Molecular analysis of barley stripe mosaic virus isolates differing in their biological properties and the development of reverse transcription loop-mediated isothermal amplification assays for their detection

Abstract

Barley stripe mosaic virus (BSMV) is an important seed-transmitted pathogen occurring worldwide. Recently, the occurrence of mild BSMV pathotypes has been observed in barley crops in Poland. In this study, the full-length genome sequences of mild and aggressive Polish and German BSMV isolates was established. Phylogenetic and recombination analysis was performed using Polish and other BSMV isolates described to date. The analysis revealed that Polish isolates differed only in 25 nucleotides, which suggests that point mutations might have had a great impact on the biological properties of the virus. The phylogenetic analysis revealed that the closest relationship was that between European and BSMV-CV42, BSMV-ND18 and BSMV-Type isolates, whereas the highest genetic distance was observed for BSMV-Qasr Ibrim and BSMV-China isolates. A recombination event within the αa protein of BSMV-De-M and BSMV-CV42 isolates was also detected. Moreover, a sensitive reverse transcription loop-mediated isothermal amplification (RT-LAMP) method was developed for rapid detection of BSMV isolates. The RT-LAMP assay can be used for routine diagnostics of BSMV in seed and plant material.

Validation and optimization of the loop-mediated isothermal amplification (LAMP) technique for rapid detection of wheat stripe mosaic virus, a wheat-infecting pathogen

“…Therefore, Francois et al 30 and Hao et al, 31 working on the identification of wheat dwarf virus by LAMP, albeit without using Loop primers, demonstrated that 1 h of incubation was required for the amplification of the target gene. Similarly, as in the aforementioned studies, Zarzyńska-Nowak et al 32 used the technique for the detection of barley stripe mosaic virus (BSMV) infecting barley.…”

Distribution of Wheat-Infecting Viruses and Genetic Variability of Wheat Streak Mosaic Virus and Barley Stripe Mosaic Virus in Kazakhstan

“…Multiplex RT-PCR has been successfully applied for the screening and quantification of WSMV and TriMV [ 56 , 57 ], and RT-qPCR has been shown to be twice and thrice more sensitive than ELISA in the detection of TriMV and HPWMoV, respectively [ 58 ]. For BSMV, Zarzyńska et al demonstrated the limitations of ELISA as a diagnostic tool: it could not detect mild infections with moderate virus titers, while RT-PCR [ 59 ] and LAMP [ 60 ] were more sensitive. RT-qPCR is a valuable tool in studying virus gene expression and virus–host interactions [ 6 ].…”

Occurrence, Genetic Variability of Tomato Yellow Ring Orthotospovirus Population and the Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Its Rapid Detection

“…LAMP amplifies target DNA at isothermal conditions (usually 60–65 °C) and obviates the need for thermal cyclers and postamplification procedures for signal detection. The significant advantages of LAMP assay make it very popular and widely used by many researchers to detect plant and animal viruses [ 37 , 38 , 39 , 40 , 41 , 42 ].…”