Genetic variability of Wheat dwarf virus

Wheat dwarf virus (WDV; family Geminiviridae, genus Mastrevirus) is a single-stranded DNA virus transmitted by the leafhopper Psammotettix alienus and it periodically causes severe damage to winter wheat in Sweden. WDV is also present in large parts of Europe. Two strains of WDV are known, the wheat strain and the barley strain. To get better understanding of the genetic diversity of WDV in Sweden and compare to the situation in the rest of the world, several isolates from wheat, triticale, wild grasses and the insect vector were collected and partially sequenced. All isolates collected in Sweden were shown to belong to the wheat strain of WDV. From Turkey and Hungary, two barley strain isolates were collected and complete genome sequences were determined. WDV infection in wild grasses was shown to occur only sporadically in Swedish grasslands, even in samples collected adjacent to heavily infected winter wheat fields. This indicates that wild grasses are not important as a primary source of WDV for the insect vector. Infected grasses might instead act as virus reservoirs, enabling WDV to prevail without winter wheat. The diversity of the Swedish wheat strain isolates and available international isolates was shown to be low. In phylogenetic analyses, no clear grouping could be seen according to geographical origin or host. The partial sequences of barley strain isolates grouped into three distinct clades: one Central-European clade with isolates from Germany, Hungary and Czech Republic, one clade with isolates from Spain and one clade with the Turkish isolates. For future studies on the host specificity determinants of the two WDV strains, infectious clones, transmissible by Agrobacterium tumefaciens, were constructed. The infectious clone of the barley strain was constructed from the Hungarian isolate WDV-Bar[HU]. The clone WDV-Bar[HU] was shown to infect barley, oat and rye. The biological activity of the barley infectious clone was further confirmed by insect transmission and typical WDV particles were visualised by electron microscopy. An infectious clone was also constructed for a Swedish wheat strain isolate and was confirmed to be able to infect wheat. PCR-based techniques were developed for rapid detection of WDV and Oat sterile dwarf virus in their respective insect vectors. The methods will be useful when trying to predict the risk of virus infection in cereal fields

Ultra-Deep Pyrosequencing of Partial Surface Protein Genes from Infectious Salmon Anaemia Virus (ISAV) Suggest Novel Mechanisms Involved in Transition to Virulence

<div><p>Uncultivable HPR0 strains of infectious salmon anaemia viruses (ISAVs) infecting gills are non-virulent putative precursors of virulent ISAVs (vISAVs) causing systemic disease in farmed Atlantic salmon (<i>Salmo salar</i>). The transition to virulence involves two molecular events, a deletion in the highly polymorphic region (HPR) of the hemagglutinin-esterase (HE) gene and a Q₂₆₆→L₂₆₆ substitution or insertion next to the putative cleavage site (R₂₆₇) in the fusion protein (F). We have performed ultra-deep pyrosequencing (UDPS) of these gene regions from healthy fish positive for HPR0 virus carrying full-length HPR sampled in a screening program, and a vISAV strain from an ISA outbreak at the same farming site three weeks later, and compared the mutant spectra. As the UDPS data shows the presence of both HE genotypes at both sampling times, and the outbreak strain was unlikely to be directly related to the HPR0 strain, this is the first report of a double infection with HPR0s and vISAVs. For F amplicon reads, mutation frequencies generating L₂₆₆ codons in screening samples and Q₂₆₆ codons in outbreak samples were not higher than at any random site. We suggest quasispecies heterogeneity as well as RNA structural properties are linked to transition to virulence. More specifically, a mechanism where selected single point mutations in the full-length HPR alter the RNA structure facilitating single- or sequential deletions in this region is proposed. The data provides stronger support for the deletion hypothesis, as opposed to recombination, as the responsible mechanism for generating the sequence deletions in HE.</p> </div

Next Generation Plasma Proteomics Identifies High-Precision Biomarker Candidates for Ovarian Cancer.

BACKGROUND: Ovarian cancer is the eighth most common cancer among women and has a 5-year survival of only 30-50%. The survival is close to 90% for patients in stage I but only 20% for patients in stage IV. The presently available biomarkers have insufficient sensitivity and specificity for early detection and there is an urgent need to identify novel biomarkers. METHODS: We employed the Explore PEA technology for high-precision analysis of 1463 plasma proteins and conducted a discovery and replication study using two clinical cohorts of previously untreated patients with benign or malignant ovarian tumours (N = 111 and N = 37). RESULTS: The discovery analysis identified 32 proteins that had significantly higher levels in malignant cases as compared to benign diagnoses, and for 28 of these, the association was replicated in the second cohort. Multivariate modelling identified three highly accurate models based on 4 to 7 proteins each for separating benign tumours from early-stage and/or late-stage ovarian cancers, all with AUCs above 0.96 in the replication cohort. We also developed a model for separating the early-stage from the late-stage achieving an AUC of 0.81 in the replication cohort. These models were based on eleven proteins in total (ALPP, CXCL8, DPY30, IL6, IL12, KRT19, PAEP, TSPAN1, SIGLEC5, VTCN1, and WFDC2), notably without MUCIN-16. The majority of the associated proteins have been connected to ovarian cancer but not identified as potential biomarkers. CONCLUSIONS: The results show the ability of using high-precision proteomics for the identification of novel plasma protein biomarker candidates for the early detection of ovarian cancer