Evidence for and against deformed wing virus spillover from honey bees to bumble bees: a reverse genetic analysis

Landscape structure affects temporal dynamics in the bumble bee virome: Landscape heterogeneity supports colony resilience

Virus spillovers from managed honey bees, Apis mellifera, are thought to contribute to the decline of wild pollinators, including bumble bees. However, data on the impact of such viruses on wild pollinators remain scarce, and the influence of landscape structure on virus dynamics is poorly understood. In this study, we deployed bumble bee colonies in an agricultural landscape and studied changes in the bumble bee virome during field placement under varying habitat composition and configuration using a multiscale analytical framework. We estimated prevalence of viruses and viral loads (i.e. number of viral genomic equivalent copies) in bumble bees before and after placing them in the field using next generation sequencing and quantitative PCR. The results show that viral loads and number of different viruses present increased during placement in the field and that the virus composition of the colonies shifted from an initial dominance of honey bee associated viruses to a higher number (in both viral loads and number of viruses present) of bumble bee associated viruses. Especially DWV-B, typical for honey bees, drastically decreased after the time in the field. Viral loads prior to placing colonies in the field showed no effect on colony development, suggesting low impacts of these viruses in field settings. Notably, we further demonstrate that increased habitat diversity results in a lower number of different viruses present in Bombus colonies, while colonies in areas with well-connected farmland patches decreased in their total viral load after field placement. Our results emphasize the importance of landscape heterogeneity and connectivity for wild pollinator health and that these influences predominate at fine spatial scales.

Caught in the act: the invasion of a viral vector changes viral prevalence and titre in native honeybees and bumblebees

Novel transmission routes change pathogen landscapes and may facilitate disease emergence. The varroa mite is a virus vector that switched to western honeybees at the beginning of the last century, leading to hive mortality, particularly in combination with RNA viruses. A recent invasion of varroa on the French island of Ushant introduced vector-mediated transmission to one of the last varroa-naive native honeybee populations and caused rapid changes in the honeybee viral community. These changes were characterized by a drastic increase in deformed wing virus type B prevalence and titre in honeybees, as well as knock-on effects in bumblebees, particularly in the year following the invasion. Slow bee paralysis virus also appeared in honeybees and bumblebees, with a 1 year delay, while black queen cell virus declined in honeybees. This study highlights the rapid and far-reaching effects of vector-borne transmission that can extend beyond the directly affected host species, and that the direction of the effect depends on the pathogen's virulence.

Host Barriers Limit Viral Spread in a Spillover Host: A Study of Deformed Wing Virus in the Bumblebee Bombus terrestris

The transmission of pathogens from reservoir to recipient host species, termed pathogen spillover, can profoundly impact plant, animal, and public health. However, why some pathogens lead to disease emergence in a novel species while others fail to establish or do not elicit disease is often poorly understood. There is strong evidence that deformed wing virus (DWV), an (+)ssRNA virus, spills over from its reservoir host, the honeybee Apis mellifera, into the bumblebee Bombus terrestris. However, the low impact of DWV on B. terrestris in laboratory experiments suggests host barriers to virus spread in this recipient host. To investigate potential host barriers, we followed the spread of DWV genotype B (DWV-B) through a host's body using RT-PCR after experimental transmission to bumblebees in comparison to honeybees. Inoculation was per os, mimicking food-borne transmission, or by injection into the bee's haemocoel, mimicking vector-based transmission. In honeybees, DWV-B was present in both honeybee faeces and haemolymph within 3 days of inoculation per os or by injection. In contrast, DWV-B was not detected in B. terrestris haemolymph after inoculation per os, suggesting a gut barrier that hinders DWV-B's spread through the body of a B. terrestris. DWV-B was, however, detected in B. terrestris faeces after injection and feeding, albeit at a lower abundance than that observed for A. mellifera, suggesting that B. terrestris sheds less DWV-B than A. mellifera in faeces when infected. Barriers to viral spread in B. terrestris following oral infection may limit DWV's impact on this spillover host and reduce its contribution to the community epidemiology of DWV.

A semi-automated and high-throughput approach for the detection of honey bee viruses in bee samples

Deformed wing virus (DWV) was first detected in dead honey bees in 1982 but has been in honey bees for at least 300 years. Due to its high prevalence and virulence, they have been linked with the ongoing decline in honey bee populations worldwide. A rapid, simple, semi-automated, high-throughput, and cost-effective method of screening colonies for viruses would benefit bee research and the beekeeping industry. Here we describe a semi-automated approach that combines an RNA-grade liquid homogenizer followed by magnetic bead capture for total virus nucleic acid extraction. We compare it to the more commonly applied nucleic acid column-based purification method and use qPCR plus Oxford Nanopore Technologies sequencing to evaluate the accuracy of analytical results for both methods. Our results showed high reproducibility and accuracy for both approaches. The semi-automated method described here allows for faster screening of viral loads in units of 96 samples at a time. We developed this method to monitor viral loads in honey bee colonies, but it could be easily applied for any PCR or genomic-based screening assays.

