Beet soil-borne mosaic virus: development of virus-specific detection tools

Fomitcheva, V. W.; Kühne, Thomas D.

doi:10.1007/s41348-019-00219-7

Cited by 5 publications

(4 citation statements)

References 16 publications

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“…The accuracy of the ELISA is less than molecular-based detection methods, however, being fast, cheap and the presence of commercial kits make the ELISA a preferred assay for the routine detection of BNYVV. RT-PCR is a more accurate tool compared to ELISA and is considered a more reliable method in virus detection studies 22,[30][31][32][33][34] hence, it is increasingly used in the detection of BNYVV [35][36][37] . The use of nucleic acid-based methods such as RT-PCR and qRT-PCR has increased the sensitivity of the virus detection by up to 100-10,000 times 27 .…”

Section: Discussionmentioning

confidence: 99%

Genome composition analysis of multipartite BNYVV reveals the occurrence of genetic re-assortment in the isolates of Asia Minor and Thrace

Özmen

Khabbazi

et al. 2020

Sci Rep

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Beet necrotic yellow vein virus (BnYVV) is the cause of rhizomania, an important disease of sugar beetaround the world. The multipartite genome of the BNYVV contains four or five single-stranded RNA that has been used to characterize the virus. Understanding genome composition of the virus not only determines the degree of pathogenicity but also is required to development of resistant varieties of sugar beet. Resistance to rhizomania has been conferred to sugar beet varieties by conventional breeding methods or modern genome engineering tools. However, over time, viruses undergo genetic alterations and develop new variants to break crop resistance. Here, we report the occurrence of genetic reassortment and emergence of new variants of BnYVV among the isolates of thrace and Asia Minor (modern-day Turkey). Our findings indicate that the isolates harbor European A-type RNA-2 and RNA-3, nevertheless, RNA-5 is closely related to East Asian J-type. Furthermore, RNA-1 and RNA-4 are either derived from A, B, and P-types or a mixture of them. The RNA-5 factor which enhance the pathogenicity, is rarely found in the isolates studied (20%). The creation of new variants of the virus emphasizes the necessity to develop new generation of resistant crops. We anticipate that these findings will be useful for future genetic characterization and evolutionary studies of BNYVV, as well as for developing sustainable strategies for the control of this destructive disease.Rhizomania is one of the most destructive soil-borne diseases of sugar beet (Beta vulgaris L.) worldwide. Since the first report of rhizomania 1 numerous studies have reported the worldwide infection of sugar beet fields with this disease. Tamada and Baba 2 first identified Beet necrotic yellow vein virus (BNYVV) as the cause of rhizomania when they isolated the virus from infected plants of sugar beet fields in Japan. This disease reduces sugar content by 8%, root yield up to 90%, and sugar yield up to 80% 3,4 . The BNYVV genome is multipartite and composed of four single-stranded RNA species designated as RNA-1, RNA-2, RNA-3, and RNA-4, coating with a 21-kDa protein 5 . In addition, a fifth RNA species (RNA-5) has been identified in some of the European and Asian BNYVV isolates 6-12 . RNA-1 and RNA-2, which contain 6746 and 4612 nt-long RNA species, respectively, encode viral "housekeeping" genes involved in virus replication, assembly, cell-to-cell movement and suppression of post transcriptional gene silencing 13,14 . Therefore, when the virus vector Polymyxa betae Keskin 15 is not present, RNA-1 and RNA-2 are required for the maintenance of BNYVV in the environment 8,14,16 . RNA-3 consisting of a 1775 nt-long RNA species, is involved in viral pathogenicity 7,10,11,17,18 . RNA-4 (1431 nt) plays a key role in transmission of the virus by P. betae 7,11,13,19 . RNA-5 (1342-1347 nt in length) is associated with rhizomania severity, but is not required for virus survival 20,21 . Comparative studies revealed that the RNA-1, RNA-4, and RNA-5 contribute to the development ...

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Section: Discussionmentioning

confidence: 99%

Genome composition analysis of multipartite BNYVV reveals the occurrence of genetic re-assortment in the isolates of Asia Minor and Thrace

Özmen

Khabbazi

et al. 2020

Sci Rep

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“…The Panel performed the pest categorisation for beet necrotic yellow vein virus, following guiding principles and steps presented in the EFSA guidance on quantitative pest risk assessment (EFSA PLH Panel, 2018) and in the International Standard for Phytosanitary Measures No 11 (FAO, 2013) and No 21 (FAO, 2004).…”

Section: Methodologiesmentioning

confidence: 99%

“…However, foliar symptoms including wilting can be confused with those resulting from other biotic or abiotic stresses. Since other soil‐borne viruses may be found in association with rhizomania, such as beet soil‐borne virus (BSBV), beet soil‐borne mosaic virus (BSBMV) (Meunier et al., 2003b), beet virus Q (BVQ) and beet black scorch virus (BBSV) (Mehrvar et al., 2009), a correct virus detection and identification relies on serological and molecular methods (Fomitcheva and Kühne, 2019). Serological methods based on enzyme‐linked immunosorbent assay (ELISA) are sensitive and robust for virus detection in particular when large sample numbers are to be tested.…”

