As regular readers of TME will have read, this past summer was a whirlwind of sampling in which I took the briefest of holidays in the Southwest of England before attending the European Phycological Congress (read about the congress here and here).
I was able to do a little serendipitous Gracilaria searching and catch up with collaborators at the Marine Biological Association.
Salcombe algal hunting
Science as art
Declan Schroeder, a Senior Fellow at the MBA, shared with me some of the latest research from his group. It is an excellent departure for it’s not about a seaweed or even something marine!
Bees are the key pollinators for agriculture, with an economic value of be than 225 billion USD. But, in the last 50 years, millions of European honeybee colonies have collapsed due to the spread of the ectoparasite Varroa destructor and its affiliation with the Deformed Wing Virus (DWV), a single-stranded RNA virus.
As a result [of rapid replication and high error rates], many RNA viruses are highly genetically heterogeneous and exist within infected population structures known as quasispecies. It has been proposed that this gives these viral pathogens an increased ability to shift to a new environmental niche, such as a new host, as a suitable mutant is more likely to already exist if the opportunity arises.
Quasispecies can exist as swarms of mutants around one variant or as master variants with their own swarm of mutants. It is the A variant of DWV that is implicated in colony collapse, but recently, DWV type B has been found to dominate the DWV population of honey bees in an isolated apiary in the UK (Mordecai et al. 2015a). DWV Type A leads to colony death, whereas Type B does not lead to the collapse of the colony. The role of the newly described Type C (Mordecai et al. 2015b) in overwintering colony losses is unclear.
Describing viral diversity is important in order to understand more about viral dynamics in honey bees to humans, but bioinformatic pipelines designed for prokaryotes and eukaryotes are not really suited to viral systems.
Mordecai et al. (2015b) used Illumina sequencing and the Vicuna de novo assembler. This assembler is designed to
assemble highly heterogeneous viral populations and is well suited to the computational challenge that the DWV quasi species present.
Figure from Mordecai et al. (2015a) showing the bioinformatics pipeline leading to the application of the VICUNA de novo assembler.
Reference assemblers likely hinder the discovery of variants. Despite the use of the Vicuna pipeline in Mordecai et al. (2015b), it is not suited to further analyzing the diversity around the variants. Yet,
the ability to determine whether recombination has occurred and to locate associated specific recombination junctions is thus of major importance in understanding emerging diseases and pathogenesis (Wood et al. 2014).
Wood et al. (2014) provide a method for determining recombinant mosaics using high-throughput sequence data using DWV as a model.
The ability to study this diversity is important on a global scale, particularly with cross-species viral transmission. For example, DWV can infect bumble bees, V. destructor and other insects.
Exploring the extent of viral diversity in RNA quasispecies, of which DWV may be a suitable model, may offer insight into the mechanisms by which viruses are able to transmit between different hosts as well as how viruses are able to develop resistance to antiviral therapies.
The future study of DWV quasispecies may
elucidate mechanisms by which it establishes a persistent infection among several hosts but only proves pathogenic in some.
Mordecai et al. (2015a) expand on this in a second paper recently published in The ISME Journal and propose a phenomenon called superinfection exclusion. Certain bee colonies survive despite high Varroa infestation and high DWV loads.
One bee keeper initiated a closed breeding program after Varroa swept across the UK in the 1990s. Mordecai et al. (2015a) studied his apiaries and demonstrated the dominance of DWV variant B, the variant that does not result in colony death.
The Swindon UK population in question could have evolved to favour DWV type B persistence as a result of husbandry practices that have selected for a new stable non-pathogenic equilibrium.
Different viral variants may compete in which the disease-causing variant (e.g., DWV Type A) may win or the avirulent variants (e.g., DWV Type B) can lead to colony survival, albeit with very high viral loads in which other variants are excluded.
Mordecai et al. (2015a) conclude superinfection exclusion could be a method by which colony decline could be limited or eradicated by using DWV Type B as a biocontrol.
References
Mordecai, GJ, LE Brettell, SJ Martin, D Dixon, IM Jones, DC Schroeder (2015a) Superinfection exclusion and the long-term survival of honey bees in Varroa-infested colonies. The ISME Journal. doi: 10.1038/ismej.2015.186
Mordecai, GJ, L Wilfert, SJ Martin, IM Jones, DC Schroeder. (2015b) Diversity in a honey bee pathogen: first report of a third master variant of the Deformed Wing Virus quasispecies. The ISME Journal. doi: 10.1038/ismej.2015.178
Wood GR, EV Ryabov, JM Fannon, JD Moore, DJ Evans, N Burroughs. (2014). MosaicSolver: a tool for determining recombinants of viral genomes from pileup data. Nucl Acids Res 42: e123 doi: 10.1093/nar/gku524