Recently accepted for publication
Wood et al., (2014) MosaicSolver: a tool for determining recombinants of viral genomes from pileup data. Nucleic Acids Research (in press)
Viral recombination is a key evolutionary mechanism, aiding escape from host immunity, changes in tropism and possibly transmission across species barriers. Determining whether recombination has occurred and the specific recombination points is thus of major importance in understanding emerging diseases and pathogenesis. This paper describes a method for determining recombinant mosaics (and their proportions) originating from two parent genomes, using high-throughput sequence data. The method involves setting the problem geometrically and the use of appropriately constrained quadratic programming. Recombinants of the honeybee deformed wing virus and the Varroa destructor virus-1 are inferred to illustrate the method, using siRNAs and sequence data sampling the viral genome population (cDNA library). Matlab software (MosaicSolver) is available.
Europic 2014 was held in Blankenberg, Belgium. The pier is without doubt the most attractive part of the town. The seafront consists of an endless row of apartments overlooking – in March at least – the cold, grey North Sea. It probably looks a whole lot better in the height of summer.
The meeting was – as usual – excellent. A good mix of talks from labs around the world, ample time to talk over dinner or a Leffe beer or two and an afternoon in the infinitely more attractive town of Bruge (Shoot first, Sightsee later).
Andrew Woodman, Fadi AlNaji and DJE presented current studies at the meeting on recombination in enteroviruses and identification of a virulent recombinant variant of deformed wing virus.
Blankenberg fashion centre
The Belfry of Bruges
Recently accepted for publication
Atkinson et al., (2014) The Influence of CpG and UpA Dinucleotide Frequencies on RNA Virus Replication and Characterisation of the Innate Cellular Pathways Underlying Virus Attenuation and Enhanced Replication. Nucleic Acids Research. January 2014
Most RNA viruses infecting mammals and other vertebrates show profound suppression of CpG and UpA dinucleotide frequencies. To investigate this functionally, mutants of the picornavirus, echovirus 7 (E7), were constructed with altered CpG and UpA compositions in two 1.1–1.3 Kbase regions. Those with increased frequencies of CpG and UpA showed impaired replication kinetics and higher RNA/infectivity ratios compared with wild-type virus. Remarkably, mutants with CpGs and UpAs removed showed enhanced replication, larger plaques and rapidly outcompeted wild-type virus on co-infections. Luciferase-expressing E7 sub-genomic replicons with CpGs and UpAs removed from the reporter gene showed 100-fold greater luminescence. E7 and mutants were equivalently sen- sitive to exogenously added interferon-b, showed no evidence for differential recognition by ADAR1 or pattern recognition receptors RIG-I, MDA5 or PKR. However, kinase inhibitors roscovitine and C16 partially or entirely reversed the attenuated phenotype of high CpG and UpA mutants, potentially through inhibition of currently uncharacterized pattern recognition receptors that respond to RNA composition. Generating viruses with enhanced replication kinetics has applications in vaccine production and reporter gene construction. More fundamentally, the findings introduce a new evolutionary paradigm where dinucleotide composition of viral genomes is subjected to selection pressures independently of coding capacity and profoundly influences host– pathogen interactions.