1
|
Lee GE, Lee HJ, Jeong RD. Comprehensive Metatranscriptomic Analysis of Plant Viruses in Imported Frozen Cherries and Blueberries. THE PLANT PATHOLOGY JOURNAL 2024; 40:377-389. [PMID: 39117336 PMCID: PMC11309839 DOI: 10.5423/ppj.oa.06.2024.0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024]
Abstract
The possibility of new viruses emerging in various regions worldwide has increased due to a combination of factors, including climate change and the expansion of international trading. Plant viruses spread through various transmission routes, encompassing well-known avenues such as pollen, seeds, and insects. However, research on potential transmission routes beyond these known mechanisms has remained limited. To address this gap, this study employed metatranscriptomic analysis to ascertain the presence of plant viruses in imported frozen fruits, specifically cherries and blueberries. This analysis aimed to identify pathways through which plant viruses may be introduced into countries. Virome analysis revealed the presence of six species of plant viruses in frozen cherries and blueberries: cherry virus A (CVA), prunus necrotic ringspot virus (PNRSV), prune dwarf virus (PDV), prunus virus F (PrVF), blueberry shock virus (BlShV), and blueberry latent virus (BlLV). Identifying these potential transmission routes is crucial for effectively managing and preventing the spread of plant viruses and crop protection. This study highlights the importance of robust quality control measures and monitoring systems for frozen fruits, emphasizing the need for proactive measures to mitigate the risk associated with the potential spread of plant viruses.
Collapse
Affiliation(s)
- Ga-Eun Lee
- Department of Applied Biology, Chonnam National University, Gwangju 61185, Korea
| | - Hyo-Jeong Lee
- Department of Applied Biology, Chonnam National University, Gwangju 61185, Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Chonnam National University, Gwangju 61185, Korea
| |
Collapse
|
2
|
Li S, Bu J, Pan X, Li Q, Zuo X, Xiao G, Du J, Zhang LK, Xia B, Gao Z. SARS-CoV-2 envelope protein-derived extracellular vesicles act as potential media for viral spillover. J Med Virol 2024; 96:e29782. [PMID: 39011762 DOI: 10.1002/jmv.29782] [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: 02/15/2024] [Revised: 06/13/2024] [Accepted: 06/25/2024] [Indexed: 07/17/2024]
Abstract
Extracellular vesicles (EVs) are shown to be a novel viral transmission model capable of increasing a virus's tropism. According to our earlier research, cells infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or transfected with envelope protein plasmids generate a novel type of EVs that are micrometer-sized and able to encase virus particles. Here, we showed the capacity of these EVs to invade various animals both in vitro and in vivo independent of the angiotensin-converting enzyme 2 receptor. First, via macropinocytosis, intact EVs produced from Vero E6 (monkey) cells were able to enter cells from a variety of animals, including cats, dogs, bats, hamsters, and minks, and vice versa. Second, when given to zebrafish with cutaneous wounds, the EVs showed favorable stability in aqueous environments and entered the fish. Moreover, infection of wild-type (WT) mice with heterogeneous EVs carrying SARS-CoV-2 particles led to a strong cytokine response and a notable amount of lung damage. Conversely, free viral particles did not infect WT mice. These results highlight the variety of processes behind viral transmission and cross-species evolution by indicating that EVs may be possible vehicles for SARS-CoV-2 spillover and raising risk concerns over EVs' potential for viral gene transfer.
