A Survey Using High-Throughput Sequencing Suggests That the Diversity of Cereal and Barley Yellow Dwarf Viruses Is Underestimated

Worldwide, barley/cereal yellow dwarf viruses (YDVs) are the most widespread and damaging group of cereal viruses. In this study, we applied high-throughput sequencing technologies (HTS) to perform a virus survey on symptomatic plants from 47 cereal fields in Estonia. HTS allowed the assembly of complete genome sequences for 22 isolates of cereal yellow dwarf virus RPS, barley yellow dwarf virus GAV, barley yellow dwarf virus PAS (BYDV-PAS), barley yellow dwarf virus PAV (BYDV-PAV), and barley yellow dwarf virus OYV (BYDV-OYV). We also assembled a near-complete genome of the putative novel species BYDV-OYV from Swedish samples of meadow fescue. Previously, partial sequencing of the central part of the coat protein gene indicated that BYDV-OYV represented a putative new species closely related to BYDV-PAV-CN, which currently is recognized as a subtype of BYDV-PAV. The present study found that whereas the 3′gene block of BYDV-OYV shares the closest relationship with BYDV-PAV-CN, the 5′gene block of BYDV-OYV shows the closest relationships to that of BYDV-PAS. Recombination detection analysis revealed that BYDV-OYV is a parental virus for both. Analysis of complete genome sequence data indicates that both BYDV-OYV and BYDV-PAV-CN meet the species criteria of genus Luteovirus. The study discusses BYDV phylogeny, and through a systematic in silico analysis of published primers for YDV detection, the existing gaps in current diagnostic practices for detection of YDVs, proposing primer pairs based on the most recent genomic information for the detection of different BYDV species. Thanks to the rising number of sequences available in databases, continuous updating of diagnostic primers can improve test specificity, e.g., inclusivity and exclusivity at species levels. This is needed to properly survey the geographical and host distribution of the different species of the YDV complex and their prevalence in cereal/barley yellow dwarf disease epidemics

Identification of a nanovirus-alphasatellite complex in Sophora alopecuroides

Viruses in the genus Nanovirus of the family Nanoviridae generally have eight individually encapsidated circular genome components and have been predominantly found infecting Fabaceae plants in Europe, Australia, Africa and Asia. For over a decade Sophora alopecuroides L. (Fabaceae) plants have been observed across Iran displaying dwarfing, yellowing, stunted leaves and yellow vein banding. Using a high-throughput sequencing approach, sequences were identified within one such plant that had similarities to nanovirus genome components. From this plant, the nanovirus-like molecules DNA-R (n\ua0=\ua04), DNA-C (n\ua0=\ua02), DNA-S (n\ua0=\ua01), DNA-M (n\ua0=\ua01), DNA-N (n\ua0=\ua01), DNA-U1 (n\ua0=\ua01), DNA-U2 (n\ua0=\ua01) and DNA-U4 (n\ua0=\ua01) were amplified, cloned and sequenced. Other than for the DNA-R, these components share less than 71% identity with those of other known nanoviruses. The four DNA-R molecules were highly diverse, sharing only 65–71% identity with each other and 64–86% identity with those of other nanoviruses. In the S. alopecuroides plant 14 molecules sharing 57.7–84.6% identity with previously determined sequences of nanovirus-associated alphasatellites were also identified. Given the research activity in the nanovirus field during the last five years coupled with high-throughput sequence technologies, many more diverse nanoviruses and nanovirus-associated satellites are likely to be identified

Diversity and evolution of potato mop-top virus

Nearly complete sequences of RNA-CP and 3'-proximal RNA-TGB were determined for 43 samples of potato mop-top virus (PMTV) originating from potato tubers and field soil from Sweden, Denmark and the USA. The results showed limited diversity and no strict geographical grouping, suggesting only a few original introductions of PMTV from the Andes. Two distinguishable types of RNA-CP and RNA-TGB were found in the samples, but no specific combination of them correlated with spraing symptoms in tubers. Lack of positive selection in the coding sequences indicates that there is no specific molecular adaptation of PMTV to new vectors or hosts

Symptom evolution following the emergence of maize streak virus

For pathogens infecting single host species evolutionary trade-offs have previously been demonstrated between pathogen-induced mortality rates and transmission rates. It remains unclear, however, how such trade-offs impact sub-lethal pathogen-inflicted damage, and whether these trade-offs even occur in broad host-range pathogens. Here, we examine changes over the past 110 years in symptoms induced in maize by the broad host-range pathogen, maize streak virus (MSV). Specifically, we use the quantified symptom intensities of cloned MSV isolates in differentially resistant maize genotypes to phylogenetically infer ancestral symptom intensities and check for phylogenetic signal associated with these symptom intensities. We show that whereas symptoms reflecting harm to the host have remained constant or decreased, there has been an increase in how extensively MSV colonizes the cells upon which transmission vectors feed

Virusförande bladlöss i potatis, oljeväxter och stråsäd – risk för lusskador 2019?

