Metagenomic analysis of Varroa-free Australian honey bees (Apis mellifera) shows a diverse Picornavirales virome

Abstract

The viral landscape of the honey bee (Apismellifera) has changed as a consequence of the global spread of the parasitic mite Varroa destructor and accompanying virulent strains of the iflavirus deformed wing virus (DWV), which the mite vectors. The presence of DWV in honey bee populations is known to influence the occurrence of other viruses, suggesting that the current known virome of A. mellifera may be undercharacterized. Here we tested this hypothesis by examining the honey bee virome in Australia, which is uniquely free of parasitic mites or DWV. Using a high-throughput sequencing (HTS) approach, we examined the RNA virome from nine pools of A. mellifera across Australia. In addition to previously reported honey bee viruses, several other insect viruses were detected, including strains related to aphid lethal paralysis virus (ALPV) and Rhopalosiphum padi virus (RhPV), which have recently been identified as infecting honey bees in the USA, as well as several other viruses recently found in Drosophila spp. A further 42 putative novel insect virus genomes spanning the order Picornavirales were assembled, which significantly increases the known viral diversity in A. mellifera. Among these novel genomes, we identified several that were similar (but different) to key A. mellifera viruses, such as DWV, that warrant further investigation. We propose that A. mellifera may be preferentially infected with viruses of the order Picornavirales and that a diverse population of these viruses may be representative of a Varroa-free landscape.

Diversity and Global Distribution of Viruses of the Western Honey Bee, Apis mellifera

“…For bees, this process started in earnest with the mass screening for possible virological links to colony collapse disorder (CCD) [43], with each subsequent effort adding to the virus diversity in bees or its ectoparasite Varroa destructor [32][33][34][44][45][46][47][48], culminating in the list in Table 1. However, this is almost certainly a vast underestimate of the true total virus diversity in bees, judging by the rate of new discoveries [49], not only of virus species and genera [50] but also of families and orders [23]. Additionally, methodological biases exist in the discovery process towards RNA viruses (preponderance of transcriptome studies in HTS), especially those with poly-A tail (e.g., Picornavirales), and a bioinformatic screening based largely on conserved replication protein domains, thereby excluding subviral entities lacking a replicase (viroids, satellite viruses), viruses replicating by other means and other non-host, replicating, bioactive nucleic acid sequences.…”

“…The typical symptoms of this pathogen, wing deformities, are closely linked to transmission by V. destructor or injection [55][56][57]. By contrast, it appears that infection through vertical, venereal or oral transmission is effectively symptomless, even if the virus titers in the affected organs can be as high as those achieved by Varroa-mediated transmission [41,49,50]. Finally, the relationship between titers and symptoms is not always straightforward, and covert infections may result in more cryptic symptoms, such as changes in behavioral maturation that may be more difficult to discern [58][59][60].…”

“…b : Viruses with DNA genomes. c : Novel picorna-like viruses identified in Australian honey bees by Roberts et al [50]. The columns on the right summarize the current experimental evidence for the presence (+, highlighted), unclear (~), absence (-) or unknown (?)…”

Expansion of the Metazoan Virosphere: Progress, Pitfalls, and Prospects

“…Tokarz et al 2018). The focus has subsequently expanded to include neglected animal lineages, identifying hundreds of new RNA viruses in arthropods and other invertebrates (Webster et al 2015;Shi et al 2016a;Roberts et al 2018;Waldron et al 2018), and recently in divergent and under-sampled chordates (Geoghegan et al 2018;Shi et al 2018).…”

Next-Generation Sequencing on Insectivorous Bat Guano: An Accurate Tool to Identify Arthropod Viruses of Potential Agricultural Concern

“…Beyond the classified Dicistrovirus species, numerous dicistroviruses which are yet to be classified have been characterized in the last two decades mainly owing to the advent of high-throughput sequencing technologies (HTS). Although numbers of them were identified in insects [12,[17][18][19][20][21][22], some were found in mammalian stools, including human beings. However, the presence of such viruses in mammalian faeces were likely linked to their dietary habits [23][24][25][26][27][28].…”