Collapse
Affiliation(s)
- Shuangqu Li
- Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiwen Bu
- State Key Laboratory of Neuroscience, Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoyan Pan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qiguang Li
- Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Zuo
- Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Jiulin Du
- State Key Laboratory of Neuroscience, Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Lei-Ke Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- Hubei Jiangxia Laboratory, Wuhan, Hubei, China
| | - Bingqing Xia
- Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhaobing Gao
- Stake Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Zhongshan Institute of Drug Discovery, Institution for Drug Discovery Innovation, 22 Chinese Academy of Science, Zhongshan, China
| |
Collapse
|
3
|
Maksimović O, Bačnik K, Rivarez MPS, Vučurović A, Mehle N, Ravnikar M, Gutiérrez-Aguirre I, Kutnjak D. Virome analysis of irrigation water sources provides extensive insights into the diversity and distribution of plant viruses in agroecosystems. WATER RESEARCH 2024; 249:120712. [PMID: 38134622 DOI: 10.1016/j.watres.2023.120712] [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: 07/05/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 12/24/2023]
Abstract
Plant viruses pose a significant threat to agriculture. Several are stable outside their hosts, can enter water bodies and remain infective for prolonged periods of time. Even though the quality of irrigation water is of increasing importance in the context of plant health, the presence of plant viruses in irrigation waters is understudied. In this study, we conducted a large-scale high-throughput sequencing (HTS)-based virome analysis of irrigation and surface water sources to obtain complete information about the abundance and diversity of plant viruses in such waters. We detected nucleic acids of plant viruses from 20 families, discovered several novel plant viruses from economically important taxa, like Tobamovirus and observed the influence of the water source on the present virome. By comparing viromes of water and surrounding plants, we observed presence of plant viruses in both compartments, especially in cases of large-scale outbreaks, such as that of tomato mosaic virus. Moreover, we demonstrated that water virome data can extensively inform us about the distribution and diversity of plant viruses for which only limited information is available from plants. Overall, the results of the study provided extensive insights into the virome of irrigation waters from the perspective of plant health. It also suggested that an HTS-based water virome surveillance system could be used to detect potential plant disease outbreaks and to survey the distribution and diversity of plant viruses in the ecosystem.
Collapse
Affiliation(s)
- Olivera Maksimović
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia; Jožef Stefan International Postgraduate School, Slovenia
| | - Katarina Bačnik
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia
| | - Mark Paul Selda Rivarez
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia; Department of Entomology and Plant Pathology, North Carolina State University, USA; College of Agriculture and Agri-Industries, Caraga State University, Philippines
| | - Ana Vučurović
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia
| | - Nataša Mehle
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia; School for Viticulture and Enology, University of Nova Gorica, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia
| | | | - Denis Kutnjak
- National Institute of Biology, Večna pot 111, Ljubljana 1000, Slovenia.
| |
Collapse
|
4
|
Mehle N, Bačnik K, Bajde I, Brodarič J, Fox A, Gutiérrez-Aguirre I, Kitek M, Kutnjak D, Loh YL, Maksimović Carvalho Ferreira O, Ravnikar M, Vogel E, Vos C, Vučurović A. Tomato brown rugose fruit virus in aqueous environments - survival and significance of water-mediated transmission. FRONTIERS IN PLANT SCIENCE 2023; 14:1187920. [PMID: 37332729 PMCID: PMC10275568 DOI: 10.3389/fpls.2023.1187920] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023]
Abstract
Tomato brown rugose fruit virus (ToBRFV) has recently emerged as a major disease of tomatoes and peppers. ToBRFV is a seed- and contact-transmitted virus. In Slovenia, ToBRFV RNA was detected in samples of wastewater, river, and water used to irrigate plants. Even though the source of detected RNA could not be clearly established, this raised the question of the significance of the detection of ToBRFV in water samples and experimental studies were performed to address this question. The data presented here confirm that the release of virus particles from the roots of infected plants is a source of infectious ToBRFV particles in water and that the virus can remain infective up to four weeks in water stored at room temperature, while its RNA can be detected for much longer. These data also indicate that irrigation with ToBRFV-contaminated water can lead to plant infection. In addition, it has been shown that ToBRFV circulated in drain water in commercial tomato greenhouses from other European countries and that an outbreak of ToBRFV can be detected by regular monitoring of drain water. A simple method for concentrating ToBRFV from water samples and a comparison of the sensitivity of different methods, including the determination of the highest ToBRFV dilution still capable of infecting test plants, were also investigated. The results of our studies fill the knowledge gaps in the epidemiology and diagnosis of ToBRFV, by studying the role of water-mediated transmission, and provide a reliable risk assessment to identify critical points for monitoring and control.
