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

Neighbors sharing pathogens: the intricate relationship between Apis mellifera and ants (Hymenoptera: Formicidae) nesting in hives

Ants are ubiquitous and eusocial insects that exhibit frequent physical contact among colony members, thereby increasing their susceptibility to diseases. Some species are often found in beehives and in their surroundings, where they exploit the food resources of honey bees. This intricate relationship may facilitate the interspecific transmission of honey bee pathogens to ants, although ants themselves may contribute to spillback phenomena. The objective of this study was to assess the presence and abundance of honey bee pathogens in ants sampled from Italian apiaries. A total of 37 colonies within 24 apiaries across 7 regions were monitored. In total, 6 pathogens were detected in adult ants and 3 in the brood. In particular, the study revealed a high prevalence of honey bee pathogens in ants, with DWV, BQCV, and CBPV being the most commonly encountered. The brood also tested positive for the same viruses. Notably, all analyzed viruses were found to be replicative in both adult ants and ant broods. Furthermore, co-infections were prevalent, suggesting complex pathogen interactions within ant populations. Statistical analysis indicated significant differences in pathogen prevalence and abundance among ant species and sample types. The findings highlight active infection in both the ants and the brood, suggesting a potential role of ants as reservoir hosts and vectors of honey bee pathogens emphasizing the need for further research to understand the implications of interspecific pathogen transmission on ant and bee health.

The multispecies stinkbug iflavirus Halyomorpha halys virus detected in the multispecies stinkbug egg parasitoid microwasp, Telenomus podisi (Ashmead) (Hymenoptera: Platygastridae)

Wasps are important parasitoids of stinkbugs and frequently exposed to various types of microorganisms through environmental contact and fecal-oral transmission route. Many parasitize stinkbug eggs and are commercially used in the field to control insect population. The parasitoid T. podisi is known for its high parasitism capacity and ability to target multiple species of stinkbugs. In this study we asked whether T. podisi exposed to eggs infected by a multispecies asymptomatic stinkbug virus, the Halyomorpha halys virus (HhV) would get infected. HhV is a geographically distributed multispecies iflavirus previously found to infect four stinkbug hosts, including three Brazilian species, Chinavia ubica, Euschistus heros and Diceraeus melacanthus, and T. posidi can parasitize all of them. As results, RT-PCR screening revealed positive samples for the HhV genome in two out of four tested pools of T. podisi, whereas the antigenome, indicative of replicative activity, was not detected. The wasps were raised in E. heros eggs that presented both the genome and the antigenome forms of the HhV genome. Subsequent RNA-deep sequencing of HhV positive T. podisi RNA pools yielded a complete genome of HhV with high coverage. Phylogenetic analysis positioned the isolate HhV-Tp (isolate Telenomus podisi) alongside with the stinkbug HhV. Analysis of transcriptomes from several hymenopteran species revealed HhV-Tp reads in four species. However, the transmission mechanism and the ecological significance of HhV remain elusive, warranting further studies to illuminate both the transmission process and its capacity for environmental propagation using T. podisi as a potential vector.

Seasonal Variability in the Prevalence of DWV Strains in Individual Colonies of European Honeybees in Hawaii

The most prevalent viral pathogen of honeybees is Deformed Wing Virus (DWV) and its two most widely studied and common master-variants are DWV-A and DWV-B. The prevalence of DWV variants in the UK and in the US is changing, with the prevalence of the DWV-A strain declining and DWV-B increasing over time. In 2012, only DWV-A was detected on the Hawaiian Islands of Oahu. In this study we focused on a colony-level survey of DWV strains in a single apiary and examined the prevalence of DWV variants over the course of two years. In 2018 and 2019, a total of 16 colonies underwent viral testing in January, May, and September. Of those 16 colonies, four were monitored in both 2018 and 2019. Individual colonies showed variability of DWV master variants throughout the sampling period. DWV-A was consistently detected; however, the detection of DWV-B was variable across time in individual colonies. Ultimately, this study demonstrated a seasonal variation in both viral prevalence and load for DWV-B, providing a perspective on the dynamic nature of DWV master variants emerging in Hawaii.

