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Plant Viruses and Their Vectors: Epidemiology and Control
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Plant Viruses and Their Vectors: Epidemiology and Control

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Viruses of Plants, Fungi and Protozoa".

Deadline for manuscript submissions: closed (31 December 2024) | Viewed by 10176

Special Issue Editors

Prof. Dr. Beata Hasiów-Jaroszewska

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Guest Editor
Institute of Plant Protection-National Research Institute, Department of Virology and Bacteriology, ul. Wł. Węgorka 20, 60-318 Poznań, Poland
Interests: evolution of plant viruses; host–pathogen interactions; subviral RNA particles; RNA interference
Special Issues, Collections and Topics in MDPI journals
Dr. Matthaios M. Mathioudakis

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Guest Editor
Institute of Olive Trees, Subtropical Plants & Viticulture-Hellenic Agricultural Organization “DIMITRA” (ELGO-DIMITRA), Laboratory of Plant Pathology, Karamanlis Ave. 167, Gr-73134 Chania, Greece
Interests: plant virus molecular characterization; plant virus diagnostics and epidemiology; plant-virus interactions; RNA silencing suppression
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Viral diseases provide a major challenge to twenty-first century agriculture. Plant viruses are considered the second greatest contributor to yield loss. To make the situation worse, plants are commonly infected by more than one virus in fields (mixed infections), leading to synergistic combinations that result in the development of severe symptoms on infected plants and their fruits. Disease management strategies require an extensive knowledge of virus infection and its effect on host plants to allow the correct control procedures to be implemented. Most viruses and vector-borne viruses are spread by infected plant material and/or insects. Plant pathogens can influence the behavior and fitness of their vectors. Hence, the detection and identification of viruses and control of their vectors are crucial for successful crop production and are of great significance in terms of world food security. In this Special Issue, we aim to highlight the importance of virus and vector epidemiology in relation to the structure and dynamics of viral populations and their vectors, host–pathogen interactions, the development of new diagnostic tools as well as efficient and durable disease control strategies.

Prof. Dr. Beata Hasiów-Jaroszewska
Dr. Matthaios M. Mathioudakis
Guest Editors

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Keywords

  • epidemiology
  • mixed infections
  • insect vectors
  • viral diagnostics
  • genome variability
  • RNA interference
  • cross-protection
  • host–pathogen–vector interactions

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Related Special Issues

Published Papers (9 papers)