Collapse
Affiliation(s)
- Nataša Mehle
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- School for Viticulture and Enology, University of Nova Gorica, Vipava, Slovenia
| | - Katarina Bačnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Irena Bajde
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Jakob Brodarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Adrian Fox
- Fera Science Ltd., York, United Kingdom
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Miha Kitek
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Olivera Maksimović Carvalho Ferreira
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Elise Vogel
- Scientia Terrae Research Institute VZW, Sint-Katelijne-Waver, Belgium
- De Ceuster Meststoffen NV (DCM), Grobbendonk, Belgium
| | - Christine Vos
- Scientia Terrae Research Institute VZW, Sint-Katelijne-Waver, Belgium
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| |
Collapse
|
5
|
Ahrens AK, Selinka HC, Wylezich C, Wonnemann H, Sindt O, Hellmer HH, Pfaff F, Höper D, Mettenleiter TC, Beer M, Harder TC. Investigating Environmental Matrices for Use in Avian Influenza Virus Surveillance-Surface Water, Sediments, and Avian Fecal Samples. Microbiol Spectr 2023; 11:e0266422. [PMID: 36700688 PMCID: PMC10100768 DOI: 10.1128/spectrum.02664-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023] Open
Abstract
Surveillance of avian influenza viruses (AIV) in wild water bird populations is important for early warning to protect poultry from incursions of high-pathogenicity (HP) AIV. Access to individual water birds is difficult and restricted and limits sampling depth. Here, we focused on environmental samples such as surface water, sediments, and environmentally deposited fresh avian feces as matrices for AIV detection. Enrichment of viral particles by ultrafiltration of 10-L surface water samples using Rexeed-25-A devices was validated using a bacteriophage ϕ6 internal control system, and AIV detection was attempted using real-time RT-PCR and virus isolation. While validation runs suggested an average enrichment of about 60-fold, lower values of 10 to 15 were observed for field water samples. In total 25/36 (60%) of water samples and 18/36 (50%) of corresponding sediment samples tested AIV positive. Samples were obtained from shallow water bodies in habitats with large numbers of waterfowl during an HPAIV epizootic. Although AIV RNA was detected in a substantial percentage of samples virus isolation failed. Virus loads in samples often were too low to allow further sub- and pathotyping. Similar results were obtained with environmentally deposited avian feces. Moreover, the spectrum of viruses detected by these active surveillance methods did not fully mirror an ongoing HPAIV epizootic among waterfowl as detected by passive surveillance, which, in terms of sensitivity, remains unsurpassed. IMPORTANCE Avian influenza viruses (AIV) have a wide host range in the avian metapopulation and, occasionally, transmission to humans also occurs. Surface water plays a particularly important role in the epidemiology of AIV, as the natural virus reservoir is found in aquatic wild birds. Environmental matrices comprising surface water, sediments, and avian fecal matter deposited in the environment were examined for their usefulness in AIV surveillance. Despite virus enrichment efforts, environmental samples regularly revealed very low virus loads, which hampered further sub- and pathotyping. Passive surveillance based on oral and cloacal swabs of diseased and dead wild birds remained unsurpassed with respect to sensitivity.