Distribution of infectious and parasitic agents among three sentinel bee species across European agricultural landscapes

Infectious and parasitic agents (IPAs) and their associated diseases are major environmental stressors that jeopardize bee health, both alone and in interaction with other stressors. Their impact on pollinator communities can be assessed by studying multiple sentinel bee species. Here, we analysed the field exposure of three sentinel managed bee species (Apis mellifera, Bombus terrestris and Osmia bicornis) to 11 IPAs (six RNA viruses, two bacteria, three microsporidia). The sentinel bees were deployed at 128 sites in eight European countries adjacent to either oilseed rape fields or apple orchards during crop bloom. Adult bees of each species were sampled before their placement and after crop bloom. The IPAs were detected and quantified using a harmonised, high-throughput and semi-automatized qPCR workflow. We describe differences among bee species in IPA profiles (richness, diversity, detection frequencies, loads and their change upon field exposure, and exposure risk), with no clear patterns related to the country or focal crop. Our results suggest that the most frequent IPAs in adult bees are more appropriate for assessing the bees' IPA exposure risk. We also report positive correlations of IPA loads supporting the potential IPA transmission among sentinels, suggesting careful consideration should be taken when introducing managed pollinators in ecologically sensitive environments.

Nursing Honeybee Behavior and Sensorial-Related Genes Are Altered by Deformed Wing Virus Variant A

Insect behavior is coordinated mainly by smell through the diverse odor-binding proteins (OBP) that allow them to identify and recognize their environment. Sensory information collected through smell is then analyzed and interpreted in the brain, allowing for correct insect functioning. The behavior of honeybees (Apis mellifera L.) can be affected by different pathogens, such as deformed wing virus (DWV). In particular, the DWV variant A (DWV-A) is capable of altering olfactory sensitivity and reducing the gene expression of different OBPs, including those associated with nursing behavior. The DWV is also capable of replicating itself in the sensory lobes of the brain, further compromising the processing of sensory information. This study evaluated the behavioral response of nurse honeybees exposed to a pheromone compound and the alterations in the gene expression of the pre- and post-synaptic neuronal genes neuroxins-1 and neurogilin-1 in the bee heads and OBP proteins in the antennae of nurse bees inoculated with DWV-A. The behavioral response of nurse bees exposed to the larval pheromone compound benzyl alcohol was analyzed using a Y-tube olfactometer. The viral load, the gene expression of OBP5 and OBP11 in antennae, and neuroxins-1 and neurogilin-1 in the bee heads were analyzed via qPCR. High viral loads significantly reduced the ability of 10- and 15-day-old nurse honeybees to choose the correct pheromone compound. Also, the gene expression of OBP5, OBP11, neuroxin-1, and neurogilin-1 in nurse honeybees decreased when they were highly infected with DWV-A. These results suggest that a DWV-A infection can disturb information processing and cause nursing honeybees to reduce their activity inside the hive, altering internal cohesion.

Widespread distribution of honey bee-associated pathogens in native bees and wasps: Trends in pathogen prevalence and co-occurrence

Pollinators have experienced significant declines in the past decade, in part due to emerging infectious diseases. Historically, studies have primarily focused on pathogens in the Western honey bee, Apis mellifera. However, recent work has demonstrated that these pathogens are shared by other pollinators and can negatively affect their health. Here, we surveyed honey bees and 15 native bee and wasp species for 13 pathogens traditionally associated with honey bees. The native bee and wasp species included 11 species not previously screened for pathogens. We found at least one honey bee-associated pathogen in 53% of native bee and wasp samples. The most widely distributed and commonly detected pathogens were the microsporidian Nosema ceranae, the bacterium Melissococcus plutonius, and the viruses deformed wing virus and black queen cell virus. The prevalence of viruses was generally higher in honey bees than in native bees and wasps. However, the prevalence of M. plutonius and the brood fungus Ascosphaera apis was significantly higher in some native bee species than in honey bees. The data also reveal novel trends in the association between co-occurring pathogens in honey bees and native bees and wasps at the pathogen community level. These results can inform the assessment of risks that native pollinator species face from pathogen stress, and indicate that many non-viral pathogens, notably M. plutonius and N. ceranae, are far more widely distributed and commonly found in native bees and wasps than previously thought.

Doomed drones? Using passage experiments and mathematical modelling to determine Deformed wing virus population dynamics in male honeybees

Varroa destructor is an ectoparasitic mite of honeybees which vectors a range of pathogenic viruses, the most notable being Deformed wing virus (DWV). Mites parasitise bees during pupal development and male honeybees, drones, have a longer development cycle than female workers (24 versus 21 days), allow for more progeny mites to develop per foundress (1.6-2.5 compared to 0.7-1.45). How this longer exposure time influences evolution of the transmitted virus population is unknown. Using uniquely tagged viruses recovered from cDNA we investigated the replication, competition and morbidity of DWV genotypes in drones. Assays examining virus replication and morbidity revealed drones are highly susceptible to both predominant genotypes of DWV. In virus passage studies using an equimolar inocula of major DNA genotypes and their recombinants, the recombinant form dominated but did not reach 100% of the virus population within 10 passages. Using an in-silico model of the virus-mite-bee system we examined bottlenecks during virus acquisition by the mite and subsequent injection of viruses into the host, which may play a significant role in shaping virus diversity. This study furthers our understanding of the variables influencing DWV diversity changes and provides insight into areas of future research in the mite-virus-bee system.