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.

Shift in virus composition in honeybees (Apis mellifera) following worldwide invasion by the parasitic mite and virus vector Varroa destructor

Invasive vectors can induce dramatic changes in disease epidemiology. While viral emergence following geographical range expansion of a vector is well known, the influence a vector can have at the level of the host's pathobiome is less well understood. Taking advantage of the formerly heterogeneous spatial distribution of the ectoparasitic mite Varroa destructor that acts as potent virus vector among honeybees Apis mellifera, we investigated the impact of its recent global spread on the viral community of honeybees in a retrospective study of historical samples. We hypothesized that the vector has had an effect on the epidemiology of several bee viruses, potentially altering their transmissibility and/or virulence, and consequently their prevalence, abundance, or both. To test this, we quantified the prevalence and loads of 14 viruses from honeybee samples collected in mite-free and mite-infested populations in four independent geographical regions. The presence of the mite dramatically increased the prevalence and load of deformed wing virus, a cause of unsustainably high colony losses. In addition, several other viruses became more prevalent or were found at higher load in mite-infested areas, including viruses not known to be actively varroa-transmitted, but which may increase opportunistically in varroa-parasitized bees.

Deformed wing virus of honey bees is inactivated by cold plasma ionized hydrogen peroxide

Deformed wing virus (DWV) is a widespread pathogen of Apis mellifera honey bees, and is considered a major causative factor for the collapse of infected honey bee colonies. DWV can be horizontally transmitted among bees through various oral routes, including via food sharing and by interactions of bees with viral-contaminated solid hive substrates. Cold plasma ionized hydrogen peroxide (iHP) is used extensively by the food production, processing and medical industries to clean surfaces of microbial contaminants. In this study, we investigated the use of iHP to inactivate DWV particles in situ on a solid substrate. iHP-treated DWV sources were ~105-fold less infectious when injected into naïve honey bee pupae compared to DWV receiving no iHP treatment, matching injected controls containing no DWV. iHP treatment also greatly reduced the incidence of overt DWV infections (i.e., pupae having >109 copies of DWV). The level of DWV inactivation achieved with iHP treatment was higher than other means of viral inactivation such as gamma irradiation, and iHP treatment is likely simpler and safer. Treatment of DWV contaminated hive substrates with iHP, even with honey bees present, may be an effective way to decrease the impacts of DWV infection on honey bees.

Omics-based analysis of honey bee (Apis mellifera) response to Varroa sp. parasitisation and associated factors reveals changes impairing winter bee generation

The extensive annual loss of honey bees (Apis mellifera L.) represents a global problem affecting agriculture and biodiversity. The parasitic mite Varroa destructor, associated with viral co-infections, plays a key role in this loss. Despite years of intensive research, the complex mechanisms of Varroa - honey bee interaction are still not fully defined. Therefore, this study employed a unique combination of transcriptomic, proteomic, metabolomic, and functional analyses to reveal new details about the effect of Varroa mites and naturally associated factors, including viruses, on honey bees. We focused on the differences between Varroa parasitised and unparasitised ten-day-old worker bees collected before overwintering from the same set of colonies reared without anti-mite treatment. Supplementary comparison to honey bees collected from colonies with standard anti-Varroa treatment can provide further insights into the effect of a pyrethroid flumethrin. Analysis of the honey bees exposed to mite parasitisation revealed alterations in the transcriptome and proteome related to immunity, oxidative stress, olfactory recognition, metabolism of sphingolipids, and RNA regulatory mechanisms. The immune response and sphingolipid metabolism were strongly activated, whereas olfactory recognition and oxidative stress pathways were inhibited in Varroa parasitised honey bees compared to unparasitised ones. Moreover, metabolomic analysis confirmed the depletion of nutrients and energy stores, resulting in a generally disrupted metabolism in the parasitised workers. The combined omics-based analysis conducted on strictly parasitised bees revealed the key molecular components and mechanisms underlying the detrimental effects of Varroa sp. and its associated pathogens. This study provides the theoretical basis and interlinked datasets for further research on honey bee response to biological threats and the development of efficient control strategies against Varroa mites.