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confidence: 99%

Pest categorisation of beet necrotic yellow vein virus

Dehnen‐Schmutz¹,

Serio²,

Gonthier³

et al. 2020

EFS2

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Following a request from the EU Commission, the Panel on Plant Health performed a categorisation of beet necrotic yellow vein virus ( BNYVV ), the causal agent of the sugar beet rhizomania disease. The virus is currently listed in Annex III as a protected zone ( PZ ) quarantine pest of the Commission Implementing Regulation ( EU ) 2019/2072. The identity of the BNYVV is well established. BNYVV is a soil‐borne virus transmitted by the obligate root plasmodiophorid endoparasite Polymyxa betae . BNYVV is widely distributed in the EU , but is not reported in the following EU PZ s: Ireland, France (Brittany), Portugal (Azores), Finland and Northern Ireland. The virus may enter, become established and spread in the PZ s via P. betae resting spores with soil and growing media as such or attached to machinery and with roots and tubercles of species other than B. vulgaris and with plants for planting. Introduction of BNYVV would have a negative impact on sugar beet and other beet crops in PZ s, because of yield and sugar content reduction. Phytosanitary measures are available to reduce the likelihood of entry and spread in the PZ s. Once the virus and its plasmodiophorid vector have entered a PZ , their eradication would be difficult due to the persistence of viruliferous resting spores in the soil. The main knowledge gaps or uncertainties identified concerning the presence of BNYVV in the PZ s and the incidence and distribution of BNYVV in Switzerland, a country to which a range of specific requirements do not apply. BNYVV meets all the criteria that are within the remit of EFSA to qualify as a potential protected zone union quarantine pest. Plants for planting are not considered as a main means of spread, and therefore BNYVV does not satisfy all the criteria evaluated by EFSA to qualify as potential Union regulated non‐quarantine pest.

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“…The qRT-PCR relies on specific primers and probes for the virus: in the case of new mutations or whenever discrimination among different strains of the virus is needed, the use of new or different probes would be sufficient to accurately detect the strain. It has also been challenging, in some cases, to distinguish between BNYVV and BSBMV (Beet soil-borne mosaic virus) applying the ELISA test, because the structure of the two viruses is similar [ 9 ]. This problem no longer exists with the qRT-PCR targeting specific nucleic acids.…”

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confidence: 99%

Quantification of rhizomania virus by automated RNA isolation and PCR based methods in sugar beet

et al. 2021

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Rhizomania is a grave disease affecting sugar beet (Beta vulgaris L.). It is caused by the Beet Necrotic Yellow Vein Virus (BNYVV), an RNA virus transmitted by the plasmodiophorid vector Polymyxa betae. Genetic resistance to the virus has been accomplished mostly using phenotype-genotype association studies. As yet, the most convenient method to ascertain plant resistance has been the quantification of viral titer in roots through the ELISA test. This method is particularly time-consuming and clashes with the necessities of modern plant breeding. Here, we propose an alternative and successful phenotyping method based on the automatic extraction of the viral RNA from sugar beet roots and its relative and absolute quantification by quantitative real-time PCR (qRT-PCR) and digital PCR (dPCR), respectively. Such a method enables an improved standardization of the study, as well as an accurate quantification of the virus also in those samples presenting low virus titer, with respect to the ELISA test. Keywords Sugar beet Á Rhizomania virus Á Highthroughput phenotyping Á Quantitative real-time PCR Á Digital PCR Abbreviations qRT-PCR Quantitative real-time PCR dPCR Digital PCR RT-PCR Reverse transcriptase PCR Rhizomania is the most destructive disease affecting sugar beet: it can decrease sugar yield by up to 70% [24, 31, 33]. Rhizomania is caused by the Beet Necrotic Yellow Vein Virus (BNYVV), a virus transmitted by the soil-borne plasmodiophorid vector Polymyxa betae. The BNYVV is a single-stranded rod-shaped virus consisting of 4 or 5 ssRNAs [28]. According to the RNA structure, the A, B, and P forms of BNYVV have been distinguished. Strains A and B have four RNAs while the P-type also has a fifth RNA strand. The function of each RNA strand has been well characterized [11]. In particular, the third one is involved in the long-distance movement of the virus in the plant [12]. The P25 virulence factor is located on this strand and is responsible for the development of one of the main root symptoms: the extensive proliferation of lateral roots [10, 32]. This gene is the one displaying the highest variability: mutations at positions 67 to 70 (hypervariable tetrad) are unique for each strain of the virus [22]. The variability within the P25 gene allows the virus to bypass the resistance. Koenig et al. [16] described the most common mutations of this tetrad in each strain: in the A-type ACHG, AHHG, AFHG, ALHG, AYHG, VCHG; in the B-type AYHR, AHHR; in the P-type SYHG have been identified. More recently, a new A-strain has been characterized, where the hypervariable tetrad presents the AYPR motif. This strain is less common than the others but more aggressive [4]. Rhizomania virus is spread worldwide, and it causes enormous damage to the crop. The only approach to control the disease is the use of host genetic resistance. The

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Beet soil-borne mosaic virus: development of virus-specific detection tools

Cited by 5 publications

References 16 publications

Genome composition analysis of multipartite BNYVV reveals the occurrence of genetic re-assortment in the isolates of Asia Minor and Thrace

Genome composition analysis of multipartite BNYVV reveals the occurrence of genetic re-assortment in the isolates of Asia Minor and Thrace

Pest categorisation of beet necrotic yellow vein virus

Quantification of rhizomania virus by automated RNA isolation and PCR based methods in sugar beet

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