Detection of honey bee viruses in larvae of Vespa orientalis

The Oriental hornet (Vespa orientalis) is one of the major predators of honey bees. It has been demonstrated that adults of V. orientalis can harbor honey bee viruses, however the transmission route of infection is still not clear. The aim of this study was to study the possible presence of honey bee viruses in V. orientalis larvae and honey bees collected from the same apiary. Therefore, 29 samples of V. orientalis larvae and 2 pools of honey bee (Apis mellifera). samples were analyzed by multiplex PCR to detect the presence of six honeybee viruses: Acute Bee Paralysis Virus (ABPV), Black Queen Cell Virus (BQCV), Chronic Bee Paralysis Virus (CBPV), Deformed Wing Virus (DWV), Kashmir Bee Virus (KBV) and Sac Brood Virus (SBV). Biomolecular analysis of V. orientalis larvae revealed that DWV was present in 24/29 samples, SBV in 10/29, BQCV in 7/29 samples and ABPV in 5/29 samples, while no sample was found positive for CBPV or KBV. From biomolecular analysis of honey bee samples DWV was the most detected virus, followed by SBV, BQCV, ABPV. No honey bee sample was found positive for CBPV or KBV. Considering the overlapping of positivities between V.orientalis larvae and honey bee samples, and that V.orientalis larvae are fed insect proteins, preferably honey bees, we can suggest the acquisition of viral particles through the ingestion of infected bees. However, future studies are needed to confirm this hypothesis and rule out any other source of infection.

CRISPR-induced DNA reorganization for multiplexed nucleic acid detection

Nucleic acid sensing powered by the sequence recognition of CRIPSR technologies has enabled major advancement toward rapid, accurate and deployable diagnostics. While exciting, there are still many challenges facing their practical implementation, such as the widespread need for a PAM sequence in the targeted nucleic acid, labile RNA inputs, and limited multiplexing. Here we report FACT (Functionalized Amplification CRISPR Tracing), a CRISPR-based nucleic acid barcoding technology compatible with Cas12a and Cas13a, enabling diagnostic outputs based on cis- and trans-cleavage from any sequence. Furthermore, we link the activation of CRISPR-Cas12a to the expression of proteins through a Reprogrammable PAIRing system (RePAIR). We then combine FACT and RePAIR to create FACTOR (FACT on RePAIR), a CRISPR-based diagnostic, that we use to detect infectious disease in an agricultural use case: honey bee viral infection. With high specificity and accuracy, we demonstrate the potential of FACTOR to be applied to the sensing of any nucleic acid of interest.

Molecular Detection and Phylogenetic Analysis of Deformed Wing Virus and Sacbrood Virus Isolated from Pollen

Among many pathogens and pests, honey bee viruses are known as one of the most common cause of diseases in honey bee colonies. In this study, we demonstrate that pollen grains and bee bread are potential sources of viral DNA. We extracted DNA from 3 types of pollen samples: directly provided by beekeepers (n = 12), purchased from trade markets (n = 5), and obtained from honeycombs (bee bread, n = 10). The extracted DNA was used for molecular detection (RT-PCR analysis) of six of the most widely distributed honey bee viruses: deformed wing virus, sacbrood virus, acute bee paralysis virus, black queen cell virus, Kashmir bee virus, Israeli acute paralysis virus, and chronic bee paralysis virus. We successfully managed to establish only the deformed wing virus (DWV) and the sacbrood virus (SBV), with different distribution frequencies depending on the territory of the country. The phylogenetic analyses of Bulgarian isolates were performed with the most similar sequences available in molecular databases from other countries. Phylogenies of Bulgarian viral strains demonstrated genetically heterogeneous populations of DWV and relatively homogenous populations of SBV. In conclusion, the results obtained from the current study have shown that pollen is a valuable source for molecular detection of honey bee pathogens. This allows epidemiological monitoring of honey bee diseases at a regional and a national level.

Trans-generational immune priming against American Foulbrood does not affect the performance of honeybee colonies

Honeybees are major pollinators for our food crops, but at the same time they face many stressors all over the world. One of the major threats to honeybee health are bacterial diseases, the most severe of which is the American Foulbrood (AFB). Recently a trans-generational vaccination approach against AFB has been proposed, showing strong potential in protecting the colonies from AFB outbreaks. Yet, what remains unstudied is whether the priming of the colony has any undesired side-effects. It is widely accepted that immune function is often a trade-off against other life-history traits, hence immune priming could have an effect on the colony performance. In this experiment we set up 48 hives, half of them with primed queens and half of them as controls. The hives were placed in six apiaries, located as pair of apiaries in three regions. Through a 2-year study we monitored the hives and measured their health and performance. We measured hive weight and frame contents such as brood amount, worker numbers, and honey yield. We studied the prevalence of the most common honeybee pathogens in the hives and expression of relevant immune genes in the offspring at larval stage. No effect of trans-generational immune priming on any of the hive parameters was found. Instead, we did find other factors contributing on various hive performance parameters. Interestingly not only time but also the region, although only 10 km apart from each other, had an effect on the performance and health of the colonies, suggesting that the local environment plays an important role in hive performance. Our results suggest that exploiting the trans-generational priming could serve as a safe tool in fighting the AFB in apiaries.

Metagenomic analysis of viromes in honey bee colonies (Apis mellifera; Hymenoptera: Apidae) after mass disappearance in Korea

After the nationwide, massive winter losses of honey bees in Korea during the winter of 2021, samplings were conducted from live honey bees in colonies and dead honey bees nearby colonies in the same bee-farms in six regions in Korea. Each sample was subjected to virome analysis using high-throughput sequencing technology. The number of viral reads was the lowest in the live honey bee group sample with 370,503 reads and the highest in the dead honey bee group sample with 42,659,622 reads. Viral contigs were matched with the viral genomes of the black queen cell virus, deformed wing virus, Israeli acute paralysis virus, and sacbrood virus, all of which have been previously reported in Korea. However, Apis rhabdovirus 5, bee macula-like virus, Varroa orthomyxovirus-1, Hubei partiti-like virus 34, Lake Sinai virus 2, 3, and 4, and the Ditton virus, were also discovered in this study, which are the first records in Korea. Plant viral sequences resembling those of Arabidopsis latent virus 1, and a novel viral sequence was also discovered. In the present study 55 complete viral genome sequences were identified. This study is the first virome analysis of domestic honey bees and provides the latest information on the diversity of honey bee viruses in Korea.