Honey Bee Pathogen Prevalence and Interactions within the Marmara Region of Turkey

Beekeeping has yet to reach its full potential in terms of productivity in Turkey where it has a relatively large role in the economy. Poor colony health is suspected to be the reason for this, but comprehensive disease monitoring programs are lacking to support this notion. We sampled a total of 115 colonies across five different apiaries throughout the Marmara region of Turkey and screened for all of the major bee pathogens using PCR and RNA-seq methods. We found that Varroa mites are more prevalent in comparison to Nosema infections. The pathogens ABPV, DWV, KV, and VDV1 are near 100% prevalent and are the most abundant across all locations, which are known to be vectored by the Varroa mite. We therefore suspect that controlling Varroa mites will be key for improving bee health in Turkey moving forward. We also documented significant interactions between DWV, KV, and VDV1, which may explain how the more virulent strain of the virus becomes abundant. ABPV had a positive interaction with VDV1, thereby possibly facilitating this more virulent viral strain, but a negative interaction with Nosema ceranae. Therefore, these complex pathogen interactions should be taken into consideration in the future to improve bee health.

Epidemiology of a major honey bee pathogen, deformed wing virus: potential worldwide replacement of genotype A by genotype B

The western honey bee (Apis mellifera) is of major economic and ecological importance, with elevated rates of colony losses in temperate regions over the last two decades thought to be largely caused by the exotic ectoparasitic mite Varroa destructor and deformed wing virus (DWV), which the mite transmits. DWV currently exists as two main genotypes: the formerly widespread DWV-A and the more recently described and rapidly expanding DWV-B. It is an excellent system to understand viral evolution and the replacement of one viral variant by another. Here we synthesise published results on the distribution and prevalence of DWV-A and -B over the period 2008-2021 and present novel data for Germany, Italy and the UK to suggest that (i) DWV-B has rapidly expanded worldwide since its first description in 2004 and (ii) that it is potentially replacing DWV-A. Both genotypes are also found in wild bee species. Based on a simple mathematical model, we suggest that interference between viral genotypes when co-infecting the same host is key to understanding their epidemiology. We finally discuss the consequences of genotype replacement for beekeeping and for wild pollinator species.

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.

Virome Analysis Reveals Diverse and Divergent RNA Viruses in Wild Insect Pollinators in Beijing, China

Insect pollinators provide major pollination services for wild plants and crops. Honeybee viruses can cause serious damage to honeybee colonies. However, viruses of other wild pollinating insects have yet to be fully explored. In the present study, we used RNA sequencing to investigate the viral diversity of 50 species of wild pollinating insects. A total of 3 pathogenic honeybee viruses, 8 previously reported viruses, and 26 novel viruses were identified in sequenced samples. Among these, 7 novel viruses were shown to be closely related to honeybee pathogenic viruses, and 4 were determined to have potential pathogenicity for their hosts. The viruses detected in wild insect pollinators were mainly from the order Picornavirales and the families Orthomyxoviridae, Sinhaliviridae, Rhabdoviridae, and Flaviviridae. Our study expanded the species range of known insect pollinator viruses, contributing to future efforts to protect economic honeybees and wild pollinating insects.

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.

Global similarity, and some key differences, in the metagenomes of Swedish varroa-surviving and varroa-susceptible honeybees

There is increasing evidence that honeybees (Apis mellifera L.) can adapt naturally to survive Varroa destructor, the primary cause of colony mortality world-wide. Most of the adaptive traits of naturally varroa-surviving honeybees concern varroa reproduction. Here we investigate whether factors in the honeybee metagenome also contribute to this survival. The quantitative and qualitative composition of the bacterial and viral metagenome fluctuated greatly during the active season, but with little overall difference between varroa-surviving and varroa-susceptible colonies. The main exceptions were Bartonella apis and sacbrood virus, particularly during early spring and autumn. Bombella apis was also strongly associated with early and late season, though equally for all colonies. All three affect colony protein management and metabolism. Lake Sinai virus was more abundant in varroa-surviving colonies during the summer. Lake Sinai virus and deformed wing virus also showed a tendency towards seasonal genetic change, but without any distinction between varroa-surviving and varroa-susceptible colonies. Whether the changes in these taxa contribute to survival or reflect demographic differences between the colonies (or both) remains unclear.

