo, Viale delle Scienze, Palermo 90128, Italy
| | - D Oliva
- Istituto Regionale del Vino e dell’Olio (IRVO), Via Libertà 66, Palermo 90143, Italy
| | - M Ayllon
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Campus Ciudad Universitaria Av. Puerta de Hierro, nº 2 - 4, Madrid 28040, Spain
| | - M Turina
- Institute for Sustainable Plant Protection (IPSP), CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - M Turina
- Institute for Sustainable Plant Protection (IPSP), CNR, Strada delle Cacce 73, Torino 10135, Italy
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40
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Coatsworth H, Bozic J, Carrillo J, Buckner EA, Rivers AR, Dinglasan RR, Mathias DK. Intrinsic variation in the vertically transmitted core virome of the mosquito Aedes aegypti. Mol Ecol 2022; 31:2545-2561. [PMID: 35229389 DOI: 10.1111/mec.16412] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/27/2022] [Accepted: 02/17/2022] [Indexed: 11/29/2022]
Abstract
Virome studies among metazoans have revealed the ubiquity of RNA viruses in animals, contributing to a fundamental re-thinking of the relationships between organisms and their microbiota. Mosquito viromes, often scrutinized due to their public health relevance, may also provide insight into broadly applicable concepts, such as a "core virome," a set of viruses consistently associated with a host species or population that may fundamentally impact its basic biology. A subset of mosquito-associated viruses (MAVs) could comprise such a core, and MAVs can be categorized as (i) arboviruses, which alternate between mosquito and vertebrate hosts, (ii) insect-specific viruses, which cannot replicate in vertebrate cells, and (iii) viruses with unknown specificity. MAVs have been widely characterized in the disease vector Aedes aegypti, and the occurrence of a core virome in this species has been proposed but remains unclear. Using a wild population previously surveyed for MAVs and a common laboratory strain, we investigated viromes in reproductive tissue via metagenomic RNA sequencing. Virome composition varied across samples, but four groups comprised >97% of virus sequences: a novel partiti-like virus (Partitiviridae), a toti-like virus (Totiviridae), unclassified Riboviria, and four orthomyxo-like viruses (Orthormyxoviridae). Whole or partial genomes for the partiti-like virus, toti-like virus, and one orthomyxo-like virus were assembled and analyzed phylogenetically. Multigenerational maintenance of these MAVs was confirmed by RT-PCR, indicating vertical transmission as a mechanism for persistence. This study provides fundamental information regarding MAV ecology and variability in A. aegypti and the potential for vertically maintained core viromes at the population level.
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Affiliation(s)
- H Coatsworth
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.,Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA.,CDC Southeastern Center of Excellence in Vector Borne Diseases, Gainesville, Florida, USA
| | - J Bozic
- CDC Southeastern Center of Excellence in Vector Borne Diseases, Gainesville, Florida, USA.,Entomology & Nematology Department, Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, Florida, USA.,Department of Entomology, the Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, PA, USA
| | - J Carrillo
- CDC Southeastern Center of Excellence in Vector Borne Diseases, Gainesville, Florida, USA.,Manatee County Mosquito Control District, Palmetto, Florida, USA.,Lacerta Therapeutics, Production and Development, Alachua Florida, USA
| | - E A Buckner
- CDC Southeastern Center of Excellence in Vector Borne Diseases, Gainesville, Florida, USA.,Entomology & Nematology Department, Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, Florida, USA
| | - A R Rivers
- CDC Southeastern Center of Excellence in Vector Borne Diseases, Gainesville, Florida, USA.,Genomics and Bioinformatics Research Unit, Agricultural Research Service, United States Department of Agriculture, Gainesville, Florida, USA
| | - R R Dinglasan
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA.,Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA.,CDC Southeastern Center of Excellence in Vector Borne Diseases, Gainesville, Florida, USA
| | - D K Mathias
- CDC Southeastern Center of Excellence in Vector Borne Diseases, Gainesville, Florida, USA.,Entomology & Nematology Department, Florida Medical Entomology Laboratory, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, Florida, USA
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41
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Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus. PLoS Genet 2022; 18:e1010100. [PMID: 35226668 PMCID: PMC8912903 DOI: 10.1371/journal.pgen.1010100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/10/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022] Open
Abstract
