Using ultradeep Illumina sequencing, the diversity of two coexisting Potato virus Y sequence pools present within a plant was investigated: RNA isolated from viral particles and virus-derived small interfering RNAs (the derivatives of a plant RNA silencing mechanism). The mutational landscape of the within-host virus population was highly similar between both pools, with no notable hotspots across the viral genome. Notably, all of the single-nucleotide polymorphisms with a frequency of higher than 1.6% were found in both pools. Some unique single-nucleotide polymorphisms (SNPs) with very low frequencies were found in each of the pools, with more of them occurring in the small RNA (sRNA) pool, possibly arising through genetic drift in localized virus populations within a plant and the errors introduced during the amplification of silencing signal. Sequencing of the viral particle pool enhanced the efficiency of consensus viral genome sequence reconstruction. Nonhomologous recombinations were commonly detected in the viral particle pool, with a hot spot in the 3′ untranslated and coat protein regions of the genome. We stress that they present an important but often overlooked aspect of virus population diversity.
COBISS.SI-ID: 3333711
The emergence of next-generation "deep" sequencing has enabled the study of virus populations with much higher resolutions. This new tool increases the possibility of observing mixed infections caused by combinations of plant viruses, which are likely to occur more frequently than previously thought. The biological impact of co-infecting viruses on their host has yet to be determined and fully understood, and the first step towards reaching this goal is the separation and purification of individual species. Ion-exchange monolith chromatography has been used successfully for the purification and concentration of different viruses, and number of them have been separated from plant homogenate or bacterial and eukaryotic lysate. Thus, the question remained as to whether different virus species present in a single sample could be separated. In this study, anion-exchange chromatography using monolithic supports was optimized for fast and efficient partial purification of three model plant viruses: Turnip yellow mosaic virus, Tomato bushy stunt virus, and Tobacco mosaic virus. The virus species, as well as two virus strains, were separated from each other in a single chromatographic experiment from an artificially mixed sample. Based on A260/280 ratios, we were able to attribute specific peaks to a certain viral morphology/structure (icosahedral or rod-shaped). This first separation of individual viruses from an artificially prepared laboratory mixture should encourage new applications of monolithic chromatographic supports in the separation of plant, bacterial, or animal viruses from all kinds of mixed samples.
COBISS.SI-ID: 3344463
Raspberry leaf blotch virus (RLBV), a member of the genus Emaravirus, has recently been reported to be associated with raspberry leaf blotch disorder in Scotland. It was found in several samples of raspberry in England, Serbia, Finland and Bulgaria. Red raspberry plants with similar symptoms were found in Montenegro in 2011 and infection with RLBV was confirmed in symptomatic plants using RT-PCR. Two RNA5 amplicons were cloned and sequenced and compared with sequences in GenBank. BLAST analysis of Montenegrin RLBV nucleotide sequence showed 93% nucleotide (nt) identity with three available RLBV RNA5 sequences (HG738849, HG738846 and FR823303) from Bulgaria and the United Kingdom. The deduced protein sequence was identical to sequences from Bulgaria (CDJ26745) and showed 96.1% identity and 100% similarity to P5 sequence from the UK (CBZ42028). Our results show that the prevalence of RLBV in red raspberry in Montenegro is high. This finding will help to improve the quality of the increasing red raspberry production in Montenegro.
COBISS.SI-ID: 4779880