Metatranscriptome Analysis of Sympatric Bee Species Identifies Bee Virus Variants and a New Virus, Andrena-Associated Bee Virus-1

Abstract

Bees are important plant pollinators in agricultural and natural ecosystems. High average annual losses of honey bee (Apis mellifera) colonies in some parts of the world, and regional population declines of some mining bee species (Andrena spp.), are attributed to multiple factors including habitat loss, lack of quality forage, insecticide exposure, and pathogens, including viruses. While research has primarily focused on viruses in honey bees, many of these viruses have a broad host range. It is therefore important to apply a community level approach in studying the epidemiology of bee viruses. We utilized high-throughput sequencing to evaluate viral diversity and viral sharing in sympatric, co-foraging bees in the context of habitat type. Variants of four common viruses (i.e., black queen cell virus, deformed wing virus, Lake Sinai virus 2, and Lake Sinai virus NE) were identified in honey bee and mining bee samples, and the high degree of nucleotide identity in the virus consensus sequences obtained from both taxa indicates virus sharing. We discovered a unique bipartite + ssRNA Tombo-like virus, Andrena-associated bee virus-1 (AnBV-1). AnBV-1 infects mining bees, honey bees, and primary honey bee pupal cells maintained in culture. AnBV-1 prevalence and abundance was greater in mining bees than in honey bees. Statistical modeling that examined the roles of ecological factors, including floral diversity and abundance, indicated that AnBV-1 infection prevalence in honey bees was greater in habitats with low floral diversity and abundance, and that interspecific virus transmission is strongly modulated by the floral community in the habitat. These results suggest that land management strategies that aim to enhance floral diversity and abundance may reduce AnBV-1 spread between co-foraging bees.

Adaptation to vector‐based transmission in a honeybee virus

“…It is common for DWV genotypes to recombine in co-infected colonies (Brettell et al, 2020;Dalmon et al, 2017;Moore et al, 2011;Ryabov et al, 2014;Zioni et al, 2011). This may have influenced which strains predominate in our M+ colonies, such that our DWV-A or DWV-B genotypes could in fact be a recombinant containing genomic portions of both A and B, as suggested by Daughenbaugh et al (2021).…”

Investigating Virus–Host Interactions in Cultured Primary Honey Bee Cells

“…After collection, larvae were surface-sterilized for 3 min in 0.6% hypochlorite (dilute bleach), followed by 3 min in 70% ethanol, and then briefly washed in sterile water for injection (Gibco) in a biological safety cabinet (Class II type A/B3, Nuaire). Larvae were placed into 200 μL of WH2 media (pH 6.4, 150 mL Schneider’s insect medium, SIGMA cat# S0146; 200 mL 0.06M L-Histidine, SIGMA cat# H5659; 50 mL heat-inactivated fetal bovine serum, Life Technologies cat# 16000044; 15 mL CMRL medium, Gibco cat# 11530-037; 5 mL Hank’s balanced salts, SIGMA cat# H9394; 2 mL insect media supplement, SIGMA cat# I7267), supplemented with 1× penicillin/streptomycin (ThermoFisher, cat# 15070063), 10 at a time [ 33 , 175 ]. Sterile 18-guage needles were used to wound larvae on the lateral cuticle of the abdomen.…”

“…PCR was performed according to standard methods [ 33 , 63 , 64 , 97 ]. In brief, 2 μL cDNA template in 12.5 μL aqueous buffer containing 10 pmol of each forward and reverse primer ( Table S1 ) was amplified with 0.5 μL (5 U/μL) ChoiceTaq polymerase (Thomas Scientific) according to the manufacturer’s instructions using the following cycling conditions: 95 °C for 5 min; 95 °C for 30 s, 55 °C for 30 s, 72 °C for 45 s, 35 cycles; final elongation 72 °C for 5 min, hold at 4 °C.…”

“…The largest group of honey-bee-infecting pathogens are small RNA viruses (reviewed in [ 23 , 32 ]). The list of honey bee-infecting and honey-bee-associated viruses is ever growing, in part due to virus discovery efforts aided by the increased use of high throughput sequencing of either total RNA or virally enriched RNA sample sequencing [ 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 ] (reviewed in [ 23 , 24 ]). The most ubiquitous and well-studied honey-bee-associated viruses include acute bee paralysis virus [ 42 ], black queen cell virus [ 43 ], chronic bee paralysis virus [ 44 , 45 ], deformed wing virus [ 46 , 47 ], Israeli acute paralysis virus [ 48 ], Kashmir bee virus [ 49 ], sacbrood virus [ 50 ], and the Lake Sinai virus group [ 40 , 51 ].…”

Virus Prevalence and Genetic Diversity Across a Wild Bumblebee Community

“…Differences in viral prevalence between hosts or locations at a given time can be explained by a variety of environmental and biotic factors. For pollinators, these can include the presence of host species like managed honeybees and their viral vector Varroa destructor (Fürst et al, 2014;Manley et al, 2019Manley et al, , 2020 or other dominant bee species (Graystock et al, 2020), all of which modify exposure to viruses, as well as landscape effects such as the intensity of agricultural land-use and habitat loss (Figueroa et al, 2020;Daughenbaugh et al, 2021) or the presence of particular floral resources (Adler et al, 2020). Here, we focus on underexplored abiotic factors, which can be important if viruses are spread by environmental contamination or aerosolisation, then abiotic factors can be important.…”