An invasive ant increases deformed wing virus loads in honey bees

The majority of invasive species are best known for their effects as predators. However, many introduced predators may also be substantial reservoirs for pathogens. Honey bee-associated viruses are found in various arthropod species including invasive ants. We examined how the globally invasive Argentine ant (Linepithema humile), which can reach high densities and infest beehives, is associated with pathogen dynamics in honey bees. Viral loads of deformed wing virus (DWV), which has been linked to millions of beehive deaths around the globe, and black queen cell virus significantly increased in bees when invasive ants were present. Microsporidian and trypanosomatid infections, which are more bee-specific, were not affected by ant invasion. The bee virome in autumn revealed that DWV was the predominant virus with the highest infection levels and that no ant-associated viruses were infecting bees. Viral spillback from ants could increase infections in bees. In addition, ant attacks could pose a significant stressor to bee colonies that may affect virus susceptibility. These viral dynamics are a hidden effect of ant pests, which could have a significant impact on disease emergence in this economically important pollinator. Our study highlights a perhaps overlooked effect of species invasions: changes in pathogen dynamics.

Dietary Supplement of Grape Wastes Enhances Honeybee Immune System and Reduces Deformed Wing Virus (DWV) Load

Ingredients rich in phenolic compounds and antioxidants of winemaking wastes, which play an important role in the prevention of various diseases and the control of viruses, are being explored. Currently, there is a concern about honeybee population loss, with deformed wing virus (DWV) being the most common virus infecting apiaries and one of the main causes of honeybee decline. Hence, the effect of grape pomace powder (GPP) as a dietary supplement to enhance the immune system of honeybees affected by DWV was evaluated. The characteristics of the ingredient GPP, obtained by spray-drying, revealed a high anthocyanin content (1102.45 mg 100 g^-1), and it was applied at doses of 0.5, 1, 2.5 and 5% as a dietary supplement for bees infected by DWV. The results showed that the GPP treatments strengthened the immune response of honeybees against DWV. Moreover, the expression of the Relish gene was significantly higher in bees fed with GPP compared to the infected control. This study, which is framed in the search of food waste valorization for environmental sustainability, proves the feasibility of using grape wastes as dietary supplements for pollinators, and provides knowledge of the influence of polyphenols on the expression profiles of immune-related genes in honeybees.

Procedures and potential pitfalls for constructing a bee-infecting RNA virus clone

Viruses are factors that can fluctuate insect populations, including honey bees. Most honey bee infecting viruses are single positive-stranded RNA viruses that may not specifically infect honey bees and can be hazardous to other pollinator insects. In addition, these viruses could synergize with other stressors to worsen the honey bee population decline. To identify the underlying detailed mechanisms, reversed genetic studies with infectious cDNA clones of the viruses are necessary. Moreover, an infectious cDNA clone can be applied to studies as an ideal virus isolate that consists of a single virus species with a uniform genotype. However, only a few infectious cDNA clones have been reported in honey bee studies since the first infectious cDNA clone was published four decades ago. This article discusses steps, rationales, and potential issues in bee-infecting RNA virus cloning. In addition, failed experiences of cloning a Deformed wing virus isolate that was phylogenetically identical to Kakugo virus were addressed. We hope the information provided in this article can facilitate further developments of reverse-genetic studies of bee-infecting viruses to clarify the roles of virus diseases in the current pollinator declines.

Quantitative and Qualitative Changes in the Deformed Wing Virus Population in Honey Bees Associated with the Introduction or Removal of Varroa destructor

Varroa destructor is an ectoparasitic mite associated with significant losses of honeybee colonies globally. The mite vectors a range of pathogenic viruses, the most important of which is the Deformed wing virus (DWV). In the absence of Varroa, DWV exists as a low-level, highly diverse virus population. However, when transmitted by Varroa, certain variants become highly elevated, and may become near-clonal and cause symptomatic infections. Mite transmission between colonies can occur when parasitised workers drift from or rob adjacent hives. These activities can result in elevated mite levels, but the resulting change in the DWV population, the primary determinant of winter colony losses, has not been determined. In reciprocal studies, we investigated the influence of the removal of mites, or their acquisition, on the DWV population. When mites were removed from heavily infested colonies, there was a striking and rapid reduction in virus load. Conversely, siting Varroa-naïve colonies in a mite-infested apiary resulted in the acquisition of mites and concomitant changes in the virus population. We observed both near-clonal and highly divergent virus populations regardless of titre, suggesting changes were stochastic and colony-specific. Our findings have implications for the outcome of strategies in areas with total or patchy implementation of Varroa control plans.