RNA interference (RNAi) is a conserved mechanism of small RNA-mediated genome regulation commonly involved in suppression of transposable elements (TEs) through both post-transcriptional silencing, and transcriptional repression via heterochromatin assembly. The fission yeast Schizosaccharomyces pombe has been extensively utilised as a model for studying RNAi pathways. However, this species is somewhat atypical in that TEs are not major targets of RNAi, and instead small RNAs correspond primarily to non-coding pericentromeric repeat sequences, reflecting a specialised role for the pathway in promoting heterochromatin assembly in these regions. In contrast, in the related fission yeast Schizosaccharomyces japonicus, sequenced small RNAs correspond primarily to TEs. This suggests there may be fundamental differences in the operation of RNAi pathways in these two related species. To investigate these differences, we probed RNAi function in S. japonicus. Unexpectedly, and in contrast to S. pombe, we found that RNAi is essential in this species. Moreover, viability of RNAi mutants can be rescued by mutations implicated in enhancing RNAi-independent heterochromatin propagation. These rescued strains retain heterochromatic marks on TE sequences, but exhibit derepression of TEs at the post-transcriptional level. Our findings indicate that S. japonicus retains the ancestral role of RNAi in facilitating suppression of TEs via both post-transcriptional silencing and heterochromatin assembly, with specifically the heterochromatin pathway being essential for viability, likely due to a function in genome maintenance. The specialised role of RNAi in heterochromatin assembly in S. pombe appears to be a derived state that emerged after the divergence of S. japonicus. The chromosomes of many species are populated by repetitive transposable elements that are able to “jump” throughout the genome. The consequences of these mobilisations can be catastrophic, resulting in disruption of genes or chromosomal rearrangements, thus organisms usually employ defence mechanisms to keep these elements inactivated. The most widespread of these systems is RNA interference, which utilises small RNA molecules to direct either packaging of transposable element DNA into repressive heterochromatin, or degradation of RNA transcripts. Many fundamental discoveries about RNAi function have been made in the model fission yeast Schizosaccharomyces pombe; however, this species is unusual as it does not generally employ RNAi to control its transposable elements. We found that in a lesser studied relative, Schizosaccharomyces japonicus, small RNAs are required to silence transposable elements, and that this silencing occurs via both formation of heterochromatin and degradation of transcripts. This dual function RNAi pathway targeting transposable elements that appear to cluster at centromeres is very similar to systems seen in complex multicellular organisms, thus our findings reveal S. japonicus to be an exciting emergent model in which to study RNAi and centromere function.
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Abstract
The COVID-19 pandemic has given the study of virus evolution and ecology new relevance. Although viruses were first identified more than a century ago, we likely know less about their diversity than that of any other biological entity. Most documented animal viruses have been sampled from just two phyla - the Chordata and the Arthropoda - with a strong bias towards viruses that infect humans or animals of economic and social importance, often in association with strong disease phenotypes. Fortunately, the recent development of unbiased metagenomic next-generation sequencing is providing a richer view of the animal virome and shedding new light on virus evolution. In this Review, we explore our changing understanding of the diversity, composition and evolution of the animal virome. We outline the factors that determine the phylogenetic diversity and genomic structure of animal viruses on evolutionary timescales and show how this impacts assessment of the risk of disease emergence in the short term. We also describe the ongoing challenges in metagenomic analysis and outline key themes for future research. A central question is how major events in the evolutionary history of animals, such as the origin of the vertebrates and periodic mass extinction events, have shaped the diversity and evolution of the viruses they carry.
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43
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Raza A, Wu Q. Diagnosis of Viral Diseases Using Deep Sequencing and Metagenomics Analyses. Methods Mol Biol 2022; 2400:225-243. [PMID: 34905206 DOI: 10.1007/978-1-0716-1835-6_22] [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: 06/14/2023]
Abstract
Viruses are ubiquitous in nature and exist in a variety of habitats. The advancement in sequencing technologies has revolutionized the understanding of viral biodiversity associated with plant diseases. Deep sequencing combined with metagenomics is a powerful approach that has proven to be revolutionary in the last decade and involves the direct analysis of viral genomes present in a diseased tissue sample. This protocol describes the details of RNA extraction and purification from wild rice plant and their yield, RNA purity, and integrity assessment. As a final step, bioinformatics data analysis including demultiplexing, quality control, de novo transcriptome assembly, taxonomic allocation and read mapping following Illumina HiSeq small and total RNA sequencing are described. Furthermore, the total RNAs extraction protocol and an additional ribosomal rRNAs depletion step which are significantly important for viral genomes construction are provided.