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19 pages, 3497 KiB  
Article
Aphid Species in Citrus Orchards in Crete: Key Vectors of Citrus Tristeza Virus and Automated Monitoring Innovations for Alate Aphids
by Matthaios M. Mathioudakis, Kyriaki Varikou, Antonia Karagianni, Panagiota Psirofonia, Nikolaos Tektonidis, Despoina Kapantaidaki, Vasiliki Evangelou, Leonidas Economou, Beata Hasiów-Jaroszewska and Ilyas Potamitis
Viruses 2025, 17(3), 395; https://doi.org/10.3390/v17030395 - 11 Mar 2025
Viewed by 541
Abstract
Citrus tristeza virus (CTV) is a vector-borne virus that poses a significant threat to citrus production worldwide, inducing a variety of symptoms. Therefore, a detailed knowledge of local aphids, identification of viruliferous species, and the development of new monitoring tools are necessary to [...] Read more.
Citrus tristeza virus (CTV) is a vector-borne virus that poses a significant threat to citrus production worldwide, inducing a variety of symptoms. Therefore, a detailed knowledge of local aphids, identification of viruliferous species, and the development of new monitoring tools are necessary to improve CTV control strategies. Herein, a 2-year survey was conducted to assess the frequency of aphid species infesting several citrus pilot orchards. Plot findings based on morphological and molecular identification revealed Aphis spiraecola (ranged from 44–100%) as the most abundant aphid species, followed by A. gossypii (<50%). Toxoptera aurantii, Myzus persicae, and A. craccivora were present in low numbers, and A. citricidus was not detected. Due to the absence of CTV detection in aphids and citrus trees from the pilot orchards, a complementary survey was conducted in CTV-infected fields. Three aphid species were identified as CTV-positive by RT-PCR, suggesting that they may be viruliferous, with A. spiraecola as predominant, followed by A. gossypii and T. aurantii. Additionally, we developed a non-invasive procedure for identifying aphid species using wingbeat analysis. This method provides a faster alternative to traditional identification techniques by taxonomic keys based on morphological features or PCR, although its accuracy is lower (approximately 95% for the two species tested). Overall, this work provides a detailed study of aphid species composition in citrus orchards, identifies the predominant local putative CTV vector, and introduces a novel sensor for aphid monitoring, contributing to improved epidemic forecasting and sustainable disease management strategies. Full article
(This article belongs to the Special Issue Plant Viruses and Their Vectors: Epidemiology and Control)
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12 pages, 1721 KiB  
Article
A Novel Multi-Gene Combined RT-PCR Assay for Rapid and Sensitive Detection of Maize Dwarf Mosaic Virus
by Yujie Jin, Xihong Chen, Min Li, Xiaoqi Zhang, Wei Cai, Jianguo Shen, Yongjiang Zhang and Fangluan Gao
Viruses 2025, 17(3), 370; https://doi.org/10.3390/v17030370 - 5 Mar 2025
Viewed by 538
Abstract
Maize, a staple food and cash crop worldwide, also serves as a critical industrial raw material. However, it is significantly threatened by viral pathogens, particularly maize dwarf mosaic virus (MDMV), the primary cause of maize dwarf mosaic disease, a debilitating condition affecting maize [...] Read more.
Maize, a staple food and cash crop worldwide, also serves as a critical industrial raw material. However, it is significantly threatened by viral pathogens, particularly maize dwarf mosaic virus (MDMV), the primary cause of maize dwarf mosaic disease, a debilitating condition affecting maize cultivation. This study aims to establish a multi-gene combined RT-PCR assay for the rapid specific, sensitive, and reliable detection of MDMV without the need for special expensive equipment. Samples of imported maize, sorghum, and barley were collected from ports in Fujian and Shanghai. Primers targeting the coat protein (CP) and cytoplasmic inclusion protein (CI) genes of MDMV were designed and optimized. Through the design and screening of primers, as well as the optimization of reaction conditions and primer concentrations, a multi-gene combined RT-PCR assay was established to simultaneously detect both genes. Additionally, a real-time fluorescent-based RT-PCR (RT-qPCR) assay was developed using the CP gene to confirm the accuracy of multi-gene combined RT-PCR assay. The sensitivity of the optimized multi-gene combined RT-PCR assay enables the detection of MDMV in infected maize leaf crude extracts at dilutions of 5.37 pg/μL. This assay exhibited excellent specificity, high sensitivity, and robust repeatability, providing swift and accurate detection of MDMV. The multi-gene combined RT-PCR assay offers precise and efficient technical support for MDMV detection and contributes to improved maize production practices. Full article
(This article belongs to the Special Issue Plant Viruses and Their Vectors: Epidemiology and Control)
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20 pages, 3296 KiB  
Article
Presence of Soybean Vein Necrosis Orthotospovirus (Tospoviridae: Orthotospovirus) in Pakistan, Pakistani Scientists’ and Farmers’ Perception of Disease Dynamics and Management, and Policy Recommendations to Improve Soybean Production
