WITHDRAWN: Exploring in-silico prediction for the development of a RT-qPCR-high resolution melting assay for the broad detection of emaraviruses

Olmedo-Velarde, Alejandro; Ochoa-Corona, F. M.; Larrea-Sarmiento, Adriana; Elbeaino, Toufic; Flores, Francisco

doi:10.1016/j.jviromet.2021.114425

Cited by 3 publications

(3 citation statements)

References 80 publications

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“…In comparison with our findings, all 137 tested trees from all cultivars were infected by at least one virus, with FMV and FLMaV-2 being the most prevalent viruses with incidence rates of 49% and 21.8% in all tested plants, respectively, followed by FLMaV-1 with an incidence rate of 10.9% in all tested plants. Our findings corroborate prior reports from a number of Mediterranean countries [ 1 , 2 , 7 , 23 , 34 , 37 – 42 ].…”

Section: Discussionsupporting

confidence: 93%

Incidence, Molecular Detection, and Partial Nucleotide Sequencing of Some Viruses Causing Fig Mosaic Disease (FMD) on Fig Plants in Egypt

Toima

M.El-Banna

Sayed

et al. 2022

International Journal of Microbiology

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Fig mosaic disease (FMD) is a viral disease that poses a significant danger to Egypt’s fig-producing economy. During the two growing seasons 2017 and 2018, fig leaves and fruits displaying a variety of symptoms linked with fig mosaic disease (FMD) were collected and differentiated from the most famous fig-growing governorates in Egypt, Mersa Matruh, Ismailia, and Giza. Symptomatic samples were tested for the presence of fig mosaic virus (FMV), fig leaf mottle-associated virus 1 (FLMaV-1), fig leaf mottle-associated virus 2 (FLMaV-2), fig mild mottle-associated virus (FMMaV), fig latent virus 1 (FLV-1), fig fleck-associated virus (FFkaV), and fig cryptic virus (FCV) using reverse transcription-polymerase chain reaction (RT-PCR) with specific primers. Three viruses were detected in mixed infections and showed positive results. FMV was detected with infection rate 49% followed by FLMaV-2 with infection rate 21.8% and FLMaV-1 with infection rate 10.9%, respectively, whereas all tested samples were negative for the other viruses. According to the sequence and phylogenetic analysis, the Egyptian FMV isolate was closely related to other FMV isolates, particularly the Argentina ones (Acc. No. KP796424), with 99% identity. While FLMaV-1 showed more than 98% identity with reference isolate FLMaV-1 (Acc. No. LN873219), on the other hand, the isolate of FLMaV-2 showed 100% identity with reference FLMaV-2 isolate (Acc. No. FJ473383) based on phylogenetic analysis. Because fig output in Egypt is expanding, our findings suggest that greater attention should be paid to improving the phytosanitary condition of fig trees in Egypt.

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Section: Discussionsupporting

confidence: 93%

Incidence, Molecular Detection, and Partial Nucleotide Sequencing of Some Viruses Causing Fig Mosaic Disease (FMD) on Fig Plants in Egypt

Toima

M.El-Banna

Sayed

et al. 2022

International Journal of Microbiology

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“…The sequences of 16 primer sets were sourced from scientific literature (Babu et al, 2016; Babu, Knox, et al, 2018; di Bello et al, 2018; Dobhal et al, 2016; Druciarek et al, 2019; Laney et al, 2011; Salazar et al, 2021; Salazar et al, 2021) and are listed in Table 1. The primers sequences in the new APC‐RRV insert are not in order and combine 14 primer sets for specific detection of diagnostic sequences of the RRV genome, including one primer set for amplification of a conserved region of the emaravirus genome (Olmedo‐Velarde et al, 2021), and two sets are primers used for the barcoding of eriophyoid mites, cytochrome c oxidase subunit I (COI, mtDNA) and rDNA (Dabert et al, 2008; Dabert et al, 2010; Druciarek et al, 2019). Two RRV primer sets were designed to perform RT‐PCR, five sets for RT‐qPCR, one set for both RRV RT‐PCR and RT‐qPCR, three sets were for RPA, two sets for RT‐LAMP.…”