Occurrence of Honey Bee (Apis mellifera L.) Pathogens in Wild Pollinators in Northern Italy

Diseases contribute to the decline of pollinator populations, which may be aggravated by the interspecific transmission of honey bee pests and pathogens. Flowers increase the risk of transmission, as they expose the pollinators to infections during the foraging activity. In this study, both the prevalence and abundance of 21 honey bee pathogens (11 viruses, 4 bacteria, 3 fungi, and 3 trypanosomatids) were assessed in the flower-visiting entomofauna sampled from March to September 2021 in seven sites in the two North-Italian regions, Emilia-Romagna and Piedmont. A total of 1,028 specimens were collected, identified, and analysed. Of the twenty-one pathogens that were searched for, only thirteen were detected. Altogether, the prevalence of the positive individuals reached 63.9%, with Nosema ceranae, deformed wing virus (DWV), and chronic bee paralysis virus (CBPV) as the most prevalent pathogens. In general, the pathogen abundance averaged 5.15 * 10⁶ copies, with CBPV, N. ceranae, and black queen cell virus (BQCV) as the most abundant pathogens, with 8.63, 1.58, and 0.48 * 10⁷ copies, respectively. All the detected viruses were found to be replicative. The sequence analysis indicated that the same genetic variant was circulating in a specific site or region, suggesting that interspecific transmission events among honey bees and wild pollinators are possible. Frequently, N. ceranae and DWV were found to co-infect the same individual. The circulation of honey bee pathogens in wild pollinators was never investigated before in Italy. Our study resulted in the unprecedented detection of 72 wild pollinator species as potential hosts of honey bee pathogens. Those results encourage the implementation of monitoring actions aiming to improve our understanding of the environmental implications of such interspecific transmission events, which is pivotal to embracing a One Health approach to pollinators’ welfare.

Detection of Honeybee Viruses in Vespa orientalis

The Oriental hornet (Vespa orientalis) is spreading across the Italian territory threatening the health and wellbeing of honeybees by feeding on adult individuals and larvae and by plundering hive resources. Considering the capacity of other hornets in harboring honeybee viruses, the aim of this study was to identify the possible role of the Oriental hornet as a vector for honeybee viruses. Adult hornets were subjected to macroscopical examination to identify the presence of lesions, and to biomolecular investigation to detect the presence of six honeybee viruses: Acute Bee Paralysis Virus (ABPV), Black Queen Cell Virus (BQCV), Chronic Bee Paralysis Virus (CBPV), Deformed Wing Virus (DWV), Kashmir Bee Virus (KBV), Sac Brood Virus (SBV). No macroscopical alterations were found while biomolecular results showed that DWV was the most detected virus (25/30), followed by ABPV (19/30), BQCV (13/30), KBV (1/30) and SBV (1/30). No sample was found positive for CBPV. In 20/30 samples several co-infections were identified. The most frequent (17/30) was the association between DWV and ABPV, often associated to BQCV (9/17). One sample (1/30) showed the presence of four different viruses namely DWV, ABPV, BQCV and KBV. The detected viruses are the most widespread in apiaries across the Italian territory suggesting the possible passage from honeybees to V. orientalis, by predation of infected adult honeybees and larvae, and cannibalization of their carcasses. However, to date, it is still not clear if these viruses are replicative but we can suggest a role as mechanical vector of V. orientalis in spreading these viruses.

An Insight Into the microRNA Profile of the Ectoparasitic Mite Varroa destructor (Acari: Varroidae), the Primary Vector of Honey Bee Deformed Wing Virus

The remarkably adaptive mite Varroa destructor is the most important honey bee ectoparasite. Varroa mites are competent vectors of deformed wing virus (DWV), and the Varroa-virus complex is a major determinant of annual honey bee colony mortality and collapse. MicroRNAs (miRNAs) are 22-24 nucleotide non-coding RNAs produced by all plants and animals and some viruses that influence biological processes through post-transcriptional regulation of gene expression. Knowledge of miRNAs and their function in mite biology remains limited. Here we constructed small RNA libraries from male and female V. destructor using Illumina's small RNA-Seq platform. A total of 101,913,208 and 91,904,732 small RNA reads (>18 nucleotides) from male and female mites were analyzed using the miRDeep2 algorithm. A conservative approach predicted 306 miRNAs, 18 of which were upregulated and 13 downregulated in female V. destructor compared with males. Quantitative real-time PCR validated the expression of selected differentially-expressed female Varroa miRNAs. This dataset provides a list of potential miRNA targets involved in regulating vital Varroa biological processes and paves the way for developing strategies to target Varroa and their viruses.

Experimental cross species transmission of a major viral pathogen in bees is predominantly from honeybees to bumblebees

Cross-species transmission of a pathogen from a reservoir to a recipient host species, spillover, can have major impacts on biodiversity, domestic species and human health. Deformed wing virus (DWV) is a panzootic RNA virus in honeybees that is causal in their elevated colony losses, and several correlative field studies have suggested spillover of DWV from managed honeybees to wild bee species such as bumblebees. Yet unequivocal demonstration of DWV spillover is lacking, while spillback, the transmission of DWV from a recipient back to the reservoir host, is rarely considered. Here, we show in fully crossed laboratory experiments that the transmission of DWV (genotype A) from honeybees to bumblebees occurs readily, yet we neither detected viral transmission from bumblebees to honeybees nor onward transmission from experimentally infected to uninoculated bumblebees. Our results support the potential for viral spillover from honeybees to other bee species in the field when robbing resources from heterospecific nests or when visiting the same flowers. They also underscore the importance of studies on the virulence of DWV in wild bee species so as to evaluate viral impact on individual and population fitness as well as viral adaption to new host species.