Collapse
Affiliation(s)
- Ann Kathrin Ahrens
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | | | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | | | - Ole Sindt
- State Laboratory of Schleswig-Holstein, Neumuenster, Germany
| | - Hartmut H. Hellmer
- Climate Sciences, Physical Oceanography of the Polar Seas, Alfred Wegener Institute, Bremerhaven, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | | | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | - Timm C. Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| |
Collapse
|
6
|
Betancourt WQ. Waterborne Plant Viruses of Importance in Agriculture. Infect Dis (Lond) 2023. [DOI: 10.1007/978-1-0716-2463-0_1096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
|
7
|
Potential risk of plant viruses entering disease cycle in surface water in protected vegetable growing areas of Eastern China. PLoS One 2023; 18:e0280303. [PMID: 36696381 PMCID: PMC9876373 DOI: 10.1371/journal.pone.0280303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 12/27/2022] [Indexed: 01/26/2023] Open
Abstract
With the expansion of protected vegetable growing areas (PVGAs), viral plant diseases have become more prevalent, causing severe economic losses to the vegetable production industry in China. At present, researches on plant viruses mainly focus on plants, but there is only a few reports on the species of viruses in surface water from PVGAs. The surface water samples in PVGAs are representative to a certain extent, which has an important reference value for studying the characteristics of plant viruses in surface water. The purpose of this study was to identify the diversity and the possibility of entering disease infection cycle of plant viruses in water samples collected from PVGAs in eastern China. A total of 144 water samples were collected, and eight plant viruses including tobacco mosaic virus (TMV, 8.33%), cucumber green mottle mosaic virus (CGMMV, 33.33%), pepper mild mottle virus (PMMoV, 6.94%), cucumber mosaic virus (CMV, 0.69%), tomato masaic virus (ToMV, 3.47%), tomato mottle mosaic virus (ToMMV, 0.69%), tomato chlorosis virus (ToCV, 4.17%), and tomato yellow leaf curl virus (TYLCV, 5.56%) were examined using RT-PCR and PCR. The species of viruses in surface water varied greatly by location. CGMMV, TMV, ToCV, ToMV, ToMMV, and TYLCV were identified in Shandong, a northern part of Eastern China, whereas only PMMoV was found in Shanghai, a southern part of Eastern China. After healthy tobacco plants were inoculated with the concentrated solutions of TMV, ToMV, CGMMV, and PMMoV, could cause disease in healthy tobacco, indicating that the plant viruses in the concentrated solution have the infectivity, and the plant viruses in surface water have the possibility of entering the infection cycle of disease. The results will improve the understanding of the potential risks of waterborne disease transmission.
Collapse
|
8
|
Hu Z, Yang L, Han J, Liu Z, Zhao Y, Jin Y, Sheng Y, Zhu L, Hu B. Human viruses lurking in the environment activated by excessive use of COVID-19 prevention supplies. ENVIRONMENT INTERNATIONAL 2022; 163:107192. [PMID: 35354102 PMCID: PMC8938188 DOI: 10.1016/j.envint.2022.107192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/24/2022] [Accepted: 03/17/2022] [Indexed: 05/09/2023]
Abstract
Due to extensive COVID-19 prevention measures, millions of tons of chemicals penetrated into natural environment. Alterations of human viruses in the environment, the neglected perceiver of environmental fluctuations, remain obscure. To decipher the interaction between human viruses and COVID-19 related chemicals, environmental samples were collected on March 2020 from surroundings of designated hospitals and receivers of wastewater treatment plant effluent in Wuhan. The virus community and chemical concentration were respectively unveiled in virtue of virome and ultra-high-performance liquid chromatography-tandem mass spectrometry. The complex relationship between virus and chemical was ulteriorly elaborated by random forest model. As an indicator, environmental viruses were corroborated to sensitively reflect the ecological disturbance originated from pandemic prevention supplies. Chemicals especially trihalomethanes restrained the virus community diversity. Confronting this adverse scenario, Human gammaherpesvirus 4 and Orf virus with resistance to trihalomethanes flourished while replication potential of Macacine alphaherpesvirus 1 ascended under glucocorticoids stress. Consequently, human viruses lurking in the environment were actuated by COVID-19 prevention chemicals, which was a constant burden to public health in this ongoing pandemic. Besides, segments of SARS-CoV-2 RNA were detected near designated hospitals, suggesting environment as a missing link in the transmission route. This research innovatively underlined the human health risk of pandemic prevention supplies from the virus - environment interaction, appealing for monitoring of environmental viruses in long term.
Collapse
Affiliation(s)
- Zhichao Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Lihua Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jian Han
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zishu Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Yihao Jin
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Yaqi Sheng
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, 310058 China
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, 310058 China.