Södra Sverige har 2018 upplevt en ovanligt mild och lång höst, och sugfällorna i Alnarp och Ingelstorp har i oktober fångat ett mycket stort antal bladlöss, vilka gynnats av vädret. Tidigare år med stora populationer av bladlöss under hösten har varit förknippade med virusangrepp på höstgrödor. Det har därför nu i höst varit en stor risk för för angrepp av rödsotvirus på höstsäd och Turnip yellows virus på höstoljeväxter. Omfattningen av skador orsakade av virusinfektion är sedan i hög grad beroende på om bladlössen bar på virus och har etablerat sig i mottagliga grödor samt i vilken utsträckning bekämpning av bladlöss har gjorts

Reservoirs of plant virus disease: Occurrence of wheat dwarf virus and barley/cereal yellow dwarf viruses in Sweden

Non-crop plants such as grasses and volunteer plants are an inseparable part of the flora of crop fields and can influence virus incidence in crop plants. The presence of grasses as virus reservoirs can lead to a higher probability of virus incidence in crop plants. However, the role of reservoirs as an inoculum source in agricultural fields has not been well studied for many viral diseases of crops. Grasses have been found to constitute potential reservoirs for cereal-infecting viruses in different parts of the world. This study revealed that cereal-infecting viruses such as wheat dwarf virus (WDV), barley yellow dwarf viruses (BYDVs), and cereal yellow dwarf virus-RPV (CYDV-RPV) can be found among ryegrass growing in or around winter wheat fields. Phylogenetic analysis showed that a WDV isolate from ryegrass was a typical WDV-E isolate that infects wheat. Similarly, a ryegrass isolate of barley yellow dwarf virus-PAV (BYDV-PAV) grouped in a clade together with other BYDV-PAV isolates. Inoculation experiments under greenhouse conditions confirmed that annual ryegrass of various genotypes can be infected with WDV to a very low titre. Moreover, leafhoppers were able to acquire WDV from infected ryegrass plants, despite the low titre, and transmit the virus to wheat, resulting in symptoms. Information from the grass reservoir may contribute to improving strategies for controlling plant virus outbreaks in the field. Knowledge of the likely levels of virus in potential reservoir plants can be used to inform decisions on insect vector control strategies and may help to prevent virus disease outbreaks in the future

Host Plant Resistance to Pathogen with Reference to Induction of Systemic Acquired Resistance (SAR) in Tobacco (Nicotiana Tabacum Var. Samsun) When Infected with Tobacco Mosaic Virus (TMV)

A model study based on induction of SAR via infecting different lines of tobacco (Nicotiana tabacum var. Samsun) with Tobacco mosaic virus (TMV) was carried out at the Department of Applied Biology, University of Helsinki, Finland in December, 2006. The objective was to demonstrate the onset of defence response, spread of SAR in tobacco plants infected with TMV and detection of expression of marker gene, PR protein gene (PR1) using northern blotting and real time polymerease chain reaction (PCR). Localized necrosis was observed at 3 and 10 days post inoculation (dpi) only in TMV-inoculated NN plants in contrast to absence of similar localized symptom in the corresponding inoculated nn plants except systemic yellowing at 10 dpi. The data generated by northern blot analysis as well as real-time PCR showed existence of variation among experimental treatments with respect to PR1 gene expression. Northern blotting and real-time PCR gave similar results except a difference that was observed for sample 10 probably signifying high precision and sensitivity of real-time PCR in indicating PR1 expression compared to northern blotting. The RNA ladder was not visible in agarose gel and it was not possible to observe the actual result. This confirmed the importance of proceeding to the application of northern blotting. The result of this study indicated localized induction of necrotic lesions in infected tobacco var. Samsun (NN) as indicator for the HR programmed cell death and PRl expression as indicator for SAR in systemic leaves. All plants of nn variety are susceptible and showed only systemic mosaic symptoms in contrast to localized lesions expressed in NN plants. The result of this study indicated that the NN gene in TMV-infected tobacco var. Samsun carrying N allele recognized the corresponding Avirulence gene of the virus inducing the SAR in systemic leaves as indicated via expression of PR1 protein and hypersensitive reaction (HR) in infected leaves as visualized by localized necrosis in infected leaves. This is in agreement with the theory of gene-for-gene interaction in plant defence responses

Milder autumns may increase risk for infection of crops with turnip yellows virus

Climate change has increased the risk for infection of crops with insect-transmitted viruses. Mild autumns provide prolonged active periods to insects, which may spread viruses to winter crops. In autumn 2018, green peach aphids (Myzus persicae) were found in suction traps in southern Sweden that presented infection risk for winter oilseed rape (OSR; Brassica napus) with turnip yellows virus (TuYV). A survey was carried out in spring 2019 with random leaf samples from 46 OSR fields in southern and central Sweden using DAS-ELISA resulting in TuYV being detected in all fields except one. In the counties of Skåne, Kalmar and Östergötland, the average incidence of TuYV-infected plants was 75% and the incidence reached 100% for nine fields. Sequence analyses of the coat protein gene revealed a close relationship between TuYV isolates from Sweden and other parts of the world. High-throughput sequencing for one of the OSR samples confirmed the presence of TuYV and revealed co-infection with TuYV-associated RNAs. Molecular analyses of seven sugar beet (Beta vulgaris) plants with yellowing, collected in 2019, revealed that two of them were infected by TuYV together with two other poleroviruses: beet mild yellowing virus and beet chlorosis virus. The presence of TuYV in sugar beet suggests a spillover from other hosts. Poleroviruses are prone to recombination, and mixed infection with three poleroviruses in the same plant poses a risk for the emergence of new polerovirus genotypes