Honey bees and climate explain viral prevalence in wild bee communities on a continental scale

Viruses are omnipresent, yet the knowledge on drivers of viral prevalence in wild host populations is often limited. Biotic factors, such as sympatric managed host species, as well as abiotic factors, such as climatic variables, are likely to impact viral prevalence. Managed and wild bees, which harbor several multi-host viruses with a mostly fecal-oral between-species transmission route, provide an excellent system with which to test for the impact of biotic and abiotic factors on viral prevalence in wild host populations. Here we show on a continental scale that the prevalence of three broad host viruses: the AKI-complex (Acute bee paralysis virus, Kashmir bee virus and Israeli acute paralysis virus), Deformed wing virus, and Slow bee paralysis virus in wild bee populations (bumble bees and solitary bees) is positively related to viral prevalence of sympatric honey bees as well as being impacted by climatic variables. The former highlights the need for good beekeeping practices, including Varroa destructor management to reduce honey bee viral infection and hive placement. Furthermore, we found that viral prevalence in wild bees is at its lowest at the extreme ends of both temperature and precipitation ranges. Under predicted climate change, the frequency of extremes in precipitation and temperature will continue to increase and may hence impact viral prevalence in wild bee communities.

Cold case: The disappearance of Egypt bee virus, a fourth distinct master strain of deformed wing virus linked to honeybee mortality in 1970's Egypt

In 1977, a sample of diseased adult honeybees (Apis mellifera) from Egypt was found to contain large amounts of a previously unknown virus, Egypt bee virus, which was subsequently shown to be serologically related to deformed wing virus (DWV). By sequencing the original isolate, we demonstrate that Egypt bee virus is in fact a fourth unique, major variant of DWV (DWV-D): more closely related to DWV-C than to either DWV-A or DWV-B. DWV-A and DWV-B are the most common DWV variants worldwide due to their close relationship and transmission by Varroa destructor. However, we could not find any trace of DWV-D in several hundred RNA sequencing libraries from a worldwide selection of honeybee, varroa and bumblebee samples. This means that DWV-D has either become extinct, been replaced by other DWV variants better adapted to varroa-mediated transmission, or persists only in a narrow geographic or host range, isolated from common bee and beekeeping trade routes.

Haplotype Analysis of Varroa destructor and Deformed Wing Virus Using Long Reads

As a phoretic parasite and virus vector, the mite Varroa destructor and the associated Deformed wing virus (DWV) form a lethal combination to the honey bee, Apis mellifera. Routine acaricide treatment has been reported to reduce the diversity of mites and select for tolerance against these treatments. Further, different DWV strains face selective pressures when transmitted via mites. In this study, the haplotypes of Varroa mites and associated DWV variants were quantified using long reads. A single haplotype dominated the mite mitochondrial gene cytochrome oxidase subunit I, reflecting an ancient bottleneck. However, highly polymorphic genes were present across the mite genome, suggesting the diversity of mites could be actively maintained at a regional level. DWV detected in both mites and honey bees show a dominant variant with only a few low-frequency alternate haplotypes. The relative abundances of DWV haplotypes isolated from honey bees and mites were highly consistent, suggesting that some variants are favored by ongoing selection.

First come, first served: superinfection exclusion in Deformed wing virus is dependent upon sequence identity and not the order of virus acquisition

Deformed wing virus (DWV) is the most important globally distributed pathogen of honey bees and, when vectored by the ectoparasite Varroa destructor, is associated with high levels of colony losses. Divergent DWV types may differ in their pathogenicity and are reported to exhibit superinfection exclusion upon sequential infections, an inevitability in a Varroa-infested colony. We used a reverse genetic approach to investigate competition and interactions between genetically distinct or related virus strains, analysing viral load over time, tissue distribution with reporter gene-expressing viruses and recombination between virus variants. Transient competition occurred irrespective of the order of virus acquisition, indicating no directionality or dominance. Over longer periods, the ability to compete with a pre-existing infection correlated with the genetic divergence of the inoculae. Genetic recombination was observed throughout the DWV genome with recombinants accounting for ~2% of the population as determined by deep sequencing. We propose that superinfection exclusion, if it occurs at all, is a consequence of a cross-reactive RNAi response to the viruses involved, explaining the lack of dominance of one virus type over another. A better understanding of the consequences of dual- and superinfection will inform development of cross-protective honey bee vaccines and landscape-scale DWV transmission and evolution.

Variant A of the Deformed Wings Virus Alters the Olfactory Sensitivity and the Expression of Odorant Binding Proteins on Antennas of Apis mellifera

Simple Summary

Honey bees, Apis melllifera, are the most commonly managed bee in the world for pollination services. However, worldwide continuous colony losses have been reported for almost a decade. One factor of these losses is associated to pathogens being the virus one of the most important problems in honey bee health. One of the known viruses that affect the honey bee population is deformed wing virus (DWV). DWV causes physical malformation and behavioral disturbances, but also, this virus can be found in the antenna affecting the anatomical integrity of infected areas, which could compromise normal antennal functioning associated to aroma perception. Thus, we evaluate olfactory sensitivity and the expression of antenna-specific odorant-binding proteins (OBP) genes in honey bees inoculated with variant A of the DWV. We performed olfactory sensitivity analysis using the essential oils Eucalyptus globulus and Mentha piperita, but also, and molecular analysis of gene expression of nine OBPs. We found that the high level of replication of DWV-A in the antennae decreased the olfactory sensitivity and led to a down-regulation of some OBPs in middle- and forager-age worker bees. Thus, DWV-A infection in adults of honey bees could compromise volatile compound recognition inside the hive and outside the hive.

