Endogenous viral elements in mosquito genomes: current knowledge and outstanding questions

Analysis of somatic piRNAs in the malaria mosquito Anopheles coluzzii reveals atypical classes of genic small RNAs

Piwi-interacting small RNAs (piRNA) play a key role in controlling the activity of transposable elements (TEs) in the animal germline. In diverse arthropod species, including the pathogen vectors mosquitoes, the piRNA pathway is also active in nongonadal somatic tissues, where its targets and functions are less clear. Here, we studied the features of small RNA production in head and thorax tissues of an uninfected laboratory strain of Anopheles coluzzii focusing on the 24-32-nt-long RNAs. Small RNAs derived from repetitive elements constitute a minor fraction while most small RNAs process from long noncoding RNAs (lncRNAs) and protein-coding gene mRNAs. The majority of small RNAs derived from repetitive elements and lncRNAs exhibited typical piRNAs features. By contrast, majority of protein-coding gene-derived 24-32 nt small RNAs lack the hallmarks of piRNAs and have signatures of nontemplated 3' end tailing. Most of the atypical small RNAs exhibit female-biased expression and originate from mitochondrial and nuclear genes involved in energy metabolism. We also identified atypical genic small RNAs in Anopheles gambiae somatic tissues, which further validates the noncanonical mechanism of their production. We discuss a novel mechanism of small RNA production in mosquito somatic tissues and the possible functional significance of genic small RNAs.

detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data

Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.

Diversity and evolution analysis of RNA viruses in three wheat aphid species

BACKGROUND

Although advances in metagenomics, viral diversity and non-retroviral endogenous viral elements (EVEs) in wheat aphids remain underexplored. By analyzing 470 publicly available datasets and one laboratory-generated transcriptome, the RNA virome and EVEs in the genomes of Sitobion avenae, Schizaphis graminum, and Rhopalosiphum padi were systematically investigated.

RESULTS

We identified 43 RNA viruses, including 12 novel and 31 known RNA viruses. These viruses were widely distributed and abundant in different geographic populations of three wheat aphid species. +ssRNA viruses were the dominant type of aphid viruses. Besides, 90 EVEs were discovered in the genomes of three aphid species. In addition, the EVEs exhibit potential domestication and novel functional roles within aphid genomes.

CONCLUSIONS

This study expands the understanding of RNA virus diversity in aphids and provides valuable insights into the potential functions of EVEs in virus-host coevolution.

Metagenome analysis of viruses associated with Anopheles mosquitoes from Ramu Upazila, Cox's Bazar District, Bangladesh

Bangladesh has a warm climate and landscapes favourable for the proliferation of mosquitoes. Mosquito-borne pathogens including malaria and arthropod-borne viruses (arboviruses) remain a serious threat to the public health requiring constant vector control and disease surveillance. From November 2018 to April 2019, Anopheles mosquitoes were collected in three unions in the Ramu Upazila (sub-district) of Cox's Bazar District, Bangladesh. The mosquito specimens were combined into pools based on date of collection, household ID, and sex. Metagenome next-generation sequencing was conducted to elucidate diversity of virus sequences in each pool. Homology-based taxonomic classification and phylogenetic analyses identified a broad diversity of putative viruses from 12 known families, with additional unclassified viruses also likely present. Analysis of male mosquitoes showed some of these viruses are likely capable of being vertically transmitted. Moreover, many of the assembled virus sequences share homology and phylogenetic affinity with segments in sequenced Anopheles genomes, and may represent endogenous viral elements derived from a past evolutionary relationship between these putative viruses and their mosquito hosts.

