Author Archives: dje

Wood et al., 2014

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)

Abstract

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.

Ryabov et al., 2014

Recently accepted for publication

Ryabov et al., (2014) A Virulent Strain of Deformed Wing Virus (DWV) of Honeybees (Apis mellifera) Prevails after Varroa destructor-Mediated, or In Vitro, Transmission. PLoS Pathogens

Abstract

The globally distributed ectoparasite Varroa destructor is a vector for viral pathogens of the Western honeybee (Apis mellifera), in particular the Iflavirus Deformed Wing Virus (DWV). In the absence of Varroa low levels DWV occur, generally causing asymptomatic infections. Conversely, Varroa-infested colonies show markedly elevated virus levels, increased overwintering colony losses, with impairment of pupal development and symptomatic workers. To determine whether changes in the virus population were due Varroa amplifying and introducing virulent virus strains and/or suppressing the host immune responses we exposed Varroa-naïve larvae to oral and Varroa-transmitted DWV. We monitored virus levels and diversity in developing pupae and associated Varroa, the resulting RNAi response and transcriptome changes in the host. Exposed pupae were stratified by Varroa association (presence/absence) and virus levels (low/high) into three groups. Varroa-free pupae all exhibited low levels of a highly diverse DWV population, with those exposed per os (group NV) exhibiting changes in the population composition. Varroa-associated pupae exhibited either low levels of a diverse DWV population (group VL) or high levels of a near-clonal virulent variant of DWV (group VH). These groups and unexposed controls (C) could be also discriminated by principal component analysis of the transcriptome changes observed, which included several genes involved in development and the immune response. All Varroa tested contained a diverse replicating DWV population implying the virulent variant present in group VH, and predominating in RNA-seq analysis of temporally and geographically separate Varroa-infested colonies, was selected upon transmission from Varroa, a conclusion supported by direct injection of pupae in vitro with mixed virus populations. Identification of a virulent variant of DWV, the role of Varroa in its transmission and the resulting host transcriptome changes furthers our understanding of this important viral pathogen of honeybees.

Lowry et al., 2014

Recently accepted for publication

Lowry et al., (2014) Recombination in enteroviruses is a biphasic replicative process involving the generation of greater-than genome length ‘imprecise’ intermediates. PLoS Pathogens DOI: 10.1371/journal.ppat.1004191

Abstract

Recombination in enteroviruses provides an evolutionary mechanism for acquiring extensive regions of novel sequence, is suggested to have a role in genotype diversity and is known to have been key to the emergence of novel neuropathogenic variants of poliovirus. Despite the importance of this evolutionary mechanism, the recombination process remains relatively poorly understood. We investigated heterologous recombination using a novel reverse genetic approach that resulted in the isolation of intermediate chimeric intertypic polioviruses bearing genomes with extensive duplicated sequences at the recombination junction. Serial passage of viruses exhibiting such imprecise junctions yielded progeny with increased fitness which had lost the duplicated sequences. Mutations or inhibitors that changed polymerase fidelity or the coalescence of replication complexes markedly altered the yield of recombinants (but did not influence non-replicative recombination) indicating both that the process is replicative and that it may be possible to enhance or reduce recombination-mediated viral evolution if required. We propose that extant recombinants result from a biphasic process in which an initial recombination event is followed by a process of resolution, deleting extraneous sequences and optimizing viral fitness. This process has implications for our wider understanding of ‘evolution by duplication’ in the positive-strand RNA viruses.

YBKA Spring Conference

I’m delighted to be talking  – twice (!) – at the Yorkshire Beekeepers Association Spring Conference in York on Saturday the 12th. With Stephen Martin (bee recognition and the Asian hornet), Jay Evans (beenomics – is that a real word?), Ben Jones (nutrition) and Liz Collison (neonicotinoids) also on the programme it promises to be an enjoyable day.

Update – it was a very enjoyable meeting, well attended and with two parallel sessions to entertain the audience. The sessions finished with breakout groups to “ask the experts” (or wonder where the expert was as I couldn’t find the room) followed by a wrap-up meeting. I’d like to thank the YBKA, Roger Chappel and Michael Badger for their excellent hospitality.

BBKA Spring Convention

DWV symptoms

DWV symptoms

I presented our work on honeybee viruses at the BBKA (British Beekeepers Association) Spring Convention during the Friday afternoon IPI (Insect Pollinators Initiative) research session. It was great to meet Dr. Brenda Ball who conducted some of the excellent early studies on transmission of deformed wing virus (DWV) by Varroa destructor. Also speaking at the convention was Jay Evans (USDA) who is also an invited speaker at the York Beekeepers Association Spring conference next week.

Europic 2014

Blankenberg pier

Blankenberg pier

Blankenberg seafront

Blankenberg seafront

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

Blankenberg fashion centre

The Belfry of Bruges

The Belfry of Bruges

 

 

Into the Lion’s Den

I’m delighted to be speaking at the Bee Farmers Association (BFA) Spring Conference on Saturday 8th March. The BFA are the voice of professional beekeeping and their members are responsible for virtually all migratory beekeeping in the UK, together with contract pollination services and bulk honey production and sales.

Update: I spent an enjoyable afternoon with the BFA talking about Varroa and viruses. I’d like to thank John Howat and Murray McGregor for their hospitality and the audience for their wide-ranging and enthusiastic questions. It was a good opportunity to discuss the practical applications of research into honeybee viruses.