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
9
|
Geballa-Koukoulas K, La Scola B, Blanc G, Andreani J. Diversity of Giant Viruses Infecting Vermamoeba vermiformis. Front Microbiol 2022; 13:808499. [PMID: 35602053 PMCID: PMC9116030 DOI: 10.3389/fmicb.2022.808499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/18/2022] [Indexed: 11/28/2022] Open
Abstract
The discovery of Acanthamoeba polyphaga mimivirus in 2003 using the free-living amoeba Acanthamoeba polyphaga caused a paradigm shift in the virology field. Twelve years later, using another amoeba as a host, i.e., Vermamoeba vermiformis, novel isolates of giant viruses have been discovered. This amoeba–virus relationship led scientists to study the evolution of giant viruses and explore the origins of eukaryotes. The purpose of this article is to review all the giant viruses that have been isolated from Vermamoeba vermiformis, compare their genomic features, and report the influence of these viruses on the cell cycle of their amoebal host. To date, viruses putatively belonging to eight different viral taxa have been described: 7 are lytic and 1 is non-lytic. The comparison of giant viruses infecting Vermamoeba vermiformis has suggested three homogenous groups according to their size, the replication time inside the host cell, and the number of encoding tRNAs. This approach is an attempt at determining the evolutionary origins and trajectories of the virus; therefore, more giant viruses infecting Vermamoeba must be discovered and studied to create a comprehensive knowledge on these intriguing biological entities.
Collapse
Affiliation(s)
- Khalil Geballa-Koukoulas
- MEPHI, APHM, IRD 198, Aix Marseille University, IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
- *Correspondence: Khalil Geballa-Koukoulas,
| | - Bernard La Scola
- MEPHI, APHM, IRD 198, Aix Marseille University, IHU-Méditerranée Infection, Marseille, France
| | - Guillaume Blanc
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Julien Andreani
- MEPHI, APHM, IRD 198, Aix Marseille University, IHU-Méditerranée Infection, Marseille, France
- Julien Andreani,
| |
Collapse
|
10
|
Filipić A, Lukežič T, Bačnik K, Ravnikar M, Ješelnik M, Košir T, Petkovšek M, Zupanc M, Dular M, Aguirre IG. Hydrodynamic cavitation efficiently inactivates potato virus Y in water. ULTRASONICS SONOCHEMISTRY 2022; 82:105898. [PMID: 34973580 PMCID: PMC8799611 DOI: 10.1016/j.ultsonch.2021.105898] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/17/2021] [Accepted: 12/26/2021] [Indexed: 05/24/2023]
Abstract
Waterborne plant viruses can destroy entire crops, leading not only to high financial losses but also to food shortages. Potato virus Y (PVY) is the most important potato viral pathogen that can also affect other valuable crops. Recently, it has been confirmed that this virus is capable of infecting host plants via water, emphasizing the relevance of using proper strategies to treat recycled water in order to prevent the spread of the infectious agents. Emerging environmentally friendly methods such as hydrodynamic cavitation (HC) provide a great alternative for treating recycled water used for irrigation. In the experiments conducted in this study, laboratory HC based on Venturi constriction with a sample volume of 1 L was used to treat water samples spiked with purified PVY virions. The ability of the virus to infect plants was abolished after 500 HC passes, corresponding to 50 min of treatment under pressure difference of 7 bar. In some cases, shorter treatments of 125 or 250 passes were also sufficient for virus inactivation. The HC treatment disrupted the integrity of viral particles, which also led to a minor damage of viral RNA. Reactive species, including singlet oxygen, hydroxyl radicals, and hydrogen peroxide, were not primarily responsible for PVY inactivation during HC treatment, suggesting that mechanical effects are likely the driving force of virus inactivation. This pioneering study, the first to investigate eukaryotic virus inactivation by HC, will inspire additional research in this field enabling further improvement of HC as a water decontamination technology.