Phylogenetic Analysis of Chandipura virus: Insights from a Preliminary Genomic Study

Chandipura virus (CHPV) is an arthropod-borne virus linked to encephalitis in humans, primarily in India. Its evolutionary dynamics and transmission pathways remain poorly understood due to limited genomic data. This study analyzed 23 publicly available CHPV genomes, including isolates from humans, sandflies, and a hedgehog, retrieved from GenBank. Phylogenetic analyses were conducted to explore host-specific and geographic evolutionary patterns. Phylogenetic analysis revealed distinct evolutionary lineages. Human-derived genomes collected in India between 2003 and 2024 formed a well-supported monophyletic clade, suggesting a unique evolutionary lineage. In contrast, sandfly-derived genomes exhibited diverse clustering patterns. Notably, Kenyan sandfly isolates from 2016-2017 were phylogenetically closer to human-derived sequences, suggesting possible shared evolutionary pressures. These findings provide preliminary insights into CHPV evolution and emphasize the need for enhanced genomic surveillance in both human and non-human populations. Expanding genomic data is essential to validate these observations and inform public health strategies.

EEfinder, a general purpose tool for identification of bacterial and viral endogenized elements in eukaryotic genomes

Horizontal gene transfer is a phenomenon of genetic material transmission between species with no parental relationship. It has been characterized among several major branches of life, including among prokaryotes, viruses and eukaryotes. The characterization of endogenous elements derived from viruses or bacteria provides a snapshot of past host-pathogen interactions and coevolution as well as reference information to remove false positive results from metagenomic studies. Currently there is a lack of general purpose standardized tools for endogenous elements screening which limits reproducibility and hinder comparative analysis between studies. Here we describe EEfinder, a new general purpose tool for identification and classification of endogenous elements derived from viruses or bacteria found in eukaryotic genomes. The tool was developed to include six common steps performed in this type of analysis: data cleaning, similarity search through sequence alignment, filtering candidate elements, taxonomy assignment, merging of truncated elements and flanks extraction. We evaluated the sensitivity of EEfinder to identify endogenous elements through comparative analysis using data from the literature and showed that EEfinder automatically detected 97 % of the EVEs compared to published results obtained by manual curation and detected an almost exact full integration of a Wolbachia genome described using wet-lab experiments. Therefore, EEfinder can effectively and systematically identify endogenous elements with bacterial/viral origin integrated in eukaryotic genomes. EEfinder is publicly available on https://github.com/WallauBioinfo/EEfinder.

Evidence of endogenous non-retroviral RNA virus sequences into the genome and transcriptome of the malaria vector Anopheles darlingi

The characterization of non-retroviral integrated RNA virus sequences (NIRVS) in mosquitoes has emerged as a significant area of research that could yield insight into virus-host interactions. This study aimed to characterize NIRVS in the Anopheles darlingi reference genome and identify putative transcribed NIRVS in field-collected mosquitoes from Colombia. The An. darlingi reference genome was analyzed to identify and characterize NIRVS by conducting a BLAST query with all the virus sequences previously identified in arthropods available in the NCBI-virus repository. In addition, An. darlingi field-collected mosquitoes were examined for NIRVS using a metatranscriptomic approach. As a result, 44 NIRVS were identified in the An. darlingi genome, constituting integrations of negative single-stranded RNA viruses (ssRNA-) from the families Rhabdoviridae, Chuviridae and Phasmaviridae, and integrations of double-stranded RNA viruses (dsRNA) from the families Partitiviridae and Sedoreoviridae. These NIRVS were not randomly distributed but clustered in specific regions of the genome enriched with BEL/Pao and Ty3/Gypsy long terminal repeat elements. Furthermore, putative NIRVS-like sequences were present in the transcriptomic data from all the Colombian An. darlingi natural populations. This study is significant as it represents the first identification of NIRVS in the most important malaria vector of the Neotropics. The findings help in understanding the intricate relationship between the mosquito and its virome, and the regulation of viruses' mechanisms in the Anopheles genus.

Unleashing Nature's Allies: Comparing the Vertical Transmission Dynamics of Insect-Specific and Vertebrate-Infecting Flaviviruses in Mosquitoes