by Asifa Hameed, Cristina Rosa, Paige Castillanos and Edwin G. Rajotte
Viruses 2025, 17(3), 315; https://doi.org/10.3390/v17030315 - 25 Feb 2025
Viewed by 363
Abstract
Soybean vein necrosis orthotospovirus (SVNV: Tospoviridae: Orthotospovirus) is a well-recognized thrips-vectored and seed-borne virus common in the United States (U.S.), Canada, and Egypt. Pakistan started the commercial cultivation of soybeans in the 1970s, when some soybean cultivars were imported from the U.S. to [...] Read more.
Soybean vein necrosis orthotospovirus (SVNV: Tospoviridae: Orthotospovirus) is a well-recognized thrips-vectored and seed-borne virus common in the United States (U.S.), Canada, and Egypt. Pakistan started the commercial cultivation of soybeans in the 1970s, when some soybean cultivars were imported from the U.S. to meet the country’s domestic requirement of oil, poultry, animal feed, and forage. A survey of farmers and scientists was conducted in the Punjab and Khyber Pakhtunkhwa provinces of Pakistan to understand perceptions of SVNV in the indigenous Pakistani community. Concurrently, soybean fields were sampled for SVNV presence at the National Agricultural Research Institute in Islamabad, Pakistan. Based upon survey and SVNV detection results through ELISA and qRT-PCR, a policy was developed. Overall, we found that SVNV was present in Islamabad, Pakistan in USDA-approved soybean cultivars. Although scientists knew about general thrips biology and insecticides, knowledge about identification of vectors (Thrips species) was not significantly different between the scientists and the farmers. Scientists at the Islamabad location were more aware of crop production technology and pests. This study reports that Pakistan needs to strengthen its research institutes, scientists’ and farmers’ capacity building, and extension programs to understand the disease complex in soybean crops. Full article
(This article belongs to the Special Issue Plant Viruses and Their Vectors: Epidemiology and Control)
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16 pages, 11435 KiB  
Article
Prevalence of Aphid-Transmitted Potyviruses in Pumpkin and Winter Squash in Georgia, USA
by Nirmala Acharya, Manish Kumar, Sudeep Bag, David G. Riley, Juan C. Diaz-Perez, Alvin M. Simmons, Timothy Coolong and Theodore McAvoy
Viruses 2025, 17(2), 233; https://doi.org/10.3390/v17020233 - 8 Feb 2025
Viewed by 951
Abstract
Viruses are a major pathogen challenging the sustainable production of cucurbits worldwide. Pumpkin and winter squash showed severe virus-like symptoms during the fall of 2022 and 2023 in Georgia, USA. Symptomatic leaves were collected from the field and processed for small RNA sequencing [...] Read more.
Viruses are a major pathogen challenging the sustainable production of cucurbits worldwide. Pumpkin and winter squash showed severe virus-like symptoms during the fall of 2022 and 2023 in Georgia, USA. Symptomatic leaves were collected from the field and processed for small RNA sequencing for virus identification using high-throughput sequencing (HTS). HTS analysis revealed the presence of two aphid-transmitted viruses (ATVs), zucchini yellow mosaic virus (ZYMV) and papaya ringspot virus (PRSV), along with three whitefly-transmitted viruses, cucurbit chlorotic yellows virus, cucurbit yellow stunting disorder virus, and cucurbit leaf crumple virus. The results of our study suggest a significant shift in ATV’s abundance in these two crops between 2022 and 2023. According to the qPCR data in the fall of 2022, pumpkins experience an incidence of 56.25% and 31.25% of PRSV and ZYMV, respectively. Similarly, winter squash shows an incidence of 50% and 32.14% of PRSV and ZYMV, respectively. Mixed infection of both viruses was also observed in these two crops. In 2023, we observed a predominance of ZYMV in pumpkin and winter squash (61.25% and 42.50%, respectively). However, PRSV was not detected in pumpkins, and it was detected at a negligible level (0.62%) in winter squash using qPCR. Phylogenetic analysis of ZYMV-encoded coat protein (CP) and helper component-protease (HC-Pro) from Georgia suggests a close relationship with the European isolates. Conversely, PRSV-encoded CP and NIa-VPg show a more diverse evolutionary history. Overall, this research will provide valuable insights into the dynamics of ZYMV and PRSV in pumpkin and winter squash crops within the southeastern United States. Full article
(This article belongs to the Special Issue Plant Viruses and Their Vectors: Epidemiology and Control)
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15 pages, 3698 KiB  
Article
Identification and Molecular Characterization of Telosma Mosaic Virus (TelMV) and East Asian Passiflora Virus (EAPV) from Patchouli in China
by Asma Aziz, Na Li, Xiaoqing Wang, Linxi Wang, Yougen Wu, Muhammad Zeeshan Ul Haq, Zhaoji Dai and Hongguang Cui
Viruses 2024, 16(12), 1837; https://doi.org/10.3390/v16121837 - 27 Nov 2024
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Abstract
Patchouli is a valuable medicinal herb and cash crop in China, but viral infections cause significant yield losses. This study identified six viruses in patchouli transcriptome data, including the first-ever detection of East Asian Passiflora Virus (EAPV) in patchouli. RT-PCR validated three viruses [...] Read more.
