High throughput sequencing and RT-qPCR assay reveal the presence of rose cryptic virus-1 in the United Kingdom

Vazquez‐Iglesias, Ines; Adams, Ian; Hodgetts, J.; Fowkes, A.; Forde, S.; Ward, R.; Buxton‐Kirk, A.; Kelly, Michael D.; Santin-Azcona, Jone; Skelton, A.; Harju, V.; Boonham, Neil; Robinson, Rebekah J.; Clover, G. R. G.; Fox, Adrian

doi:10.1007/s42161-019-00307-5

Cited by 8 publications

(4 citation statements)

References 18 publications

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“…Several viruses have been reported affecting roses in Europe, including arabis mosaic virus (ArMV; genus Nepovirus ), strawberry latent ringspot virus (SLRSV; family Secoviridae ), apple mosaic virus (ApMV, genus Ilarvirus ), and prunus necrotic ringspot virus (PNRSV; genus Ilarvirus ; King et al ., 2012). Rose mosaic disease (RMD) is one of the most common diseases of roses worldwide, and is caused by single or mixed infections of these viruses (Vazquez‐Iglesias et al ., 2019). Differences have been established between viruses involved in RMD occurring in North America and Europe, although PNRSV has been identified as the most frequent virus associated with this disease in both continents (Horst et al ., 1983; Manners, 1997; Sertkaya, 2010).…”

Section: Rose Viruses Reported In Europementioning

confidence: 99%

“…Rose cryptic virus‐1 (RoCV1), also known as Rosa multiflora cryptic virus (Martin and Tzanetakis, 2008), is a partitivirus first reported in the USA (Sabanadzovic and Ghanem‐Sabanadzovic, 2008) and subsequently in Canada (James et al ., 2015), New Zealand (Milleza et al ., 2013), and recently in the UK (Vazquez‐Iglesias et al ., 2019). Cryptic viruses escaped detection for many years because most cause no visible symptoms or, in a few cases, very mild symptoms (Milleza et al ., 2013).…”

Section: Rose Viruses Reported In Europementioning

confidence: 99%

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Facing Rose rosette virus: A risk to European rose cultivation

et al. 2020

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Roses (Rosa) are one of the most valuable ornamental flowering shrubs around the globe. They are susceptible to numerous pathogens that require management, increasing the cost of cultivation. Rose rosette virus (RRV; genus Emaravirus) is a devastating virus that has been spreading since the 1940s in the United States and Canada. It is an emerging risk to European and worldwide rose cultivation, causing symptoms such as witches' broom, malformations, excessive thorn production, and eventually plant death. RRV is transmitted by the eriophyid mite Phyllocoptes fructiphilus and by grafting. Research is being undertaken to understand RRV and to find control measures and resistant cultivars, as they are not currently available. Early detection of the disease is the key to prevent the establishment and spread of RRV and its vector. Different molecular and serological diagnostic methods have been designed and implemented, including ELISA, RT‐PCR, RT‐qPCR, LAMP, and high‐throughput sequencing. RRV infected plants can remain symptomless for long periods, so these diagnostic assays are necessary in conjunction with visual assessment to facilitate early detection. Significant social, economic, and environmental impacts are expected if RRV and its vector establish and spread in Europe. Rose trade between countries is the most likely pathway of introduction of RRV into Europe. In this review we describe current knowledge about RRV, the molecular and serological methods available for the detection of this virus, pathways to entry, and the possible impact if it establishes and spreads in Europe.