Ten Years of Deformed Wing Virus (DWV) in Hawaiian Honey Bees (Apis mellifera), the Dominant DWV-A Variant Is Potentially Being Replaced by Variants with a DWV-B Coding Sequence

The combination of Deformed wing virus (DWV) and Varroa destructor is arguably one of the greatest threats currently facing western honey bees, Apis mellifera. Varroa's association with DWV has decreased viral diversity and increased loads of DWV within honey bee populations. Nowhere has this been better studied than in Hawaii, where the arrival of Varroa progressively led to the dominance of the single master variant (DWV-A) on both mite-infested Hawaiian Islands of Oahu and Big Island. Now, exactly 10 years following the original study, we find that the DWV population has changed once again, with variants containing the RdRp coding sequence pertaining to the master variant B beginning to co-dominate alongside variants with the DWV-A RdRp sequence on the mite-infested islands of Oahu and Big Island. In speculation, based on other studies, it appears this could represent a stage in the journey towards the complete dominance of DWV-B, a variant that appears better adapted to be transmitted within honey bee colonies.

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.

Adaptation to vector-based transmission in a honeybee virus

Global pollinator declines as a result of emerging infectious diseases are of major concern. Managed honeybees Apis mellifera are susceptible to numerous parasites and pathogens, many of which appear to be transmissible to sympatric non-Apis taxa. The ectoparasitic mite Varroa destructor is considered to be the most significant threat to honeybees due to its role in vectoring RNA viruses, particularly Deformed wing virus (DWV). Vector transmission of DWV has resulted in the accumulation of high viral loads in honeybees and is often associated with colony death. DWV has two main genotypes, A and B. DWV-A was more prevalent during the initial phase of V. destructor establishment. In recent years, the global prevalence of DWV-B has increased, suggesting that DWV-B is better adapted to vector transmission than DWV-A. We aimed to determine the role vector transmission plays in DWV genotype prevalence at a colony level. We experimentally increased or decreased the number of V. destructor mites in honeybee colonies, and tracked DWV-A and DWV-B loads over a period of 10 months. Our results show that the two DWV genotypes differ in their response to mite numbers. DWV-A accumulation in honeybees was positively correlated with mite numbers yet DWV-A was largely undetected in the absence of the mite. In contrast, colonies had high loads of DWV-B even when mite numbers were low. DWV-B loads persisted in miticide-treated colonies, indicating that this genotype has a competitive advantage over DWV-A irrespective of mite numbers. Our findings suggest that the global increase in DWV-B prevalence is not driven by selective pressure by the vector. Rather, DWV-B is able to persist in colonies at higher viral loads relative to DWV-A in the presence and absence of V. destructor. The interplay between V. destructor and DWV genotypes within honeybee colonies may have broad consequences upon viral diversity in sympatric taxa as a result of spillover.

Detection of deformed wing virus (DWV) in the Vietnamese walking stick Medauroidea extradentata (Phasmatodea)

Deformed wing virus (DWV) is a single-stranded positive sense RNA virus that mainly infects honey bees (Apis mellifera) and can have devastating impacts on the colony. Recent studies have shown the presence of this virus in several species of Apis spp. and some other Hymenoptera, but our knowledge of their host range is very limited. We screened previously sequenced RNAseq libraries from different tissues of Vietnamese Walking Stick, Medauroidea extradentata (Phasmatodea) for DWV. We only found this virus in six libraries from anterior and posterior midgut tissue. From the midgut libraries we were able to construct a complete DWV genome sequence, which consisted of 10,140 nucleotides and included one open reading frame. Pairwise genome comparison confirmed strong similarity (98.89 %) of these assembled sequences with only 113 SNPs to the original DWV genome. We hypothesize the M. extradentata acquired this virus via a foodborne transmission by consuming DWV-infected material such as pollen or leaves contaminated with virus infected bee faeces.