Patchouli is a valuable medicinal herb and cash crop in China, but viral infections cause significant yield losses. This study identified six viruses in patchouli transcriptome data, including the first-ever detection of East Asian Passiflora Virus (EAPV) in patchouli. RT-PCR validated three viruses from diseased patchouli plants in Haikou, China: telosma tosaic virus (TelMV), broad bean wilt virus-2 (BBWV-2), and pogostemom alphacytorhabdovirus 1 (PogACRV1_Pog). The complete genomic sequence of TelMV from patchouli (TelMV) was determined, revealing a 9691-nucleotide RNA genome encoding a 3083-amino-acid polyprotein. Comparative analysis showed 77.66% to 81.01% nucleotide sequence identity with previously reported TelMV isolates. TelMV was also shown to be infectious in Nicotiana benthamiana through sap rub-inoculation. Additionally, a large portion of the EAPV genome was reconstructed from RNA-seq data, with coat protein analysis confirming its identity. This study presents the first complete TelMV genome in patchouli and the first detection of EAPV in the plant. Full article
(This article belongs to the Special Issue Plant Viruses and Their Vectors: Epidemiology and Control)
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14 pages, 1343 KiB  
Article
Demonstration of Insect Vector-Mediated Transfer of a Betasatellite between Two Helper Viruses
by Noun Fouad, Martine Granier, Stéphane Blanc, Gaël Thébaud and Cica Urbino
Viruses 2024, 16(9), 1420; https://doi.org/10.3390/v16091420 - 5 Sep 2024
Viewed by 1348
Abstract
Begomoviruses, transmitted by the whitefly Bemisia tabaci, pose significant threats to global agriculture due to their severe impact on various crops. Among the satellite molecules associated with begomoviruses, betasatellites play a crucial role in enhancing disease severity and yield losses. The spread [...] Read more.
Begomoviruses, transmitted by the whitefly Bemisia tabaci, pose significant threats to global agriculture due to their severe impact on various crops. Among the satellite molecules associated with begomoviruses, betasatellites play a crucial role in enhancing disease severity and yield losses. The spread and association of these molecules with helper viruses in host plants are thus matters of concern. Here, we focus on the propagation of betasatellites and, more specifically, on their transfer between different helper viruses and hosts through vector transmission. Our results show that the cotton leaf curl Gezira betasatellite (CLCuGeB), initially acquired with its helper virus cotton leaf curl Gezira virus (CLCuGeV) from an okra plant, can be transmitted and assisted by a different helper virus, tomato yellow leaf curl virus (TYLCV), in a different host plant (tomato plant). The new association can be formed whether TYLCV and CLCuGeB encounter each other in a host plant previously infected with TYLCV or in whiteflies having acquired the different components separately. Our findings reveal two pathways by which betasatellites can be transferred between helper viruses and host plants and highlight the ability of betasatellites to spread in begomovirus-infected environments. Full article
(This article belongs to the Special Issue Plant Viruses and Their Vectors: Epidemiology and Control)
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20 pages, 3188 KiB  
Article
Characterization of Caulimovirid-like Sequences from Upland Cotton (Gossypium hirsutum L.) Exhibiting Terminal Abortion in Georgia, USA
by Surendra R. Edula, Lavesta C. Hand, Phillip M. Roberts, Edward Beasley, John L. Snider, Robert C. Kemerait, Peng W. Chee and Sudeep Bag
Viruses 2024, 16(7), 1111; https://doi.org/10.3390/v16071111 - 11 Jul 2024
Cited by 2 | Viewed by 1960
Abstract
In this study, we investigated the potential involvement of endogenous viral elements (EVEs) in the development of apical tissue necrosis, resulting in the terminal abortion of upland cotton (Gossypium hirsutum L.) in Georgia. The high-throughput sequence analysis of symptomatic and asymptomatic plant [...] Read more.
In this study, we investigated the potential involvement of endogenous viral elements (EVEs) in the development of apical tissue necrosis, resulting in the terminal abortion of upland cotton (Gossypium hirsutum L.) in Georgia. The high-throughput sequence analysis of symptomatic and asymptomatic plant tissue samples revealed near-complete EVE-Georgia (EVE-GA) sequences closely related to caulimoviruses. The analysis of EVE-GA’s putative open reading frames (ORFs) compared to cotton virus A and endogenous cotton pararetroviral elements (eCPRVE) revealed their similarity in putative ORFs 1–4. However, in the ORF 5 and ORF 6 encoding putative coat protein and reverse transcriptase, respectively, the sequences from EVE-GA have stop codons similar to eCPRVE sequences from Mississippi. In silico mining of the cotton genome database using EVE-GA as a query uncovered near-complete viral sequence insertions in the genomes of G. hirsutum species (~7 kb) but partial in G. tomentosum (~5.3 kb) and G. mustelinum (~5.1 kb) species. Furthermore, cotton EVEs’ episomal forms and messenger RNA (mRNA) transcripts were detected in both symptomatic and asymptomatic plants collected from cotton fields. No significant yield difference was observed between symptomatic and asymptomatic plants of the two varieties evaluated in the experimental plot. Additionally, EVEs were also detected in cotton seeds and seedlings. This study emphasizes the need for future research on EVE sequences, their coding capacity, and any potential role in host immunity or pathogenicity. Full article