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Affiliation(s)
- Ali Raza
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Qingfa Wu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China.
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44
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Male Age and Wolbachia Dynamics: Investigating How Fast and Why Bacterial Densities and Cytoplasmic Incompatibility Strengths Vary. mBio 2021; 12:e0299821. [PMID: 34903056 PMCID: PMC8686834 DOI: 10.1128/mbio.02998-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Endosymbionts can influence host reproduction and fitness to favor their maternal transmission. For example, endosymbiotic Wolbachia bacteria often cause cytoplasmic incompatibility (CI) that kills uninfected embryos fertilized by Wolbachia-modified sperm. Infected females can rescue CI, providing them a relative fitness advantage. Wolbachia-induced CI strength varies widely and tends to decrease as host males age. Since strong CI drives Wolbachia to high equilibrium frequencies, understanding how fast and why CI strength declines with male age is crucial to explaining age-dependent CI’s influence on Wolbachia prevalence. Here, we investigate if Wolbachia densities and/or CI gene (cif) expression covary with CI-strength variation and explore covariates of age-dependent Wolbachia-density variation in two classic CI systems. wRi CI strength decreases slowly with Drosophila simulans male age (6%/day), but wMel CI strength decreases very rapidly (19%/day), yielding statistically insignificant CI after only 3 days of Drosophila melanogaster adult emergence. Wolbachia densities and cif expression in testes decrease as wRi-infected males age, but both surprisingly increase as wMel-infected males age, and CI strength declines. We then tested if phage lysis, Octomom copy number (which impacts wMel density), or host immune expression covary with age-dependent wMel densities. Only host immune expression correlated with density. Together, our results identify how fast CI strength declines with male age in two model systems and reveal unique relationships between male age, Wolbachia densities, cif expression, and host immunity. We discuss new hypotheses about the basis of age-dependent CI strength and its contributions to Wolbachia prevalence.
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Metatranscriptomic Sequencing Suggests the Presence of Novel RNA Viruses in Rice Transmitted by Brown Planthopper. Viruses 2021; 13:v13122464. [PMID: 34960733 PMCID: PMC8708968 DOI: 10.3390/v13122464] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
Viral pathogens are a major threat to stable crop production. Using a backcross strategy, we find that integrating a dominant brown planthopper (BPH) resistance gene Bph3 into a high-yield and BPH-susceptible indica rice variety significantly enhances BPH resistance. However, when Bph3-carrying backcross lines are infested with BPH, these BPH-resistant lines exhibit sterile characteristics, displaying panicle enclosure and failure of seed production at their mature stage. As we suspected, BPH-mediated viral infections could cause the observed sterile symptoms, and we characterized rice-infecting viruses using deep metatranscriptomic sequencing. Our analyses revealed eight novel virus species and five known viruses, including a highly divergent virus clustered within a currently unclassified family. Additionally, we characterized rice plant antiviral responses using small RNA sequencing. The results revealed abundant virus-derived small interfering RNAs in sterile rice plants, providing evidence for Dicer-like and Argonaute-mediated immune responses in rice plants. Together, our results provide insights into the diversity of viruses in rice plants, and our findings suggest that multiple virus infections occur in rice plants.