Insect-specific viruses (ISVs) include viruses that are restricted to the infection of mosquitoes and are spread mostly through transovarial transmission. Despite using a distinct mode of transmission, ISVs are often phylogenetically related to arthropod-borne viruses (arboviruses) that are responsible for human diseases and able to infect both mosquitoes and vertebrates. ISVs can also induce a phenomenon called "superinfection exclusion", whereby a primary ISV infection in an insect inhibits subsequent viral infections of the insect. This has sparked interest in the use of ISVs for the control of pathogenic arboviruses transmitted by mosquitoes. In particular, insect-specific flaviviruses (ISFs) have been shown to inhibit infection of vertebrate-infecting flaviviruses (VIFs) both in vitro and in vivo. This has shown potential as a new and ecologically friendly biological approach to the control of arboviral disease. For this intervention to have lasting impacts for biological control, it is imperative that ISFs are maintained in mosquito populations with high rates of vertical transmission. Therefore, these strategies will need to optimise vertical transmission of ISFs in order to establish persistently infected mosquito lines for sustainable arbovirus control. This review compares recent observations of vertical transmission of arboviral and insect-specific flaviviruses and potential determinants of transovarial transmission rates to understand how the vertical transmission of ISFs may be optimised for effective arboviral control.

Genetic diversity of Flaviviridae and Rhabdoviridae EVEs in Aedes aegypti and Aedes albopictus on Hainan Island and the Leizhou Peninsula, China

BACKGROUND

Hainan Island and the Leizhou Peninsula, the southernmost part of mainland China, are areas where Aedes aegypti and Ae. albopictus are sympatric and are also high-incidence areas of dengue outbreaks in China. Many studies have suggested that Aedes endogenous viral components (EVEs) are enriched in piRNA clusters which can silence incoming viral genomes. Investigation the EVEs present in the piRNA clusters associated with viral infection of Aedes mosquitoes in these regions may provide a theoretical basis for novel transmission-blocking vector control strategies.

METHODS

In this study, specific primers for endogenous Flaviviridae elements (EFVEs) and endogenous Rhabdoviridae elements (ERVEs) were used to detect the distribution of Zika virus infection associated EVEs in the genomes of individuals of the two Aedes mosquitoes. Genetic diversity of EVEs with a high detection rate was also analyzed.

RESULTS

The results showed that many EVEs associated with Zika virus infection were detected in both Aedes species, with the detection rates were 47.68% to 100% in Ae. aegypti and 36.15% to 92.31% in sympatric Ae. albopictus populations. EVEs detection rates in another 17 Ae. albopictus populations ranged from 29.39% to 89.85%. Genetic diversity analyses of the four EVEs (AaFlavi53, AaRha61, AaRha91 and AaRha100) of Ae. aegypti showed that each had high haplotype diversity and low nucleotide diversity. The number of haplotypes in AaFlavi53 was 8, with the dominant haplotype being Hap_1 and the other 7 haplotypes being further mutated from Hap_1 in a lineage direction. In contrast, the haplotype diversity of the other three ERVEs (AaRha61, AaRha91 and AaRha100) was more diverse and richer, with the haplotype numbers were 9, 15 and 19 respectively. In addition, these EVEs all showed inconsistent patterns of both population differentiation and dispersal compared to neutral evolutionary genes such as the Mitochondrial COI gene.

CONCLUSION

The EFVEs and ERVEs tested were present at high frequencies in the field Aedes mosquito populations. The haplotype diversity of the EFVE AaFlavi53 was relatively lower and the three ERVEs (AaRha61, AaRha91, AaRha100) were higher. None of the four EVEs could be indicative of the genetic diversity of the Ae. aegypti population. This study provided theoretical support for the use of EVEs to block arbovirus transmission, but further research is needed into the mechanisms by which these EVEs are antiviral to Aedes mosquitoes.

Transposon and Transgene Tribulations in Mosquitoes: A Perspective of piRNA Proportions

