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Emerging and Re-emerging Plant Viruses in a Context of Global Change

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A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Viral Pathogens".

Deadline for manuscript submissions: closed (15 January 2024) | Viewed by 30052

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Special Issue Editors

Dr. Sudeep Bag

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Guest Editor

Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA
Interests: plant viruses; epidemiology; diagnosis; host–virus interaction; HTS

Prof. Dr. Albert K. Culbreath

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Guest Editor

Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA
Interests: epidemiology and management of foliar fungal diseases and tomato spotted wilt virus (TSWV) of peanut

Prof. Dr. Rajagopalbabu Srinivasan

E-Mail Website
Guest Editor

Department of Entomology, University of Georgia, Griffin, GA 30223, USA
Interests: whitefly and aphid- transmitted plant viruses

Special Issue Information

Dear Colleagues,

Extant plant viruses and diseases caused by them severely impact yields of many economically important crops. In addition, new plant viruses are becoming increasingly common at the interface of cultivated and natural vegetations. Numerous factors driving the emergence of new viruses include virus evolution, genomic recombination, reassortment, agricultural diversification, urbanization, global trade, and human migration. Furthermore, climate change and intensification practices could aggravate the risk of new and emerging viruses. These emerging viruses impact the regional agroecosystem and pose a risk to food security and the local economy. To what extent do these new emerging and re-emerging viruses threaten native plant communities and diversity is not well investigated. This Special Issue highlights the impact of emerging and re-emerging viruses in the newly introduced regions, assays to detect the virus in managed and natural vegetation, vector, beneficial population, high-throughput sequencing, host–virus-vector interaction, virus management using conventional and genomic tools, and steps to mitigate virus spread.

Dr. Sudeep Bag
Prof. Dr. Albert K. Culbreath
Prof. Dr. Rajagopalbabu Srinivasan
Guest Editors

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Keywords

molecular and field epidemiology
emerging and re-emerging viruses
adaptation
weeds
overwintering host
non-crop host
quarantine and regulation
decision-making tools
omics
genomic surveillance and modelling
phylogenomic
disease management

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Published Papers (9 papers)

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Research

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14 pages, 2162 KiB

Open AccessArticle

Identification of a Novel Polerovirus in Cocoa (Theobroma cacao) Germplasm and Development of Molecular Methods for Use in Diagnostics

by Ihsan Ullah, Muhammad Kamran and Jim M. Dunwell

Pathogens 2023, 12(11), 1284; https://doi.org/10.3390/pathogens12111284 - 26 Oct 2023

Cited by 2 | Viewed by 2113

Abstract

The cocoa crop (Theobroma cacao L.) is known to be a host for several badnaviruses, some of which cause severe disease, while others are asymptomatic. Recently, the first preliminary evidence has been published concerning the occurrence of a polerovirus in cacao. We report here the first near-complete genome sequence of cacao polerovirus (CaPV) by combining bioinformatic searches of cacao transcript databases, with cloning from the infected germplasm. The reported novel genome has all the genome features known for poleroviruses from other species. Pairwise identity analyses of RNA-dependent RNA polymerase and coat protein indicates < 60% similarity of CaPV with any reported poleroviruses; hence, we propose that the polerovirus isolate reported in this study is a novel polerovirus. The genome sequence information was also used to develop a multiplex RT-PCR assay, which was applied to screen a selected range of germplasms and to identify several infected clones. Although there is no evidence that this virus causes any severe disease, this new information, together with a robust diagnostic assay, are of strategic importance in developing protocols for the safe international transfer of cacao germplasms. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Plant Viruses in a Context of Global Change)

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14 pages, 9317 KiB

Open AccessEditor’s ChoiceArticle

Effects of Host Plants and Their Infection Status on Acquisition and Inoculation of A Plant Virus by Its Hemipteran Vector

by Saurabh Gautam, Kiran R. Gadhave, James W. Buck, Bhabesh Dutta, Timothy Coolong, Scott Adkins, Alvin M. Simmons and Rajagopalbabu Srinivasan

Pathogens 2023, 12(9), 1119; https://doi.org/10.3390/pathogens12091119 - 1 Sep 2023