Collapse
Affiliation(s)
- Arijana Filipić
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia.
| | - Tadeja Lukežič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Katarina Bačnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Meta Ješelnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Tamara Košir
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Martin Petkovšek
- University of Ljubljana, Faculty of Mechanical Engineering, Aškerčeva 6, 1000 Ljubljana, Slovenia
| | - Mojca Zupanc
- University of Ljubljana, Faculty of Mechanical Engineering, Aškerčeva 6, 1000 Ljubljana, Slovenia
| | - Matevž Dular
- University of Ljubljana, Faculty of Mechanical Engineering, Aškerčeva 6, 1000 Ljubljana, Slovenia
| | - Ion Gutierrez Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| |
Collapse
|
11
|
Rivarez MPS, Vučurović A, Mehle N, Ravnikar M, Kutnjak D. Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing. Front Microbiol 2021; 12:671925. [PMID: 34093492 PMCID: PMC8175903 DOI: 10.3389/fmicb.2021.671925] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/12/2021] [Indexed: 11/30/2022] Open
Abstract
Viruses cause a big fraction of economically important diseases in major crops, including tomato. In the past decade (2011–2020), many emerging or re-emerging tomato-infecting viruses were reported worldwide. In this period, 45 novel viral species were identified in tomato, 14 of which were discovered using high-throughput sequencing (HTS). In this review, we first discuss the role of HTS in these discoveries and its general impact on tomato virome research. We observed that the rate of tomato virus discovery is accelerating in the past few years due to the use of HTS. However, the extent of the post-discovery characterization of viruses is lagging behind and is greater for economically devastating viruses, such as the recently emerged tomato brown rugose fruit virus. Moreover, many known viruses still cause significant economic damages to tomato production. The review of databases and literature revealed at least 312 virus, satellite virus, or viroid species (in 22 families and 39 genera) associated with tomato, which is likely the highest number recorded for any plant. Among those, here, we summarize the current knowledge on the biology, global distribution, and epidemiology of the most important species. Increasing knowledge on tomato virome and employment of HTS to also study viromes of surrounding wild plants and environmental samples are bringing new insights into the understanding of epidemiology and ecology of tomato-infecting viruses and can, in the future, facilitate virus disease forecasting and prevention of virus disease outbreaks in tomato.
Collapse
Affiliation(s)
- Mark Paul Selda Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Faculty of Agriculture, University of Belgrade, Belgrade, Serbia
| | - Nataša Mehle
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,School for Viticulture and Enology, University of Nova Gorica, Nova Gorica, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| |
Collapse
|
12
|
Filipić A, Dobnik D, Tušek Žnidarič M, Žegura B, Štern A, Primc G, Mozetič M, Ravnikar M, Žel J, Gutierrez Aguirre I. Inactivation of Pepper Mild Mottle Virus in Water by Cold Atmospheric Plasma. Front Microbiol 2021; 12:618209. [PMID: 33584622 PMCID: PMC7877120 DOI: 10.3389/fmicb.2021.618209] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/04/2021] [Indexed: 11/18/2022] Open
Abstract
Water scarcity is one of the greatest threats for human survival and quality of life, and this is increasingly contributing to the risk of human, animal and plant infections due to waterborne viruses. Viruses are transmitted through polluted water, where they can survive and cause infections even at low concentrations. Plant viruses from the genus Tobamovirus are highly mechanically transmissible, and cause considerable damage to important crops, such as tomato. The release of infective tobamoviruses into environmental waters has been reported, with the consequent risk for arid regions, where these waters are used for irrigation. Virus inactivation in water is thus very important and cold atmospheric plasma (CAP) is emerging in this field as an efficient, safe, and sustainable alternative to classic waterborne virus inactivation methods. In the present study we evaluated CAP-mediated inactivation of pepper mild mottle virus (PMMoV) in water samples. PMMoV is a very resilient water-transmissible tobamovirus that can survive transit through the human digestive tract. The efficiency of PMMoV inactivation was characterized for infectivity and virion integrity, and at the genome level, using test plant infectivity assays, transmission electron microscopy, and molecular methods, respectively. Additionally, the safety of CAP treatment was determined by testing the cytotoxic and genotoxic properties of CAP-treated water on the HepG2 cell line. 5-min treatment with CAP was sufficient to inactivate PMMoV without introducing any cytotoxic or genotoxic effects in the in-vitro cell model system. These data on inactivation of such stable waterborne virus, PMMoV, will encourage further examination of CAP as an alternative for treatment of potable and irrigation waters, and even for other water sources, with emphasis on inactivation of various viruses including enteric viruses.