Section: Methodsmentioning

confidence: 99%

An artificial positive control for routine detection of rose rosette virus and Phyllocoptes fructiphilus that fit most primers for PCR, LAMP and RPA based assays

Ruschel

Taylor

Ochoa-Corona

et al. 2023

Annals of Applied Biology

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Rose (Rosa spp.) is a very important ornamental shrub cultivated worldwide and of value for the pharmaceutical industry. The plant is broadly susceptible to pathogens, including viruses. Rose rosette virus (RRV; virus species Emaravirus rosae) causes multiple symptoms typically rosettes, ultimately leading to death. The virus transmission is by grafting and a wind-dispersed eriophyoid mite, Phyllocoptes fructiphilus, which survives in winter-dormant plants. Due to extensive globalization RRV is a threat for the European rose, landscape, nursery and tourism industries. The most common and reliable method used for RRV detection is RT-PCR. Positive control is indispensable for PCR reliability and can be difficult to obtain for emerging or highly contagious pathogens and are subject to BSL-2 quarantine. A synthetic artificial positive control (APC) using custom DNA inserts of sense and anti-sense primers was designed de novo and inserted in a circular plasmid vector to create a positive control for use with most RRV reported primers and eriophyoid mites. This study describes a functional demonstration and development of a rapid, consistent, adaptable and cost-effective alternative to infected true-tissue positive control for detection of RRV. The inserted RRV primers are for end point and quantitative RT-PCR, reverse transcription loop-mediated isothermal amplification (RT-LAMP), recombinase-polymerase amplification (RPA), broad detection of emaravirus and the eriophyoid mite vector Phyllocoptes fructiphilus. The APC-RRV and RRV infected rose (leaf tissue) were tested side to side. Results demonstrated APC-RRV is a safe, cloneable and reliable approach subjected to quality control with application in quarantine surveillance and routine diagnostics of RRV.

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“…The negative-sense, single-stranded RNA (-ssRNA) genus Emaravirus (family Fimoviridae ; order Bunyavirales ) is an emerging group of eriophyoid-transmitted viruses comprising more than 30 classified and putative species with worldwide distribution and economic impact [2,11]. Emaravirus rosae (member: rose rosette emaravirus, RRV) is considered one of the most economically significant emaraviruses, as infected plants die within two to five years after the onset of symptoms [5], affecting the profitability and sustainability of commercial operations and landscapers in the United States [7,12].…”

Section: Introductionmentioning

confidence: 99%

Quantification of rose rosette emaravirus (RRV) titers in eriophyoid mites: insights into viral dynamics and vector competency

Druciarek,

Rojas,

Tzanetakis

2024

Preprint

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Understanding the interaction between rose rosette emaravirus (RRV) and its vectors is pivotal in addressing the epidemic outbreak of rose rosette disease. This study employed quantitative real-time RT-PCR to assess RRV genome copy numbers in Phyllocoptes fructiphilus and P. adalius, providing insights into the viral dynamics and vector competency. Our findings suggest active virus replication within P. fructiphilus, a confirmed vector species, unlike P. adalius, highlighting its non-vector status. Furthermore, the study highlights the variability in virus concentration in mites over time, underlining possible developmental stage-specific response and influence of mite lifestyle on RRV retention and replication. This research is the first step in understanding the virus-mite interactome, which is essential for developing effective management strategies against rose rosette disease.

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WITHDRAWN: Exploring in-silico prediction for the development of a RT-qPCR-high resolution melting assay for the broad detection of emaraviruses

Cited by 3 publications

References 80 publications

Incidence, Molecular Detection, and Partial Nucleotide Sequencing of Some Viruses Causing Fig Mosaic Disease (FMD) on Fig Plants in Egypt

Incidence, Molecular Detection, and Partial Nucleotide Sequencing of Some Viruses Causing Fig Mosaic Disease (FMD) on Fig Plants in Egypt

An artificial positive control for routine detection of rose rosette virus and Phyllocoptes fructiphilus that fit most primers for PCR, LAMP and RPA based assays

Quantification of rose rosette emaravirus (RRV) titers in eriophyoid mites: insights into viral dynamics and vector competency

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