Cited by 6 | Viewed by 2254

Abstract

Whitefly, Bemisia tabaci Gennadius (B cryptic species), transmits cucurbit leaf crumple virus (CuLCrV) in a persistent fashion. CuLCrV affects several crops such as squash and snap bean in the southeastern United States. CuLCrV is often found as a mixed infection with whitefly transmitted criniviruses, such as cucurbit yellow stunting disorder virus (CYSDV) in hosts such as squash, or as a single infection in hosts such as snap bean. The implications of different host plants (inoculum sources) with varying infection status on CuLCrV transmission/epidemics is not clear. This study conducted a series of whitefly mediated CuLCrV transmission experiments. In the first experiment, three plants species: squash, snap bean, and tobacco were inoculated by whiteflies feeding on field-collected mixed-infected squash plants. In the second experiment, three plant species, namely squash, snap bean, and tobacco with varying infection status (squash infected with CuLCrV and CYSDV and snap bean and tobacco infected with CuLCrV), were used as inoculum sources. In the third experiment, squash plants with differential CuLCrV accumulation levels and infection status (either singly infected with CuLCrV or mixed infected with CuLCrV and CYSDV) were used as inoculum sources. Irrespective of plant species and its infection status, CuLCrV accumulation in whiteflies was dependent upon the CuLCrV accumulation in the inoculum source plants. Furthermore, differential CuLCrV accumulation in whiteflies resulted in differential transmission, CuLCrV accumulation, and disease phenotype in the recipient squash plants. Overall, results demonstrate that whitefly mediated CuLCrV transmission between host plants follows a virus density dependent phenomenon with implications for epidemics. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Plant Viruses in a Context of Global Change)

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17 pages, 9957 KiB

Open AccessEditor’s ChoiceArticle

Evaluation of Wild Peanut Species and Their Allotetraploids for Resistance against Thrips and Thrips-Transmitted Tomato Spotted Wilt Orthotospovirus (TSWV)

by Yi-Ju Chen, Sudeep Pandey, Michael Catto, Soraya Leal-Bertioli, Mark R. Abney, Sudeep Bag, Mark Hopkins, Albert Culbreath and Rajagopalbabu Srinivasan

Pathogens 2023, 12(9), 1102; https://doi.org/10.3390/pathogens12091102 - 28 Aug 2023

Cited by 6 | Viewed by 2468

Abstract

Thrips-transmitted tomato spotted wilt orthotospovirus (TSWV) causes spotted wilt disease in peanut (Arachis hypogaea L.) and limits yield. Breeding programs have been developing TSWV-resistant cultivars, but availability of sources of resistance against TSWV in cultivated germplasm is extremely limited. Diploid wild Arachis species can serve as important sources of resistance, and despite ploidy barriers (cultivated peanut is tetraploid), their usage in breeding programs is now possible because of the knowledge and development of induced interspecific allotetraploid hybrids. This study screened 10 wild diploid Arachis and six induced allotetraploid genotypes via thrips-mediated TSWV transmission assays and thrips’ feeding assays in the greenhouse. Three parameters were evaluated: percent TSWV infection, virus accumulation, and temporal severity of thrips feeding injury. Results indicated that the diploid A. stenosperma accession V10309 and its derivative-induced allotetraploid ValSten1 had the lowest TSWV infection incidences among the evaluated genotypes. Allotetraploid BatDur1 had the lowest thrips-inflicted damage at each week post thrips release, while diploid A. batizocoi accession K9484 and A. duranensis accession V14167 had reduced feeding damage one week post thrips release, and diploids A. valida accession GK30011 and A. batizocoi had reduced feeding damage three weeks post thrips releasethan the others. Overall, plausible TSWV resistance in diploid species and their allotetraploid hybrids was characterized by reduced percent TSWV infection, virus accumulation, and feeding severity. Furthermore, a few diploids and tetraploid hybrids displayed antibiosis against thrips. These results document evidence for resistance against TSWV and thrips in wild diploid Arachis species and peanut-compatible-induced allotetraploids. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Plant Viruses in a Context of Global Change)

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16 pages, 3150 KiB

Open AccessArticle

A Simplified Multiplex PCR Assay for Simultaneous Detection of Six Viruses Infecting Diverse Chilli Species in India and Its Application in Field Diagnosis

by Oinam Priyoda Devi, Susheel Kumar Sharma, Keithellakpam Sanatombi, Konjengbam Sarda Devi, Neeta Pathaw, Subhra Saikat Roy, Ngathem Taibangnganbi Chanu, Rakesh Sanabam, Huirem Chandrajini Devi, Akoijam Ratankumar Singh and Virendra Kumar Baranwal

Pathogens 2023, 12(1), 6; https://doi.org/10.3390/pathogens12010006 - 21 Dec 2022