Collapse
Affiliation(s)
- Arijana Filipić
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Bojana Žegura
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Alja Štern
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Gregor Primc
- Department of Surface Engineering, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Miran Mozetič
- Department of Surface Engineering, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,University of Nova Gorica, Nova Gorica, Slovenia
| | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Ion Gutierrez Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| |
Collapse
|
13
|
Bačnik K, Kutnjak D, Pecman A, Mehle N, Tušek Žnidarič M, Gutiérrez Aguirre I, Ravnikar M. Viromics and infectivity analysis reveal the release of infective plant viruses from wastewater into the environment. WATER RESEARCH 2020; 177:115628. [PMID: 32299020 DOI: 10.1016/j.watres.2020.115628] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 05/06/2023]
Abstract
Viruses represent one of the most important threats to agriculture. Several viral families include highly stable pathogens, which remain infective and can be transported long distances in water. The diversity of plant viruses in wastewater remains understudied; however, their potential impact is increasing with the increased irrigation usage of reclaimed wastewater. To determine the abundance, diversity and biological relevance of plant viruses in wastewater influents and effluents we applied an optimized virus concentration method followed by high-throughput sequencing and infectivity assays. We detected representatives of 47 plant virus species, including emerging crop threats. We also demonstrated infectivity for pathogenic and economically relevant plant viruses from the genus Tobamovirus (family Virgaviridae), which remain infective even after conventional wastewater treatment. These results demonstrate the potential of metagenomics to capture the diversity of plant viruses circulating in the environment and expose the potential risk of the uncontrolled use of reclaimed water for irrigation.
Collapse
Affiliation(s)
- Katarina Bačnik
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Denis Kutnjak
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Anja Pecman
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Nataša Mehle
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Ion Gutiérrez Aguirre
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Maja Ravnikar
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000, Ljubljana, Slovenia; University of Nova Gorica, Vipavska cesta, 5000, Nova Gorica, Slovenia.
| |
Collapse
|
14
|
Filipić A, Gutierrez-Aguirre I, Primc G, Mozetič M, Dobnik D. Cold Plasma, a New Hope in the Field of Virus Inactivation. Trends Biotechnol 2020; 38:1278-1291. [PMID: 32418663 PMCID: PMC7164895 DOI: 10.1016/j.tibtech.2020.04.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022]
Abstract
Viruses can infect all cell-based organisms, from bacteria to humans, animals, and plants. They are responsible for numerous cases of hospitalization, many deaths, and widespread crop destruction, all of which result in an enormous medical, economical, and biological burden. Each of the currently used decontamination methods has important drawbacks. Cold plasma (CP) has entered this field as a novel, efficient, and clean solution for virus inactivation. We present recent developments in this promising field of CP-mediated virus inactivation, and describe the applications and mechanisms of the inactivation. This is particularly relevant because viral pandemics, such as COVID-19, highlight the need for alternative virus inactivation methods to replace, complement, or upgrade existing procedures. Pathogenic viruses are becoming an increasing burden for health, agriculture, and the global economy. Classic disinfection methods have several drawbacks, and innovative solutions for virus inactivation are urgently needed. CP can be used as an environmentally friendly tool for virus inactivation. It can inactivate different human, animal, and plant viruses in various matrices. When using CP for virus inactivation it is important to set the correct parameters and to choose treatment durations that allow particles to interact with the contaminated material. Reactive oxygen and/or nitrogen species have been shown to be responsible for virus inactivation through effects on capsid proteins and/or nucleic acids. The development of more accurate methods will provide information on which plasma particles are crucial in each experiment, and how exactly they affect viruses.
Collapse
Affiliation(s)
- Arijana Filipić
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000 Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova Cesta 39, 1000 Ljubljana, Slovenia.
| | - Ion Gutierrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
| | - Gregor Primc
- Department of Surface Engineering and Optoelectronics, Jožef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia
| | - Miran Mozetič
- Department of Surface Engineering and Optoelectronics, Jožef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
| |
Collapse
|