Phylogenetic analysis of Wheat dwarf virus isolates from Iran

Wheat dwarf virus (WDV) adversely affects cereal production in Asia, Europe, and North Africa. In this study, sequences of several WDV isolates from Iran which is located in the Fertile Crescent were analyzed. Analysis revealed a new geographic cluster for WDV-Wheat from Iran. Recombination analysis demonstrated the existence of several breakpoints in different regions of the viral genome. Data analysis demonstrated that WDV-Barley has an older history and lower diversity than WDV-Wheat. Sequence analysis identified a rare occasion of a co-infection of wheat with WDV-Wheat and WDV-Barley.

Discrimination and genetic diversity of Wheat dwarf virus in the Czech Republic

Cereal-infecting Mastreviruses are one of the most ubiquitous of viruses, having caused huge yield losses during the last decade in the Czech Republic. The presence of two strains of Wheat dwarf virus (WDV), one of which is wheat adapted and one barley adapted, have been confirmed from among field samples of wheat and barley plants. The virus typing was conducted by both PCR-RFLP and sequencing-based methods. The Czech WDV isolates of the barley strain are more variable than the isolates of the wheat strain, separating them into two clades, one representing a pool of divergent isolates. The RFLP analysis confirmed the separation of the Czech isolates into two strains and highlights a powerful method for the rapid diagnosis of both the wheat and barley strains. Additionally, both RFLP and sequence analysis have shown that the barley strain is restricted to the barley host, while the wheat strain is present in both wheat and barley plants.

Surveying cereal-infecting geminiviruses in Germany--diagnostics and direct sequencing using rolling circle amplification

Geminiviruses have spread in German cereal crops during the last few years. In order to identify and classify them, we have compared conventional techniques (enzyme-linked immunosorbent assays, polymerase chain reaction, bacterial cloning, and sequencing) with a newly developed method which uses rolling circle amplification (RCA), restriction fragment length polymorphism (RFLP), and direct sequencing without a bacterial cloning step. Whereas immunological methods utilising polyclonal antibodies were reliable for detection of geminiviruses, they did not discriminate between different German mastrevirus species, in contrast to RCA/RFLP. Direct sequencing gave high fidelity results with the same quality as conventional cloning and sequencing but with significantly reduced effort and costs. Based on a survey of field-derived cereal samples and on DNA sequences of distinct virus isolates we propose two new mastrevirus species, to be named Barley dwarf virus (BDV), and Oat dwarf virus (ODV) according to sequence differences and host range studies. The results show the applicability of RCA-based techniques for field studies and the possibility of sequencing a geminiviral genome without cloning. This approach will accelerate genomics studies of all viruses with small circular DNA genomes. In addition, RCA proves to be a reliable technique allowing for the detection of new geminivirus species as it does not depend on the knowledge of specific primers.