Cited by 8 | Viewed by 3095

Abstract

Chilli is infected by at least 65 viruses globally, with a mixed infection of multiple viruses leading to severe losses being a common occurrence. A simple diagnostic procedure that can identify multiple viruses at once is required to track their spread, initiate management measures and manage them using virus-free planting supplies. The present study, for the first time, reports a simplified and robust multiplex PCR (mPCR) assay for the simultaneous detection of five RNA viruses, capsicum chlorosis orthotospovirus (CaCV), chilli veinal mottle virus (ChiVMV), large cardamom chirke virus (LCCV), cucumber mosaic virus (CMV), and pepper mild mottle virus (PMMoV), and a DNA virus, chilli leaf curl virus (ChiLCV) infecting chilli. The developed mPCR employed six pairs of primer from the conserved coat protein (CP) region of the respective viruses. Different parameters viz., primer concentration (150–450 nM) and annealing temperature (50 °C), were optimized in order to achieve specific and sensitive amplification of the target viruses in a single reaction tube. The detection limit of the mPCR assay was 5.00 pg/µL to simultaneously detect all the target viruses in a single reaction, indicating a sufficient sensitivity of the developed assay. The developed assay showed high specificity and showed no cross-amplification. The multiplex PCR assay was validated using field samples collected across Northeast India. Interestingly, out of 61 samples collected across the northeastern states, only 22 samples (36%) were positive for single virus infection while 33 samples (54%) were positive for three or more viruses tested in mPCR, showing the widespread occurrence of mixed infection under field conditions. To the best of our knowledge, this is the first report on the development and field validation of the mPCR assay for six chilli viruses and will have application in routine virus indexing and virus management. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Plant Viruses in a Context of Global Change)

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14 pages, 4991 KiB

Open AccessArticle

Silencing of Thrips palmi UHRF1BP1 and PFAS Using Antisense Oligos Induces Mortality and Reduces Tospovirus Titer in Its Vector

by Priti, Sunil Kumar Mukherjee and Amalendu Ghosh

Pathogens 2022, 11(11), 1319; https://doi.org/10.3390/pathogens11111319 - 10 Nov 2022

Cited by 12 | Viewed by 3014

Abstract

Thrips palmi (Thysanoptera: Thripidae) is an important pest of vegetables, legumes, and ornamentals. In addition, it transmits several plant viruses. T. palmi genes associated with innate immunity, endocytosis-related pathways, and cuticular development are highly enriched in response to Groundnut bud necrosis orthotospovirus (GBNV, genus Orthotospovirus, family Tospoviridae) infection. As the previous transcriptomic study suggested the involvement of T. palmi UHRF1BP1 and PFAS in GBNV infection, these two genes were targeted for silencing using antisense oligonucleotides (ASOs), and the effects on thrips’ fitness and virus acquisition were observed. Phosphorothioate modification of ASOs was carried out by replacing the nonbridging oxygen atom with a sulfur atom at the 3′ position to increase nuclease stability. The modified ASOs were delivered orally through an artificial diet. Exposure to ASOs reduced the target mRNA expression up to 2.70-fold optimally. Silencing of T. palmi UHRF1BP1 and PFAS induced 93.33% mortality that further increased up to 100% with an increase in exposure. Silencing of T. palmi UHRF1BP1 and PFAS also produced morphological deformities in the treated T. palmi. GBNV titer in T. palmi significantly declined post-exposure to ASOs. This is the first-ever report of silencing T. palmi UHRF1BP1 and PFAS using modified ASO to induce mortality and impair virus transmission in T. palmi. T. palmi UHRF1BP1 and PFAS would be novel genetic targets to manage thrips and restrict the spread of tospovirus. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Plant Viruses in a Context of Global Change)

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13 pages, 2138 KiB

Open AccessArticle

Homeobox 27, a Homeodomain Transcription Factor, Confers Tolerances to CMV by Associating with Cucumber Mosaic Virus 2b Protein

by Usha Kumari Rattan, Surender Kumar, Reenu Kumari, Monika Bharti and Vipin Hallan

Pathogens 2022, 11(7), 788; https://doi.org/10.3390/pathogens11070788 - 12 Jul 2022

Cited by 2 | Viewed by 2577

Abstract

Transcription factors (TFs) play an important role in plant development; however, their role during viral infection largely remains unknown. The present study was designed to uncover the role transcription factors play in Cucumber mosaic virus (CMV) infection. During the screening of an Arabidopsis thaliana (Col-0) transcription factor library, using the CMV 2b protein as bait in the yeast two-hybrid system, the 2b protein interacted with Homeobox protein 27 (HB27). HB27 belongs to the zinc finger homeodomain family and is known to have a regulatory role in flower development, and responses to biotic and abiotic stress. The interaction between CMV 2b and HB27 proteins was further validated using in planta (bimolecular fluorescence complementation assay) and in vitro far-Western blotting (FWB) methods. In the bimolecular fluorescence complementation assay, these proteins reconstituted YFP fluorescence in the nucleus and the cytoplasmic region as small fluorescent dots. In FWB, positive interaction was detected using bait anti-MYC antibody on the target HB27-HA protein. During CMV infection, upregulation (~3-fold) of the HB27 transcript was observed at 14 days post-infection (dpi) in A. thaliana plants, and expression declined to the same as healthy plants at 21 dpi. To understand the role of the HB27 protein during CMV infection, virus accumulation was determined in HB27-overexpressing (HB27 OE) and knockout mutants. In HB27-overexpressing lines, infected plants developed mild symptoms, accumulating a lower virus titer at 21 dpi compared to wild-type plants. Additionally, knockout HB27 mutants had more severe symptoms and a higher viral accumulation than wild-type plants. These results indicate that HB27 plays an important role in the regulation of plant defense against plant virus infection. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Plant Viruses in a Context of Global Change)