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Pennemann FL, Mussabekova A, Urban C, Stukalov A, Andersen LL, Grass V, Lavacca TM, Holze C, Oubraham L, Benamrouche Y, Girardi E, Boulos RE, Hartmann R, Superti-Furga G, Habjan M, Imler JL, Meignin C, Pichlmair A. Cross-species analysis of viral nucleic acid interacting proteins identifies TAOKs as innate immune regulators. Nat Commun 2021; 12:7009. [PMID: 34853303 PMCID: PMC8636641 DOI: 10.1038/s41467-021-27192-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 11/02/2021] [Indexed: 12/11/2022] Open
Abstract
The cell intrinsic antiviral response of multicellular organisms developed over millions of years and critically relies on the ability to sense and eliminate viral nucleic acids. Here we use an affinity proteomics approach in evolutionary distant species (human, mouse and fly) to identify proteins that are conserved in their ability to associate with diverse viral nucleic acids. This approach shows a core of orthologous proteins targeting viral genetic material and species-specific interactions. Functional characterization of the influence of 181 candidates on replication of 6 distinct viruses in human cells and flies identifies 128 nucleic acid binding proteins with an impact on virus growth. We identify the family of TAO kinases (TAOK1, -2 and -3) as dsRNA-interacting antiviral proteins and show their requirement for type-I interferon induction. Depletion of TAO kinases in mammals or flies leads to an impaired response to virus infection characterized by a reduced induction of interferon stimulated genes in mammals and impaired expression of srg1 and diedel in flies. Overall, our study shows a larger set of proteins able to mediate the interaction between viral genetic material and host factors than anticipated so far, attesting to the ancestral roots of innate immunity and to the lineage-specific pressures exerted by viruses.
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Affiliation(s)
- Friederike L Pennemann
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Assel Mussabekova
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Christian Urban
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Alexey Stukalov
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Line Lykke Andersen
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Vincent Grass
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Teresa Maria Lavacca
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Cathleen Holze
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Lila Oubraham
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany
| | - Yasmine Benamrouche
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Enrico Girardi
- CeMM - Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Rasha E Boulos
- Computer Science and Mathematics Department, School of Arts and Science, Lebanese American University, Byblos, Lebanon
| | - Rune Hartmann
- Aarhus University, Department of Molecular Biology and Genetics - Structural Biology, Aarhus, Denmark
| | - Giulio Superti-Furga
- CeMM - Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Matthias Habjan
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Jean-Luc Imler
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Carine Meignin
- Université de Strasbourg, CNRS UPR9022, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Andreas Pichlmair
- Technical University of Munich, School of Medicine, Institute of Virology, 81675, Munich, Germany.
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany.
- German Center for Infection Research (DZIF), Munich partner site, Munich, Germany.
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Possible Arbovirus Found in Virome of Melophagus ovinus. Viruses 2021; 13:v13122375. [PMID: 34960644 PMCID: PMC8707155 DOI: 10.3390/v13122375] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/22/2022] Open
Abstract
Members of the Lipopteninae subfamily are blood-sucking ectoparasites of mammals. The sheep ked (Melophagus ovinus) is a widely distributed ectoparasite of sheep. It can be found in most sheep-rearing areas and can cause skin irritation, restlessness, anemia, weight loss and skin injuries. Various bacteria and some viruses have been detected in M. ovinus; however, the virome of this ked has never been studied using modern approaches. Here, we study the virome of M. ovinus collected in the Republic of Tuva, Russia. In our research, we were able to assemble full genomes for five novel viruses, related to the Rhabdoviridae (Sigmavirus), Iflaviridae, Reoviridae and Solemoviridae families. Four viruses were found in all five of the studied pools, while one virus was found in two pools. Phylogenetically, all of the novel viruses clustered together with various recently described arthropod viruses. All the discovered viruses were tested on their ability to replicate in the mammalian porcine embryo kidney (PEK) cell line. Aksy-Durug Melophagus sigmavirus RNA was detected in the PEK cell line cultural supernate after the first, second and third passages. Such data imply that this virus might be able to replicate in mammalian cells, and thus, can be considered as a possible arbovirus.
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Cogni R, Ding SD, Pimentel AC, Day JP, Jiggins FM. Wolbachia reduces virus infection in a natural population of Drosophila. Commun Biol 2021; 4:1327. [PMID: 34824354 PMCID: PMC8617179 DOI: 10.1038/s42003-021-02838-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/25/2021] [Indexed: 12/31/2022] Open
Abstract
Wolbachia is a maternally transmitted bacterial symbiont that is estimated to infect approximately half of arthropod species. In the laboratory it can increase the resistance of insects to viral infection, but its effect on viruses in nature is unknown. Here we report that in a natural population of Drosophila melanogaster, individuals that are infected with Wolbachia are less likely to be infected by viruses. By characterising the virome by metagenomic sequencing and then testing individual flies for infection, we found the protective effect of Wolbachia was virus-specific, with the prevalence of infection being up to 15% greater in Wolbachia-free flies. The antiviral effects of Wolbachia may contribute to its extraordinary ecological success, and in nature the symbiont may be an important component of the antiviral defences of insects.
