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Virus Detection and Quantification in Plants
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Virus Detection and Quantification in Plants

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Protection and Biotic Interactions".

Deadline for manuscript submissions: closed (20 June 2023) | Viewed by 11355

Special Issue Editors

Dr. Ana Vučurović

E-Mail Website
Guest Editor
Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
Interests: plant pathology; virology; microbiology; molecular biology
Prof. Dr. Masamichi Nishiguchi

E-Mail Website
Guest Editor
Department of Biological Resources, Ehime University, Matsuyama 790-8566, Japan
Interests: plant virus; gene silencing; biotic stress; virus resistance; pathogen resistance; high-temperature stress; transgenic plants; plant biotechnology

Special Issue Information

Dear Colleagues,

Plant viruses account for a significant proportion of economically important diseases in major crops. The global economic damage caused by plant viruses is very difficult to estimate; however, rough estimates suggest that yield losses range from $30 to $50 billion annually.

The recent emergence of several novel virus species, such as tomato brown rugose fruit virus, threatens the production of several important crops and has required a rapid response by diagnosticians to develop rapid and reliable diagnostics. Increasing international trade in plants, climate change, and further reductions in the use of chemical pesticides will certainly lead to the spread of pests and the emergence of new virus species/strains. Therefore, to prevent losses and achieve sustainable plant production, it is critical to prevent or limit the damage caused by plant viruses. A basis for successful pest control is the fast, reliable, and accurate detection of causal agents.

On the other hand, to successfully control viruses in plants, it is necessary to know the events involved in disease development. Quantitative analysis can be used to estimate the viral load in plants as an indicator of active infection, stage of infection, progress of infection, and to study host defenses during the infection process. Quantitative changes in viral titers during infection may indicate bottlenecks in virus infection cycles that can be used to develop new control strategies.

In this Special Issue, we focus on state-of-the-art methods for the detection and quantification of plant viruses based on nucleic acid amplification, next-generation sequencing, etc. We invite you to contribute your original studies or review articles on these topics.

Dr. Ana Vučurović
Prof. Dr. Masamichi Nishiguchi
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • detection
  • identification
  • diagnostics
  • quantification
  • ddPCR
  • PCR
  • qPCR
  • HTS
  • RT-qPCR
  • RT-PCR
  • emerging viruses
  • plant viruses

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Published Papers (4 papers)