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19 pages, 2394 KiB

Open AccessReview

Natural and Engineered Resistance Mechanisms in Plants against Phytoviruses

by Anik Majumdar, Abhishek Sharma and Rakesh Belludi

Pathogens 2023, 12(4), 619; https://doi.org/10.3390/pathogens12040619 - 19 Apr 2023

Cited by 3 | Viewed by 3871

Abstract

Plant viruses, as obligate intracellular parasites, rely exclusively on host machinery to complete their life cycle. Whether a virus is pathogenic or not depends on the balance between the mechanisms used by both plants and viruses during the intense encounter. Antiviral defence mechanisms in plants can be of two types, i.e., natural resistance and engineered resistance. Innate immunity, RNA silencing, translational repression, autophagy-mediated degradation, and resistance to virus movement are the possible natural defence mechanisms against viruses in plants, whereas engineered resistance includes pathogen-derived resistance along with gene editing technologies. The incorporation of various resistance genes through breeding programmes, along with gene editing tools such as CRISPR/Cas technologies, holds great promise in developing virus-resistant plants. In this review, different resistance mechanisms against viruses in plants along with reported resistance genes in major vegetable crops are discussed. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Plant Viruses in a Context of Global Change)

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20 pages, 5734 KiB

Open AccessEditor’s ChoiceReview

Occurrence, Distribution, and Management of Aphid-Transmitted Viruses in Cucurbits in Spain

by Celia De Moya-Ruiz, Pedro Gómez and Miguel Juárez

Pathogens 2023, 12(3), 422; https://doi.org/10.3390/pathogens12030422 - 7 Mar 2023

Cited by 12 | Viewed by 4855

Abstract

The effectiveness of pest and disease management in crops relies on knowledge about their presence and distribution in crop-producing areas. Aphids and whiteflies are among the main threats to vegetable crops since these hemipterans feed on plants, causing severe damage, and are also able to transmit a large number of devastating plant viral diseases. In particular, the widespread occurrence of aphid-transmitted viruses in cucurbit crops, along with the lack of effective control measures, makes surveillance programs and virus epidemiology necessary for providing sound advice and further integration into the management strategies that can ensure sustainable food production. This review describes the current presence and distribution of aphid-transmitted viruses in cucurbits in Spain, providing valuable epidemiological information, including symptom expressions of virus-infected plants for further surveillance and viral detection. We also provide an overview of the current measures for virus infection prevention and control strategies in cucurbits and indicate the need for further research and innovative strategies against aphid pests and their associated viral diseases. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Plant Viruses in a Context of Global Change)

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26 pages, 1800 KiB

Open AccessReview

Emerging and Re-Emerging Diseases Caused by Badnaviruses

by Alangar Ishwara Bhat, Ramasamy Selvarajan and Velusamy Balasubramanian

Pathogens 2023, 12(2), 245; https://doi.org/10.3390/pathogens12020245 - 3 Feb 2023

Cited by 7 | Viewed by 4048

Abstract

New and emerging plant diseases are caused by different pathogens including viruses that often cause significant crop losses. Badnaviruses are pararetroviruses that contain a single molecule of ds DNA genome of 7 to 9 kb in size and infect a large number of economically important crops such as banana and plantains, black pepper, cacao, citrus, grapevine, pineapple, sugarcane, sweet potato, taro, and yam, causing significant yield losses. Many of the species in the genus have a restricted host range and several of them are known to infect a single crop. Combined infections of different virus species and strains offer conditions that favor the development of new strains via recombination, especially in vegetatively propagated crops. The primary spread of badnaviruses is through vegetative propagating materials while for the secondary spread, they depend on insects such as mealybugs and aphids. Disease emerges as a consequence of the interactions between host and pathogens under favorable environmental conditions. The viral genome of the pararetroviruses is known to be integrated into the chromosome of the host and a few plants with integrants when subjected to different kinds of abiotic stress will give rise to episomal forms of the virus and cause disease. Attempts have been made to develop management strategies for badnaviruses both conventionally and using precision breeding techniques such as genome editing. Until 2016 only 32 badnavirus species infecting different crops were known, but in a span of six years, this number has gone up to 68. The current review highlights the emerging disease problems and management options for badnaviruses infecting economically important crops. Full article

(This article belongs to the Special Issue Emerging and Re-emerging Plant Viruses in a Context of Global Change)

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