Abstract

Insects have a highly sensitive sense of smell, allowing them to perform complex behaviors, such as foraging and peer recognition. Their sense of smell is based on the recognition of ligands and is mainly coordinated by odorant-binding proteins (OBPs). In Apis mellifera, behavior can be affected by different pathogens, including deformed wing virus (DWV) and its variants. In particular, it has been shown that variant A of DWV (DWV-A) is capable of altering the ultra-cellular structure associated with olfactory activity. In this study was evaluated olfactory sensitivity and the expression of OBP genes in honey bees inoculated with DWV-A. Electroantennographic analyses (EAG) were carried out to determine the olfactory sensitivity to the essential oils Eucalyptus globulus and Mentha piperita. The expression of nine antenna-specific OBP genes and DWV-A load in inoculated bees was also quantified by qPCR. We observed an inverse relationship between viral load and olfactory sensitivity and the expression of some OBP proteins. Thus, high viral loads reduced olfactory sensitivity to essential oils and the gene expression of the OBP2, OBP5, OBP11, and OBP12 proteins on the antennas of middle- and forager-age bees. These results suggest that DWV-A could have negative effects on the processes of aroma perception by worker bees, affecting their performance in tasks carried out in and outside the colony.

Pathogens Spillover from Honey Bees to Other Arthropods

Honey bees, and pollinators in general, play a major role in the health of ecosystems. There is a consensus about the steady decrease in pollinator populations, which raises global ecological concern. Several drivers are implicated in this threat. Among them, honey bee pathogens are transmitted to other arthropods populations, including wild and managed pollinators. The western honey bee, Apis mellifera, is quasi-globally spread. This successful species acted as and, in some cases, became a maintenance host for pathogens. This systematic review collects and summarizes spillover cases having in common Apis mellifera as the mainteinance host and some of its pathogens. The reports are grouped by final host species and condition, year, and geographic area of detection and the co-occurrence in the same host. A total of eighty-one articles in the time frame 1960-2021 were included. The reported spillover cases cover a wide range of hymenopteran host species, generally living in close contact with or sharing the same environmental resources as the honey bees. They also involve non-hymenopteran arthropods, like spiders and roaches, which are either likely or unlikely to live in close proximity to honey bees. Specific studies should consider host-dependent pathogen modifications and effects on involved host species. Both the plasticity of bee pathogens and the ecological consequences of spillover suggest a holistic approach to bee health and the implementation of a One Health approach.

Replicative Deformed Wing Virus Found in the Head of Adults from Symptomatic Commercial Bumblebee (Bombus terrestris) Colonies

The deformed wing virus (DWV) is one of the most common honey bee pathogens. The virus may also be detected in other insect species, including Bombus terrestris adults from wild and managed colonies. In this study, individuals of all stages, castes, and sexes were sampled from three commercial colonies exhibiting the presence of deformed workers and analysed for the presence of DWV. Adults (deformed individuals, gynes, workers, males) had their head exscinded from the rest of the body and the two parts were analysed separately by RT-PCR. Juvenile stages (pupae, larvae, and eggs) were analysed undissected. All individuals tested positive for replicative DWV, but deformed adults showed a higher number of copies compared to asymptomatic individuals. Moreover, they showed viral infection in their heads. Sequence analysis indicated that the obtained DWV amplicons belonged to a strain isolated in the United Kingdom. Further studies are needed to characterize the specific DWV target organs in the bumblebees. The result of this study indicates the evidence of DWV infection in B. terrestris specimens that could cause wing deformities, suggesting a relationship between the deformities and the virus localization in the head. Further studies are needed to define if a specific organ could be a target in symptomatic bumblebees.

Evaluating competition for forage plants between honey bees and wild bees in Denmark

A recurrent concern in nature conservation is the potential competition for forage plants between wild bees and managed honey bees. Specifically, that the highly sophisticated system of recruitment and large perennial colonies of honey bees quickly exhaust forage resources leading to the local extirpation of wild bees. However, different species of bees show different preferences for forage plants. We here summarize known forage plants for honey bees and wild bee species at national scale in Denmark. Our focus is on floral resources shared by honey bees and wild bees, with an emphasis on both threatened wild bee species and foraging specialist species. Across all 292 known bee species from Denmark, a total of 410 plant genera were recorded as forage plants. These included 294 plant genera visited by honey bees and 292 plant genera visited by different species of wild bees. Honey bees and wild bees share 176 plant genera in Denmark. Comparing the pairwise niche overlap for individual bee species, no significant relationship was found between their overlap and forage specialization or conservation status. Network analysis of the bee-plant interactions placed honey bees aside from most other bee species, specifically the module containing the honey bee had fewer links to any other modules, while the remaining modules were more highly inter-connected. Despite the lack of predictive relationship from the pairwise niche overlap, data for individual species could be summarized. Consequently, we have identified a set of operational parameters that, based on a high foraging overlap (>70%) and unfavorable conservation status (Vulnerable+Endangered+Critically Endangered), can guide both conservation actions and land management decisions in proximity to known or suspected populations of these species.