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Research

14 pages, 2540 KiB  
Article
qPCR Assay as a Tool for Examining Cotton Resistance to the Virus Complex Causing CLCuD: Yield Loss Inversely Correlates with Betasatellite, Not Virus, DNA Titer
by Zafar Iqbal, Muhammad Shafiq, Sajed Ali, Muhammad Arslan Mahmood, Hamid Anees Siddiqui, Imran Amin and Rob W. Briddon
Plants 2023, 12(14), 2645; https://doi.org/10.3390/plants12142645 - 14 Jul 2023
Cited by 5 | Viewed by 1962
Abstract
Cotton leaf curl disease (CLCuD) is a significant constraint to the economies of Pakistan and India. The disease is caused by different begomoviruses (genus Begomovirus, family Geminiviridae) in association with a disease-specific betasatellite. However, another satellite-like molecule, alphasatellite, is occasionally found [...] Read more.
Cotton leaf curl disease (CLCuD) is a significant constraint to the economies of Pakistan and India. The disease is caused by different begomoviruses (genus Begomovirus, family Geminiviridae) in association with a disease-specific betasatellite. However, another satellite-like molecule, alphasatellite, is occasionally found associated with this disease complex. A quantitative real-time PCR assay for the virus/satellite components causing CLCuD was used to investigate the performance of selected cotton varieties in the 2014–2015 National Coordinated Varietal Trials (NCVT) in Pakistan. The DNA levels of virus and satellites in cotton plants were determined for five cotton varieties across three geographic locations and compared with seed cotton yield (SCY) as a measure of the plant performance. The highest virus titer was detected in B-10 (0.972 ng·µg−1) from Vehari and the lowest in B-3 (0.006 ng·µg−1) from Faisalabad. Likewise, the highest alphasatellite titer was found in B-1 (0.055 ng·µg−1) from Vehari and the lowest in B-1 and B-2 (0.001 ng·µg−1) from Faisalabad. The highest betasatellite titer was found in B-23 (1.156 ng·µg−1) from Faisalabad and the lowest in B-12 (0.072 ng·µg−1) from Multan. Virus/satellite DNA levels, symptoms, and SCY were found to be highly variable between the varieties and between the locations. Nevertheless, statistical analysis of the results suggested that betasatellite DNA levels, rather than virus or alphasatellite DNA levels, were the important variable in plant performance, having an inverse relationship with SCY (−0.447). This quantitative assay will be useful in breeding programs for development of virus resistant plants and varietal trials, such as the NCVT, to select suitable varieties of cotton with mild (preferably no) symptoms and low (preferably no) virus/satellite. At present, no such molecular techniques are used in resistance breeding programs or varietal trials in Pakistan. Full article
(This article belongs to the Special Issue Virus Detection and Quantification in Plants)
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18 pages, 1048 KiB  
Article
Applicability of Different Methods for Quantifying Virucidal Efficacy Using MENNO Florades and Tomato Brown Rugose Fruit Virus as an Example
by Shaheen Nourinejhad Zarghani, Jens Ehlers, Mehran Monavari, Susanne von Bargen, Joachim Hamacher, Carmen Büttner and Martina Bandte
Plants 2023, 12(4), 894; https://doi.org/10.3390/plants12040894 - 16 Feb 2023
Cited by 8 | Viewed by 2839
Abstract
After entry of a quarantine/regulated pathogen, infected plants shall be destroyed, and the cultivated area (e.g., greenhouse) shall be disinfected. Therefore, the selection of an effective disinfectant plays an important role. With the availability of different methods for virus quantification, we investigated the [...] Read more.
After entry of a quarantine/regulated pathogen, infected plants shall be destroyed, and the cultivated area (e.g., greenhouse) shall be disinfected. Therefore, the selection of an effective disinfectant plays an important role. With the availability of different methods for virus quantification, we investigated the application of quantitative ELISA (qELISA), RT-qPCR (reverse transcription-quantitative polymerase chain reaction), and bioassays for the quantification of disinfectant efficacy. Therefore, we estimated the titer reduction in tomato brown rugose fruit virus (ToBRFV), a regulated pathogen, in plant sap and on germ carriers after treatment with MENNO Florades 4% for 16 h. The virus load before and after the treatment was measured with the mentioned methods. The RT-qPCR and qELISA methods showed very low efficacy in the presence of the disinfectant. Although bioassays are time-consuming, need purified particles for establishing the quantification models, and are less sensitive than RT-qPCR, they were able to quantify the differences in virus titer in the presence/absence of disinfectant. Interestingly, the bioassays reached at least the lower limit sensitivity of a qELISA. By being less sensitive to the presence of the disinfectant, bioassays proved to be the only technique for the determination of the disinfectant efficacy against ToBRFV on different germ carriers as well as on virus-infected plant sap. Full article
(This article belongs to the Special Issue Virus Detection and Quantification in Plants)
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16 pages, 2641 KiB  
Article
Comparison of Models for Quantification of Tomato Brown Rugose Fruit Virus Based on a Bioassay Using a Local Lesion Host
by Shaheen Nourinejhad Zarghani, Mehran Monavari, Jens Ehlers, Joachim Hamacher, Carmen Büttner and Martina Bandte
Plants 2022, 11(24), 3443; https://doi.org/10.3390/plants11243443 - 9 Dec 2022
Cited by 8 | Viewed by 2900
Abstract
Considering the availability of serological and molecular biological methods, the bioassay has been paled into insignificance, although it is the only experimental method that can be used to demonstrate the infectivity of a virus. We compared goodness-of-fit and predictability power of five models [...] Read more.
Considering the availability of serological and molecular biological methods, the bioassay has been paled into insignificance, although it is the only experimental method that can be used to demonstrate the infectivity of a virus. We compared goodness-of-fit and predictability power of five models for the quantification of tomato brown rugose fruit virus (ToBRFV) based on local lesion assays: the Kleczkowski model, Furumoto and Mickey models I and II, the Gokhale and Bald model (growth curve model), and the modified Poisson model. For this purpose, mechanical inoculations onto Nicotiana tabacum L. cv. Xanthi nc and N. glutionosa L. with defined virus concentrations were first performed with half-leaf randomization in a Latin square design. Subsequently, models were implemented using Python software and fitted to the number of local lesions. All models could fit to the data for quantifying ToBRFV based on local lesions, among which the modified Poisson model had the best prediction of virus concentration in spike samples based on local lesions, although data of individual indicator plants showed variations. More accurate modeling was obtained from the test plant N. glutinosa than from N. tabacum cv. Xanthi nc. The position of the half-leaves on the test plants had no significant effect on the number of local lesions. Full article
(This article belongs to the Special Issue Virus Detection and Quantification in Plants)
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16 pages, 2888 KiB  
Article
Grapevine Leafroll-Associated Virus 3 Replication in Grapevine Hosts Changes through the Dormancy Stage
by Mate Čarija, Silvija Černi, Darija Stupin-Polančec, Tomislav Radić, Emanuel Gaši and Katarina Hančević
Plants 2022, 11(23), 3250; https://doi.org/10.3390/plants11233250 - 26 Nov 2022
Cited by 4 | Viewed by 2105
Abstract
Grapevine leafroll-associated virus 3 (GLRaV-3) is a graft-transmissible virus present in every viticultural region of the world and poses a large threat to grapevine production. Frequent coinfections with other viruses, the large number of grapevine varieties, the complexity of processes involved in plant [...] Read more.
Grapevine leafroll-associated virus 3 (GLRaV-3) is a graft-transmissible virus present in every viticultural region of the world and poses a large threat to grapevine production. Frequent coinfections with other viruses, the large number of grapevine varieties, the complexity of processes involved in plant response to virus infection, and the lack of studies on GLRaV-3 replication limit our knowledge of GLRaV-3 damaging effects and their background. In this study, five different inocula, one containing GLRaV-3 and others containing GLRaV-3 in combination with different grapevine viruses were green grafted to 52 different grapevine plants of four varieties to analyze the influence of the phenological stage and virus composition on GLRaV-3 replication. Relative concentration analysis by quantitative PCR conducted over a 16-month period revealed that other viruses as well as plant stage had a significant effect on GLRaV-3 replication and symptoms expression. The replication was most pronounced in the deep dormancy stage at the beginning of the infection, and the least at the exit of the dormancy stage. This study brings new insight into GLRaV-3 replication and discusses about viral interactions in one of the most economically important perennial plants, the grapevine. Full article
(This article belongs to the Special Issue Virus Detection and Quantification in Plants)
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