Mosquitoes, like Drosophila, are dipterans, the order of "true flies" characterized by a single set of two wings. Drosophila are prime model organisms for biomedical research, while mosquito researchers struggle to establish robust molecular biology in these that are arguably the most dangerous vectors of human pathogens. Both insects utilize the RNA interference (RNAi) pathway to generate small RNAs to silence transposons and viruses, yet details are emerging that several RNAi features are unique to each insect family, such as how culicine mosquitoes have evolved extreme genomic feature differences connected to their unique RNAi features. A major technical difference in the molecular genetic studies of these insects is that generating stable transgenic animals are routine in Drosophila but still variable in stability in mosquitoes, despite genomic DNA-editing advances. By comparing and contrasting the differences in the RNAi pathways of Drosophila and mosquitoes, in this review we propose a hypothesis that transgene DNAs are possibly more intensely targeted by mosquito RNAi pathways and chromatin regulatory pathways than in Drosophila. We review the latest findings on mosquito RNAi pathways, which are still much less well understood than in Drosophila, and we speculate that deeper study into how mosquitoes modulate transposons and viruses with Piwi-interacting RNAs (piRNAs) will yield clues to improving transgene DNA expression stability in transgenic mosquitoes.

In vitro characterization of cell-fusing agent virus DNA forms in Aedes aegypti mosquitoes

How non-retroviral endogenous viral elements (EVEs) are established is a long-standing question. Viral DNA (vDNA) forms of RNA viruses are likely to be EVE precursors. Cell-fusing agent virus (CFAV) is a major insect-specific virus (ISV) in the Aedes aegypti mosquitoes and one of the few existing non-retroviral RNA viruses found as EVEs. We characterized CFAV-derived vDNA in the cell line to understand the mechanism of why current viruses are rarely endogenized. vDNA production was affected by cell culture media independent of CFAV replication. vDNAs that correspond to different regions covering the entire viral genome were detected, implying multiple initiation sites exist. A considerable proportion of vDNAs corresponded to ssDNA. Higher vDNA copies were detected in the cytoplasm than the nucleus. Our findings provide valuable insights into the intracellular characteristics of ISV-derived vDNAs, which will aid in understanding the underlying mechanisms of non-retroviral EVE formation.

A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data

Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses. Here, we systematically assess the effects of EVEs on a prototypical virus discovery pipeline, evaluate their impact on data integrity and classification accuracy, and provide some recommendations for better practices. We examined EVEs and exogenous viral sequences linked to Orthomyxoviridae, a diverse family of negative-sense segmented RNA viruses, in 13 genomic and 538 transcriptomic datasets of Culicinae mosquitoes. Our analysis revealed a substantial number of viral sequences in transcriptomic datasets. However, a significant portion appeared not to be exogenous viruses but transcripts derived from EVEs. Distinguishing between transcribed EVEs and exogenous virus sequences was especially difficult in samples with low viral abundance. For example, three transcribed EVEs showed full-length segments, devoid of frameshift and nonsense mutations, exhibiting sufficient mean read depths that qualify them as exogenous virus hits. Mapping reads on a host genome containing EVEs before assembly somewhat alleviated the EVE burden, but it led to a drastic reduction of viral hits and reduced quality of assemblies, especially in regions of the viral genome relatively similar to EVEs. Our study highlights that our knowledge of the genetic diversity of viruses can be altered by the underestimated presence of EVEs in transcriptomic datasets, leading to false positives and altered or missing sequence information. Thus, recognizing and addressing the influence of EVEs in virus discovery pipelines will be key in enhancing our ability to capture the full spectrum of viral diversity.

Co-option of a non-retroviral endogenous viral element in planthoppers

Non-retroviral endogenous viral elements (nrEVEs) are widely dispersed throughout the genomes of eukaryotes. Although nrEVEs are known to be involved in host antiviral immunity, it remains an open question whether they can be domesticated as functional proteins to serve cellular innovations in arthropods. In this study, we found that endogenous toti-like viral elements (ToEVEs) are ubiquitously integrated into the genomes of three planthopper species, with highly variable distributions and polymorphism levels in planthopper populations. Three ToEVEs display exon‒intron structures and active transcription, suggesting that they might have been domesticated by planthoppers. CRISPR/Cas9 experiments revealed that one ToEVE in Nilaparvata lugens, NlToEVE14, has been co-opted by its host and plays essential roles in planthopper development and fecundity. Large-scale analysis of ToEVEs in arthropod genomes indicated that the number of arthropod nrEVEs is currently underestimated and that they may contribute to the functional diversity of arthropod genes.

Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole genome DNA sequencing data

Flaviviruses are a diverse group of RNA viruses, which include the etiological agents of Zika, dengue and yellow fever that are transmitted by mosquitoes. Flaviviruses do not encode reverse transcriptase and cannot reverse transcribe into DNA, yet DNA sequences of flaviviruses are found both integrated in the chromosomes of Aedes aegypti mosquitoes and as extrachromosomal sequences. We have previously examined the Ae. aegypti reference genome to identify flavivirus integrations and analyzed conservation of these sequences among whole-genome data of 464 Ae. aegypti collected across 10 countries globally. Here, we extended this analysis by identifying flavivirus sequences in these samples independently of the Ae. aegypti reference assembly. Our aim was to identify the complete set of viral sequences, including those absent in the reference genome, and their geographical distribution. We compared the identified sequences using BLASTn and applied machine learning methods to identify clusters of similar sequences. Apart from clusters of sequences that correspond to the four viral integration events that we had previously described, we identified 19 smaller clusters. The only cluster with a strong geographic association consisted of Cell-fusing agent virus-like sequences specific to Thailand. The remaining clusters did not have a geographic association and mostly consisted of near identical short sequences without strong similarity to any known flaviviral genomes. The short read sequencing data did not permit us to determine whether identified sequences were extrachromosomal or integrated into Ae. aegypti chromosomes. Our results suggest that Liverpool strain and field Ae. aegypti mosquitoes have a similar variety of conserved flaviviral DNA, whose functional role should be investigated in follow-up studies.

Ancient origin of Jingchuvirales derived glycoproteins integrated in arthropod genomes

Endogenous virus elements (EVEs) are viral-derived sequences integrated into their host genomes. EVEs of the Jingchuvirales order were detected in a wide range of insect genomes covering several distantly related families. Moreover, Jingchuvirales-derived glycoproteins were recently associated by our group with the origin of a putative new retrovirus based on a glycoprotein captured by a mosquito retrotransposon. But, except for mosquitoes, there is a lack of a more detailed understanding of the endogenization mechanism, timing, and frequency per Jingchuvirales viral lineages. Here we screened Jingchuvirales glycoprotein-derived EVEs (Jg-EVEs) in eukaryotic genomes. We found six distinct endogenization events of Jg-EVEs, that belong to two out of five known Jingchuvirales families (Chuviridae and Natareviridae). For seven arthropod families bearing Jg-EVEs there is no register of bona fide circulating chuvirus infection. Hence, our results show that Jingchuvirales viruses infected or still infect these host families. Although we found abundant evidence of LTR-Gypsy retrotransposons fragments associated with the glycoprotein in Hymenoptera and other insect orders, our results show that the widespread distribution of Jingchuvirales glycoproteins in extant Arhtropods is a result of multiple ancient endogenization events and that these virus fossils are being vertically inherited in Arthropods genomes for millions of years.

What Are the Functional Roles of Piwi Proteins and piRNAs in Insects?

Research on Piwi proteins and piRNAs in insects has focused on three experimental models: oogenesis and spermatogenesis in Drosophila melanogaster, the antiviral response in Aedes mosquitoes and the molecular analysis of primary and secondary piRNA biogenesis in Bombyx mori-derived BmN4 cells. Significant unique and complementary information has been acquired and has led to a greater appreciation of the complexity of piRNA biogenesis and Piwi protein function. Studies performed in other insect species are emerging and promise to add to the current state of the art on the roles of piRNAs and Piwi proteins. Although the primary role of the piRNA pathway is genome defense against transposons, particularly in the germline, recent findings also indicate an expansion of its functions. In this review, an extensive overview is presented of the knowledge of the piRNA pathway that so far has accumulated in insects. Following a presentation of the three major models, data from other insects were also discussed. Finally, the mechanisms for the expansion of the function of the piRNA pathway from transposon control to gene regulation were considered.