(This article belongs to the Special Issue Plant Viruses and Their Vectors: Epidemiology and Control)
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16 pages, 11913 KiB  
Article
Molecular Surveillance, Prevalence, and Distribution of Cacao Infecting Badnavirus Species in Côte d’Ivoire and Ghana
by George A. Ameyaw, Koffié Kouakou, Mohammed Javed Iqbal, Luc Belé, Valentin L. F. Wolf, Cory V. Keith, Bolou A. Bolou Bi, Christophe Kouamé, Donald Livingstone, Owusu Domfeh, Ebenezer A. Gyamera, Jean-Philippe Marelli and Judith K. Brown
Viruses 2024, 16(5), 735; https://doi.org/10.3390/v16050735 - 6 May 2024
Cited by 1 | Viewed by 1723
Abstract
The cacao swollen shoot disease (CSSD) caused by a complex of badnavirus species presents a major challenge for cacao production in West Africa, especially Ghana and Côte d’Ivoire. In this study, CSSD species detection efficiency, diversity, and geographic distribution patterns in cacao plantations [...] Read more.
The cacao swollen shoot disease (CSSD) caused by a complex of badnavirus species presents a major challenge for cacao production in West Africa, especially Ghana and Côte d’Ivoire. In this study, CSSD species detection efficiency, diversity, and geographic distribution patterns in cacao plantations in Ghana and Côte d’Ivoire were investigated through field surveillance, PCR detection assays, sequencing of positive amplicons, and phylogeographic clustering. Cumulatively, the detection efficiency of the tested CSSD primer sets that were targeting the movement protein domain of the virus ranged from 0.15% (CSSD-3 primer) to 66.91% (CSSD-1 primer) on all the symptomatic cacao leaf samples assessed. The identified CSSD species differed phylogenetically and overlapped in distribution, with the cacao swollen shoot Togo B virus (CSSTBV) (n = 588 sequences) being the most prevalent and widely distributed compared to the other CSSD species that were encountered in both countries. Geographically, the cacao swollen shoot CE virus (CSSCEV) species (n = 124 sequences) that was identified was largely restricted to the bordering regions of Ghana and Côte d’Ivoire. These results provide updated knowledge of the geographic distribution of the key CSSD species and their diagnostic efficiency and, thus, provide guidance in identifying locations for structured testing of cacao germplasm and optimal diagnostics for the predominant CSSD species in Ghana and Côte d’Ivoire. Full article
(This article belongs to the Special Issue Plant Viruses and Their Vectors: Epidemiology and Control)
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13 pages, 1354 KiB  
Perspective
The Temporal Order of Mixed Viral Infections Matters: Common Events That Are Neglected in Plant Viral Diseases
by Celia de Moya-Ruiz, Inmaculada Ferriol and Pedro Gómez
Viruses 2024, 16(12), 1954; https://doi.org/10.3390/v16121954 - 20 Dec 2024
Viewed by 1056
Abstract
Mixed infections of plant viruses are common in crops and represent a critical biotic factor with substantial epidemiological implications for plant viral diseases. Compared to single-virus infections, mixed infections arise from simultaneous or sequential infections, which can inevitably affect the ecology and evolution [...] Read more.
Mixed infections of plant viruses are common in crops and represent a critical biotic factor with substantial epidemiological implications for plant viral diseases. Compared to single-virus infections, mixed infections arise from simultaneous or sequential infections, which can inevitably affect the ecology and evolution of the diseases. These infections can either exacerbate or ameliorate symptom severity, including virus–virus interactions within the same host that may influence a range of viral traits associated with disease emergence. This underscores the need for a more comprehensive understanding of how the order of virus arrival to the host can impact plant disease dynamics. From this perspective, we reviewed the current evidence regarding the impact of mixed infections within the framework of simultaneous and sequential infections in plants, considering the mode of viral transmission. We also examined how the temporal order of mixed infections could affect the dynamics of viral populations and present a case study of two aphid-transmitted viruses infecting melon plants, suggesting that the order of virus arrival significantly affects viral load and disease outcomes. Finally, we anticipate future research that reconciles molecular epidemiology and evolutionary ecology, underlining the importance of biotic interactions in shaping viral epidemiology and plant disease dynamics in agroecosystems. Full article
(This article belongs to the Special Issue Plant Viruses and Their Vectors: Epidemiology and Control)
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