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Section: Rose Viruses Reported In Europementioning

confidence: 99%

Section: Rose Viruses Reported In Europementioning

confidence: 99%

Facing Rose rosette virus: A risk to European rose cultivation

et al. 2020

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“…Rose rosette virus (RRV) of the genus Emaravirus is the causal agent of RRD and can be effectively spread by the eriophyid mite (Phyllocoptes fructiphilus) [6,8]. RMD is generally associated with mixed infections of viruses that belong to different taxa, especially apple mosaic virus (ApMV) and prunus necrotic ringspot virus (PNRSV) of the genus Ilarvirus and Arabis mosaic virus (ArMV) and strawberry latent ringspot virus (SLRSV) of the genus Nepovirus [9]. Symptoms associated with RMD are highly variable, depending primarily on rose cultivars, virus agents and environmental factors.…”

Section: Introductionmentioning

confidence: 99%

Rose Virome Analysis and Identification of A Novel Ilarvirus In Taiwan

Chen¹,

Lin²,

Lin³

et al. 2022

Preprint

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Rose (Rosa spp.), especially R. hybrida, is one of the most popular ornamental plants in the world and the third largest cut flower crop in Taiwan. Rose mosaic disease (RMD), showing mosaic, line patterns and ringspots on leaves, is a common rose disease caused by complex infection of various viruses. Due to pests and diseases, the rose planting area in Taiwan has been decreasing since 2008; however, no rose virus disease has been reported in the past five decades. In the spring of 2020, rose samples showing RMD-like symptoms were observed at an organic farm in Chiayi, central Taiwan. The virome in the farm was analyzed by RNA-seq. Rose genomic sequences were filtered from the obtained reads. The remaining reads were de novo assembled to generate 294 contigs, 50 of which were annotated as viral sequences corresponding to 10 viruses. Through reverse transcription-polymerase chain reaction validation, a total of seven viruses were detected, including six known rose viruses, namely apple mosaic virus, prunus necrotic ringspot virus, rose partitivirus, apple stem grooving virus, rose spring dwarf-associated virus and rose cryptic virus 1, and a novel ilarvirus. After completing the whole genome sequencing and sequence analysis, the unknown ilarvirus was demonstrated as a new species, tentatively named rose ilarvirus 2. This is the first report of the rose viruses in Taiwan.

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“…However, classifying an infected disease requires skill and experience. For example, rose mosaic disease is a common disease worldwide and can sometimes be caused by more than one pathogen [3]. Image processing methods for plant disease classification are currently being studied [4] combined with machine learning such as Support Vector Machine (SVM) [5] or K-Nearest Neighbors (KNN) [6].…”

Section: Introductionmentioning

confidence: 99%

A Hybrid Deep Learning and Optimized Machine Learning Approach for Rose Leaf Disease Classification

Nuanmeesri

2021

Eng. Technol. Appl. Sci. Res.

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Analysis of the symptoms of rose leaves can identify up to 15 different diseases. This research aims to develop Convolutional Neural Network models for classifying the diseases on rose leaves using hybrid deep learning techniques with Support Vector Machine (SVM). The developed models were based on the VGG16 architecture and early or late fusion techniques were applied to concatenate the output from a fully connected layer. The results showed that the developed models based on early fusion performed better than the developed models on either late fusion or VGG16 alone. In addition, it was found that the models using the SVM classifier had better efficiency in classifying the diseases appearing on rose leaves than the models using the softmax function classifier. In particular, a hybrid deep learning model based on early fusion and SVM, which applied the categorical hinge loss function, yielded a validation accuracy of 88.33% and a validation loss of 0.0679, which were higher than the ones of the other models. Moreover, this model was evaluated by 10-fold cross-validation with 90.26% accuracy, 90.59% precision, 92.44% recall, and 91.50% F1-score for disease classification on rose leaves.

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High throughput sequencing and RT-qPCR assay reveal the presence of rose cryptic virus-1 in the United Kingdom

Cited by 8 publications

References 18 publications

Facing Rose rosette virus: A risk to European rose cultivation

Facing Rose rosette virus: A risk to European rose cultivation

Rose Virome Analysis and Identification of A Novel Ilarvirus In Taiwan

A Hybrid Deep Learning and Optimized Machine Learning Approach for Rose Leaf Disease Classification

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