The Metagenomic Analysis of Viral Diversity in Colorado Potato Beetle Public NGS Data

The Colorado potato beetle (CPB) is one of the most serious insect pests due to its high ecological plasticity and ability to rapidly develop resistance to insecticides. The use of biological insecticides based on viruses is a promising approach to control insect pests, but the information on viruses which infect leaf feeding beetles is scarce. We performed a metagenomic analysis of 297 CPB genomic and transcriptomic samples from the public National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) database. The reads that were not aligned to the reference genome were assembled with metaSPAdes, and 13314 selected contigs were analyzed with BLAST tools. The contigs and non-aligned reads were also analyzed with Kraken2 software. A total of 3137 virus-positive contigs were attributed to different viruses belonging to 6 types, 17 orders, and 32 families, matching over 97 viral species. The annotated sequences can be divided into several groups: those that are homologous to genetic sequences of insect viruses (Adintoviridae, Ascoviridae, Baculoviridae, Dicistroviridae, Chuviridae, Hytrosaviridae, Iflaviridae, Iridoviridae, Nimaviridae, Nudiviridae, Phasmaviridae, Picornaviridae, Polydnaviriformidae, Xinmoviridae etc.), plant viruses (Betaflexiviridae, Bromoviridae, Kitaviridae, Potyviridae), and endogenous retroviral elements (Retroviridae, Metaviridae). Additionally, the full-length genomes and near-full length genome sequences of several viruses were assembled. We also found sequences belonging to Bracoviriform viruses and, for the first time, experimentally validated the presence of bracoviral genetic fragments in the CPB genome. Our work represents the first attempt to discover the viral genetic material in CPB samples, and we hope that further studies will help to identify new viruses to extend the arsenal of biopesticides against CPB.

Virome and nrEVEome diversity of Aedes albopictus mosquitoes from La Reunion Island and China

Background

Aedes albopictus is a public health threat for its worldwide spread and ability to transmit arboviruses. Understanding mechanisms of mosquito immunity can provide new tools to control arbovirus spread. The genomes of Aedes mosquitoes contain hundreds of nonretroviral endogenous viral elements (nrEVEs), which are enriched in piRNA clusters and produce piRNAs, with the potential to target cognate viruses. Recently, one nrEVE was shown to limit cognate viral infection through nrEVE-derived piRNAs. These findings suggest that nrEVEs constitute an archive of past viral infection and that the landscape of viral integrations may be variable across populations depending on their viral exposure.

Methods

We used bioinformatics and molecular approaches to identify known and novel (i.e. absent in the reference genome) viral integrations in the genome of wild collected Aedes albopictus mosquitoes and characterize their virome.

Results

We showed that the landscape of viral integrations is dynamic with seven novel viral integrations being characterized, but does not correlate with the virome, which includes both viral species known and unknown to infect mosquitoes. However, the small RNA coverage profile of nrEVEs and the viral genomic contigs we identified confirmed an interaction among these elements and the piRNA and siRNA pathways in mosquitoes.

Conclusions

Mosquitoes nrEVEs have been recently described as a new form of heritable, sequence-specific mechanism of antiviral immunity. Our results contribute to understanding the dynamic distribution of nrEVEs in the genomes of wild Ae. albopictus and their interaction with mosquito viruses.

Critical View on the Importance of Host Defense Strategies on Virus Distribution of Bee Viruses: What Can We Learn from SARS-CoV-2 Variants?

Bees, both wild and domesticated ones, are hosts to a plethora of viruses, with most of them infecting a wide range of bee species and genera. Although viral discovery and research on bee viruses date back over 50 years, the last decade is marked by a surge of new studies, new virus discoveries, and reports on viral transmission in and between bee species. This steep increase in research on bee viruses was mainly initiated by the global reports on honeybee colony losses and the worldwide wild bee decline, where viruses are regarded as one of the main drivers. While the knowledge gained on bee viruses has significantly progressed in a short amount of time, we believe that integration of host defense strategies and their effect on viral dynamics in the multi-host viral landscape are important aspects that are currently still missing. With the large epidemiological dataset generated over the last two years on the SARS-CoV-2 pandemic, the role of these defense mechanisms in shaping viral dynamics has become eminent. Integration of these dynamics in a multi-host system would not only greatly aid the understanding of viral dynamics as a driver of wild bee decline, but we believe bee pollinators and their viruses provide an ideal system to study the multi-host viruses and their epidemiology.