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Affiliation(s)
- Rodrigo Cogni
- Department of Ecology, University of São Paulo, São Paulo, Brazil.
| | | | - André C Pimentel
- Department of Ecology, University of São Paulo, São Paulo, Brazil
| | - Jonathan P Day
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Francis M Jiggins
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
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Xu L, Guo M, Hu B, Zhou H, Yang W, Hui L, Huang R, Zhan J, Shi W, Wu Y. Tick virome diversity in Hubei Province, China, and the influence of host ecology. Virus Evol 2021; 7:veab089. [PMID: 34804590 PMCID: PMC8599308 DOI: 10.1093/ve/veab089] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/14/2021] [Accepted: 11/02/2021] [Indexed: 12/16/2022] Open
Abstract
Ticks are important vector hosts of pathogens which cause human and animal
diseases worldwide. Diverse viruses have been discovered in ticks; however,
little is known about the ecological factors that affect the tick virome
composition and evolution. Herein, we employed RNA sequencing to study the
virome diversity of the Haemaphysalis longicornis and
Rhipicephalus microplus ticks sampled in Hubei Province in
China. Twelve RNA viruses with complete genomes were identified, which belonged
to six viral families: Flaviviridae, Matonaviridae, Peribunyaviridae,
Nairoviridae, Phenuiviridae, and Rhabdoviridae.
These viruses showed great diversity in their genome organization and evolution,
four of which were proposed to be novel species. The virome diversity and
abundance of R. microplus ticks fed on cattle were evidently
high. Further ecological analyses suggested that host species and feeding status
may be key factors affecting the tick virome structure. This study described a
number of novel viral species and variants from ticks and, more importantly,
provided insights into the ecological factors shaping the virome structures of
ticks, although it clearly warrants further investigation.
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Affiliation(s)
- Lin Xu
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian 271016, China
| | - Moujian Guo
- State Key Laboratory of Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Bing Hu
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Hong Zhou
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian 271000, China
| | - Wei Yang
- State Key Laboratory of Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Lixia Hui
- State Key Laboratory of Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Rui Huang
- State Key Laboratory of Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Jianbo Zhan
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Weifeng Shi
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian 271016, China
| | - Ying Wu
- State Key Laboratory of Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
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50
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Silva JMF, Nagata T, Melo FL, Elena SF. Heterogeneity in the Response of Different Subtypes of Drosophila melanogaster Midgut Cells to Viral Infections. Viruses 2021; 13:2284. [PMID: 34835089 PMCID: PMC8623525 DOI: 10.3390/v13112284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/05/2021] [Accepted: 11/13/2021] [Indexed: 11/29/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) offers the possibility to monitor both host and pathogens transcriptomes at the cellular level. Here, public scRNA-seq datasets from Drosophila melanogaster midgut cells were used to compare the differences in replication strategy and cellular responses between two fly picorna-like viruses, Thika virus (TV) and D. melanogaster Nora virus (DMelNV). TV exhibited lower levels of viral RNA accumulation but infected a higher number of cells compared to DMelNV. In both cases, viral RNA accumulation varied according to cell subtype. The cellular heat shock response to TV and DMelNV infection was cell-subtype- and virus-specific. Disruption of bottleneck genes at later stages of infection in the systemic response, as well as of translation-related genes in the cellular response to DMelNV in two cell subtypes, may affect the virus replication.
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Affiliation(s)
- João M. F. Silva
- Departamento de Biologia Celular, Universidade de Brasília, Brasília 70910-900, Brazil; (J.M.F.S.); (T.N.); (F.L.M.)
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, 46980 Paterna, València, Spain
| | - Tatsuya Nagata
- Departamento de Biologia Celular, Universidade de Brasília, Brasília 70910-900, Brazil; (J.M.F.S.); (T.N.); (F.L.M.)
| | - Fernando L. Melo
- Departamento de Biologia Celular, Universidade de Brasília, Brasília 70910-900, Brazil; (J.M.F.S.); (T.N.); (F.L.M.)
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, 46980 Paterna, València, Spain
- The Santa Fe Institute, Santa Fe, NM 87501, USA
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