Detection of Lotmaria passim, Crithidia mellificae and Replicative Forms of Deformed Wing Virus and Kashmir Bee Virus in the Small Hive Beetle (Aethina tumida)

Knowledge regarding the honey bee pathogens borne by invasive bee pests remains scarce. This investigation aimed to assess the presence in Aethina tumida (small hive beetle, SHB) adults of honey bee pathogens belonging to the following groups: (i) bacteria (Paenibacillus larvae and Melissococcus plutonius), (ii) trypanosomatids (Lotmaria passim and Crithidia mellificae), and (iii) viruses (black queen cell virus, Kashmir bee virus, deformed wing virus, slow paralysis virus, sacbrood virus, Israeli acute paralysis virus, acute bee paralysis virus, chronic bee paralysis virus). Specimens were collected from free-flying colonies in Gainesville (Florida, USA) in summer 2017. The results of the molecular analysis show the presence of L. passim, C. mellificae, and replicative forms of deformed wing virus (DWV) and Kashmir bee virus (KBV). Replicative forms of KBV have not previously been reported. These results support the hypothesis of pathogen spillover between managed honey bees and the SHB, and these dynamics require further investigation.

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

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.

Possible Spillover of Pathogens between Bee Communities Foraging on the Same Floral Resource

Simple Summary

Floral resource availability is one of the keys to preserving the health of bee communities. However, flowers also present a risk of pathogen transmission, as infected pollinators could deposit pathogens while foraging, exposing other pollinators to infection via the consumption of contaminated nectar or pollen. Here, we studied, over time, the prevalence of seven viruses in bee communities that share the same small surface of floral resource in order to assess the risk of virus spillover. In total, 2057 bee specimens from 30 species were caught, identified and checked for the presence of viruses. Specimens from the Halictidae family were the dominant wild bees. The prevalence of viruses was quite high: at least one virus was detected in 78% of the samples, and co-infections were frequent. The genetic diversity of the viruses was also investigated to look for the possible association of geographic origin or host with shared ancestry.

Abstract

Viruses are known to contribute to bee population decline. Possible spillover is suspected from the co-occurrence of viruses in wild bees and honey bees. In order to study the risk of virus transmission between wild and managed bee species sharing the same floral resource, we tried to maximize the possible cross-infections using Phacelia tanacetifolia, which is highly attractive to honey bees and a broad range of wild bee species. Virus prevalence was compared over two years in Southern France. A total of 1137 wild bees from 29 wild bee species (based on COI barcoding) and 920 honey bees (Apis mellifera) were checked for the seven most common honey bee RNA viruses. Halictid bees were the most abundant. Co-infections were frequent, and Sacbrood virus (SBV), Black queen cell virus (BQCV), Acute bee paralysis virus (ABPV) and Israeli acute paralysis virus (IAPV) were widespread in the hymenopteran pollinator community. Conversely, Deformed wing virus (DWV) was detected at low levels in wild bees, whereas it was highly prevalent in honey bees (78.3% of the samples). Both wild bee and honey bee virus isolates were sequenced to look for possible host-specificity or geographical structuring. ABPV phylogeny suggested a specific cluster for Eucera bees, while isolates of DWV from bumble bees (Bombus spp.) clustered together with honey bee isolates, suggesting a possible spillover.

Varroa destructor mites vector and transmit pathogenic honey bee viruses acquired from an artificial diet

The ectoparasitic mite Varroa destructor is one of the most destructive pests of the honey bee (Apis mellifera) and the primary biotic cause of colony collapse in many regions of the world. These mites inflict physical injury on their honey bee hosts from feeding on host hemolymph and fat body cells/cellular components, and serve as the vector for deadly honey bee viruses, including Deformed wing virus (DWV) and the related Varroa destructor virus-1 (VDV-1) (i.e., DWV-like viruses). Studies focused on elucidating the dynamics of Varroa-mediated vectoring and transmission of DWV-like viruses may be confounded by viruses present in ingested host tissues or the mites themselves. Here we describe a system that includes an artificial diet free of insect tissue-derived components for maintaining Varroa mites for in vitro experimentation. Using this system, together with the novel engineered cDNA clone-derived genetically tagged VDV-1 and wild-type DWV, we demonstrated for the first time that Varroa mites provided an artificial diet supplemented with engineered viruses for 36 hours could acquire and transmit sufficient numbers of virus particles to establish an infection in virus-naïve hosts. While the in vitro system described herein provides for only up to five days of mite survival, precluding study of the long-term impacts of viruses on mite health, the system allows for extensive insights into the dynamics of Varroa-mediated vectoring and transmission of honey bee viruses.

RNAseq of Deformed Wing Virus and Other Honey Bee-Associated Viruses in Eight Insect Taxa with or without Varroa Infestation

The global spread of a parasitic mite (Varroa destructor) has resulted in Deformed wing virus (DWV), a previously rare pathogen, now dominating the viromes in honey bees and contributing to large-scale honey bee colony losses. DWV can be found in diverse insect taxa and has been implicated in spilling over from honey bees into associated ("apiary") and other ("non-apiary") insects. Here we generated next generation sequence data from 127 insect samples belonging to diverse taxa collected from Hawaiian islands with and without Varroa to identify whether the mite has indirectly affected the viral landscapes of key insect taxa across bees, wasps, flies and ants. Our data showed that, while Varroa was associated with a dramatic increase in abundance of (predominantly recombinant) DWV in honey bees (and no other honey bee-associated RNA virus), this change was not seen in any other taxa sampled. Honey bees share their environment with other insect populations and exist as a homogenous group, frequently sharing common viruses, albeit at low levels. Our data suggest that the threat of Varroa to increase viral load in an apiary does not automatically translate to an increase in virus load in other insects living in the wider community.